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Sample records for natural bacterial assemblages

  1. 2,4,6-Trinitrotoluene mineralization and bacterial production rates of natural microbial assemblages from coastal sediments

    International Nuclear Information System (INIS)

    Montgomery, Michael T.; Coffin, Richard B.; Boyd, Thomas J.; Smith, Joseph P.; Walker, Shelby E.; Osburn, Christopher L.

    2011-01-01

    The nitrogenous energetic constituent, 2,4,6-Trinitrotoluene (TNT), is widely reported to be resistant to bacterial mineralization (conversion to CO 2 ); however, these studies primarily involve bacterial isolates from freshwater where bacterial production is typically limited by phosphorus. This study involved six surveys of coastal waters adjacent to three biome types: temperate broadleaf, northern coniferous, and tropical. Capacity to catabolize and mineralize TNT ring carbon to CO 2 was a common feature of natural sediment assemblages from these coastal environments (ranging to 270+/-38 μg C kg -1 d -1 ). More importantly, these mineralization rates comprised a significant proportion of total heterotrophic production. The finding that most natural assemblages surveyed from these ecosystems can mineralize TNT ring carbon to CO 2 is consistent with recent reports that assemblage components can incorporate TNT ring carbon into bacterial biomass. These data counter the widely held contention that TNT is recalcitrant to bacterial catabolism of the ring carbon in natural environments. - Highlights: → TNT mineralization is a common feature of natural bacterial assemblages in coastal sediments. → TNT mineralization rates comprised a significant proportion of total heterotrophic production. → These data counter the widely held contention that TNT is recalcitrant to bacterial catabolism of the ring carbon in natural environments. - The capacity to mineralize TNT ring carbon to CO 2 is a common feature of natural bacterial assemblages in coastal sediment.

  2. 2,4,6-Trinitrotoluene mineralization and bacterial production rates of natural microbial assemblages from coastal sediments

    Energy Technology Data Exchange (ETDEWEB)

    Montgomery, Michael T., E-mail: michael.montgomery@nrl.navy.mil [Naval Research Laboratory, Marine Biogeochemistry Section, Code 6114, 4555 Overlook Avenue, Washington, DC 20375 (United States); Coffin, Richard B., E-mail: richard.coffin@nrl.navy.mil [Naval Research Laboratory, Marine Biogeochemistry Section, Code 6114, 4555 Overlook Avenue, Washington, DC 20375 (United States); Boyd, Thomas J., E-mail: thomas.boyd@nrl.navy.mil [Naval Research Laboratory, Marine Biogeochemistry Section, Code 6114, 4555 Overlook Avenue, Washington, DC 20375 (United States); Smith, Joseph P., E-mail: joseph.smith@nrl.navy.mil [Naval Research Laboratory, Marine Biogeochemistry Section, Code 6114, 4555 Overlook Avenue, Washington, DC 20375 (United States); Walker, Shelby E., E-mail: Shelby.Walker@noaa.gov [Naval Research Laboratory, Marine Biogeochemistry Section, Code 6114, 4555 Overlook Avenue, Washington, DC 20375 (United States); Osburn, Christopher L., E-mail: chris_osburn@ncsu.edu [Marine, Earth and Atmospheric Sciences, North Carolina State University, Raleigh, NC 27695 (United States)

    2011-12-15

    The nitrogenous energetic constituent, 2,4,6-Trinitrotoluene (TNT), is widely reported to be resistant to bacterial mineralization (conversion to CO{sub 2}); however, these studies primarily involve bacterial isolates from freshwater where bacterial production is typically limited by phosphorus. This study involved six surveys of coastal waters adjacent to three biome types: temperate broadleaf, northern coniferous, and tropical. Capacity to catabolize and mineralize TNT ring carbon to CO{sub 2} was a common feature of natural sediment assemblages from these coastal environments (ranging to 270+/-38 {mu}g C kg{sup -1} d{sup -1}). More importantly, these mineralization rates comprised a significant proportion of total heterotrophic production. The finding that most natural assemblages surveyed from these ecosystems can mineralize TNT ring carbon to CO{sub 2} is consistent with recent reports that assemblage components can incorporate TNT ring carbon into bacterial biomass. These data counter the widely held contention that TNT is recalcitrant to bacterial catabolism of the ring carbon in natural environments. - Highlights: > TNT mineralization is a common feature of natural bacterial assemblages in coastal sediments. > TNT mineralization rates comprised a significant proportion of total heterotrophic production. > These data counter the widely held contention that TNT is recalcitrant to bacterial catabolism of the ring carbon in natural environments. - The capacity to mineralize TNT ring carbon to CO{sub 2} is a common feature of natural bacterial assemblages in coastal sediment.

  3. Sulfonamide and tetracycline resistance genes in total- and culturable-bacterial assemblages in South African aquatic environments

    Directory of Open Access Journals (Sweden)

    Satoru eSuzuki

    2015-08-01

    Full Text Available Antibiotic resistant bacteria (ARB are ubiquitous in the natural environment. The introduction of effluent derived antibiotic resistance genes (ARGs into aquatic environments is of concern in the spreading of genetic risk. This study showed the prevalence of sulfonamide and tetracycline resistance genes, sul1, sul2, sul3 and tet(M, in the total bacterial assemblage and colony forming bacterial assemblage in river and estuarine water and sewage treatment plants (STP in South Africa. There was no correlation between antibiotic concentrations and ARGs, suggesting the targeted ARGs are spread in a wide area without connection to selection pressure. Among sul genes, sul1 and sul2 were major genes in the total (over 10-2 copies/16S and colony forming bacteria assemblages (approx 10-1 copies/16S. In urban waters, the sul3 gene was mostly not detectable in total and culturable assemblages, suggesting sul3 is not abundant. tet(M was found in natural assemblages with 10-3 copies/16S level in STP, but was not detected in colony forming bacteria, suggesting the non-culturable (yet-to-be cultured bacterial community in urban surface waters and STP effluent possess the tet(M gene. Sulfamethoxazole resistant (SMXr and oxytetracycline resistant (OTCr bacterial communities in urban waters possessed not only sul1 and sul2 but also sul3 and tet(M genes. These genes are widely distributed in SMXr and OTCr bacteria. In conclusion, urban river and estuarine water and STP effluent in the Durban area were highly contaminated with ARGs, and the yet-to-be cultured bacterial community may act as a non-visible ARG reservoir in certain situations.

  4. Environmental Factors Support the Formation of Specific Bacterial Assemblages on Microplastics

    Science.gov (United States)

    Oberbeckmann, Sonja; Kreikemeyer, Bernd; Labrenz, Matthias

    2018-01-01

    While the global distribution of microplastics (MP) in the marine environment is currently being critically evaluated, the potential role of MP as a vector for distinct microbial assemblages or even pathogenic bacteria is hardly understood. To gain a deeper understanding, we investigated how different in situ conditions contribute to the composition and specificity of MP-associated bacterial communities in relation to communities on natural particles. Polystyrene (PS), polyethylene (PE), and wooden pellets were incubated for 2 weeks along an environmental gradient, ranging from marine (coastal Baltic Sea) to freshwater (waste water treatment plant, WWTP) conditions. The associated assemblages as well as the water communities were investigated applying high-throughput 16S rRNA gene sequencing. Our setup allowed for the first time to determine MP-dependent and -independent assemblage factors as subject to different environmental conditions in one system. Most importantly, plastic-specific assemblages were found to develop solely under certain conditions, such as lower nutrient concentration and higher salinity, while the bacterial genus Erythrobacter, known for the ability to utilize polycyclic aromatic hydrocarbons (PAH), was found specifically on MP across a broader section of the gradient. We discovered no enrichment of potential pathogens on PE or PS; however, the abundant colonization of MP in a WWTP by certain bacteria commonly associated with antibiotic resistance suggests MP as a possible hotspot for horizontal gene transfer. Taken together, our study clarifies that the surrounding environment prevailingly shapes the biofilm communities, but that MP-specific assemblage factors exist. These findings point to the ecological significance of specific MP-promoted bacterial populations in aquatic environments and particularly in plastic accumulation zones. PMID:29403454

  5. Environmental Factors Support the Formation of Specific Bacterial Assemblages on Microplastics

    Directory of Open Access Journals (Sweden)

    Sonja Oberbeckmann

    2018-01-01

    Full Text Available While the global distribution of microplastics (MP in the marine environment is currently being critically evaluated, the potential role of MP as a vector for distinct microbial assemblages or even pathogenic bacteria is hardly understood. To gain a deeper understanding, we investigated how different in situ conditions contribute to the composition and specificity of MP-associated bacterial communities in relation to communities on natural particles. Polystyrene (PS, polyethylene (PE, and wooden pellets were incubated for 2 weeks along an environmental gradient, ranging from marine (coastal Baltic Sea to freshwater (waste water treatment plant, WWTP conditions. The associated assemblages as well as the water communities were investigated applying high-throughput 16S rRNA gene sequencing. Our setup allowed for the first time to determine MP-dependent and -independent assemblage factors as subject to different environmental conditions in one system. Most importantly, plastic-specific assemblages were found to develop solely under certain conditions, such as lower nutrient concentration and higher salinity, while the bacterial genus Erythrobacter, known for the ability to utilize polycyclic aromatic hydrocarbons (PAH, was found specifically on MP across a broader section of the gradient. We discovered no enrichment of potential pathogens on PE or PS; however, the abundant colonization of MP in a WWTP by certain bacteria commonly associated with antibiotic resistance suggests MP as a possible hotspot for horizontal gene transfer. Taken together, our study clarifies that the surrounding environment prevailingly shapes the biofilm communities, but that MP-specific assemblage factors exist. These findings point to the ecological significance of specific MP-promoted bacterial populations in aquatic environments and particularly in plastic accumulation zones.

  6. Airborne bacterial assemblage in a zero carbon building: A case study.

    Science.gov (United States)

    Leung, M H Y; Tong, X; Tong, J C K; Lee, P K H

    2018-01-01

    Currently, there is little information pertaining to the airborne bacterial communities of green buildings. In this case study, the air bacterial community of a zero carbon building (ZCB) in Hong Kong was characterized by targeting the bacterial 16S rRNA gene. Bacteria associated with the outdoor environment dominated the indoor airborne bacterial assemblage, with a modest contribution from bacteria associated with human skin. Differences in overall community diversity, membership, and composition associated with short (day-to-day) and long-term temporal properties were detected, which may have been driven by specific environmental genera and taxa. Furthermore, time-decay relationships in community membership (based on unweighted UniFrac distances) and composition (based on weighted UniFrac distances) differed depending on the season and sampling location. A Bayesian source-tracking approach further supported the importance of adjacent outdoor air bacterial assemblage in sourcing the ZCB indoor bioaerosol. Despite the unique building attributes, the ZCB microbial assemblage detected and its temporal characteristics were not dissimilar to that of conventional built environments investigated previously. Future controlled experiments and microbial assemblage investigations of other ZCBs will undoubtedly uncover additional knowledge related to how airborne bacteria in green buildings may be influenced by their distinctive architectural attributes. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  7. Brood size modifications affect plumage bacterial assemblages of European starlings.

    Science.gov (United States)

    Lucas, Françoise S; Moureau, Benoit; Jourdie, Violaine; Heeb, Philipp

    2005-02-01

    During reproduction, birds face trade-offs between time and energy devoted to parental effort and traits associated with self-maintenance. We manipulated brood sizes to investigate the effects of such trade-offs on feather bacterial densities and the structure of bacterial assemblages on feathers in adult European starlings, Sturnus vulgaris, and in vitro feather degradation. As predicted by a trade-off between parental effort and self-maintenance, we found that birds with enlarged broods had more free-living bacteria on their feathers than birds with reduced broods. Furthermore, we found a significant interaction between brood manipulation and original brood size on free-living bacterial densities suggesting that the trade-off is mediated by the adults' initial reproductive investment. In contrast, brood size manipulations had no significant effect on densities of attached bacteria. Using ribosomal intergenic spacer analysis (RISA), we demonstrated that brood manipulations significantly modified the structure (band pattern) of feather-degrading bacterial assemblages, but had no significant effect on their richness (number of bands) or the in vitro feather degradation. In vitro feather degradation varied in relation to the premanipulation brood size and positively with the richness of the feather degrading bacterial community. Besides brood manipulation effect, we found that ecological factors and individual traits, such as the age, the nest location or the capture date, shaped bacterial assemblages and feather degradation capacities.

  8. Disentangling the effects of solar radiation, wrack macroalgae and beach macrofauna on associated bacterial assemblages.

    Science.gov (United States)

    Rodil, Iván F; Fernandes, Joana P; Mucha, Ana P

    2015-12-01

    Wrack detritus plays a significant role in shaping community dynamics and food-webs on sandy beaches. Macroalgae is the most abundant beach wrack, and it is broken down by the combination of environmental processes, macrofauna grazing, and microbial degradation before returning to the sea as nutrients. The role of solar radiation, algal species and beach macrofauna as ecological drivers for bacterial assemblages associated to wrack was investigated by experimental manipulation of Laminaria ochroleuca and Sargassum muticum. We examined the effects of changes in solar radiation on wrack-associated bacterial assemblages by using cut-off filters: PAR + UVA + UVB (280-700 nm; PAB), PAR + UVA (320-700 nm; PA), PAR (400-700 nm; P), and a control with no filter (C). Results showed that moderate changes in UVR are capable to promote substantial differences on bacterial assemblages so that wrack patches exposed to full sunlight treatments (C and PAB) showed more similar assemblages among them than compared to patches exposed to treatments that blocked part of the solar radiation (P and PA). Our findings also suggested that specific algal nutrient quality-related variables (i.e. nitrogen, C:N ratio and phlorotannins) are main determinants of bacterial dynamics on wrack deposits. We showed a positive relationship between beach macrofauna, especially the most abundant and active wrack-users, the amphipod Talitrus saltator and the coleopteran Phaleria cadaverina, and both bacterial abundance and richness. Moderate variations in natural solar radiation and shifts in the algal species entering beach ecosystems can modify the role of wrack in the energy-flow of nearshore environments with unknown ecological implications for coastal ecosystems. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Bacterial assemblages of the eastern Atlantic Ocean reveal both vertical and latitudinal biogeographic signatures

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    C. J. Friedline

    2012-06-01

    Full Text Available Microbial communities are recognized as major drivers of the biogeochemical processes in the oceans. However, the genetic diversity and composition of those communities is poorly understood. The aim of this study is to investigate the composition of bacterial assemblages in three different water layer habitats: surface (2–20 m, deep chlorophyll maximum (DCM; 28–90 m, and deep (100–4600 m at nine stations along the eastern Atlantic Ocean from 42.8° N to 23.7° S. The sampling of three discrete, predefined habitat types from different depths, Longhurstian provinces, and geographical locations allowed us to investigate whether marine bacterial assemblages show spatial variation and to determine if the observed spatial variation is influenced by current environmental conditions, historical/geographical contingencies, or both. The PCR amplicons of the V6 region of the 16S rRNA from 16 microbial assemblages were pyrosequenced, generating a total of 352 029 sequences; after quality filtering and processing, 257 260 sequences were clustered into 2871 normalized operational taxonomic units (OTU using a definition of 97% sequence identity. Community ecology statistical analyses demonstrate that the eastern Atlantic Ocean bacterial assemblages are vertically stratified and associated with water layers characterized by unique environmental signals (e.g., temperature, salinity, and nutrients. Genetic compositions of bacterial assemblages from the same water layer are more similar to each other than to assemblages from different water layers. The observed clustering of samples by water layer allows us to conclude that contemporary environments are influencing the observed biogeographic patterns. Moreover, the implementation of a novel Bayesian inference approach that allows a more efficient and explicit use of all the OTU abundance data shows a distance effect suggesting the influence of historical contingencies on the composition of bacterial

  10. Bacterial assemblages of the eastern Atlantic Ocean reveal both vertical and latitudinal biogeographic signatures

    Science.gov (United States)

    Friedline, C. J.; Franklin, R. B.; McCallister, S. L.; Rivera, M. C.

    2012-06-01

    Microbial communities are recognized as major drivers of the biogeochemical processes in the oceans. However, the genetic diversity and composition of those communities is poorly understood. The aim of this study is to investigate the composition of bacterial assemblages in three different water layer habitats: surface (2-20 m), deep chlorophyll maximum (DCM; 28-90 m), and deep (100-4600 m) at nine stations along the eastern Atlantic Ocean from 42.8° N to 23.7° S. The sampling of three discrete, predefined habitat types from different depths, Longhurstian provinces, and geographical locations allowed us to investigate whether marine bacterial assemblages show spatial variation and to determine if the observed spatial variation is influenced by current environmental conditions, historical/geographical contingencies, or both. The PCR amplicons of the V6 region of the 16S rRNA from 16 microbial assemblages were pyrosequenced, generating a total of 352 029 sequences; after quality filtering and processing, 257 260 sequences were clustered into 2871 normalized operational taxonomic units (OTU) using a definition of 97% sequence identity. Community ecology statistical analyses demonstrate that the eastern Atlantic Ocean bacterial assemblages are vertically stratified and associated with water layers characterized by unique environmental signals (e.g., temperature, salinity, and nutrients). Genetic compositions of bacterial assemblages from the same water layer are more similar to each other than to assemblages from different water layers. The observed clustering of samples by water layer allows us to conclude that contemporary environments are influencing the observed biogeographic patterns. Moreover, the implementation of a novel Bayesian inference approach that allows a more efficient and explicit use of all the OTU abundance data shows a distance effect suggesting the influence of historical contingencies on the composition of bacterial assemblages. Surface

  11. Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder.

    Science.gov (United States)

    Denef, Vincent J; Carrick, Hunter J; Cavaletto, Joann; Chiang, Edna; Johengen, Thomas H; Vanderploeg, Henry A

    2017-01-01

    One approach to improve forecasts of how global change will affect ecosystem processes is to better understand how anthropogenic disturbances alter bacterial assemblages that drive biogeochemical cycles. Species invasions are important contributors to global change, but their impacts on bacterial community ecology are rarely investigated. Here, we studied direct impacts of invasive dreissenid mussels (IDMs), one of many invasive filter feeders, on freshwater lake bacterioplankton. We demonstrated that direct effects of IDMs reduced bacterial abundance and altered assemblage composition by preferentially removing larger and particle-associated bacteria. While this increased the relative abundances of many free-living bacterial taxa, some were susceptible to filter feeding, in line with efficient removal of phytoplankton cells of <2 μm. This selective removal of particle-associated and larger bacteria by IDMs altered inferred bacterial functional group representation, defined by carbon and energy source utilization. Specifically, we inferred an increased relative abundance of chemoorganoheterotrophs predicted to be capable of rhodopsin-dependent energy generation. In contrast to the few previous studies that have focused on the longer-term combined direct and indirect effects of IDMs on bacterioplankton, our study showed that IDMs act directly as a biological disturbance to which freshwater bacterial assemblages are sensitive. The negative impacts on particle-associated bacteria, which have been shown to be more active than free-living bacteria, and the inferred shifts in functional group representation raise the possibility that IDMs may directly alter bacterially mediated ecosystem functions. IMPORTANCE Freshwater bacteria play fundamental roles in global elemental cycling and are an intrinsic part of local food webs. Human activities are altering freshwater environments, and much has been learned regarding the sensitivity of bacterial assemblages to a variety of

  12. Consequences of organ choice in describing bacterial pathogen assemblages in a rodent population.

    Science.gov (United States)

    Villette, P; Afonso, E; Couval, G; Levret, A; Galan, M; Tatard, C; Cosson, J F; Giraudoux, P

    2017-10-01

    High-throughput sequencing technologies now allow for rapid cost-effective surveys of multiple pathogens in many host species including rodents, but it is currently unclear if the organ chosen for screening influences the number and identity of bacteria detected. We used 16S rRNA amplicon sequencing to identify bacterial pathogens in the heart, liver, lungs, kidneys and spleen of 13 water voles (Arvicola terrestris) collected in Franche-Comté, France. We asked if bacterial pathogen assemblages within organs are similar and if all five organs are necessary to detect all of the bacteria present in an individual animal. We identified 24 bacteria representing 17 genera; average bacterial richness for each organ ranged from 1·5 ± 0·4 (mean ± standard error) to 2·5 ± 0·4 bacteria/organ and did not differ significantly between organs. The average bacterial richness when organ assemblages were pooled within animals was 4·7 ± 0·6 bacteria/animal; Operational Taxonomic Unit accumulation analysis indicates that all five organs are required to obtain this. Organ type influences bacterial assemblage composition in a systematic way (PERMANOVA, 999 permutations, pseudo-F 4,51 = 1·37, P = 0·001). Our results demonstrate that the number of organs sampled influences the ability to detect bacterial pathogens, which can inform sampling decisions in public health and wildlife ecology.

  13. Plumage bacterial assemblages in a breeding wild passerine: relationships with ecological factors and body condition.

    Science.gov (United States)

    Saag, Pauli; Tilgar, Vallo; Mänd, Raivo; Kilgas, Priit; Mägi, Marko

    2011-05-01

    Microorganisms have been shown to play an important role in shaping the life histories of animals, and it has recently been suggested that feather-degrading bacteria influence the trade-off between parental effort and self-preening behavior in birds. We studied a wild breeding population of great tits (Parus major) to explore habitat-, seasonal-, and sex-related variation in feather-degrading and free-living bacteria inhabiting the birds' yellow ventral feathers and to investigate associations with body condition. The density and species richness of bacterial assemblages was studied using flow cytometry and ribosomal intergenic spacer analysis. The density of studied bacteria declined between the nest-building period and the first brood. The number of bacterial phylotypes per bird was higher in coniferous habitat, while bacterial densities were higher in deciduous habitat. Free-living bacterial density was positively correlated with female mass; conversely, there was a negative correlation between attached bacterial density and female mass during the period of peak reproductive effort. Bacterial species richness was sex dependent, with more diverse bacterial assemblages present on males than females. Thus, this study revealed that bacterial assemblages on the feathers of breeding birds are affected both by life history and ecological factors and are related to body condition.

  14. Balanced Fertilization Decreases Environmental Filtering on Soil Bacterial Community Assemblage in North China

    Directory of Open Access Journals (Sweden)

    Youzhi Feng

    2017-12-01

    Full Text Available Although increasing evidences have emerged for responses of soil microorganisms to fertilizations, the knowledge regarding community assemblages that cause variations in composition is still lacking, as well as the possible feedback to soil fertility. Phylogenetic conservatism of species indicates their similar environmental preferences and/or function traits and phylogenetic signals further can infer community assemblages and influenced ecological processes. Here, we calculated the mean pairwise phylogenetic distance and nearest relative index, characterizing phylogenetic signal and the undergone ecological process to evaluate the community assembly of soil bacterial phylotypes in 20-year fertilized soils. The bacterial community assembly is structured by environmental filtering, regardless of fertilization regime. Soil phosphorous (P availability imposes selection on community assemblage and influences their community turnover among fertilizations. When P nutrient lacks, the effect of environmental filtering becomes stronger, hence bacterial functional traits become more coherent; this process results into increased intraspecific interactions characterized by co-occurrence network analysis. In contrast, when P nutrient becomes abundant, the environmental selection is mitigated; function traits are evened. This process reduces intraspecific interactions and increases carbon sequestration efficiency, which is finally of great favor to the increases in soil fertility. This study has made the first attempt, at the bacterial level, to understand how fertilization affects agroecosystems. When more phylogenetic information on how nutrient cycling-related microbes respond to fertilization becomes available, the systematic knowledge will eventually provide guidance to optimal fertilization strategies.

  15. Composition of Bacterial Assemblages in Different Components of Reed Warbler Nests and a Possible Role of Egg Incubation in Pathogen Regulation.

    Directory of Open Access Journals (Sweden)

    Hanja B Brandl

    Full Text Available Bacteria play a central role in animal health. Yet, little is known about the acquisition of bacteria and the extent to which bacteria are acquired from different environmental sources. For example, bird nests host diverse bacteria associated with the eggs, nestlings and nesting material, but previous research has typically focussed on only a limited number of nest components at a time. It therefore remains unknown to what extent bacteria are transmitted between these components. Using both molecular and culture techniques, we characterised nest-associated bacterial assemblages throughout the entire nesting cycle of reed warblers by sampling bacteria on eggs before and during incubation, within nestling faeces, and on the nesting material of post-breeding nests. We found that bacterial assemblages clustered by nest component. Yet some overlap existed between nest components, suggesting that bacterial transmission across components is likely to occur. Eggs and nestlings from the same nest harboured more similar bacteria than expected by chance, suggesting an influence of environment or genetics on bacterial assemblages. Bacterial loads were not lower on incubated eggs. Instead, incubation was associated with a change in the structure of assemblages, including a decrease in potentially-harmful Gram-negative bacteria. In addition we show for the first time, that incubation is associated with the complete extinction of harmful haemolytic bacteria. Overall, our study appears to be the first to demonstrate differences in bacterial assemblages between bird nest components. In addition, we highlight the complexity of nest bacterial assemblages and provide new insights into the benefits of incubation.

  16. Microplastic-associated bacterial assemblages in the intertidal zone of the Yangtze Estuary.

    Science.gov (United States)

    Jiang, Peilin; Zhao, Shiye; Zhu, Lixin; Li, Daoji

    2018-05-15

    Plastic trash is common in oceans. Terrestrial and marine ecosystem interactions occur in the intertidal zone where accumulation of plastic frequently occurs. However, knowledge of the plastic-associated microbial community (the plastisphere) in the intertidal zone is scanty. We used high-throughput sequencing to profile the bacterial communities attached to microplastic samples from intertidal locations around the Yangtze estuary in China. The structure and composition of plastisphere communities varied significantly among the locations. We found the taxonomic composition on microplastic samples was related to their sedimentary and aquatic origins. Correlation network analysis was used to identify keystone bacterial genera (e.g. Rhodobacterales, Sphingomonadales and Rhizobiales), which represented important microbial associations within the plastisphere community. Other species (i.e. potential pathogens) were considered as hitchhikers in the plastic attached microbial communities. Metabolic pathway analysis suggested adaptations of these bacterial assemblages to the plastic surface-colonization lifestyle. These adaptations included reduced "cell motility" and greater "xenobiotics biodegradation and metabolism." The findings illustrate the diverse microbial assemblages that occur on microplastic and increase our understanding of plastisphere ecology. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Comparison of cell-specific activity between free-living and attached bacteria using isolates and natural assemblages

    DEFF Research Database (Denmark)

    Grossart, H.P.; Tang, K.W.; Kiørboe, Thomas

    2007-01-01

    Marine snow aggregates are microbial hotspots that support high bacterial abundance and activities. We conducted laboratory experiments to compare cell-specific bacterial protein production (BPP) and protease activity between free-living and attached bacteria. Natural bacterial assemblages attached...... bacteria increasing their metabolism upon attachment to surfaces. In subsequent experiments, we used four strains of marine snow bacteria isolates to test the hypothesis that bacteria could up- and down-regulate their metabolism while on and off an aggregate. The protease activity of attached bacteria...... to model aggregates (agar spheres) had threefold higher BPP and two orders of magnitude higher protease activity than their free-living counterpart. These observations could be explained by preferential colonization of the agar spheres by bacteria with inherently higher metabolic activity and/or individual...

  18. Effects of immune supplementation and immune challenge on bacterial assemblages in the avian cloaca

    NARCIS (Netherlands)

    Matson, Kevin D.; Versteegh, Maaike A.; van der Velde, Marco; Tieleman, B. Irene

    Relationships between avian physiology and bacterial assemblages in the cloaca are poorly understood. We used molecular techniques to analyze cloacal swabs from pigeons that were subjected to two immunological manipulations: lysozyme supplementation and endotoxin challenge. From the swabs, we

  19. TBT toxicity on a natural planktonic assemblage exposed to enhanced ultraviolet-B radiation.

    Science.gov (United States)

    Sargian, Peggy; Pelletier, Emilien; Mostajir, Behzad; Ferreyra, Gustavo A; Demers, Serge

    2005-07-01

    A microcosm approach was designed to study the combined effects of tributyltin (TBT) from antifouling paints and ultraviolet-B radiation (UVBR: 280-320 nm), on a natural planktonic assemblage (TBT (120 ng l -1) and enhanced UVBR (giving a biologically weighted UVBR 2.15-fold higher than natural light condition) were monitored in the samples coming from following treatments: (i) NUVBR light condition without TBT (NUVBR), (ii) NUVBR light condition with TBT-added (NUVBR+TBT), (iii) HUVBR light condition without TBT (HUVBR) and (iv) HUVBR light condition with TBT-added (HUVBR+TBT). Each treatment was conducted in triplicate microcosms. Different parameters were then measured during 5 days, including TBT analysis, bacterial abundance and productivity, phytoplankton abundance, cellular characteristics and growth rates, as well as in vivo chlorophyll a (Chl a) fluorescence. Following TBT addition (NUVBR+TBT treatment), Chl a concentrations never exceeded 1 microg l-1 whereas final values as high as 54 microg l-1 were observed in TBT-free treatments (NUVBR and HUVBR). TBT addition resulted also in the lost of fluorescence signal of the maximum efficiency of the photosystem II in phytoplankton assemblage. TBT toxicity caused on phytoplankton TBT resulted in a final abundance of phytoplankton TBT relative to NUVBR treatment (i.e., 31,846+/-312 cells ml-1). Moreover, when cells were submitted to TBT under enhanced UVBR (HUVBR+TBT treatment), final abundance of phytoplankton TBT and UVBR during the last 2 days of the experiment. The same type of interaction was also observed for bacterial abundance in NUVBR+TBT and HUVBR+TBT with stimulation of 226 and of 403%, respectively due to TBT addition relative to NUVBR treatment. When considering bacterial productivity, TBT addition resulted in an inhibition of 32%, and this inhibition was significantly more pronounced under dual stresses (i.e., 77% in HUVBR+TBT). These results clearly demonstrate that the combination of TBT and UVBR

  20. TBT toxicity on a natural planktonic assemblage exposed to enhanced ultraviolet-B radiation

    International Nuclear Information System (INIS)

    Sargian, Peggy; Pelletier, Emilien; Mostajir, Behzad; Ferreyra, Gustavo A.; Demers, Serge

    2005-01-01

    A microcosm approach was designed to study the combined effects of tributyltin (TBT) from antifouling paints and ultraviolet-B radiation (UVBR: 280-320 nm), on a natural planktonic assemblage ( -1 ) and enhanced UVBR (giving a biologically weighted UVBR 2.15-fold higher than natural light condition) were monitored in the samples coming from following treatments: (i) NUVBR light condition without TBT (NUVBR) (ii) NUVBR light condition with TBT-added (NUVBR + TBT) (iii) HUVBR light condition without TBT (HUVBR) and (iv) HUVBR light condition with TBT-added (HUVBR + TBT). Each treatment was conducted in triplicate microcosms. Different parameters were then measured during 5 days, including TBT analysis, bacterial abundance and productivity, phytoplankton abundance, cellular characteristics and growth rates, as well as in vivo chlorophyll a (Chl a) fluorescence. Following TBT addition (NUVBR + TBT treatment), Chl a concentrations never exceeded 1 μg l -1 whereas final values as high as 54 μg l -1 were observed in TBT-free treatments (NUVBR and HUVBR). TBT addition resulted also in the lost of fluorescence signal of the maximum efficiency of the photosystem II in phytoplankton assemblage. TBT toxicity caused on phytoplankton -1 in NUVBR + TBT relative to NUVBR treatment (i.e., 31,846 ± 312 cells ml -1 ). Moreover, when cells were submitted to TBT under enhanced UVBR (HUVBR + TBT treatment), final abundance of phytoplankton -1 , with a significant interaction between TBT and UVBR during the last 2 days of the experiment. The same type of interaction was also observed for bacterial abundance in NUVBR + TBT and HUVBR + TBT with stimulation of 226 and of 403%, respectively due to TBT addition relative to NUVBR treatment. When considering bacterial productivity, TBT addition resulted in an inhibition of 32%, and this inhibition was significantly more pronounced under dual stresses (i.e., 77% in HUVBR + TBT). These results clearly demonstrate that the combination of TBT

  1. Vertical and horizontal assemblage patterns of bacterial communities in a eutrophic river receiving domestic wastewater in southeast China.

    Science.gov (United States)

    Gao, Yan; Wang, Chengcheng; Zhang, Weiguo; Di, Panpan; Yi, Neng; Chen, Chengrong

    2017-11-01

    Bacterial communities in rivers receiving untreated domestic wastewater may show specific spatial assemblage patterns due to a wide range of physicochemical conditions created by periodic algal bloom. However, there are significant gaps in understanding environmental forces that drive changes in microbial assemblages in polluted rivers. In this study, we applied high-throughput sequencing of 16S rRNA gene amplicons to perform comprehensive spatio-temporal profiling of bacterial community structure in a local river segment receiving domestic wastewater discharge in southeast China. Multivariate statistics were then used to analyse links between bacterial community structure and environmental factors. Non-metric multidimensional scaling (NMDS) plots showed that the bacterial community structure was different between upstream and downstream sections of the river. While the upstream water contained a high proportion of bacteria degrading xenobiotic aromatic compounds, the downstream water experiencing stronger algal bloom had a more diverse bacterial community which included the genus Aeromonas comprising 14 species, most of which are human pathogens. Least discriminant analysis (LDA) effect size revealed that the surface water was mainly inhabited by aerobic microorganisms capable of degrading aromatic compounds, and also contained bacterial genera including pathogenic species. In contrast, in the bottom water we found, along with aromatic compound-degrading species, anaerobic denitrifiers and Fe 3+ -reducing and fermentative bacteria. Variance partitioning canonical correspondence analysis (VPA) showed that nutrient ratios had a stronger contribution to bacterial dissimilarities than other major physicochemical factors (temperature, pH, dissolved oxygen, total organic carbon, and chlorophyll a). These results show that microbial communities in rivers continuously receiving domestic wastewater have specific longitudinal and vertical assemblage patterns and may contain

  2. Covariation of viral parameters with bacterial assemblage richness and diversity in the water column and sediments

    Science.gov (United States)

    Hewson, Ian; Fuhrman, Jed A.

    2007-05-01

    Viruses are hypothesized to maintain diversity in microbial assemblages by regulating the abundance of dominant competitors and thereby allowing less-dominant competitors to persist in assemblages; however, there have been few empirical data sets to support this idea. In this study, we examined the relationship between the ratio of viral abundance to bacterial abundance, viral production, and the relative richness and diversity of bacterial assemblage fingerprints, in samples taken from geographically widespread locations (North Pacific gyre, the Amazon River plume and adjacent North Atlantic gyre, Gulf of Mexico, Southern California Bight and Arafura—Coral Seas) which are oligo- to mesotrophic. Bacterial assemblage richness and diversity as measured by automated rRNA intergenic spacer (ARISA) fingerprinting were significantly and positively correlated with the ratio of virus abundance to bacteria abundance (VBR) and to the rate of virus production only in the oligotrophic North Pacific gyre. ARISA fingerprint richness/diversity were not significantly correlated to viral parameters when assessed across all samples in surface waters, suggesting there is not a singular global quantitative relationship between viral pressure and host diversity within well evolved host/virus systems in different geographic locations in plankton. In sediments off Southern California, viral parameters significantly and negatively correlated with ARISA diversity, suggesting strong viral interactions in this habitat. To examine covariation of viral parameters and the relative abundance and diversity of rarer bacterial taxa (i.e., less-dominant competitor), the richness and diversity of diazotroph communities was measured using terminal restriction fragment length polymorphism (TRFLP) of a portion ( nifH) of the nitrogenase gene. The richness and diversity of diazotrophic communities were significantly and negatively correlated with viral parameters across all locations. Since diazotrophs

  3. Microplastic-associated Bacterial Assemblages in the Intertidal Zone

    Science.gov (United States)

    Jiang, P.; Zhao, S.; Zhu, L.; Li, D.

    2017-12-01

    Plastic debris is posing a planetary-scale threat. As a zone where terrestrial and marine ecosystems interactions occur, the accumulation of plastic marine debris (PMD) in intertidal environments has been well documented. But the information of plastic-associated microbial community (the "Plastisphere") in the intertidal zone is scanty. Utilizing the high-throughput sequencing, we profiled the bacterial communities attached to microplastic samples from the intertidal locations around Yangtze estuary. The structure and composition of Plastisphere communities in current study varied significantly with geographical stations. The taxonomic composition on microplastic samples implied their sedimental and aquatic origins. Some members of hydrocarbon degrading microorganisms and potential pathogens were detected on microplastic. Overall, our findings fuel the evidence for the occurrence of diverse microbial assemblages on PMD and improving our understanding of Plastisphere ecology, which could support the management action and policy change related to PMD.

  4. Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

    Directory of Open Access Journals (Sweden)

    Justin Wright

    2017-11-01

    ranges, indicating niche-specific responses of these autochthonous populations. Altogether, our findings suggest that monitored natural attenuation is an appropriate remediation strategy for DCM contamination, and that high-throughput sequencing technologies are a robust method for assessing the potential role of biodegrading bacterial assemblages in the apparent reduction of DCM concentrations in environmental scenarios.

  5. TBT toxicity on a natural planktonic assemblage exposed to enhanced ultraviolet-B radiation

    Energy Technology Data Exchange (ETDEWEB)

    Sargian, Peggy [Institut des Sciences de la Mer de Rimouski (ISMER), Universite du Quebec a Rimouski, 310, Allee des Ursulines, Rimouski, Que., G5L 3A1 (Canada)]. E-mail: peggy_sargian@uqar.qc.ca; Pelletier, Emilien [Institut des Sciences de la Mer de Rimouski (ISMER), Universite du Quebec a Rimouski, 310, Allee des Ursulines, Rimouski, Que., G5L 3A1 (Canada); Mostajir, Behzad [Reseaux trophiques pelagiques (GDR 2476) et Ecologie Microbienne des milieux Aquatiques, UMR 5119 Ecosystemes lagunaires, CNRS-Universite Montpellier II, Case 093, 34095 Montpellier Cedex 5 (France); Ferreyra, Gustavo A. [Institut des Sciences de la Mer de Rimouski (ISMER), Universite du Quebec a Rimouski, 310, Allee des Ursulines, Rimouski, Que., G5L 3A1 (Canada); Instituto Antartico Argentino (IAA), Cerrito 1248 (C1010AAZ), Buenos Aires (Argentina); Demers, Serge [Institut des Sciences de la Mer de Rimouski (ISMER), Universite du Quebec a Rimouski, 310, Allee des Ursulines, Rimouski, Que., G5L 3A1 (Canada)

    2005-07-01

    A microcosm approach was designed to study the combined effects of tributyltin (TBT) from antifouling paints and ultraviolet-B radiation (UVBR: 280-320 nm), on a natural planktonic assemblage (<150 {mu}m) isolated from the St. Lawrence Estuary at the end of the springtime. Microcosms (9 l, cylindrical Teflon[reg] bags, 75 cm height x 25 cm width) were immersed in the water column of mesocosms (1800 l, polyethylene bags, 2.3 m depth) and exposed to two different UVBR regimes: natural ambient UVBR (NUVBR), and enhanced level of UVBR (HUVBR). During consecutive 5 days, effects of TBT (120 ng l{sup -1}) and enhanced UVBR (giving a biologically weighted UVBR 2.15-fold higher than natural light condition) were monitored in the samples coming from following treatments: (i) NUVBR light condition without TBT (NUVBR) (ii) NUVBR light condition with TBT-added (NUVBR + TBT) (iii) HUVBR light condition without TBT (HUVBR) and (iv) HUVBR light condition with TBT-added (HUVBR + TBT). Each treatment was conducted in triplicate microcosms. Different parameters were then measured during 5 days, including TBT analysis, bacterial abundance and productivity, phytoplankton abundance, cellular characteristics and growth rates, as well as in vivo chlorophyll a (Chl a) fluorescence. Following TBT addition (NUVBR + TBT treatment), Chl a concentrations never exceeded 1 {mu}g l{sup -1} whereas final values as high as 54 {mu}g l{sup -1} were observed in TBT-free treatments (NUVBR and HUVBR). TBT addition resulted also in the lost of fluorescence signal of the maximum efficiency of the photosystem II in phytoplankton assemblage. TBT toxicity caused on phytoplankton <20 {mu}m an increase of mean cell size and changes in shape reflected a drastic disturbance of the cell cycle leading to an inhibition of the apparent growth rate. These negative effects of TBT resulted in a final abundance of phytoplankton <20 {mu}m of 591 {+-} 35 cells ml{sup -1} in NUVBR + TBT relative to NUVBR treatment (i

  6. Bacterial abundance, communities and heterotrophic activities in the coastal waters off Tamil Nadu

    Digital Repository Service at National Institute of Oceanography (India)

    Ramaiah, N.; Raghukumar, C.; Sheelu, G.; Chandramohan, D.

    Culturable aerobic heterotrophic bacterial (CAHB) numbers, total direct counts (TDC), bacterial generic composition and uptake of labelled glucose by natural microbial assemblages were studied from a few selected coastal sites off Tamil Nadu. A high...

  7. Assessing Interactions of Multiple Agrichemicals by Using Bacterial Assemblages in a Wetland Mesocosm System

    Directory of Open Access Journals (Sweden)

    Bruce Libman

    2005-08-01

    Full Text Available Agrichemicals may enter wetlands located adjacent to or downstream from agricultural fields. We investigated the individual and interactive effects of three agrichemicals [atrazine, chlorpyrifos, and monosodium acid methanearsonate (MSMA] and methyl mercury on abundance and heterotrophic potential of wetland heterotrophic bacteria assemblages. We used a factorial experimental design, in which chemicals were introduced in all possible combinations to 66 500-liter mesocosms at the Biological Field Station of the University of Mississippi. Methyl mercury was added to bring the total mercury (HG concentration to 0.4 mg/Kg wet weight at the sediment surface. Atrazine, chlorpyrifos, and MSMA were added at concentrations of 192, 51, and 219μg/L, respectively. Over 32 days of exposure, microbial heterotrophic activity was sensitive to only the interactive effect of HG*ATR*CPF in the sediments and only CPF in the water. Total bacterial numbers did not exhibit any significant treatment effects. Therefore, the effects of agrichemicals were reflected on cell-specific bacterial heterotrophic activity rather than bacterial population size.

  8. Who possesses drug resistance genes in the aquatic environment?: sulfamethoxazole (SMX) resistance genes among the bacterial community in water environment of Metro-Manila, Philippines.

    Science.gov (United States)

    Suzuki, Satoru; Ogo, Mitsuko; Miller, Todd W; Shimizu, Akiko; Takada, Hideshige; Siringan, Maria Auxilia T

    2013-01-01

    Recent evidence has shown that antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are ubiquitous in natural environments, including sites considered pristine. To understand the origin of ARGs and their dynamics, we must first define their actual presence in the natural bacterial assemblage. Here we found varying distribution profiles of sul genes in "colony forming bacterial assemblages" and "natural bacterial assemblages." Our monitoring for antibiotic contamination revealed that sulfamethoxazole (SMX) is a major contaminant in aquatic environments of Metro-Manila, which would have been derived from human and animal use, and subsequently decreased through the process of outflow from source to the sea. The SMX-resistant bacterial rate evaluated by the colony forming unit showed 10 to 86% of the total colony numbers showed higher rates from freshwater sites compared to marine sites. When sul genes were quantified by qPCR, colony-forming bacteria conveyed sul1 and sul2 genes in freshwater and seawater (10(-5)-10(-2) copy/16S) but not sul3. Among the natural bacterial assemblage, all sul1, sul2, and sul3 were detected (10(-5)-10(-3) copy/16S), whereas all sul genes were at an almost non-detectable level in the freshwater assemblage. This study suggests that sul1 and sul2 are main sul genes in culturable bacteria, whereas sul3 is conveyed by non-culturable bacteria in the sea. As a result marine bacteria possess sul1, sul2 and sul3 genes in the marine environment.

  9. Who Possesses Drug Resistance Genes in the Aquatic Environment? : Sulfamethoxazole (SMX Resistance Genes among the Bacterial Community in Water Environment of Metro-Manila, Philippines

    Directory of Open Access Journals (Sweden)

    Satoru eSuzuki

    2013-04-01

    Full Text Available Recent evidence has shown that antibiotic resistant bacteria (ARB and antibiotic resistance genes (ARG are ubiquitous in natural environments, including sites considered pristine. To understand the origin of ARGs and their dynamics, we must first define their actual presence in the natural bacterial assemblage. Here we found varying distribution profiles of sul genes in colony forming bacterial assemblages and natural bacterial assemblages. Our monitoring for antibiotic contamination revealed that sulfamethoxazole (SMX is a major contaminant in aquatic environments of Metro-Manila, which would have been derived from human and animal use, and subsequently decreased through the process of outflow from source to the sea. The SMX-resistant bacterial rate evaluated by the colony forming unit showed 10 to 86 % of the total colony numbers showed higher rates from freshwater sites compared to marine sites. When sul genes were quantified by qPCR, colony-forming bacteria conveyed sul1 and sul2 genes in freshwater and seawater (10-5-10-2 copy/16S but not sul3. Among the natural bacterial assemblage, all sul1, sul2 and sul3 were detected (10-5-10-3 copy/16S, whereas all sul genes were at an almost non-detectable level in the freshwater assemblage. This study suggests that sul1 and sul2 are main sul genes in culturable bacteria, whereas sul3 is conveyed by non-culturable bacteria in the sea. As a result marine bacteria possess sul1, sul2 and sul3 genes in the marine environment.

  10. Butterfly (Papilionoidea and Hesperioidea) assemblages associated with natural, exotic, and restored riparian habitats along the lower Colorado River, USA

    Science.gov (United States)

    Nelson, S.M.; Andersen, D.C.

    1999-01-01

    Butterfly assemblages were used to compare revegetated and natural riparian areas along the lower Colorado River. Species richness and correspondence analyses of assemblages showed that revegetated sites had fewer biological elements than more natural sites along the Bill Williams River. Data suggest that revegetated sites do not provide resources needed by some members of the butterfly assemblage, especially those species historically associated with the cottonwood/willow ecosystem. Revegetated sites generally lacked nectar resources, larval host plants, and closed canopies. The riparian system along the regulated river segment that contains these small revegetated sites also appears to have diminished habitat heterogeneity and uncoupled riparian corridors.Revegetated sites were static environments without the successional stages caused by flooding disturbance found in more natural systems. We hypothesize that revegetation coupled with a more natural hydrology is important for restoration of butterfly assemblages along the lower Colorado River. 

  11. Key Issues Concerning Biolog Use for Aerobic and Anaerobic Freshwater Bacterial Community-Level Physiological Profiling

    Science.gov (United States)

    Christian, Bradley W.; Lind, Owen T.

    2006-06-01

    Bacterial heterotrophy in aquatic ecosystems is important in the overall carbon cycle. Biolog MicroPlates provide information into the metabolic potential of bacteria involved in carbon cycling. Specifically, Biolog EcoPlatesTM were developed with ecologically relevant carbon substrates to allow investigators to measure carbon substrate utilization patterns and develop community-level physiological profiles from natural bacterial assemblages. However, understanding of the functionality of these plates in freshwater research is limited. We explored several issues of EcoPlate use for freshwater bacterial assemblages including inoculum density, incubation temperature, non-bacterial color development, and substrate selectivity. Each of these has various effects on plate interpretation. We offer suggestions and techniques to resolve these interpretation issues. Lastly we propose a technique to allow EcoPlate use in anaerobic freshwater bacterial studies.

  12. Differences in stability of seed-associated microbial assemblages in response to invasion by phytopathogenic microorganisms

    Directory of Open Access Journals (Sweden)

    Samir Rezki

    2016-04-01

    Full Text Available Seeds are involved in the vertical transmission of microorganisms from one plant generation to another and consequently act as reservoirs for the plant microbiota. However, little is known about the structure of seed-associated microbial assemblages and the regulators of assemblage structure. In this work, we have assessed the response of seed-associated microbial assemblages of Raphanus sativus to invading phytopathogenic agents, the bacterial strain Xanthomonas campestris pv. campestris (Xcc 8004 and the fungal strain Alternaria brassicicola Abra43. According to the indicators of bacterial (16S rRNA gene and gyrB sequences and fungal (ITS1 diversity employed in this study, seed transmission of the bacterial strain Xcc 8004 did not change the overall composition of resident microbial assemblages. In contrast seed transmission of Abra43 strongly modified the richness and structure of fungal assemblages without affecting bacterial assemblages. The sensitivity of seed-associated fungal assemblage to Abra43 is mostly related to changes in relative abundance of closely related fungal species that belong to the Alternaria genus. Variation in stability of the seed microbiota in response to Xcc and Abra43 invasions could be explained by differences in seed transmission pathways employed by these micro-organisms, which ultimately results in divergence in spatio-temporal colonization of the seed habitat.

  13. Phosphatized algal-bacterial assemblages in Late Cretaceous phosphorites of the Voronezh Anteclise

    Science.gov (United States)

    Maleonkina, Svetlana Y.

    2003-01-01

    Late Cretaceous phosphogenesis of the Voronezh Anteclise has occurred during Cenomanian and Early Campanian. SEM studies show the presence of phosphatized algal-bacterial assemblages both in Cenomanian and Campanian phosphorites. In some Cenomanian nodular phosphorite samples revealed empty tubes 1 - 5 microns in diameter, which are most likely trichomes of cyanobacterial filaments. Other samples contained accumulations of spheres 0,5-3 microns, similar to coccoidal bacteria. Complicated tubular forms with variable diameter 2 - 5 microns occur on surface of some quartz grains in nodules. They are probably pseudomorphs after algae. We found similar formations in the Campanian phosphate grains. Frequently, grain represents a cyanobacterial mat, which is sometimes concentrically coated by phosphatic films. The films of some grains retain the primary structure, their concentric layers are formed by pseudomorphs after different bacterial types and obviously they represent oncolite. In other cases, the primary structure is unobservable because of recrystallization process erases them. Occasionally, the central part retains the coccoidal structure and the recrystallization affects only films. Besides the core of such oncolite can be represented not only by phosphatic grain, but also by grains of other minerals, such as quartz, glauconite and heavy minerals, which serve as a substrate for cyanobacterial colonies. Bacteria also could settle on cavity surfaces and interiors frames of sponge fragments, teeth and bones.

  14. Temporal variability of fish larvae assemblages: influence of natural and anthropogenic disturbances

    Directory of Open Access Journals (Sweden)

    David A. Reynalte-Tataje

    Full Text Available Natural and induced disturbances greatly influence the temporal distribution of ichthyoplankton abundance. This study assesses and compares the temporal variability of fish larvae assemblages in controlled and free environments to determine the influence of environment variables on the main taxa in these systems. The study was conducted at the Chapecó (without dam impact and Ligeiro (with dam impact river mouths, which are located in the upper Uruguay River. Samples were made between October 2001 and March 2004 during three reproductive periods. The larvae assemblages were composed of small and medium-sized Characiformes and Siluriformes. The variation in the distribution of larvae was mainly temporal (>85%. When the three reproductive periods were compared, it was observed in the second period, characterized by a larger water flow and a lower temperature, that there was a reduction in abundance, a lower number of taxa, an absence of stages in post-flexion and a high dissimilarity in larvae assemblage structure. In general, the environmental variables of water flow and temperature most influenced the distribution of egg and larvae abundance. In the studied area, a smaller temporal variability was observed in the structure of larvae assemblages at the sampling sites in the Chapecó River mouth than in in the Ligeiro River mouth under the influence of dams.

  15. Phytoplankton-Associated Bacterial Community Composition and Succession during Toxic Diatom Bloom and Non-Bloom Events.

    Science.gov (United States)

    Sison-Mangus, Marilou P; Jiang, Sunny; Kudela, Raphael M; Mehic, Sanjin

    2016-01-01

    Pseudo-nitzschia blooms often occur in coastal and open ocean environments, sometimes leading to the production of the neurotoxin domoic acid that can cause severe negative impacts to higher trophic levels. Increasing evidence suggests a close relationship between phytoplankton bloom and bacterial assemblages, however, the microbial composition and succession during a bloom process is unknown. Here, we investigate the bacterial assemblages before, during and after toxic and non-toxic Pseudo-nitzschia blooms to determine the patterns of bacterial succession in a natural bloom setting. Opportunistic sampling of bacterial community profiles were determined weekly at Santa Cruz Municipal Wharf by 454 pyrosequencing and analyzed together with domoic acid levels, phytoplankton community and biomass, nutrients and temperature. We asked if the bacterial communities are similar between bloom and non-bloom events and if domoic acid or the presence of toxic algal species acts as a driving force that can significantly structure phytoplankton-associated bacterial communities. We found that bacterial diversity generally increases when Pseudo-nitzschia numbers decline. Furthermore, bacterial diversity is higher when the low-DA producing P. fraudulenta dominates the algal bloom while bacterial diversity is lower when high-DA producing P. australis dominates the algal bloom, suggesting that the presence of algal toxin can structure bacterial community. We also found bloom-related succession patterns among associated bacterial groups; Gamma-proteobacteria, were dominant during low toxic P. fraudulenta blooms comprising mostly of Vibrio spp., which increased in relative abundance (6-65%) as the bloom progresses. On the other hand, Firmicutes bacteria comprising mostly of Planococcus spp. (12-86%) dominate during high toxic P. australis blooms, with the bacterial assemblage showing the same bloom-related successional patterns in three independent bloom events. Other environmental

  16. Phytoplankton-associated bacterial community composition and succession during toxic diatom bloom and non-bloom events

    Directory of Open Access Journals (Sweden)

    Marilou P. Sison-Mangus

    2016-09-01

    Full Text Available Pseudo-nitzschia blooms often occur in coastal and open ocean environments, sometimes leading to the production of the neurotoxin domoic acid that can cause severe negative impacts to higher trophic levels. Increasing evidence suggests a close relationship between phytoplankton bloom and bacterial assemblages, however, the microbial composition and succession during a bloom process is unknown. Here, we investigate the bacterial assemblages before, during and after toxic and non-toxic Pseudo-nitzschia blooms to determine the patterns of bacterial succession in a natural bloom setting. Opportunistic sampling of bacterial community profiles were determined weekly at Santa Cruz Municipal Wharf by 454 pyrosequencing and analyzed together with domoic acid levels, phytoplankton community and biomass, nutrients and temperature. We asked if the bacterial communities are similar between bloom and non-bloom events and if domoic acid or the presence of toxic algal species acts as a driving force that can significantly structure phytoplankton-associated bacterial communities. We found that bacterial diversity generally increases when Pseudo-nitzschia numbers decline. Furthermore, bacterial diversity is higher when the low-DA producing P. fraudulenta dominates the algal bloom while bacterial diversity is lower when high-DA producing P. australis dominates the algal bloom, suggesting that the presence of algal toxin can structure bacterial community. We also found bloom-related succession patterns among associated bacterial groups; Gamma-proteobacteria, were dominant during low toxic P. fraudulenta blooms comprising mostly of Vibrio spp., which increased in relative abundance (6%-65% as the bloom progresses. On the other hand, Firmicutes bacteria comprising mostly of Planococcus spp. (12%- 86% dominate during high toxic P. australis blooms, with the bacterial assemblage showing the same bloom-related successional patterns in 3 independent bloom events. Other

  17. Impacts of temperature on primary productivity and respiration in naturally structured macroalgal assemblages.

    Directory of Open Access Journals (Sweden)

    Leigh W Tait

    Full Text Available Rising global temperatures caused by human-mediated change has already triggered significant responses in organismal physiology, distribution and ecosystem functioning. Although the effects of rising temperature on the physiology of individual organisms are well understood, the effect on community-wide processes has remained elusive. The fixation of carbon via primary productivity is an essential ecosystem function and any shifts in the balance of primary productivity and respiration could alter the carbon balance of ecosystems. Here we show through a series of tests that respiration of naturally structured algal assemblages in southern New Zealand greatly increases with rising temperature, with implications for net primary productivity (NPP. The NPP of in situ macroalgal assemblages was minimally affected by natural temperature variation, possibly through photo-acclimation or temperature acclimation responses, but respiration rates and compensating irradiance were negatively affected. However, laboratory experiments testing the impacts of rising temperature on several photosynthetic parameters showed a decline in NPP, increasing respiration rates and increasing compensating irradiance. The respiration Q10 of laboratory assemblages (the difference in metabolic rates over 10°C averaged 2.9 compared to a Q10 of 2 often seen in other autotrophs. However, gross primary productivity (GPP Q10 averaged 2, indicating that respiration was more severely affected by rising temperature. Furthermore, combined high irradiance and high temperature caused photoinhibition in the laboratory, and resulted in 50% lower NPP at high irradiance. Our study shows that communities may be more severely affected by rising global temperatures than would be expected by responses of individual species. In particular, enhanced respiration rates and rising compensation points have the potential to greatly affect the carbon balance of macroalgal assemblages through declines in

  18. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    Energy Technology Data Exchange (ETDEWEB)

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMcahon, Katherine D.; Mamlstrom, Rex R.

    2014-05-12

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ecotype model? of diversification, but not previously observed in natural populations.

  19. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    Energy Technology Data Exchange (ETDEWEB)

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMahon, Katherine D.; Malmstrom, Rex R.

    2014-06-18

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ‘ecotype model’ of diversification, but not previously observed in natural populations.

  20. How complementary are epibenthic assemblages in artificial and nearby natural rocky reefs?

    KAUST Repository

    Carvalho, Susana

    2013-12-01

    The present study analyses the composition, structure and trophic function of epibenthic assemblages in two artificial reefs (ARs) 16 years after deployment and in nearby natural reefs (NRs), aiming at providing insights on the complementarity between both habitats. Current findings suggest that after 16 years the ARs (concrete blocks), located in southern Portugal, do not act as surrogates for NRs, as epibenthic assemblages differed between reef types in composition, structure and trophic function. NRs showed higher diversity and complementarity (i.e. beta-diversity) than ARs, evidencing higher redundancy. Higher heterogeneity within NRs was also evidenced by the multi-dimensional scaling analysis based on abundance, biomass and trophic composition. NRs presented higher abundance of molluscs and biomass of sponges, resulting in differences in the trophic function: suspension-feeding dominated the NRs, while within ARs there was an ascendency of carnivory. Although not acting as surrogates for NRs and provided that no adverse effects (e.g. establishment of non-native species) were detected, ARs may have a significant contribution for the increase of regional diversity, as evidenced by the highest complementarity levels observed between assemblages in both reefs. © 2013 Elsevier Ltd.

  1. How complementary are epibenthic assemblages in artificial and nearby natural rocky reefs?

    KAUST Repository

    Carvalho, Susana; Moura, Ana; Cú rdia, Joã o; Cancela da Fonseca, Luí s; Santos, Miguel N.

    2013-01-01

    The present study analyses the composition, structure and trophic function of epibenthic assemblages in two artificial reefs (ARs) 16 years after deployment and in nearby natural reefs (NRs), aiming at providing insights on the complementarity between both habitats. Current findings suggest that after 16 years the ARs (concrete blocks), located in southern Portugal, do not act as surrogates for NRs, as epibenthic assemblages differed between reef types in composition, structure and trophic function. NRs showed higher diversity and complementarity (i.e. beta-diversity) than ARs, evidencing higher redundancy. Higher heterogeneity within NRs was also evidenced by the multi-dimensional scaling analysis based on abundance, biomass and trophic composition. NRs presented higher abundance of molluscs and biomass of sponges, resulting in differences in the trophic function: suspension-feeding dominated the NRs, while within ARs there was an ascendency of carnivory. Although not acting as surrogates for NRs and provided that no adverse effects (e.g. establishment of non-native species) were detected, ARs may have a significant contribution for the increase of regional diversity, as evidenced by the highest complementarity levels observed between assemblages in both reefs. © 2013 Elsevier Ltd.

  2. No correlation between the diversity and productivity of assemblages: evidence from the phytophage and predator assemblages in various cotton agroecosystems.

    Science.gov (United States)

    Gao, Feng; Men, XingYuan; Ge, Feng

    2014-09-01

    Biodiversity research has shown that primary productivity increases with plant species number, especially in many experimental grassland systems. Here, we assessed the correlation between productivity and diversity of phytophages and natural enemy assemblages associated with planting date and intercropping in four cotton agroecosystems. Twenty-one pairs of data were used to determine Pearson correlations between species richness, total number of individuals, diversity indices and productivity for each assemblage every five days from 5 June to 15 September 2012. At the same trophic level, the productivity exhibited a significant positive correlation with species richness of the phytophage or predator assemblage. A significant correlation was found between productivity and total number of individuals in most cotton fields. However, no significant correlations were observed between productivity and diversity indices (including indices of energy flow diversity and numerical diversity) in most cotton fields for either the phytophage or the predator assemblages. Species richness of phytophage assemblage and total individual numbers were significantly correlated with primary productivity. Also, species richness of natural enemy assemblage and total number of individuals correlated with phytophage assemblage productivity. A negative but not significant correlation occurred between the indices of numerical diversity and energy flow diversity and lower trophic-level productivity in the cotton-phytophage and phytophage-predator assemblages for most intercropped cotton agroecosystems. Our results clearly showed that there were no correlations between diversity indices and productivity within the same or lower trophic levels within the phytophage and predator assemblages in cotton agroecosystems, and inter-cropped cotton fields had a stronger ability to support the natural enemy assemblage and potentially to reduce phytophages.

  3. Marine heatwaves and optimal temperatures for microbial assemblage activity.

    Science.gov (United States)

    Joint, Ian; Smale, Dan A

    2017-02-01

    The response of microbial assemblages to instantaneous temperature change was measured in a seasonal study of the coastal waters of the western English Channel. On 18 occasions between November 1999 and December 2000, bacterial abundance was assessed and temperature responses determined from the incorporation of 3 H leucine, measured in a temperature gradient from 5°C to 38°C. Q 10 values varied, being close to 2 in spring and summer but were >3 in autumn. There was a seasonal pattern in the assemblage optimum temperature (T opt ), which was out of phase with sea surface temperature. In July, highest 3 H-leucine incorporation rates were measured at temperatures that were only 2.8°C greater than ambient sea surface temperature but in winter, T opt was ∼20°C higher than the ambient sea surface temperature. Sea surface temperatures for the adjacent English Channel and Celtic Sea for 1982-2014 have periodically been >3°C higher than climatological mean temperatures. This suggests that discrete periods of anomalously high temperatures might be close to, or exceed, temperatures at which maximum microbial assemblage activity occurs. The frequency and magnitude of marine heatwaves are likely to increase as a consequence of anthropogenic climate change and extreme temperatures may influence the role of bacterial assemblages in biogeochemical processes. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  4. Bacterial biogeography influenced by shelf-basin exchange in the Arctic surface sediment at the Chukchi Borderland.

    Science.gov (United States)

    Han, Dukki; Nam, Seung-Il; Ha, Ho Kyung; Kim, Hyoungjun; Sadowsky, Michael J; Lee, Yoo Kyung; Hur, Hor-Gil

    2016-02-01

    It has been known that continental shelves around the Arctic Ocean play a major role in the ventilation of the deep basins as a consequence of shelf-basin exchange. In the present study, we found that bacterial assemblage of the surface sediment was different from that of seawater while seawater harboured local bacterial assemblages in response to the Arctic hydrography. This finding suggests that the Arctic seafloor sediments may have distinctive bacterial biogeography. Moreover, the distribution of bacterial assemblages and physicochemical properties in surface sediments changed gradually from the Arctic continental shelf to deep-sea basin. Based on the results, bacterial biogeography in the Arctic seafloor sediments may be influenced by winnowing and re-deposition of surface sediments through the sediment gravity flow. The present study offers a deeper understanding of shelf convection and its role for the construction of bacterial assemblages in the Arctic Ocean. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  5. Bacterial growth and DOC consumption in a tropical coastal lagoon

    Directory of Open Access Journals (Sweden)

    V. F. Farjalla

    Full Text Available The aims of this research were to determine the main limiting nutrient to bacterial growth in Imboassica lagoon, southeastern Brazil, to estimate the percentage of dissolved organic carbon (DOC available for bacterial growth, and to determine the bacterial growth efficiency (BGE of natural assemblages. Bacterial growth and DOC consumption were determined in batch culture experiments, in which water samples were supplemented with nitrogen and phosphorus together or separately, or incubated without nutrient additions. When added together, N and P stimulated higher bacterial growth rates and production, as well as higher DOC consumption. The BGEs and DOC consumption rates were strongly dependent on the method used to determine bacterial production. The BGE ranged from 11 to 72%. However, only a minor fraction of bulk DOC was consumed by the planktonic bacteria (from 0.7 to 3.4%. The results suggest that low availability of phosphorus and nitrogen coupled with excess organic carbon was the main factor responsible for the relatively low bacterial utilization of DOC in Imboassica lagoon.

  6. In Situ Hydrocarbon Degradation by Indigenous Nearshore Bacterial Populations

    International Nuclear Information System (INIS)

    Cherrier, J.

    2005-01-01

    Potential episodic hydrocarbon inputs associated with oil mining and transportation together with chronic introduction of hydrocarbons via urban runoff into the relatively pristine coastal Florida waters poses a significant threat to Florida's fragile marine environment. It is therefore important to understand the extent to which indigenous bacterial populations are able to degrade hydrocarbon compounds and also determine factors that could potentially control and promote the rate at which these compounds are broken down in situ. Previous controlled laboratory experiments carried out by our research group demonstrated that separately both photo-oxidation and cometabolism stimulate bacterial hydrocarbon degradation by natural bacterial assemblages collected from a chronically petroleum contaminated site in Bayboro Bay, Florida. Additionally, we also demonstrated that stable carbon and radiocarbon abundances of respired CO 2 could be used to trace in situ hydrocarbon degradation by indigenous bacterial populations at this same site. This current proposal had two main objectives: (a) to evaluate the cumulative impact of cometabolism and photo-oxidation on hydrocarbon degradation by natural bacterial assemblages collected the same site in Bayboro Bay, Florida and (b) to determine if in situ hydrocarbon degradation by indigenous bacterial populations this site could be traced using natural radiocarbon and stable carbon abundances of assimilated bacterial carbon. Funds were used for 2 years of full support for one ESI Ph.D. student, April Croxton. To address our first objective a series of closed system bacterial incubations were carried out using photo-oxidized petroleum and pinfish (i.e. cometabolite). Bacterial production of CO 2 was used as the indicator of hydrocarbon degradation and (delta) 13 C analysis of the resultant CO 2 was used to evaluate the source of the respired CO 2 (i.e. petroleum hydrocarbons or the pinfish cometabolite). Results from these time

  7. Natural and human-induced variability in the composition of fish assemblages in the Northwestern Cuban shelf.

    Science.gov (United States)

    González-Sansón, Gaspar; Aguilar, Consuelo; Hernández, Ivet; Cabrera, Yureidy; Suarez-Montes, Noelis; Bretos, Fernando; Guggenheim, David

    2009-09-01

    The main goal of the study was to obtain field data to build a baseline of fish assemblage composition that can be used comparatively for future analyses of the impact of human actions in the region. A basic network of 68 sampling stations was defined for the entire region (4,050 km2). Fish assemblage species and size composition was estimated using visual census methods at three different spatial scales: a) entire region, b) inside the main reef area and c) along a human impact coastal gradient. Multivariate numerical analyses revealed habitat type as the main factor inducing spatial variability of fish community composition, while the level of human impact appears to play the main role in fish assemblage composition changes along the coast. A trend of decreasing fish size toward the east supports the theory of more severe human impact due to overfishing and higher urban pollution in that direction. This is the first detailed study along the northwest coast of Cuba that focuses on fish community structure and the natural and human-induced variations at different spatial scales for the entire NW shelf. This research also provides input for a more comprehensive understanding of coastal marine fish communities' status in the Gulf of Mexico basin.

  8. Disease-induced assemblage of a plant-beneficial bacterial consortium

    DEFF Research Database (Denmark)

    Berendsen, Roeland L.; Vismans, Gilles; Yu, Ke

    2018-01-01

    Disease suppressive soils typically develop after a disease outbreak due to the subsequent assembly of protective microbiota in the rhizosphere. The role of the plant immune system in the assemblage of a protective rhizosphere microbiome is largely unknown. In this study, we demonstrate...... in a second population of plants growing in the same soil. Together our results indicate that plants can adjust their root microbiome upon pathogen infection and specifically recruit a group of disease resistance-inducing and growth-promoting beneficial microbes, therewith potentially maximizing the chance...

  9. Bacterial profiling of White Plague Disease in a comparative coral species framework.

    KAUST Repository

    Roder, Cornelia

    2014-01-01

    Coral reefs are threatened throughout the world. A major factor contributing to their decline is outbreaks and propagation of coral diseases. Due to the complexity of coral-associated microbe communities, little is understood in terms of disease agents, hosts and vectors. It is known that compromised health in corals is correlated with shifts in bacterial assemblages colonizing coral mucus and tissue. However, general disease patterns remain, to a large extent, ambiguous as comparative studies over species, regions, or diseases are scarce. Here, we compare bacterial assemblages of samples from healthy (HH) colonies and such displaying signs of White Plague Disease (WPD) of two different coral species (Pavona duerdeni and Porites lutea) from the same reef in Koh Tao, Thailand, using 16S rRNA gene microarrays. In line with other studies, we found an increase of bacterial diversity in diseased (DD) corals, and a higher abundance of taxa from the families that include known coral pathogens (Alteromonadaceae, Rhodobacteraceae, Vibrionaceae). In our comparative framework analysis, we found differences in microbial assemblages between coral species and coral health states. Notably, patterns of bacterial community structures from HH and DD corals were maintained over species boundaries. Moreover, microbes that differentiated the two coral species did not overlap with microbes that were indicative of HH and DD corals. This suggests that while corals harbor distinct species-specific microbial assemblages, disease-specific bacterial abundance patterns exist that are maintained over coral species boundaries.

  10. Macroinvertebrate assemblages and biodiversity levels: ecological role of constructed wetlands and artificial ponds in a natural park

    Directory of Open Access Journals (Sweden)

    Laura Sartori

    2014-02-01

    Full Text Available Normal 0 14 false false false MicrosoftInternetExplorer4 Constructed wetlands play an important role in water supply, floodwater retention and nutrient removal, at the same time allowing the restoration of lost habitat and the preservation of biodiversity. There is little knowledge about the biodiversity that can be found in these artificial environments along time, especially at the invertebrate community level. Macroinvertebrate assemblages, water chemistry, morphology, and environmental characteristics of natural ponds, artificial pools and constructed wetlands in Parco Pineta (Northern Italy were studied to evaluate the effects of local factors on macroinvertebrate communities. The objective was to verify if each ecosystem could equally contribute to local biodiversity, regardless of its natural or artificial origin. Principal Components Analysis showed that ponds were divided into clusters, based on their morphology and their water quality, independently from their origin. The composition of macroinvertebrate communities was similar among natural wetlands and ponds artificially created to provide new habitats in the park, while it was different among natural wetlands and constructed wetlands created for wastewater treatment purposes. Biodiversity of natural ponds and constructed wetlands, evaluated using taxa richness, Shannon index, and Pielou index, was comparable. Canonical Correspondence Analysis highlighted differences in macroinvertebrate community composition and pointed out the relationships among macroinvertebrates and various environmental variables: habitat heterogeneity resulted as the most relevant factor that influences taxa richness. Water quality also affects the macroinvertebrate community structure. We determined that constructed wetlands with higher pollutant concentrations show different assemblage compositions but comparable overall macroinvertebrate biodiversity. Constructed wetlands became valuable ecological elements

  11. High bacterial biodiversity increases degradation performance of hydrocarbons during bioremediation of contaminated harbor marine sediments

    International Nuclear Information System (INIS)

    Dell'Anno, Antonio; Beolchini, Francesca; Rocchetti, Laura; Luna, Gian Marco; Danovaro, Roberto

    2012-01-01

    We investigated changes of bacterial abundance and biodiversity during bioremediation experiments carried out on oxic and anoxic marine harbor sediments contaminated with hydrocarbons. Oxic sediments, supplied with inorganic nutrients, were incubated in aerobic conditions at 20 °C and 35 °C for 30 days, whereas anoxic sediments, amended with organic substrates, were incubated in anaerobic conditions at the same temperatures for 60 days. Results reported here indicate that temperature exerted the main effect on bacterial abundance, diversity and assemblage composition. At higher temperature bacterial diversity and evenness increased significantly in aerobic conditions, whilst decreased in anaerobic conditions. In both aerobic and anaerobic conditions, biodegradation efficiencies of hydrocarbons were significantly and positively related with bacterial richness and evenness. Overall results presented here suggest that bioremediation strategies, which can sustain high levels of bacterial diversity rather than the selection of specific taxa, may significantly increase the efficiency of hydrocarbon degradation in contaminated marine sediments. - Highlights: ► Bioremediation performance was investigated on hydrocarbon contaminated sediments. ► Major changes in bacterial diversity and assemblage composition were observed. ► Temperature exerted the major effect on bacterial assemblages. ► High bacterial diversity increased significantly biodegradation performance. ► This should be considered for sediment remediation by bio-treatments. - Bioremediation strategies which can sustain high levels of bacterial diversity may significantly increase the biodegradation of hydrocarbons in contaminated marine sediments.

  12. Fish assemblages associated with natural and anthropogenically-modified habitats in a marine embayment: comparison of baited videos and opera-house traps.

    Directory of Open Access Journals (Sweden)

    Corey B Wakefield

    Full Text Available Marine embayments and estuaries play an important role in the ecology and life history of many fish species. Cockburn Sound is one of a relative paucity of marine embayments on the west coast of Australia. Its sheltered waters and close proximity to a capital city have resulted in anthropogenic intrusion and extensive seascape modification. This study aimed to compare the sampling efficiencies of baited videos and fish traps in determining the relative abundance and diversity of temperate demersal fish species associated with naturally occurring (seagrass, limestone outcrops and soft sediment and modified (rockwall and dredge channel habitats in Cockburn Sound. Baited videos sampled a greater range of species in higher total and mean abundances than fish traps. This larger amount of data collected by baited videos allowed for greater discrimination of fish assemblages between habitats. The markedly higher diversity and abundances of fish associated with seagrass and limestone outcrops, and the fact that these habitats are very limited within Cockburn Sound, suggests they play an important role in the fish ecology of this embayment. Fish assemblages associated with modified habitats comprised a subset of species in lower abundances when compared to natural habitats with similar physical characteristics. This suggests modified habitats may not have provided the necessary resource requirements (e.g. shelter and/or diet for some species, resulting in alterations to the natural trophic structure and interspecific interactions. Baited videos provided a more efficient and non-extractive method for comparing fish assemblages and habitat associations of smaller bodied species and juveniles in a turbid environment.

  13. Interactive effects of solar radiation and dissolved organic matter on bacterial activity and community structure.

    Science.gov (United States)

    Pérez, María Teresa; Sommaruga, Ruben

    2007-09-01

    We studied the interactive effects of dissolved organic matter (DOM) and solar radiation on the activity and community structure of bacteria from an alpine lake. Activity was assessed both at the community level as leucine incorporation rates and at the single-cell level by microautoradiography. Fluorescent in situ hybridization and signal amplification by catalysed reporter deposition (CARD-FISH) was used to track changes in the bacterial community composition. Bacteria-free filtrates of different DOM sources (lake, algae or soil) were incubated either in the dark or exposed to solar radiation. Afterwards, the natural bacterial assemblage was inoculated and the cultures incubated in the dark for 24-48 h. Bacterial activity was enhanced in the first 24 h in the soil and algal DOM amendments kept in the dark. After 48 h, the enhancement effect was greatly reduced. The initial bacterial community was dominated by Betaproteobacteria followed by Actinobacteria. The relative abundance (expressed as a percentage of DAPI-stained cells) of Betaproteobacteria increased first in dark incubated DOM amendments, but after 48 h no significant differences were detected among treatments. In contrast, the relative abundance of Actinobacteria increased in pre-irradiated DOM treatments. Although Betaproteobacteria dominated at the end of the experiment, the relative abundance of their R-BT subgroup differed among treatments. Changes in bacterial community activity were significantly correlated with those of the relative abundance and activity of Betaproteobacteria, whereas the contribution of Actinobacteria to the bulk activity was very modest. Our results indicate a negative effect of DOM photoalteration on the bulk bacterial activity. The magnitude of this effect was time-dependent and related to rapid changes in the bacterial assemblage composition.

  14. A bacterial community-based index to assess the ecological status of estuarine and coastal environments

    KAUST Repository

    Aylagas, Eva

    2016-10-23

    Biotic indices for monitoring marine ecosystems are mostly based on the analysis of benthic macroinvertebrate communities. Due to their high sensitivity to pollution and fast response to environmental changes, bacterial assemblages could complement the information provided by benthic metazoan communities as indicators of human-induced impacts, but so far, this biological component has not been well explored for this purpose. Here we performed 16S rRNA gene amplicon sequencing to analyze the bacterial assemblage composition of 51 estuarine and coastal stations characterized by different environmental conditions and human-derived pressures. Using the relative abundance of putative indicator bacterial taxa, we developed a biotic index that is significantly correlated with a sediment quality index calculated on the basis of organic and inorganic compound concentrations. This new index based on bacterial assemblage composition can be a sensitive tool for providing a fast environmental assessment and allow a more comprehensive integrative ecosystem approach for environmental management. © 2016.

  15. Comparison of bacterial and fungal communities between natural and planted pine forests in subtropical China.

    Science.gov (United States)

    Nie, Ming; Meng, Han; Li, Ke; Wan, Jia-Rong; Quan, Zhe-Xue; Fang, Chang-Ming; Chen, Jia-Kuan; Li, Bo

    2012-01-01

    To improve our understanding of the changes in bacterial and fungal diversity in natural pine and planted forests in subtropical region of China, we examined bacterial and fungal communities from a native and a nearby planted pine forest of the Mt. Lushan by constructing clone libraries of 16S and 18S rRNA genes. For bacterial communities, Proteobacteria and Acidobacteria were dominant bacterial taxa in both two types of forest soils. The Shannon-Wiener diversity index, rarefaction curve analysis, and LibShuff analysis suggest that these two forests contained similar diversity of bacterial communities. Low soil acidity (pH ≈ 4) of our study forests might be one of the most important selection factors determining growth of acidophilic Acidobacteria and Proteobacteria. However, the natural forest harbored greater level of fungal diversity than the planted forest according to the Shannon-Wiener diversity index and rarefaction curve analysis. Basidiomycota and Ascomycota were dominant fungal taxa in the soils of natural and planted forests, respectively. Our results suggest that fungal community was more sensitive than the bacterial community in characterizing the differences in plant cover impacts on the microbial flora in the natural and planted forests. The natural and planted forests may function differently due to the differences in soil fungal diversity and relative abundance.

  16. Bacterial community of cushion plant Thylacospermum ceaspitosum on elevational gradient in the Himalayan cold desert.

    Science.gov (United States)

    Řeháková, Klára; Chroňáková, Alica; Krištůfek, Václav; Kuchtová, Barbora; Čapková, Kateřina; Scharfen, Josef; Čapek, Petr; Doležal, Jiří

    2015-01-01

    Although bacterial assemblages are important components of soils in arid ecosystems, the knowledge about composition, life-strategies, and environmental drivers is still fragmentary, especially in remote high-elevation mountains. We compared the quality and quantity of heterotrophic bacterial assemblages between the rhizosphere of the dominant cushion-forming plant Thylacospermum ceaspitosum and its surrounding bulk soil in two mountain ranges (East Karakoram: 4850-5250 m and Little Tibet: 5350-5850 m), in communities from cold steppes to the subnival zone in Ladakh, arid Trans-Himalaya, northwest India. Bacterial communities were characterized by molecular fingerprinting in combination with culture-dependent methods. The effects of environmental factors (elevation, mountain range, and soil physico-chemical parameters) on the bacterial community composition and structure were tested by multivariate redundancy analysis and conditional inference trees. Actinobacteria dominate the cultivable part of community and represent a major bacterial lineage of cold desert soils. The most abundant genera were Streptomyces, Arthrobacter, and Paenibacillus, representing both r- and K-strategists. The soil texture is the most important factor for the community structure and the total bacteria counts. Less abundant and diverse assemblages are found in East Karakoram with coarser soils derived from leucogranite bedrock, while more diverse assemblages in Little Tibet are associated with finer soils derived from easily weathering gneisses. Cushion rhizosphere is in general less diverse than bulk soil, and contains more r-strategists. K-strategists are more associated with the extremes of the gradient, with drought at lowest elevations (4850-5000 m) and frost at the highest elevations (5750-5850 m). The present study illuminates the composition of soil bacterial assemblages in relation to the cushion plant T. ceaspitosum in a xeric environment and brings important information about

  17. The impact of natural transformation on adaptation in spatially structured bacterial populations.

    Science.gov (United States)

    Moradigaravand, Danesh; Engelstädter, Jan

    2014-06-20

    Recent studies have demonstrated that natural transformation and the formation of highly structured populations in bacteria are interconnected. In spite of growing evidence about this connection, little is known about the dynamics of natural transformation in spatially structured bacterial populations. In this work, we model the interdependency between the dynamics of the bacterial gene pool and those of environmental DNA in space to dissect the effect of transformation on adaptation. Our model reveals that even with only a single locus under consideration, transformation with a free DNA fragment pool results in complex adaptation dynamics that do not emerge in previous models focusing only on the gene shuffling effect of transformation at multiple loci. We demonstrate how spatial restriction on population growth and DNA diffusion in the environment affect the impact of transformation on adaptation. We found that in structured bacterial populations intermediate DNA diffusion rates predominantly cause transformation to impede adaptation by spreading deleterious alleles in the population. Overall, our model highlights distinctive evolutionary consequences of bacterial transformation in spatially restricted compared to planktonic bacterial populations.

  18. Marine Microphytobenthic Assemblage Shift along a Natural Shallow-Water CO2 Gradient Subjected to Multiple Environmental Stressors

    OpenAIRE

    Johnson, V; Brownlee, C; Milazzo, M; Hall-Spencer, J

    2015-01-01

    Predicting the effects of anthropogenic CO2 emissions on coastal ecosystems requires an understanding of the responses of algae, since these are a vital functional component of shallow-water habitats. We investigated microphytobenthic assemblages on rock and sandy habitats along a shallow subtidal pCO2 gradient near volcanic seeps in the Mediterranean Sea. Field studies of natural pCO2 gradients help us understand the likely effects of ocean acidification because entire communities are subjec...

  19. Effects of non-steroidal anti-inflammatory drugs on cyanobacteria and algae in laboratory strains and in natural algal assemblages.

    Science.gov (United States)

    Bácsi, István; B-Béres, Viktória; Kókai, Zsuzsanna; Gonda, Sándor; Novák, Zoltán; Nagy, Sándor Alex; Vasas, Gábor

    2016-05-01

    In recent years measurable concentrations of non-steroidal anti-inflammatory drugs (NSAIDs) have been shown in the aquatic environment as a result of increasing human consumption. Effects of five frequently used non-steroidal anti-inflammatory drugs (diclofenac, diflunisal, ibuprofen, mefenamic acid and piroxicam in 0.1 mg ml(-1) concentration) in batch cultures of cyanobacteria (Synechococcus elongatus, Microcystis aeruginosa, Cylindrospermopsis raciborskii), and eukaryotic algae (Desmodesmus communis, Haematococcus pluvialis, Cryptomonas ovata) were studied. Furthermore, the effects of the same concentrations of NSAIDs were investigated in natural algal assemblages in microcosms. According to the changes of chlorophyll-a content, unicellular cyanobacteria seemed to be more tolerant to NSAIDs than eukaryotic algae in laboratory experiments. Growth of eukaryotic algae was reduced by all drugs, the cryptomonad C. ovata was the most sensitive to NSAIDs, while the flagellated green alga H. pluvialis was more sensitive than the non-motile green alga D. communis. NSAID treatments had weaker impact in the natural assemblages dominated by cyanobacteria than in the ones dominated by eukaryotic algae, confirming the results of laboratory experiments. Diversity and number of functional groups did not change notably in cyanobacteria dominated assemblages, while they decreased significantly in eukaryotic algae dominated ones compared to controls. The results highlight that cyanobacteria (especially unicellular ones) are less sensitive to the studied, mostly hardly degradable NSAIDs, which suggest that their accumulation in water bodies may contribute to the expansion of cyanobacterial mass productions in appropriate environmental circumstances by pushing back eukaryotic algae. Thus, these contaminants require special attention during wastewater treatment and monitoring of surface waters. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. A comparison of resident fish assemblages in managed and unmanaged coastal wetlands in North Carolina and South Carolina

    Science.gov (United States)

    Robinson, Kelly F.; Jennings, Cecil A.

    2014-01-01

    The dominant fish species within impounded coastal wetlands in the southeastern US may be different from the species that dominate natural marshes. We tested the hypothesis that resident fish assemblages inhabiting impounded coastal wetlands in South Carolina would differ from resident assemblages in natural marshes of the southeastern United States. We used rarefied species richness, Shannon's H' diversity,J' evenness, Morisita's index of similarity, and the percent similarity index to compare resident fish assemblages from two impoundments to 12 open-marsh resident fish assemblages from previously published studies in North and South Carolina. We used rotenone to sample fish assemblages in impoundments. The assemblages in natural marsh habitat had been sampled with rotenone and seines. We classified comparisons yielding a similarity index ≥0.50 as moderately similar and those with an index ≥0.75 as very similar. Fifty-three percent of the among-impoundment comparisons (Morisita's index) were at least moderately similar, whereas 7% of impoundment—natural marsh comparisons were moderately similar. A difference in tidal influence was the only parameter in the best-fitting model describing the observed Morisita's indices. The index of similarity decreased by 63% when tidal influence differed between compared assemblages. Species richness and diversity were greater in impoundments than natural marshes, but evenness was similar between habitat types. Our results support the hypothesis that resident fish assemblages in impounded wetlands and natural marshes are different, and suggest that a degree of tidal influence is the most important factor behind the difference.

  1. Benthic assemblages of mega epifauna on the Oregon continental margin

    Science.gov (United States)

    Hemery, Lenaïg G.; Henkel, Sarah K.; Cochrane, Guy R.

    2018-01-01

    Environmental assessment studies are usually required by a country's administration before issuing permits for any industrial activities. One of the goals of such environmental assessment studies is to highlight species assemblages and habitat composition that could make the targeted area unique. A section of the Oregon continental slope that had not been previously explored was targeted for the deployment of floating wind turbines. We carried out an underwater video survey, using a towed camera sled, to describe its benthic assemblages. Organisms were identified to the lowest taxonomic level possible and assemblages described related to the nature of the seafloor and the depth. We highlighted six invertebrate assemblages and three fish assemblages. For the invertebrates within flat soft sediments areas we defined three different assemblages based on primarily depth: a broad mid-depth (98–315 m) assemblage dominated by red octopus, sea pens and pink shrimps; a narrower mid-depth (250–270 m) assemblage dominated by box crabs and various other invertebrates; and a deeper (310–600 m) assemblage dominated by sea urchins, sea anemones, various snails and zoroasterid sea stars. The invertebrates on mixed sediments also were divided into three different assemblages: a shallow (~100 m deep) assemblage dominated by plumose sea anemones, broad mid-depth (170–370 m) assemblage dominated by sea cucumbers and various other invertebrates; and, again, a narrower mid-depth (230–270 m) assemblage, dominated by crinoids and encrusting invertebrates. For the fish, we identified a rockfish assemblage on coarse mixed sediments at 170–370 m and another fish assemblage on smaller mixed sediments within that depth range (250–370 m) dominated by thornyheads, poachers and flatfishes; and we identified a wide depth-range (98–600 m) fish assemblage on flat soft sediments dominated by flatfishes, eelpouts and thornyheads. Three of these assemblages (the two

  2. Benthic assemblages of mega epifauna on the Oregon continental margin

    Science.gov (United States)

    Hemery, Lenaïg G.; Henkel, Sarah K.; Cochrane, Guy R.

    2018-05-01

    Environmental assessment studies are usually required by a country's administration before issuing permits for any industrial activities. One of the goals of such environmental assessment studies is to highlight species assemblages and habitat composition that could make the targeted area unique. A section of the Oregon continental slope that had not been previously explored was targeted for the deployment of floating wind turbines. We carried out an underwater video survey, using a towed camera sled, to describe its benthic assemblages. Organisms were identified to the lowest taxonomic level possible and assemblages described related to the nature of the seafloor and the depth. We highlighted six invertebrate assemblages and three fish assemblages. For the invertebrates within flat soft sediments areas we defined three different assemblages based on primarily depth: a broad mid-depth (98-315 m) assemblage dominated by red octopus, sea pens and pink shrimps; a narrower mid-depth (250-270 m) assemblage dominated by box crabs and various other invertebrates; and a deeper (310-600 m) assemblage dominated by sea urchins, sea anemones, various snails and zoroasterid sea stars. The invertebrates on mixed sediments also were divided into three different assemblages: a shallow ( 100 m deep) assemblage dominated by plumose sea anemones, broad mid-depth (170-370 m) assemblage dominated by sea cucumbers and various other invertebrates; and, again, a narrower mid-depth (230-270 m) assemblage, dominated by crinoids and encrusting invertebrates. For the fish, we identified a rockfish assemblage on coarse mixed sediments at 170-370 m and another fish assemblage on smaller mixed sediments within that depth range (250-370 m) dominated by thornyheads, poachers and flatfishes; and we identified a wide depth-range (98-600 m) fish assemblage on flat soft sediments dominated by flatfishes, eelpouts and thornyheads. Three of these assemblages (the two broad fish assemblages and the deep

  3. An Improved DNA Extraction Method for Efficient and Quantitative Recovery of Phytoplankton Diversity in Natural Assemblages.

    Directory of Open Access Journals (Sweden)

    Jian Yuan

    Full Text Available Marine phytoplankton are highly diverse with different species possessing different cell coverings, posing challenges for thoroughly breaking the cells in DNA extraction yet preserving DNA integrity. While quantitative molecular techniques have been increasingly used in phytoplankton research, an effective and simple method broadly applicable to different lineages and natural assemblages is still lacking. In this study, we developed a bead-beating protocol based on our previous experience and tested it against 9 species of phytoplankton representing different lineages and different cell covering rigidities. We found the bead-beating method enhanced the final yield of DNA (highest as 2 folds in comparison with the non-bead-beating method, while also preserving the DNA integrity. When our method was applied to a field sample collected at a subtropical bay located in Xiamen, China, the resultant ITS clone library revealed a highly diverse assemblage of phytoplankton and other micro-eukaryotes, including Archaea, Amoebozoa, Chlorophyta, Ciliphora, Bacillariophyta, Dinophyta, Fungi, Metazoa, etc. The appearance of thecate dinoflagellates, thin-walled phytoplankton and "naked" unicellular organisms indicates that our method could obtain the intact DNA of organisms with different cell coverings. All the results demonstrate that our method is useful for DNA extraction of phytoplankton and environmental surveys of their diversity and abundance.

  4. Bacterial growth in humic waters exposed to UV-radiation and simulated sunlight

    DEFF Research Database (Denmark)

    Corin, N.; Backlund, P.; Wiklund, T.

    1998-01-01

    Sterile filtered (0.45 mu m) humic lake water was exposed to simulated sunlight (300-800 nm) or W-radiation (254 run)for various periods of times and the dissolved organic carbon content, absorbance at 254 and 460 nm and PH were recorded. The irradiated water was inoculated with a natural bacterial...... assemblage and the number of viable bacteria war estimated 3 and 5 days after the inoculation using the plate count technique. The number of viable bacteria increased with the irradiation time indicating that the chemical changes of the humus macromolecules observed during irradiation resulted...

  5. Long-term nitrogen amendment alters the diversity and assemblage of soil bacterial communities in tallgrass prairie.

    Directory of Open Access Journals (Sweden)

    Joseph D Coolon

    Full Text Available Anthropogenic changes are altering the environmental conditions and the biota of ecosystems worldwide. In many temperate grasslands, such as North American tallgrass prairie, these changes include alteration in historically important disturbance regimes (e.g., frequency of fires and enhanced availability of potentially limiting nutrients, particularly nitrogen. Such anthropogenically-driven changes in the environment are known to elicit substantial changes in plant and consumer communities aboveground, but much less is known about their effects on soil microbial communities. Due to the high diversity of soil microbes and methodological challenges associated with assessing microbial community composition, relatively few studies have addressed specific taxonomic changes underlying microbial community-level responses to different fire regimes or nutrient amendments in tallgrass prairie. We used deep sequencing of the V3 region of the 16S rRNA gene to explore the effects of contrasting fire regimes and nutrient enrichment on soil bacterial communities in a long-term (20 yrs experiment in native tallgrass prairie in the eastern Central Plains. We focused on responses to nutrient amendments coupled with two extreme fire regimes (annual prescribed spring burning and complete fire exclusion. The dominant bacterial phyla identified were Proteobacteria, Verrucomicrobia, Bacteriodetes, Acidobacteria, Firmicutes, and Actinobacteria and made up 80% of all taxa quantified. Chronic nitrogen enrichment significantly impacted bacterial community diversity and community structure varied according to nitrogen treatment, but not phosphorus enrichment or fire regime. We also found significant responses of individual bacterial groups including Nitrospira and Gammaproteobacteria to long-term nitrogen enrichment. Our results show that soil nitrogen enrichment can significantly alter bacterial community diversity, structure, and individual taxa abundance, which have

  6. Bacterial diversity and biogeochemistry of different chemosynthetic habitats of the REGAB cold seep (West African margin, 3160 m water depth

    Directory of Open Access Journals (Sweden)

    P. Pop Ristova

    2012-12-01

    Full Text Available The giant pockmark REGAB (West African margin, 3160 m water depth is an active methane-emitting cold seep ecosystem, where the energy derived from microbially mediated oxidation of methane supports high biomass and diversity of chemosynthetic communities. Bare sediments interspersed with heterogeneous chemosynthetic assemblages of mytilid mussels, vesicomyid clams and siboglinid tubeworms form a complex seep ecosystem. To better understand if benthic bacterial communities reflect the patchy distribution of chemosynthetic fauna, all major chemosynthetic habitats at REGAB were investigated using an interdisciplinary approach combining pore water geochemistry, in situ quantification of fluxes and consumption of methane, as well as bacterial community fingerprinting. This study revealed that sediments populated by different fauna assemblages show distinct biogeochemical activities and are associated with distinct sediment bacterial communities. The methane consumption rates and methane effluxes ranged over one to two orders of magnitude across habitats, and reached highest values at the mussel habitat, which hosted a different bacterial community compared to the other habitats. Clam assemblages had a profound impact on the sediment geochemistry, but less so on the bacterial community structure. Moreover, all clam assemblages at REGAB were restricted to sediments characterized by complete methane consumption in the seafloor, and intermediate biogeochemical activity. Overall, variations in the sediment geochemistry were reflected in the distribution of both fauna and microbial communities; and were mostly determined by methane flux.

  7. The importance of bacterial utilization of released phytoplankton photosynthate in two humic forest lakes in southern Finland

    International Nuclear Information System (INIS)

    Jones, R.I.; Salonen, K.

    1985-01-01

    Bacterial utilization of photosynthetically fixed dissolved organic carbon (PDOC) released from natural phytoplankton assemblages was studied in two small, extremely humic, forest lakes in southern Finland. Bacterial activity (measured us uptake of 14 C-glucose) and phytoplankton photosynthesis (measured as light uptake of 14 CO 2 ) could be most effectively separated using Nuclepore filters of pore 1-2 μm. Released PDOC was 10-67% of total phytoplankton carbon fixation during in situ experiments, and represented about 0.1% of total DOC. Net uptake of PDOC by bacteria was found to be about 20% during 24 hour laboratory incubations, although about 40% of PDOC present at the start of an experiment could be utilized by bacteria during a 24 hour period. PDOC does not provide a quantitatively important substrate supply fo bacterial respiration in humic forest lakes. (author)

  8. Marine heatwaves and optimal temperatures for microbial assemblage activity

    OpenAIRE

    Joint, IR; Smale, DA

    2016-01-01

    The response of microbial assemblages to instantaneous temperature change was measured in a seasonal study of the coastal waters of the western English Channel. On 18 occasions between November 1999 and December 2000, bacterial abundance was assessed and temperature responses determined from the incorporation of 3H leucine, measured in a temperature gradient from 5°C to 38°C. Q10 values varied, being close to 2 in spring and summer but were >3 in autumn. There was a seasonal pattern in the as...

  9. Asymptomatic cattle naturally infected with Mycobacterium bovis present exacerbated tissue pathology and bacterial dissemination.

    Directory of Open Access Journals (Sweden)

    Álvaro Menin

    Full Text Available Rational discovery of novel immunodiagnostic and vaccine candidate antigens to control bovine tuberculosis (bTB requires knowledge of disease immunopathogenesis. However, there remains a paucity of information on the Mycobacterium bovis-host immune interactions during the natural infection. Analysis of 247 naturally PPD+ M. bovis-infected cattle revealed that 92% (n = 228 of these animals were found to display no clinical signs, but presented severe as well as disseminated bTB-lesions at post-mortem examination. Moreover, dissemination of bTB-lesions positively correlated with both pathology severity score (Spearman r = 0.48; p<0.0001 and viable tissue bacterial loads (Spearman r = 0.58; p = 0.0001. Additionally, granuloma encapsulation negatively correlated with M. bovis growth as well as pathology severity, suggesting that encapsulation is an effective mechanism to control bacterial proliferation during natural infection. Moreover, multinucleated giant cell numbers were found to negatively correlate with bacterial counts (Spearman r = 0.25; p = 0.03 in lung granulomas. In contrast, neutrophil numbers in the granuloma were associated with increased M. bovis proliferation (Spearman r = 0.27; p = 0.021. Together, our findings suggest that encapsulation and multinucleated giant cells control M. bovis viability, whereas neutrophils may serve as a cellular biomarker of bacterial proliferation during natural infection. These data integrate host granuloma responses with mycobacterial dissemination and could provide useful immunopathological-based biomarkers of disease severity in natural infection with M. bovis, an important cattle pathogen.

  10. Penicillin-mediated changes in viable benthic diatom assemblages – insights about the relevance of bacteria across spatial and seasonal scales.

    Digital Repository Service at National Institute of Oceanography (India)

    DeCosta, P.M.; Anil, A.C.

    environment) and seasonal (post-monsoon, pre-monsoon, monsoon) scales. Penicillin treatment resulted in bacterial suppression and a reduction in diatoms at the intertidal and mangrove sites having stable pennate-dominated assemblages. Diatom response...

  11. Bacterial assemblages differ between compartments within the coral holobiont

    Science.gov (United States)

    Sweet, M. J.; Croquer, A.; Bythell, J. C.

    2011-03-01

    It is widely accepted that corals are associated with a diverse and host species-specific microbiota, but how they are organized within their hosts remains poorly understood. Previous sampling techniques (blasted coral tissues, coral swabs and milked mucus) may preferentially sample from different compartments such as mucus, tissue and skeleton, or amalgamate them, making comparisons and generalizations between studies difficult. This study characterized bacterial communities of corals with minimal mechanical disruption and contamination from water, air and sediments from three compartments: surface mucus layer (SML), coral tissue and coral skeleton. A novel apparatus (the `snot sucker') was used to separate the SML from tissues and skeleton, and these three compartments were compared to swab samples and milked mucus along with adjacent environmental samples (water column and sediments). Bacterial 16S rRNA gene diversity was significantly different between the various coral compartments and environmental samples (PERMANOVA, F = 6.9, df = 8, P = 0.001), the only exceptions being the complete crushed coral samples and the coral skeleton, which were similar, because the skeleton represents a proportionally large volume and supports a relatively rich microflora. Milked mucus differed significantly from the SML collected with the `snot sucker' and was contaminated with zooxanthellae, suggesting that it may originate at least partially from the gastrovascular cavity rather than the tissue surface. A common method of sampling the SML, surface swabs, produced a bacterial community profile distinct from the SML sampled using our novel apparatus and also showed contamination from coral tissues. Our results indicate that microbial communities are spatially structured within the coral holobiont, and methods used to describe these need to be standardized to allow comparisons between studies.

  12. Mangrove macrobenthos: Assemblages, services, and linkages

    Science.gov (United States)

    Lee, S. Y.

    2008-02-01

    Macrobenthic assemblages are relatively poorly known compared to other components of the mangrove ecosystem. Tropical mangroves support macrobenthic biodiversity resources yet to be properly documented and interpreted. Some methodological challenges, such as the generally high spatial heterogeneity and complexity of the habitat, evidently reduce sampling efficiency and accuracy, while also leaving some microhabitats under-sampled. Macrobenthic assemblage structure seems to be influenced by local environmental conditions, such as hydroperiod, organic matter availability and sediment characteristics. Brachyurans, gastropods and oligochaetes dominate in the sediment, with the former two groups also common on hard surfaces provided by tree trunks, while insects and arachnids inhabit the canopy. Traditionally, studies of mangrove macrobenthos have focused on assemblage structure or the biology of individual species, but more complex inter-specific interactions and the inter-relationship between habitat and the biota are recently being addressed. Brachyuran crabs are the best-studied macrobenthos group, but many issues about their role in mangrove ecosystem dynamics are still controversial. Despite many species of mangrove macrobenthos being referred to as 'trophic dead ends', most serve as important links between recalcitrant mangrove organic matter and estuarine secondary production, through feeding excursion by mobile nekton during the high tide, and macrobenthos-mediated processing and exportation of organic matter. A significant difference in the standing crop biomass of forests between the Indo-west-Pacific (IWP)' and Atlantic-east-Pacific (AEP) mangroves may be related to the difference in species richness of mangrove as well as macrobenthos diversity in the two bioregions. Such differences in assemblage structure may also result in different ecosystem functioning, but the nature of the links is, however, yet to be explored. There is also a strong need for

  13. Soil nematode assemblages as bioindicators of radiation impact in the Chernobyl Exclusion Zone

    International Nuclear Information System (INIS)

    Lecomte-Pradines, C.; Bonzom, J.-M.; Della-Vedova, C.; Beaugelin-Seiller, K.; Villenave, C.; Gaschak, S.; Coppin, F.; Dubourg, N.; Maksimenko, A.; Adam-Guillermin, C.; Garnier-Laplace, J.

    2014-01-01

    In radioecology, the need to understand the long-term ecological effects of radioactive contamination has been emphasised. This requires that the health of field populations is evaluated and linked to an accurate estimate of received radiological dose. The aim of the present study was to assess the effects of current radioactive contamination on nematode assemblages at sites affected by the fallout from the Chernobyl accident. First, we estimated the total dose rates (TDRs) absorbed by nematodes, from measured current soil activity concentrations, Dose Conversion Coefficients (DCCs, calculated using EDEN software) and soil-to-biota concentration ratios (from the ERICA tool database). The impact of current TDRs on nematode assemblages was then evaluated. Nematodes were collected in spring 2011 from 18 forest sites in the Chernobyl Exclusion Zone (CEZ) with external gamma dose rates, measured using radiophotoluminescent dosimeters, varying from 0.2 to 22 μGy h −1 . These values were one order of magnitude below the TDRs. A majority of bacterial-, plant-, and fungal-feeding nematodes and very few of the disturbance sensitive families were identified. No statistically significant association was observed between TDR values and nematode total abundance or the Shannon diversity index (H′). The Nematode Channel Ratio (which defines the relative abundance of bacterial- versus fungal-feeding nematodes) decreased significantly with increasing TDR, suggesting that radioactive contamination may influence nematode assemblages either directly or indirectly by modifying their food resources. A greater Maturity Index (MI), usually characterising better soil quality, was associated with higher pH and TDR values. These results suggest that in the CEZ, nematode assemblages from the forest sites were slightly impacted by chronic exposure at a predicted TDR of 200 μGy h −1 . This may be imputable to a dominant proportion of pollutant resistant nematodes in all sites. This might

  14. Soil nematode assemblages as bioindicators of radiation impact in the Chernobyl Exclusion Zone

    Energy Technology Data Exchange (ETDEWEB)

    Lecomte-Pradines, C., E-mail: catherine.lecomte-pradines@irsn.fr [Institute for Radioprotection and Nuclear Safety, IRSN/PRP-ENV/SERIS, LECO, Building 186, Cadarache 13115 Saint Paul lez Durance cedex (France); Bonzom, J.-M. [Institute for Radioprotection and Nuclear Safety, IRSN/PRP-ENV/SERIS, LECO, Building 186, Cadarache 13115 Saint Paul lez Durance cedex (France); Della-Vedova, C. [Magelis, 6, rue Frederic Mistral, 84160 Cadenet (France); Beaugelin-Seiller, K. [Institute for Radioprotection and Nuclear Safety, IRSN/PRP-ENV/SERIS, LM2E, Building 159, Cadarache 13115 Saint Paul lez Durance cedex (France); Villenave, C. [ELISOL Environment, Building 12, Campus de la Gaillarde, 2 place Viala, 34060 Montpellier cedex 2 (France); Gaschak, S. [Chernobyl Center for Nuclear Safety, Radioactive Waste and Radioecology, International Radioecology Laboratory, 07100 Slavutych (Ukraine); Coppin, F. [Institute for Radioprotection and Nuclear Safety, IRSN/PRP-ENV/SERIS, L2BT, Building 186, Cadarache 13115 Saint Paul lez Durance cedex (France); Dubourg, N. [Institute for Radioprotection and Nuclear Safety, IRSN/PRP-ENV/SERIS, GARM Building 186, Cadarache 13115 Saint Paul lez Durance cedex (France); Maksimenko, A. [Chernobyl Center for Nuclear Safety, Radioactive Waste and Radioecology, International Radioecology Laboratory, 07100 Slavutych (Ukraine); Adam-Guillermin, C. [Institute for Radioprotection and Nuclear Safety, IRSN/PRP-ENV/SERIS, LECO, Building 186, Cadarache 13115 Saint Paul lez Durance cedex (France); Garnier-Laplace, J. [Institute for Radioprotection and Nuclear Safety, IRSN/PRP-ENV/SERIS, Building 159, Cadarache 13115 Saint Paul lez Durance cedex (France)

    2014-08-15

    In radioecology, the need to understand the long-term ecological effects of radioactive contamination has been emphasised. This requires that the health of field populations is evaluated and linked to an accurate estimate of received radiological dose. The aim of the present study was to assess the effects of current radioactive contamination on nematode assemblages at sites affected by the fallout from the Chernobyl accident. First, we estimated the total dose rates (TDRs) absorbed by nematodes, from measured current soil activity concentrations, Dose Conversion Coefficients (DCCs, calculated using EDEN software) and soil-to-biota concentration ratios (from the ERICA tool database). The impact of current TDRs on nematode assemblages was then evaluated. Nematodes were collected in spring 2011 from 18 forest sites in the Chernobyl Exclusion Zone (CEZ) with external gamma dose rates, measured using radiophotoluminescent dosimeters, varying from 0.2 to 22 μGy h{sup −1}. These values were one order of magnitude below the TDRs. A majority of bacterial-, plant-, and fungal-feeding nematodes and very few of the disturbance sensitive families were identified. No statistically significant association was observed between TDR values and nematode total abundance or the Shannon diversity index (H′). The Nematode Channel Ratio (which defines the relative abundance of bacterial- versus fungal-feeding nematodes) decreased significantly with increasing TDR, suggesting that radioactive contamination may influence nematode assemblages either directly or indirectly by modifying their food resources. A greater Maturity Index (MI), usually characterising better soil quality, was associated with higher pH and TDR values. These results suggest that in the CEZ, nematode assemblages from the forest sites were slightly impacted by chronic exposure at a predicted TDR of 200 μGy h{sup −1}. This may be imputable to a dominant proportion of pollutant resistant nematodes in all sites

  15. Patterns of Spatial Variation of Assemblages Associated with Intertidal Rocky Shores: A Global Perspective

    Science.gov (United States)

    Cruz-Motta, Juan José; Miloslavich, Patricia; Palomo, Gabriela; Iken, Katrin; Konar, Brenda; Pohle, Gerhard; Trott, Tom; Benedetti-Cecchi, Lisandro; Herrera, César; Hernández, Alejandra; Sardi, Adriana; Bueno, Andrea; Castillo, Julio; Klein, Eduardo; Guerra-Castro, Edlin; Gobin, Judith; Gómez, Diana Isabel; Riosmena-Rodríguez, Rafael; Mead, Angela; Bigatti, Gregorio; Knowlton, Ann; Shirayama, Yoshihisa

    2010-01-01

    Assemblages associated with intertidal rocky shores were examined for large scale distribution patterns with specific emphasis on identifying latitudinal trends of species richness and taxonomic distinctiveness. Seventy-two sites distributed around the globe were evaluated following the standardized sampling protocol of the Census of Marine Life NaGISA project (www.nagisa.coml.org). There were no clear patterns of standardized estimators of species richness along latitudinal gradients or among Large Marine Ecosystems (LMEs); however, a strong latitudinal gradient in taxonomic composition (i.e., proportion of different taxonomic groups in a given sample) was observed. Environmental variables related to natural influences were strongly related to the distribution patterns of the assemblages on the LME scale, particularly photoperiod, sea surface temperature (SST) and rainfall. In contrast, no environmental variables directly associated with human influences (with the exception of the inorganic pollution index) were related to assemblage patterns among LMEs. Correlations of the natural assemblages with either latitudinal gradients or environmental variables were equally strong suggesting that neither neutral models nor models based solely on environmental variables sufficiently explain spatial variation of these assemblages at a global scale. Despite the data shortcomings in this study (e.g., unbalanced sample distribution), we show the importance of generating biological global databases for the use in large-scale diversity comparisons of rocky intertidal assemblages to stimulate continued sampling and analyses. PMID:21179546

  16. Patterns of spatial variation of assemblages associated with intertidal rocky shores: a global perspective.

    Directory of Open Access Journals (Sweden)

    Juan José Cruz-Motta

    2010-12-01

    Full Text Available Assemblages associated with intertidal rocky shores were examined for large scale distribution patterns with specific emphasis on identifying latitudinal trends of species richness and taxonomic distinctiveness. Seventy-two sites distributed around the globe were evaluated following the standardized sampling protocol of the Census of Marine Life NaGISA project (www.nagisa.coml.org. There were no clear patterns of standardized estimators of species richness along latitudinal gradients or among Large Marine Ecosystems (LMEs; however, a strong latitudinal gradient in taxonomic composition (i.e., proportion of different taxonomic groups in a given sample was observed. Environmental variables related to natural influences were strongly related to the distribution patterns of the assemblages on the LME scale, particularly photoperiod, sea surface temperature (SST and rainfall. In contrast, no environmental variables directly associated with human influences (with the exception of the inorganic pollution index were related to assemblage patterns among LMEs. Correlations of the natural assemblages with either latitudinal gradients or environmental variables were equally strong suggesting that neither neutral models nor models based solely on environmental variables sufficiently explain spatial variation of these assemblages at a global scale. Despite the data shortcomings in this study (e.g., unbalanced sample distribution, we show the importance of generating biological global databases for the use in large-scale diversity comparisons of rocky intertidal assemblages to stimulate continued sampling and analyses.

  17. Landform-Sediment Assemblages Units of the Upper Mississippi River Valley

    Data.gov (United States)

    Iowa State University GIS Support and Research Facility — Wisconsinan and Holocene Landform-Sediment Assemblages of the Upper Mississippi River Valley. Knowledge of the spatial distribution of natural and cultural resources...

  18. Bacterial Diversity across Individual Lichens▿ †

    Science.gov (United States)

    Mushegian, Alexandra A.; Peterson, Celeste N.; Baker, Christopher C. M.; Pringle, Anne

    2011-01-01

    Symbioses are unique habitats for bacteria. We surveyed the spatial diversity of bacterial communities across multiple individuals of closely related lichens using terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing. Centers of lichens house richer, more consistent assemblages than species-poor and compositionally disparate lichen edges, suggesting that ecological succession plays a role in structuring these communities. PMID:21531831

  19. Soil nematode assemblages as bioindicators of radiation impact in the Chernobyl Exclusion Zone.

    Science.gov (United States)

    Lecomte-Pradines, C; Bonzom, J-M; Della-Vedova, C; Beaugelin-Seiller, K; Villenave, C; Gaschak, S; Coppin, F; Dubourg, N; Maksimenko, A; Adam-Guillermin, C; Garnier-Laplace, J

    2014-08-15

    In radioecology, the need to understand the long-term ecological effects of radioactive contamination has been emphasised. This requires that the health of field populations is evaluated and linked to an accurate estimate of received radiological dose. The aim of the present study was to assess the effects of current radioactive contamination on nematode assemblages at sites affected by the fallout from the Chernobyl accident. First, we estimated the total dose rates (TDRs) absorbed by nematodes, from measured current soil activity concentrations, Dose Conversion Coefficients (DCCs, calculated using EDEN software) and soil-to-biota concentration ratios (from the ERICA tool database). The impact of current TDRs on nematode assemblages was then evaluated. Nematodes were collected in spring 2011 from 18 forest sites in the Chernobyl Exclusion Zone (CEZ) with external gamma dose rates, measured using radiophotoluminescent dosimeters, varying from 0.2 to 22 μGy h(-1). These values were one order of magnitude below the TDRs. A majority of bacterial-, plant-, and fungal-feeding nematodes and very few of the disturbance sensitive families were identified. No statistically significant association was observed between TDR values and nematode total abundance or the Shannon diversity index (H'). The Nematode Channel Ratio (which defines the relative abundance of bacterial- versus fungal-feeding nematodes) decreased significantly with increasing TDR, suggesting that radioactive contamination may influence nematode assemblages either directly or indirectly by modifying their food resources. A greater Maturity Index (MI), usually characterising better soil quality, was associated with higher pH and TDR values. These results suggest that in the CEZ, nematode assemblages from the forest sites were slightly impacted by chronic exposure at a predicted TDR of 200 μGy h(-1). This may be imputable to a dominant proportion of pollutant resistant nematodes in all sites. This might

  20. Bacterial diversity and composition during rain events with and without Saharan dust influence reaching a high mountain lake in the Alps.

    Science.gov (United States)

    Peter, Hannes; Hörtnagl, Paul; Reche, Isabel; Sommaruga, Ruben

    2014-12-01

    The diversity of airborne microorganisms that potentially reach aquatic ecosystems during rain events is poorly explored. Here, we used a culture-independent approach to characterize bacterial assemblages during rain events with and without Saharan dust influence arriving to a high mountain lake in the Austrian Alps. Bacterial assemblage composition differed significantly between samples with and without Saharan dust influence. Although alpha diversity indices were within the same range in both sample categories, rain events with Atlantic or continental origins were dominated by Betaproteobacteria, whereas those with Saharan dust intrusions were dominated by Gammaproteobacteria. The high diversity and evenness observed in all samples suggests that different sources of bacteria contributed to the airborne assemblage collected at the lake shore. During experiments with bacterial assemblages collected during rain events with Saharan dust influence, cell numbers rapidly increased in sterile lake water from initially ∼3 × 103 cell ml-1 to 3.6-11.1 x105 cells ml-1 within 4-5 days, and initially, rare taxa dominated at the end of the experiment. Our study documents the dispersal of viable bacteria associated to Saharan dust intrusions travelling northwards as far as 47° latitude.

  1. Habitat segregation in fish assemblages

    OpenAIRE

    Ibbotson, A.T.

    1990-01-01

    The segregation of habitats of fish assemblages found in the chalk streams and rivers within the Wessex, South West and Southern Water Authority boundaries in southern England have been examined. Habitat segregation is the most frequent type of resource partitioning in natural communities. The habitat of individual fish species will be defined in order to determine the following: (1) the requirements of each species in terms of depth, current velocity, substrate, cover etc.; (2) identify the ...

  2. The relative importance of regional, local, and evolutionary factors structuring cryptobenthic coral-reef assemblages

    Science.gov (United States)

    Ahmadia, Gabby N.; Tornabene, Luke; Smith, David J.; Pezold, Frank L.

    2018-03-01

    Factors shaping coral-reef fish species assemblages can operate over a wide range of spatial scales (local versus regional) and across both proximate and evolutionary time. Niche theory and neutral theory provide frameworks for testing assumptions and generating insights about the importance of local versus regional processes. Niche theory postulates that species assemblages are an outcome of evolutionary processes at regional scales followed by local-scale interactions, whereas neutral theory presumes that species assemblages are formed by largely random processes drawing from regional species pools. Indo-Pacific cryptobenthic coral-reef fishes are highly evolved, ecologically diverse, temporally responsive, and situated on a natural longitudinal diversity gradient, making them an ideal group for testing predictions from niche and neutral theories and effects of regional and local processes on species assemblages. Using a combination of ecological metrics (fish density, diversity, assemblage composition) and evolutionary analyses (testing for phylogenetic niche conservatism), we demonstrate that the structure of cryptobenthic fish assemblages can be explained by a mixture of regional factors, such as the size of regional species pools and broad-scale barriers to gene flow/drivers of speciation, coupled with local-scale factors, such as the relative abundance of specific microhabitat types. Furthermore, species of cryptobenthic fishes have distinct microhabitat associations that drive significant differences in assemblage community structure between microhabitat types, and these distinct microhabitat associations are phylogenetically conserved over evolutionary timescales. The implied differential fitness of cryptobenthic fishes across varied microhabitats and the conserved nature of their ecology are consistent with predictions from niche theory. Neutral theory predictions may still hold true for early life-history stages, where stochastic factors may be more

  3. Snake assemblages of Marajó Island, Pará state, Brazil

    Directory of Open Access Journals (Sweden)

    Gerson Moreira Rodrigues

    2016-01-01

    Full Text Available ABSTRACT We describe the diversity, natural history and structure of snake assemblages from Marajó Island, state of Pará, Brazil, after analyzing 439 specimens deposited in herpetological collections. We tested the hypothesis that snake assemblages from forest and open areas of Marajó Island are distinct with regard to their structure, composition and functional groups. To compare the snake composition of the forest and open areas of Marajó with other comparable assemblages in Brazil, Principal Coordinate Analysis and Clustering tests were performed. A total of 61 species of snakes was recorded for Marajó, with ten species cited for the first time for the study area (Atractus natans Hoogmoed & Prudente, 2003, A. schach (Boie, 1827, Dendrophidion dendrophis (Schlegel, 1837, Helicops hagmanni Roux, 1910, Hydrops martii (Wagler in Spix, 1824, Lygophis meridionalis (Schenkel, 1901, Erythrolamprus typhlus (Linnaeus, 1758, Philodryas argentea (Daudin, 1803, Siphlophis cervinus (Laurenti, 1768, and Thamnodynastes sp.. The composition and structure of snake assemblages between forested and open were different, with five functional groups of snakes in forest areas, and three groups in open areas, based on habit and habitat. In all, 19 species were exclusive to forest areas, 10 were exclusive to open areas and 26 species were recorded in both areas. Our results revealed greater richness for forested areas, probably due to greater habitat heterogeneity. The species composition for forested area in Marajó was similar to that found in other Amazonian assemblages, while that for open areas was more similar to the Pantanal region than other open area assemblages. The general structure of the snake assemblage of Marajó was dominated by anurophagous, terrestrial and diurnal species. Terrestrial, arboreal and semi-arboreal snakes showed a seasonal offspring production pattern, while the pattern for aquatic and semi-aquatic species was aseasonal. The

  4. Long-term organic-inorganic fertilization ensures great soil productivity and bacterial diversity after natural-to-agricultural ecosystem conversion.

    Science.gov (United States)

    Xun, Weibing; Xu, Zhihui; Li, Wei; Ren, Yi; Huang, Ting; Ran, Wei; Wang, Boren; Shen, Qirong; Zhang, Ruifu

    2016-09-01

    Natural ecosystems comprise the planet's wild plant and animal resources, but large tracts of land have been converted to agroecosystems to support the demand for agricultural products. This conversion limits the number of plant species and decreases the soil biological diversity. Here we used high-throughput 16S rRNA gene sequencing to evaluate the responses of soil bacterial communities in long-term converted and fertilized red soils (a type of Ferralic Cambisol). We observed that soil bacterial diversity was strongly affected by different types of fertilization management. Oligotrophic bacterial taxa demonstrated large relative abundances in chemically fertilized soil, whereas copiotrophic bacterial taxa were found in large relative abundances in organically fertilized and fallow management soils. Only organic-inorganic fertilization exhibited the same local taxonomic and phylogenetic diversity as that of a natural ecosystem. However, the independent use of organic or inorganic fertilizer reduced local taxonomic and phylogenetic diversity and caused biotic homogenization. This study demonstrated that the homogenization of bacterial communities caused by natural-to-agricultural ecosystem conversion can be mitigated by employing rational organic-inorganic fertilization management.

  5. Role of riparian shade on the fish assemblage of a reservoir littoral

    Science.gov (United States)

    Raines, C. D.; Miranda, Leandro E.

    2016-01-01

    Research into the effects of shade on reservoir fish assemblages is lacking, with most investigations focused on streams. Unlike many streams, the canopy in a reservoir shades only a narrow fringe of water adjacent to the shoreline, and may not have the influential effect on the aquatic environment reported in streams. We compared fish assemblages between shaded and unshaded sites in a shallow reservoir. Overall species richness (gamma diversity) was higher in shaded sites, and fish assemblage composition differed between shaded and unshaded sites. Average light intensity was 66 % lower in shaded sites, and differences in average temperature and dissolved oxygen were small. Unlike streams where shade can have large effects on water physicochemistry, in reservoirs shade-related differences in fish assemblages seemed to be linked principally to differences in light intensity. Diversity in light intensity in shaded and unshaded sites in reservoirs can create various mosaics of light-based habitats that enable diversity of species assemblages. Managing to promote the habitat diversity provided by shade may require coping with the artificial nature of reservoir riparian zones and water level fluctuations.

  6. Bacterial natural transformation by highly fragmented and damaged DNA

    DEFF Research Database (Denmark)

    Overballe-Petersen, Søren; Harms, Klaus; Orlando, Ludovic Antoine Alexandre

    2013-01-01

    for microbes, but not as potential substrate for bacterial evolution. Here, we show that fragmented DNA molecules (≥20 bp) that additionally may contain abasic sites, cross-links, or miscoding lesions are acquired by the environmental bacterium Acinetobacter baylyi through natural transformation. With uptake......DNA molecules are continuously released through decomposition of organic matter and are ubiquitous in most environments. Such DNA becomes fragmented and damaged (often DNA is recognized as nutrient source...... of DNA from a 43,000-y-old woolly mammoth bone, we further demonstrate that such natural transformation events include ancient DNA molecules. We find that the DNA recombination is RecA recombinase independent and is directly linked to DNA replication. We show that the adjacent nucleotide variations...

  7. Influence of environmental variables on the structure and composition of soil bacterial communities in natural and constructed wetlands.

    Science.gov (United States)

    Arroyo, Paula; Sáenz de Miera, Luis E; Ansola, Gemma

    2015-02-15

    Bacteria are key players in wetland ecosystems, however many essential aspects regarding the ecology of wetland bacterial communities remain unknown. The present study characterizes soil bacterial communities from natural and constructed wetlands through the pyrosequencing of 16S rDNA genes in order to evaluate the influence of wetland variables on bacterial community composition and structure. The results show that the composition of soil bacterial communities was significantly associated with the wetland type (natural or constructed wetland), the type of environment (lagoon, Typha or Salix) and three continuous parameters (SOM, COD and TKN). However, no clear associations were observed with soil pH. Bacterial diversity values were significantly lower in the constructed wetland with the highest inlet nutrient concentrations. The abundances of particular metabolic groups were also related to wetland characteristics. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Antagonistic interactions between honey bee bacterial symbionts and implications for disease

    Directory of Open Access Journals (Sweden)

    Armstrong Tamieka-Nicole

    2006-03-01

    Full Text Available Abstract Background Honey bees, Apis mellifera, face many parasites and pathogens and consequently rely on a diverse set of individual and group-level defenses to prevent disease. One route by which honey bees and other insects might combat disease is through the shielding effects of their microbial symbionts. Bees carry a diverse assemblage of bacteria, very few of which appear to be pathogenic. Here we explore the inhibitory effects of these resident bacteria against the primary bacterial pathogen of honey bees, Paenibacillus larvae. Results Here we isolate, culture, and describe by 16S rRNA and protein-coding gene sequences 61 bacterial isolates from honey bee larvae, reflecting a total of 43 distinct bacterial taxa. We culture these bacteria alongside the primary larval pathogen of honey bees, Paenibacillus larvae, and show that many of these isolates severely inhibit the growth of this pathogen. Accordingly, symbiotic bacteria including those described here are plausible natural antagonists toward this widespread pathogen. Conclusion The results suggest a tradeoff in social insect colonies between the maintenance of potentially beneficial bacterial symbionts and deterrence at the individual and colony level of pathogenic species. They also provide a novel mechanism for recently described social components behind disease resistance in insect colonies, and point toward a potential control strategy for an important bee disease.

  9. Bacterial profiling of White Plague Disease in a comparative coral species framework.

    KAUST Repository

    Roder, Cornelia; Arif, Chatchanit; Bayer, Till; Aranda, Manuel; Daniels, Camille Arian; Shibl, Ahmed A.; Chavanich, Suchana; Voolstra, Christian R.

    2014-01-01

    agents, hosts and vectors. It is known that compromised health in corals is correlated with shifts in bacterial assemblages colonizing coral mucus and tissue. However, general disease patterns remain, to a large extent, ambiguous as comparative studies

  10. Fish assemblages in borrow-pit lakes of the Lower Mississippi River

    Science.gov (United States)

    Miranda, Leandro E.; Killgore, K. J.; Hoover, J.J.

    2013-01-01

    Borrow-pit lakes encompass about a third of the lentic water habitats (by area) in the active floodplain of the Lower Mississippi River, yet little is known about their fish assemblages. We investigated whether fish assemblages supported by borrow-pit lakes resembled those in oxbow lakes to help place the ecological relevance of borrow-pit lakes in context with that of natural floodplain lakes. In all, we collected 75 fish species, including 65 species in eight borrow-pit lakes, 52 species in four riverside oxbow lakes, and 44 species in eight landside oxbow lakes. Significant differences in several species richness metrics were evident between borrow-pit lakes and landside oxbow lakes but not between borrow-pit lakes and riverside oxbow lakes. All three lake types differed in fish assemblage composition. Borrow-pit lakes and riverside oxbow lakes tended to include a greater representation of fish species that require access to diverse environments, including lentic, lotic, and palustrine habitats; fish assemblages in landside oxbow lakes included a higher representation of lacustrine species. None of the fish species collected in borrow-pit lakes was federally listed as threatened or endangered, but several were listed as species of special concern by state governments in the region, suggesting that borrow-pit lakes provide habitat for sensitive riverine and wetland fish species. Differences in fish assemblages among borrow-pit lakes were linked to engineered morphologic features, suggesting that diversity in engineering can contribute to diversity in fish assemblages; however, more research is needed to match engineering designs with fish assemblage structures that best meet conservation needs.

  11. Patterns in reef fish assemblages: Insights from the Chagos Archipelago.

    Science.gov (United States)

    Samoilys, Melita; Roche, Ronan; Koldewey, Heather; Turner, John

    2018-01-01

    Understanding the drivers of variability in the composition of fish assemblages across the Indo-Pacific region is crucial to support coral reef ecosystem resilience. Whilst numerous relationships and feedback mechanisms between the functional roles of coral reef fishes and reef benthic composition have been investigated, certain key groups, such as the herbivores, are widely suggested to maintain reefs in a coral-dominated state. Examining links between fishes and reef benthos is complicated by the interactions between natural processes, disturbance events and anthropogenic impacts, particularly fishing pressure. This study examined fish assemblages and associated benthic variables across five atolls within the Chagos Archipelago, where fishing pressure is largely absent, to better understand these relationships. We found high variability in fish assemblages among atolls and sites across the archipelago, especially for key groups such as a suite of grazer-detritivore surgeonfish, and the parrotfishes which varied in density over 40-fold between sites. Differences in fish assemblages were significantly associated with variable levels of both live and recently dead coral cover and rugosity. We suggest these results reflect differing coral recovery trajectories following coral bleaching events and a strong influence of 'bottom-up' control mechanisms on fish assemblages. Species level analyses revealed that Scarus niger, Acanthurus nigrofuscus and Chlorurus strongylocephalos were key species driving differences in fish assemblage structure. Clarifying the trophic roles of herbivorous and detritivorous reef fishes will require species-level studies, which also examine feeding behaviour, to fully understand their contribution in maintaining reef resilience to climate change and fishing impacts.

  12. Patterns in reef fish assemblages: Insights from the Chagos Archipelago

    Science.gov (United States)

    Roche, Ronan; Koldewey, Heather; Turner, John

    2018-01-01

    Understanding the drivers of variability in the composition of fish assemblages across the Indo-Pacific region is crucial to support coral reef ecosystem resilience. Whilst numerous relationships and feedback mechanisms between the functional roles of coral reef fishes and reef benthic composition have been investigated, certain key groups, such as the herbivores, are widely suggested to maintain reefs in a coral-dominated state. Examining links between fishes and reef benthos is complicated by the interactions between natural processes, disturbance events and anthropogenic impacts, particularly fishing pressure. This study examined fish assemblages and associated benthic variables across five atolls within the Chagos Archipelago, where fishing pressure is largely absent, to better understand these relationships. We found high variability in fish assemblages among atolls and sites across the archipelago, especially for key groups such as a suite of grazer-detritivore surgeonfish, and the parrotfishes which varied in density over 40-fold between sites. Differences in fish assemblages were significantly associated with variable levels of both live and recently dead coral cover and rugosity. We suggest these results reflect differing coral recovery trajectories following coral bleaching events and a strong influence of ‘bottom-up’ control mechanisms on fish assemblages. Species level analyses revealed that Scarus niger, Acanthurus nigrofuscus and Chlorurus strongylocephalos were key species driving differences in fish assemblage structure. Clarifying the trophic roles of herbivorous and detritivorous reef fishes will require species-level studies, which also examine feeding behaviour, to fully understand their contribution in maintaining reef resilience to climate change and fishing impacts. PMID:29351566

  13. Sexually transmitted bacteria affect female cloacal assemblages in a wild bird

    Science.gov (United States)

    White, Joël; Mirleau, Pascal; Danchin, Etienne; Mulard, Hervé; Hatch, Scott A.; Heeb, Phillipp; Wagner, Richard H.

    2010-01-01

    Sexual transmission is an important mode of disease propagation, yet its mechanisms remain largely unknown in wild populations. Birds comprise an important model for studying sexually transmitted microbes because their cloaca provides a potential for both gastrointestinal pathogens and endosymbionts to become incorporated into ejaculates. We experimentally demonstrate in a wild population of kittiwakes (Rissa tridactyla) that bacteria are transmitted during copulation and affect the composition and diversity of female bacterial communities. We used an anti-insemination device attached to males in combination with a molecular technique (automated ribosomal intergenic spacer analysis) that describes bacterial communities. After inseminations were experimentally blocked, the cloacal communities of mates became increasingly dissimilar. Moreover, female cloacal diversity decreased and the extinction of mate-shared bacteria increased, indicating that female cloacal assemblages revert to their pre-copulatory state and that the cloaca comprises a resilient microbial ecosystem.

  14. Emerging Perspectives on the Natural Microbiome of Fresh Produce Vegetables

    Directory of Open Access Journals (Sweden)

    Colin R. Jackson

    2015-04-01

    Full Text Available Plants harbor a diverse microbiome existing as bacterial populations on the leaf surface (the phyllosphere and within plant tissues (endophytes. The composition of this microbiome has been largely unexplored in fresh produce vegetables, where studies have tended to focus on pathogen detection and survival. However, the application of next-generation 16S rRNA gene sequencing approaches is beginning to reveal the diversity of this produce-associated bacterial community. In this article we review what is known about the composition of the microbiome of fresh produce vegetables, placing it in the context of general phyllosphere research. We also demonstrate how next-generation sequencing can be used to assess the bacterial assemblages present on fresh produce, using fresh herbs as an example. That data shows how the use of such culture-independent approaches can detect groups of taxa (anaerobes, psychrophiles that may be missed by traditional culture-based techniques. Other issues discussed include questions as to whether to determine the microbiome during plant growth or at point of purchase or consumption, and the potential role of the natural bacterial community in mitigating pathogen survival.

  15. nirS-type denitrifying bacterial assemblages respond to environmental conditions of a shallow estuary.

    Science.gov (United States)

    Lisa, Jessica A; Jayakumar, Amal; Ward, Bess B; Song, Bongkeun

    2017-12-01

    Molecular analysis of dissimilatory nitrite reductase genes (nirS) was conducted using a customized microarray containing 165 nirS probes (archetypes) to identify members of sedimentary denitrifying communities. The goal of this study was to examine denitrifying community responses to changing environmental variables over spatial and temporal scales in the New River Estuary (NRE), NC, USA. Multivariate statistical analyses revealed three denitrifier assemblages and uncovered 'generalist' and 'specialist' archetypes based on the distribution of archetypes within these assemblages. Generalists, archetypes detected in all samples during at least one season, were commonly world-wide found in estuarine and marine ecosystems, comprised 8%-29% of the abundant NRE archetypes. Archetypes found in a particular site, 'specialists', were found to co-vary based on site specific conditions. Archetypes specific to the lower estuary in winter were designated Cluster I and significantly correlated by sediment Chl a and porewater Fe 2+ . A combination of specialist and more widely distributed archetypes formed Clusters II and III, which separated based on salinity and porewater H 2 S respectively. The co-occurrence of archetypes correlated with different environmental conditions highlights the importance of habitat type and niche differentiation among nirS-type denitrifying communities and supports the essential role of individual community members in overall ecosystem function. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  16. Examining shifts in Carabidae assemblages across a forest-agriculture ecotone.

    Science.gov (United States)

    Leslie, T W; Biddinger, D J; Rohr, J R; Hulting, A G; Mortensen, D A; Fleischer, S J

    2014-02-01

    Northeastern U.S. farms are often situated adjacent to forestland due to the heterogeneous nature of the landscape. We investigated how forested areas influence Carabidae diversity within nearby crop fields by establishing transects of pitfall traps. Trapping extended across a forest-agriculture ecotone consisting of maize, an intermediate mowed grass margin, and a forest edge. Carabidae diversity was compared among the three habitats, and community and population dynamics were assessed along the transect. We used a principal response curve to examine and visualize community change across a spatial gradient. The highest levels of richness and evenness were observed in the forest community, and carabid assemblages shifted significantly across the ecotone, especially at the forest-grass interface. Despite strong ecotone effects, population distributions showed that some species were found in all three habitats and seemed to thrive at the ecotone. Based on similarity indices, carabid assemblages collected in maize adjacent to forest differed from carabid assemblages in maize not adjacent to forest. We conclude that forest carabid assemblages exhibit high degrees of dissimilarity with those found in agricultural fields and forested areas should thus be retained in agricultural landscapes to increase biodiversity at the landscape scale. However, ecotone species found at forest edges can still noticeably influence carabid community composition within neighboring agricultural fields. Further studies should determine how these shifts in carabid assemblages influence agroecosystem services in relation to ecosystem services observed in fields embedded in an agricultural matrix.

  17. Investigation of bacterial communities in peat land of the Gahai Lake natural conservation area

    Science.gov (United States)

    Bai, Yani; Wang, Jinchang; Zhan, Zhigao; Guan, Limei; Jin, Liang; Zheng, Guohua

    2017-10-01

    Peat is involved in the global carbon cycle and water conservation; therefore, it is implicated in global environmental change. Microorganisms play an important role in the function of peat. To investigate the bacterial communities in peat of Gahai Lake, different locations and depths were sampled and Illumina Miseq sequencing was used to analyze the microbial community. Chemical properties of peat samples were analyzed by China state standard methods (GB methods). The results showed that bacterial communities were affected by depth, with bacterial diversity and community structure at 90 and 120 cm significantly different from that at 10, 30 and 50 cm depth from the peat surface. Chemical properties of peat land including organic matter, total nitrogen and humus content did not significantly influence bacterial community structure in peat, with only one group from genus Rhizomicrobium that was significantly correlated with total nitrogen. A substantial proportion of the bacterial sequences were unclassified (1.4%), which indicates the great application potential of peat in the Gahai Lake natural conservation area in the future.

  18. A bacterial community-based index to assess the ecological status of estuarine and coastal environments

    KAUST Repository

    Aylagas, Eva; Borja, Á ngel; Tangherlini, Michael; Dell'Anno, Antonio; Corinaldesi, Cinzia; Michell, Craig; Irigoien, Xabier; Danovaro, Roberto; Rodrí guez-Ezpeleta, Naiara

    2016-01-01

    Biotic indices for monitoring marine ecosystems are mostly based on the analysis of benthic macroinvertebrate communities. Due to their high sensitivity to pollution and fast response to environmental changes, bacterial assemblages could complement

  19. Changes in the repertoire of natural antibodies caused by immunization with bacterial antigens

    DEFF Research Database (Denmark)

    Shilova, N V; Navakouski, M J; Huflejt, M

    2011-01-01

    The repertoire of natural anti-glycan antibodies in naïve chickens and in chickens immunized with bacteria Burkholderia mallei, Burkholderia pseudomallei, and Francisella tularensis as well as with peptides from an outer membrane protein of B. pseudomallei was studied. A relatively restricted pat...... pattern of natural antibodies (first of all IgY against bacterial cell wall peptidoglycan fragments, L-Rha, and core N-acetyllactosamine) shrank and, moreover, the level of detectable antibodies decreased as a result of immunization....

  20. Recent saltmarsh foraminiferal assemblages from Iceland

    Science.gov (United States)

    Lübbers, Julia; Schönfeld, Joachim

    2018-01-01

    This study reports for the first time boreal to subarctic intertidal foraminiferal assemblages from saltmarshes at Borgarnes and Faskrudsfjördur on Iceland. The composition of living and dead foraminiferal assemblages was investigated along transects from the tidal flat to the highest reach of halophytic plants. The foraminiferal assemblages from Borgarnes showed 18 species in the total foraminiferal assemblage of which only 7 species were recorded in the living fauna. The assemblages were dominated by agglutinated taxa, whereas 3 calcareous species were recorded, of which only Haynesina orbicularis was found in the living fauna. The distribution limit of calcifying species corresponds to the lower boundary of the lower saltmarsh vegetation zone. Furthermore, calcareous tests showed many features of dissolution, which is an indication of a carbonate corrosive environment. The species forming the dead assemblages were mainly derived from the ambient intertidal areas and were displaced by tidal currents into the saltmarsh. The foraminiferal assemblages from Faskrudsfjördur showed two species, of which only one species was recorded in the living fauna. The assemblage was dominated by the agglutinated foraminifer Trochaminita irregularis. The foraminiferal species recorded on Iceland were the same as commonly found elsewhere in Europa. Since no species was found which is endemic to North America, Iceland is considered part of the European bio province. The foraminiferal could have been immigrated to Iceland from Europe through warm water currents, migratory birds or marine traffic since the last Ice Age.

  1. Mnemiopsis leidyi Gut Harbors Seasonally Variant and Commensal Microbial Assemblages

    Science.gov (United States)

    Mariita, R. M.; Hossain, M. J.; Liles, M. R.; Moss, A.

    2016-02-01

    Studies have shown that with widespread use of antibiotics in human and domestic animal populations, antibiotic resistance becomes increasingly common in the environment. Estuaries provide ideal conditions for acquisition and dissemination of drug resistance genes because they serve as sinks for pollution. This study aimed to identify M. leidyi microbial diversity and richness and their potential to act as vectors for antibiotic resistance determinants (ARDs). M. leidyi, although native to study area are highly invasive. Metagenomic analyses indicate that there are temporal variations of bacterioplankton assemblages in M. leidyi gut. Overall, Proteobacteria and Actinobacteria are the most abundant phyla. Despite the temporal dynamics in the microbial assemblages in M. leidyi gut, they seem to retain Propionibacterium acnes (gut microbiota in some insects) and select proteobacteria across all seasons. The results contradict previous studies that suggest that M. leidyi does not have constant a microbiota, but only seasonally variant microbial assemblages. Here we reveal the presence of M. leidyi gut ARDs in winter and summer, probably because of the ctenophores' positive geotaxis during rough surface conditions. Genes responsible for resistance to fluoroquinolones, multidrug resistance efflux pumps, mercuric reductase, copper homeostasis and blaR1 genes were observed. This is the first study to demonstrate that M. leidyi harbors constant microbiota and provides a baseline for understanding M. leidyi gut microbial and ARDs ecology. It also suggests that M. leidyi bacterial taxonomic and functional dynamics is influenced by season. Funding: Alabama EPSCoR GRSP fellowship, AU-CMB fellowship, NSF EPS-1158862, USDA-Hatch 370225-310100 (AGM, ML).

  2. Fish assemblage relationships with physical characteristics and presence of dams in three eastern Iowa rivers

    Science.gov (United States)

    Pierce, Clay; Nicholas L. Ahrens,; Anna K. Loan-Wilsey,; Gregory A. Simmons,; Gregory T. Gelwicks,

    2013-01-01

    Fish assemblages in rivers of the Midwestern United States are an important component of the region's natural resources and biodiversity. We characterized the physical environment and presence of dams in a series of reaches in three eastern Iowa rivers tributary to the Mississippi River and related these characteristics to the fish assemblages present. Some physical characteristics were similar among the 12 study reaches, whereas others differed substantially. We found a total of 68 species across the 12 study reaches; 56 in the Turkey River, 51 in the Maquoketa River and 50 in the Wapsipinicon River. Seventeen species could be described as ‘downstream-distributed’; 15 being found only in the lowest reach of one or more rivers and the other two being found only in the lowest reaches or two or more contiguous reaches including the lowest reach. Two species could be described as ‘upstream-distributed’, being found only in an uppermost reach. Non-metric multidimensional scaling ordination illustrated similarities among reaches, and five physical variables were significantly correlated with assemblage similarities. Catchment area and number of dams between reaches and the Mississippi River were strongly correlated with assemblage similarities, but the directions of their effects were opposite. Catchment area and number of dams were confounded. The collective evidence to date suggests that the pervasiveness of dams on rivers significantly alters fish assemblages, making underlying patterns of species change and relationships with naturally varying and human-influenced physical characteristics along a river's course difficult to discern.

  3. Depth as an organizer of fish assemblages in floodplain lakes

    Science.gov (United States)

    Miranda, L.E.

    2011-01-01

    Depth reduction is a natural process in floodplain lakes, but in many basins has been accelerated by anthropogenic disturbances. A diverse set of 42 floodplain lakes in the Yazoo River Basin (Mississippi, USA) was examined to test the hypothesis of whether depth reduction was a key determinant of water quality and fish assemblage structure. Single and multiple variable analyses were applied to 10 commonly monitored water variables and 54 fish species. Results showed strong associations between depth and water characteristics, and between depth and fish assemblages. Deep lakes provided less variable environments, clearer water, and a wider range of microhabitats than shallow lakes. The greater environmental stability was reflected by the dominant species in the assemblages, which included a broader representation of large-body species, species less tolerant of extreme water quality, and more predators. Stability in deep lakes was further reflected by reduced among-lake variability in taxa representation. Fish assemblages in shallow lakes were more variable than deep lakes, and commonly dominated by opportunistic species that have early maturity, extended breeding seasons, small adult size, and short lifespan. Depth is a causal factor that drives many physical and chemical variables that contribute to organizing fish assemblages in floodplain lakes. Thus, correlations between fish and water transparency, temperature, oxygen, trophic state, habitat structure, and other environmental descriptors may ultimately be totally or partly regulated by depth. In basins undergoing rapid anthropogenic modifications, local changes forced by depth reductions may be expected to eliminate species available from the regional pool and could have considerable ecological implications. ?? 2010 Springer Basel AG (outside the USA).

  4. Ultraviolet-B radiation effects on inorganic nitrogen uptake by natural assemblages of oceanic plankton

    International Nuclear Information System (INIS)

    Behrenfeld, M.J.; Lean, D.R.S.; Lee, H. II

    1995-01-01

    Ultraviolet-B radiation (UVBR: 290-320 nm) inhibited ammonium uptake (ρ NH4 ) and nitrate uptake (ρ NO3 ) in natural plankton assemblages collected during a transect from 37 degrees N to 55 degrees N in the Pacific Ocean. Comparison of responses in ρ NH4 to ambient solar- and lamp-enhanced UVBR spectra allowed calculation of an action spectrum for ρ NH4 inhibition. The slope of the action spectrum for ρ NH4 is half as steep as action spectra for UVBR inhibition of photosynthetic carbon uptake. Consequently, UVBR-induced photoinhibition of ρ NH4 extends to greater depths than inhibition of carbon fixation due to the greater relative effect of longer UVBR wavelengths. Inhibition of ρ NH4 was dependent upon UVBR dose when doses were weighted by the ρ NH4 action spectrum. Dependence of UVBR inhibition of ρ NH4 on dose rate was not apparent. We found that near-surface ρ NH4 and ρ NO3 can be overestimated in excess of 50% when measured using standard incubation vessels made of UVBR-absorbing materials such as polycarbonate. 68 refs., 9 figs., 1 tab

  5. Functional and Taxonomic Differentiation of Macrophyte Assemblages Across the Yangtze River Floodplain Under Human Impacts.

    Science.gov (United States)

    Zhang, Min; García Molinos, Jorge; Zhang, Xiaolin; Xu, Jun

    2018-01-01

    Human activities and the consequent extirpations of species have been changing the composition of species assemblages worldwide. These anthropogenic impacts alter not only the richness of assemblages but also the biological dissimilarity among them. One of the main gaps in the assessment of biodiversity change in freshwater ecosystems is our limited understanding regarding how taxonomic and functional facets of macrophyte assemblages respond to human impacts on regional scales. Here, we assess the temporal (before 1970s against after 2000s) changes in taxonomic and functional richness and compositional dissimilarities, partitioned into its turnover and nestedness components, of freshwater macrophyte assemblages across the floodplain lakes of the Yangtze River in China. We found that functional and taxonomic assemblage differentiation occurred simultaneously under increasing human impact, concomitant to a general decrease in functional and taxonomic richness. However, this effect weakened when the historical level of taxonomic dissimilarity among assemblages was high. Macrophyte species with large dispersal range and submersed life form were significantly more susceptible to extirpation. The impact of human activities on differentiation was complex but habitat loss and fishery intensity were consistently the main drivers of assemblage change in these lakes, whereas water quality (i.e., light pollution and nutrient enrichment) had weaker effects. Further, macrophyte taxonomic and functional differentiation was mainly driven by the nestedness component of dissimilarity, accounting for changes in assemblage composition related to changes in species richness independent of species replacement. This result, markedly different from previous studies on freshwater fish assemblages conducted in these lakes, represents a novel contribution toward achieving a more holistic understanding of how human impacts contribute to shape community assemblages in natural ecosystems.

  6. Bacteremia and bacterial translocation in the naturally occurring canine gastric dilatation-volvulus patient.

    Science.gov (United States)

    Winkler, Kevin P; Greenfield, Cathy L; Schaeffer, David J

    2003-01-01

    This prospective study was performed to determine the prevalence of bacteremia in the naturally occurring gastric dilatation-volvulus (GDV) patient, the possible relationship between bacteremia and survival, and whether bacteremia was a result of translocation from the stomach. Blood cultures were collected from each patient. Bacterial cultures were collected from the liver, mesenteric lymph node, and stomach. Forty-three percent of the GDV cases and 40% of the controls developed positive blood cultures. Gram-negative rods were the most frequently isolated organisms. Evidence of bacterial translocation from the stomach could not be demonstrated in GDV patients, and survival was not affected by the presence of bacteremia.

  7. Spatial variability in intertidal macroalgal assemblages on the North Portuguese coast: consistence between species and functional group approaches

    Science.gov (United States)

    Veiga, P.; Rubal, M.; Vieira, R.; Arenas, F.; Sousa-Pinto, I.

    2013-03-01

    Natural assemblages are variable in space and time; therefore, quantification of their variability is imperative to identify relevant scales for investigating natural or anthropogenic processes shaping these assemblages. We studied the variability of intertidal macroalgal assemblages on the North Portuguese coast, considering three spatial scales (from metres to 10 s of kilometres) following a hierarchical design. We tested the hypotheses that (1) spatial pattern will be invariant at all the studied scales and (2) spatial variability of macroalgal assemblages obtained by using species will be consistent with that obtained using functional groups. This was done considering as univariate variables: total biomass and number of taxa as well as biomass of the most important species and functional groups and as multivariate variables the structure of macroalgal assemblages, both considering species and functional groups. Most of the univariate results confirmed the first hypothesis except for the total number of taxa and foliose macroalgae that showed significant variability at the scale of site and area, respectively. In contrast, when multivariate patterns were examined, the first hypothesis was rejected except at the scale of 10 s of kilometres. Both uni- and multivariate results indicated that variation was larger at the smallest scale, and thus, small-scale processes seem to have more effect on spatial variability patterns. Macroalgal assemblages, both considering species and functional groups as surrogate, showed consistent spatial patterns, and therefore, the second hypothesis was confirmed. Consequently, functional groups may be considered a reliable biological surrogate to study changes on macroalgal assemblages at least along the investigated Portuguese coastline.

  8. Fishy Business: Response of Stream Fish Assemblages to Small Hydro-power Plant Induced Flow Alteration in the Western Ghats, Karnataka

    Science.gov (United States)

    Rao, S. T.; Krishnaswamy, J.; Bhalla, R. S.

    2017-12-01

    Alteration of natural flow regimes is considered as a major threat to freshwater fish assemblages as it disturbs the water quality and micro-habitat features of rivers. Small hydro-power (SHP), which is being promoted as a clean and green substitute for large hydro-power generation, alters the natural flow regime of head-water streams by flow diversion and regulation. The effects of altered flow regime on tropical stream fish assemblages, driven by seasonality induced perturbations to water quality and microhabitat parameters are largely understudied. My study examined the potential consequences of flow alteration by SHPs on fish assemblages in two tributaries of the west-flowing Yettinahole River which flows through the reserved forests of Sakleshpur in the Western Ghats of Karnataka. The flow in one of the tributaries followed natural flow regime while the other comprised three regimes: a near-natural flow regime above the dam, rapidly varying discharge below the dam and a dewatered regime caused by flow diversion. The study found that the altered flow regime differed from natural flow regime in terms of water quality, microhabitat heterogeneity and fish assemblage response, each indicative of the type of flow alteration. Fish assemblage in the natural flow regime was characterized by a higher catch per site, a strong association of endemic and trophic specialist species. The flow regime above the dam was found to mimic some components of the natural flow regime, both ecological and environmental. Non endemic, generalist and pool tolerant species were associated with the dewatered regime. There was a lack of strong species-regime association and an overall low catch per site for the flow regulated regime below the dam. This study highlights the consequences of altered flows on the composition of freshwater fish assemblages and portrays the potential of freshwater fish as indicators of the degree and extent of flow alteration. The study recommends the need for

  9. Characterisation of the gill mucosal bacterial communities of four butterflyfish species: a reservoir of bacterial diversity in coral reef ecosystems.

    Science.gov (United States)

    Reverter, Miriam; Sasal, Pierre; Tapissier-Bontemps, N; Lecchini, D; Suzuki, M

    2017-06-01

    While recent studies have suggested that fish mucus microbiota play an important role in homeostasis and prevention of infections, very few studies have investigated the bacterial communities of gill mucus. We characterised the gill mucus bacterial communities of four butterflyfish species and although the bacterial diversity of gill mucus varied significantly between species, Shannon diversities were high (H = 3.7-5.7) in all species. Microbiota composition differed between butterflyfishes, with Chaetodon lunulatus and C. ornatissimus having the most similar bacterial communities, which differed significantly from C. vagabundus and C. reticulatus. The core bacterial community of all species consisted of mainly Proteobacteria followed by Actinobacteria and Firmicutes. Chaetodonlunulatus and C. ornatissimus bacterial communities were mostly dominated by Gammaproteobacteria with Vibrio as the most abundant genus. Chaetodonvagabundus and C. reticulatus presented similar abundances of Gammaproteobacteria and Alphaproteobacteria, which were well represented by Acinetobacter and Paracoccus, respectively. In conclusion, our results indicate that different fish species present specific bacterial assemblages. Finally, as mucus layers are nutrient hotspots for heterotrophic bacteria living in oligotrophic environments, such as coral reef waters, the high bacterial diversity found in butterflyfish gill mucus might indicate external fish mucus surfaces act as a reservoir of coral reef bacterial diversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. The endemic Patagonian vespertilionid assemblage is a depauperate ecomorphological vicariant of species-rich neotropical assemblages

    Institute of Scientific and Technical Information of China (English)

    Analía L.GIM(E)NEZ; Norberto P. GIANNINI

    2017-01-01

    Vespertilionidae is the most diverse chiropteran family,and its diversity is concentrated in warm regions of the World;however,due to physiological and behavioral adaptations,these bats also dominate bat faunas in temperate regions.Here we performed a comparative study of vespertilionid assemblages from two broad regions of the New World,the cold and harsh Patagonia,versus the remaining temperate-to-subtropical,extra-Patagonian eco-regions of the South American Southern Cone.We took an ecomorphological approach and analyzed the craniodental morphological structure of these assemblages within a phylogenetic framework.We measured 17 craniodental linear variables from 447 specimens of 22 currently recognized vespertilionid species of the study regions.We performed a multivariate analysis to define the morphofunctional space,and calculated the pattern and degree of species packing for each assemblage.We assessed the importance of phylogeny and biogeography,and their impact on depauperate (Patagonian) versus rich (extra-Patagonian) vespertilionid assemblages as determinants of morphospace structuring.We implemented a sensitivity analysis associated to small samples of rare species.The morphological patterns were determined chiefly by the evolutionary history of the family.The Patagonian assemblage can be described as a structurally similar but comparatively depauperate ecomorphological version of those assemblages from neighboring extra-Patagonian eco-regions.The Patagonian assemblage seems to have formed by successively adding populations from Northern regions that eventually speciated in the region,leaving corresponding sisters (vicariants) in extraPatagonian eco-regions that continued to be characteristically richer.Despite being structurally akin,degree of species packing in Patagonia was comparatively very low,which may reflect the effect of limited dispersal success into a harsh region for bat survival.

  11. Effects of dams in river networks on fish assemblages in non-impoundment sections of rivers in Michigan and Wisconsin, USA

    Science.gov (United States)

    Stewart, Jana S.; Lizhu Wang,; Infante, Dana M.; Lyons, John D.; Arthur Cooper,

    2011-01-01

    Regional assessment of cumulative impacts of dams on riverine fish assemblages provides resource managers essential information for dam operation, potential dam removal, river health assessment and overall ecosystem management. Such an assessment is challenging because characteristics of fish assemblages are not only affected by dams, but also influenced by natural variation and human-induced modification (in addition to dams) in thermal and flow regimes, physicochemical habitats and biological assemblages. This study evaluated the impacts of dams on river fish assemblages in the non-impoundment sections of rivers in the states of Michigan and Wisconsin using multiple fish assemblage indicators and multiple approaches to distinguish the influences of dams from those of other natural and human-induced factors. We found that environmental factors that influence fish assemblages in addition to dams should be incorporated when evaluating regional effects of dams on fish assemblages. Without considering such co-influential factors, the evaluation is inadequate and potentially misleading. The role of dams alone in determining fish assemblages at a regional spatial scale is relatively small (explained less than 20% of variance) compared with the other environmental factors, such as river size, flow and thermal regimes and land uses jointly. However, our results do demonstrate that downstream and upstream dams can substantially modify fish assemblages in the non-impoundment sections of rivers. After excluding river size and land-use influences, our results clearly demonstrate that dams have significant impacts on fish biotic-integrity and habitat-and-social-preference indicators. The influences of the upstream dams, downstream dams, distance to dams, and dam density differ among the fish indicators, which have different implications for maintaining river biotic integrity, protecting biodiversity and managing fisheries.

  12. Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment.

    Directory of Open Access Journals (Sweden)

    Fabian Staubach

    Full Text Available The fruit fly Drosophila is a classic model organism to study adaptation as well as the relationship between genetic variation and phenotypes. Although associated bacterial communities might be important for many aspects of Drosophila biology, knowledge about their diversity, composition, and factors shaping them is limited. We used 454-based sequencing of a variable region of the bacterial 16S ribosomal RNA gene to characterize the bacterial communities associated with wild and laboratory Drosophila isolates. In order to specifically investigate effects of food source and host species on bacterial communities, we analyzed samples from wild Drosophila melanogaster and D. simulans collected from a variety of natural substrates, as well as from adults and larvae of nine laboratory-reared Drosophila species. We find no evidence for host species effects in lab-reared flies; instead, lab of origin and stochastic effects, which could influence studies of Drosophila phenotypes, are pronounced. In contrast, the natural Drosophila-associated microbiota appears to be predominantly shaped by food substrate with an additional but smaller effect of host species identity. We identify a core member of this natural microbiota that belongs to the genus Gluconobacter and is common to all wild-caught flies in this study, but absent from the laboratory. This makes it a strong candidate for being part of what could be a natural D. melanogaster and D. simulans core microbiome. Furthermore, we were able to identify candidate pathogens in natural fly isolates.

  13. Bacterial profiling of White Plague Disease across corals and oceans indicates a conserved and distinct disease microbiome

    KAUST Repository

    Roder, C.; Arif, C.; Daniels, C.; Weil, E.; Voolstra, Christian R.

    2014-01-01

    microarrays to assay differences in bacterial assemblages of healthy and diseased colonies displaying White Plague Disease (WPD) signs from two closely related Caribbean coral species, Orbicella faveolata and Orbicella franksi. Analysis of differentially

  14. Natural Sunlight Shapes Crude Oil-Degrading Bacterial Communities in Northern Gulf of Mexico Surface Waters.

    Science.gov (United States)

    Bacosa, Hernando P; Liu, Zhanfei; Erdner, Deana L

    2015-01-01

    Following the Deepwater Horizon (DWH) spill in 2010, an enormous amount of oil was observed in the deep and surface waters of the northern Gulf of Mexico. Surface waters are characterized by intense sunlight and high temperature during summer. While the oil-degrading bacterial communities in the deep-sea plume have been widely investigated, the effect of natural sunlight on those in oil polluted surface waters remains unexplored to date. In this study, we incubated surface water from the DWH site with amendments of crude oil, Corexit dispersant, or both for 36 days under natural sunlight in the northern Gulf of Mexico. The bacterial community was analyzed over time for total abundance, density of alkane and polycyclic aromatic hydrocarbon degraders, and community composition via pyrosequencing. Our results showed that, for treatments with oil and/or Corexit, sunlight significantly reduced bacterial diversity and evenness and was a key driver of shifts in bacterial community structure. In samples containing oil or dispersant, sunlight greatly reduced abundance of the Cyanobacterium Synechococcus but increased the relative abundances of Alteromonas, Marinobacter, Labrenzia, Sandarakinotalea, Bartonella, and Halomonas. Dark samples with oil were represented by members of Thalassobius, Winogradskyella, Alcanivorax, Formosa, Pseudomonas, Eubacterium, Erythrobacter, Natronocella, and Coxiella. Both oil and Corexit inhibited the Candidatus Pelagibacter with or without sunlight exposure. For the first time, we demonstrated the effects of light in structuring microbial communities in water with oil and/or Corexit. Overall, our findings improve understanding of oil pollution in surface water, and provide unequivocal evidence that sunlight is a key factor in determining bacterial community composition and dynamics in oil polluted marine waters.

  15. Elevated land runoff after European settlement perturbs persistent foraminiferal assemblages on the Great Barrier Reef.

    Science.gov (United States)

    Uthicke, S; Patel, F; Ditchburn, R

    2012-01-01

    Coral reefs are under pressure from a variety of human-induced disturbances, but demonstration of ecosystem changes and identification of stressors are often difficult. We tested whether global change or increased agricultural runoff after European settlement of Northeast Australia (ca. 1860) has affected inshore reefs of the Great Barrier Reef. Eleven sediment cores were retrieved from inner reefs, intermediate reefs, and outer-island reefs, and benthic foraminiferal assemblages were analyzed in dated (14C, 210Pb, 137Cs) core sections (N = 82 samples). Data were grouped into six age bands ( 1500 yr). Principal component analysis and two-factor (Zone and Age) permutational analysis of variance (PERMANOVA) suggested that assemblages from the three zones were significantly different from each other over several millennia, with symbiont-bearing (mixotrophic) species dominating the outer reefs. A significant interaction term indicated that within-zone patterns varied. Assemblages in outer reefs unaffected from increased land runoff were persistent until present times. In both other zones, assemblages were also persistent until 150 yr ago, suggesting that benthic foraminiferal assemblages are naturally highly persistent over long (> 2000 yr) timescales. Assemblages in core sections PERMANOVA. With some exceptions, changes on the inner and intermediate reefs were consistent with a model predicting that increased nutrients and higher turbidity enhance relative abundance of heterotrophic species. Given that assemblages did not change in outer-island reefs (not impacted by runoff) we argue that changes in assemblages due to global change can be rejected as an explanation. Thus, the findings are more consistent with the hypothesis that agricultural runoff since European settlement altered foraminiferal assemblages than with the hypothesis that global forcing caused changes.

  16. Affects and assemblages

    DEFF Research Database (Denmark)

    Samson, Kristine

    the paper raises the questions where to locate aesthetics when planners and architects wishes to design for aesthetical experiences and sensations rather than formal objects. The paper will proceed through a brief outline of the recent notion of assemblage and affect in urban studies, planning theory...... happens to aesthetics and how does it change the existing social and geographical understanding of urban space? The paper sets out to reintroduce aesthetical aspects of affects and assemblages in relation to urban space and urban planning. It presupposes urban space as a continuous state of becoming where...

  17. The Role of Regional Factors in Structuring Ouachita Mountain Stream Assemblages

    Science.gov (United States)

    Lance R. Williams; Christopher M. Taylor; Melvin L. Warren; J. Alan Clingenpeel

    2004-01-01

    Abstract - We used Basin Area Stream Survey data from the USDA Forest Service, Ouachita National Forest to evaluate the relationship between regional fish and macroinvertebrate assemblages and environmental variability (both natural and anthropogenic). Data were collected for three years (1990-1992) from six hydrologically variable stream systems in...

  18. Altered vegetative assemblage trajectories within an urban brownfield

    Energy Technology Data Exchange (ETDEWEB)

    Gallagher, Frank J., E-mail: Gallagher@sebs.rutgers.edu [Urban Forestry Program, Department of Ecology, Evolution and Natural Resources, Rutgers, State University, 14 College Farm Road, New Brunswick, NJ 08901-8551 (United States); Pechmann, Ildiko; Holzapfel, Claus [Department of Biological Sciences, Rutgers, State University, 195 University Avenue, Newark, NJ 07102 (United States); Grabosky, Jason [Urban Forestry Program, Department of Ecology, Evolution and Natural Resources, Rutgers, State University, 14 College Farm Road, New Brunswick, NJ 08901-8551 (United States)

    2011-05-15

    Recognizing the growing importance of both structure (maintenance of biodiversity) and function (fostering natural cycles) of urban ecologies, we examine coarse scale (herbaceous, shrub and forest) beta guild trajectory in an urban brownfield. The distribution of the pioneer forest assemblage dominated by Betula populifolia Marsh. and Populus spp. could be correlated positively with total soil metal load (arsenic, cadmium, chromium, copper, lead, zinc, lead and vanadium),whereas herbaceous and shrub guilds were negatively correlated. Distinct assemblage development trajectories above and below a critical soil metal threshold are demonstrated. In addition, we postulate that the translocation of metals into the plant tissue of several dominant species may provide a positive feedback loop, maintaining relatively high concentrations of metals in the litter and soil. Therefore assembly theory, which allows for the development of alternate stable states, may provide a better model for the establishment of restoration objectives on degraded urban sites. - Highlights: > Forest distribution and total soil metal load yield strong positive correlations. > Shrub and herbaceous guild distribution and TML are negative and weaker. > Below a critical TML threshold transition between guilds exhibit a standard trajectory. > Above the critical TML threshold the shrub guild is virtually absent. > Metal cycling has the potential to lead to an alternative steady state. - High concentrationsof soil metals, impact the trajectory of vegetative assemblages in an urban brownfield leading to the speculation of an alternate stable state.

  19. Gradients in Catostomid assemblages along a reservoir cascade

    Science.gov (United States)

    Miranda, Leandro E.; Keretz, Kevin R.; Gilliland, Chelsea R.

    2017-01-01

    Serial impoundment of major rivers leads to alterations of natural flow dynamics and disrupts longitudinal connectivity. Catostomid fishes (suckers, family Catostomidae) are typically found in riverine or backwater habitats yet are able to persist in impounded river systems. To the detriment of conservation, there is limited information about distribution of catostomid fishes in impounded rivers. We examined the longitudinal distribution of catostomid fishes over 23 reservoirs of the Tennessee River reservoir cascade, encompassing approximately 1600 km. Our goal was to develop a basin-scale perspective to guide conservation efforts. Catostomid species composition and assemblage structure changed longitudinally along the reservoir cascade. Catostomid species biodiversity was greatest in reservoirs lower in the cascade. Assemblage composition shifted from dominance by spotted sucker Minytrema melanops and buffalos Ictiobus spp. in the lower reservoirs to carpsuckers Carpiodes spp. midway through the cascade and redhorses Moxostoma spp. in the upper reservoirs. Most species did not extend the length of the cascade, and some species were rare, found in low numbers and in few reservoirs. The observed gradients in catostomid assemblages suggest the need for basin-scale conservation measures focusing on three broad areas: (1) conservation and management of the up-lake riverine reaches of the lower reservoirs, (2) maintenance of the access to quality habitat in tributaries to the upper reservoirs and (3) reintroductions into currently unoccupied habitat within species' historic distributions

  20. Relations between altered stramflow variability and fish assemblages in Eastern USA streams

    Science.gov (United States)

    Meador, Michael R.; Carlisle, Daren M.

    2012-01-01

    Although altered streamflow has been implicated as a major factor affecting fish assemblages, understanding the extent of streamflow alteration has required quantifying attributes of the natural flow regime. We used predictive models to quantify deviation from expected natural streamflow variability for streams in the eastern USA. Sites with >25% change in mean daily streamflow variability compared with what would be expected in a minimally disturbed environment were defined as having altered streamflow variability, based on the 10th and 90th percentiles of the distribution of streamflow variability at 1279 hydrological reference sites. We also used predictive models to assess fish assemblage condition and native species loss based on the proportion of expected native fish species that were observed. Of the 97 sites, 49 (50.5%) were classified as altered with reduced streamflow variability, whereas no sites had increased streamflow variability. Reduced streamflow variability was related to a 35% loss in native fish species, on average, and a >50% loss of species with a preference for riffle habitats. Conditional probability analysis indicated that the probability of fish assemblage impairment increased as the severity of altered streamflow variability increased. Reservoir storage capacity and wastewater discharges were important predictors of reduced streamflow variability as revealed by random forest analysis. Management and conservation of streams will require careful consideration of natural streamflow variation and potential factors contributing to altered streamflow within the entire watershed to limit the loss of critical stream habitats and fish species uniquely adapted to live in those habitats.

  1. Bacterial microbiota compositions of naturally fermented milk are shaped by both geographic origin and sample type.

    Science.gov (United States)

    Zhong, Z; Hou, Q; Kwok, L; Yu, Z; Zheng, Y; Sun, Z; Menghe, B; Zhang, H

    2016-10-01

    Naturally fermented dairy products contain a rich microbial biodiversity. This study aimed to provide an overview on the bacterial microbiota biodiversity of 85 samples, previously collected across a wide region of China, Mongolia, and Russia. Data from these 85 samples, including 55 yogurts, 18 naturally fermented yak milks, 6 koumisses, and 6 cheeses, were retrieved and collectively analyzed. The most prevalent phyla shared across samples were Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria, which together accounted for 99% of bacterial sequences. The predominant genera were Lactobacillus, Lactococcus, Streptococcus, Acetobacter, Acinetobacter, Leuconostoc, and Macrococcus, which together corresponded to 96.63% of bacterial sequences. Further multivariate statistical analyses revealed significant differences in the microbiota structure across sample geographic origin and type. First, on the principal coordinate score plot, samples representing the 3 main sample collection regions (Russia, Xinjiang, and Tibet) were mostly located respectively in the upper left, lower right, and lower left quadrants, although slight overlapping occurred. In contrast, samples from the minor sampling areas (Inner Mongolia, Mongolia, Gansu, and Sichuan) were predominantly distributed in the lower left quadrant. These results suggest a possible association between sample geographical origin and microbiota composition. Second, bacterial microbiota structure was stratified by sample type. In particular, the microbiota of cheese was largely distinct from the other sample types due to its high abundances of Lactococcus and Streptococcus. The fermented yak milk microbiota was most like that of the yogurts. Koumiss samples had the lowest microbial diversity and richness. In conclusion, both geographic origin and sample type shape the microbial diversity of naturally fermented milk. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights

  2. Investigation of phagotrophy in natural assemblages of the benthic dinoflagellates Ostreopsis, Prorocentrum and Coolia

    Directory of Open Access Journals (Sweden)

    Eliliane Vasconcelos Corrêa Almada

    Full Text Available Abstract Mixotrophy has been shown to be a common trait among dinoflagellates and its importance in the nutritional ecology of harmful algae has been hypothesized. Benthic harmful species have not been extensively investigated as their planktonic counterparts and there are major gaps in the knowledge of their nutritional strategies. In this study the occurrence of phagotrophy was investigated in natural assemblages of benthic dinoflagellates using epi-fluorescence microscopy with DAPI and LysoSensor staining. The study was conducted at five sites along the coast of Rio de Janeiro that were visited in January, August and December 2010. In total, 1659 dinoflagellate cells were observed. From these, only 0.4% of 1195 Ostreopsis cf. ovata and 2.2% of 134 Coolia spp. cells presented evidence of phagotrophy with vacuoles stained by LysoSensor or a DAPI (4',6-diamidino-2-phenylindole stained inclusion. Stained vacuoles were not registered in the 330 Prorocentrum spp. cells observed. Few O. cf. ovata cells contained round red inclusions ("red spots" that were not stained either by DAPI or LysoSensor, suggesting that these structures are not ingested prey. The results showed that phagotrophy was not a frequent nutritional strategy in benthic dinoflagellates during the study period.

  3. The dynamic nature and territory of transcriptional machinery in the bacterial chromosome

    Directory of Open Access Journals (Sweden)

    Ding Jun Jin

    2015-05-01

    Full Text Available Our knowledge of the regulation of genes involved in bacterial growth and stress responses is extensive; however, we have only recently begun to understand how environmental cues influence the dynamic, three-dimensional distribution of RNA polymerase (RNAP in Escherichia coli on the level of single cell, using wide-field fluorescence microscopy and state-of-the-art imaging techniques. Live-cell imaging using either an agarose-embedding procedure or a microfluidic system further underscores the dynamic nature of the distribution of RNAP in response to changes in the environment. A general agreement between live-cell and fixed-cell images has validated the formaldehyde-fixing procedure, which is a technical breakthrough in the study of the cell biology of RNAP. In this review we use a systems biology perspective to summarize the advances in the cell biology of RNAP in E. coli, including the discoveries of the bacterial nucleolus, the spatial compartmentalization of the transcription machinery at the periphery of the nucleoid, and the segregation of the chromosome territories for the two major cellular functions of transcription and replication in fast-growing cells. Our understanding of the coupling of transcription and bacterial chromosome (or nucleoid structure is also summarized. Using E. coli as a simple model system, co-imaging of RNAP with DNA and other factors during growth and stress responses will continue to be a useful tool for studying bacterial growth and adaptation in changing environment.

  4. Strange Assemblage

    Directory of Open Access Journals (Sweden)

    David Robert Cole

    2014-08-01

    Full Text Available This paper contends that the power of Deleuze & Guattari’s (1988 notion of assemblage as theorised in 1000 Plateaus can be normalised and reductive with reference to its application to any social-cultural context where an open system of dynamic and fluid elements are located. Rather than determining the assemblage in this way, this paper argues for an alternative conception of ‘strange assemblage’ that must be deliberately and consciously created through rigorous and focused intellectual, creative and philosophical work around what makes assemblages singular. The paper will proceed with examples of ‘strange assemblage’ taken from a film by Peter Greenaway (A Zed and 2 Noughts; the film ‘Performance’; educational research with Sudanese families in Australia; the book, Bomb Culture by Jeff Nuttall (1970; and the band Hawkwind. Fittingly, these elements are themselves chosen to demonstrate the concept of ‘strange assemblage’, and how it can be presented. How exactly the elements of a ‘strange assemblage’ come together and work in the world is unknown until they are specifically elaborated and created ‘in the moment’. Such spontaneous methodology reminds us of the 1960s ‘Happenings’, the Situationist International and Dada/Surrealism. The difference that will be opened up by this paper is that all elements of this ‘strange assemblage’ cohere in terms of a rendering of ‘the unacceptable.'

  5. Cryo-electron tomography of bacterial viruses

    Energy Technology Data Exchange (ETDEWEB)

    Guerrero-Ferreira, Ricardo C. [Division of Pediatric Infectious Diseases, Emory University School of Medicine, Children' s Healthcare of Atlanta, Atlanta, GA 30322 (United States); Wright, Elizabeth R., E-mail: erwrigh@emory.edu [Division of Pediatric Infectious Diseases, Emory University School of Medicine, Children' s Healthcare of Atlanta, Atlanta, GA 30322 (United States)

    2013-01-05

    Bacteriophage particles contain both simple and complex macromolecular assemblages and machines that enable them to regulate the infection process under diverse environmental conditions with a broad range of bacterial hosts. Recent developments in cryo-electron tomography (cryo-ET) make it possible to observe the interactions of bacteriophages with their host cells under native-state conditions at unprecedented resolution and in three-dimensions. This review describes the application of cryo-ET to studies of bacteriophage attachment, genome ejection, assembly and egress. Current topics of investigation and future directions in the field are also discussed.

  6. Transient shifts in bacterial communities associated with the temperate gorgonian Paramuricea clavata in the Northwestern Mediterranean Sea.

    Directory of Open Access Journals (Sweden)

    Marie La Rivière

    Full Text Available BACKGROUND: Bacterial communities that are associated with tropical reef-forming corals are being increasingly recognized for their role in host physiology and health. However, little is known about the microbial diversity of the communities associated with temperate gorgonian corals, even though these communities are key structural components of the ecosystem. In the Northwestern Mediterranean Sea, gorgonians undergo recurrent mass mortalities, but the potential relationship between these events and the structure of the associated bacterial communities remains unexplored. Because microbial assemblages may contribute to the overall health and disease resistance of their host, a detailed baseline of the associated bacterial diversity is required to better understand the functioning of the gorgonian holobiont. METHODOLOGY/PRINCIPAL FINDINGS: The bacterial diversity associated with the gorgonian Paramuricea clavata was determined using denaturing gradient gel electrophoresis, terminal-restriction fragment length polymorphism and the construction of clone libraries of the bacterial 16S ribosomal DNA. Three study sites were monitored for 4 years to assess the variability of communities associated with healthy colonies. Bacterial assemblages were highly dominated by one Hahellaceae-related ribotype and exhibited low diversity. While this pattern was mostly conserved through space and time, in summer 2007, a deep shift in microbiota structure toward increased bacterial diversity and the transient disappearance of Hahellaceae was observed. CONCLUSION/SIGNIFICANCE: This is the first spatiotemporal study to investigate the bacterial diversity associated with a temperate shallow gorgonian. Our data revealed an established relationship between P. clavata and a specific bacterial group within the Oceanospirillales. These results suggest a potential symbiotic role of Hahellaceae in the host-microbe association, as recently suggested for tropical corals

  7. Bacterial dynamics and metabolite changes in solid-state acetic acid fermentation of Shanxi aged vinegar.

    Science.gov (United States)

    Li, Sha; Li, Pan; Liu, Xiong; Luo, Lixin; Lin, Weifeng

    2016-05-01

    Solid-state acetic acid fermentation (AAF), a natural or semi-controlled fermentation process driven by reproducible microbial communities, is an important technique to produce traditional Chinese cereal vinegars. Highly complex microbial communities and metabolites are involved in traditional Chinese solid-state AAF, but the association between microbiota and metabolites during this process are still poorly understood. In this study, we performed amplicon 16S rRNA gene sequencing on the Illumina MiSeq platform, PCR-denaturing gradient gel electrophoresis, and metabolite analysis to trace the bacterial dynamics and metabolite changes under AAF process. A succession of bacterial assemblages was observed during the AAF process. Lactobacillales dominated all the stages. However, Acetobacter species in Rhodospirillales were considerably accelerated during AAF until the end of fermentation. Quantitative PCR results indicated that the biomass of total bacteria showed a "system microbe self-domestication" process in the first 3 days, and then peaked at the seventh day before gradually decreasing until the end of AAF. Moreover, a total of 88 metabolites, including 8 organic acids, 16 free amino acids, and 66 aroma compounds were detected during AAF. Principal component analysis and cluster analyses revealed the high correlation between the dynamics of bacterial community and metabolites.

  8. Natural and human-induced variability in the composition of fish assemblages in the Northwestern Cuban shelf

    Directory of Open Access Journals (Sweden)

    Gaspar González-Sansón

    2009-09-01

    Full Text Available The main goal of the study was to obtain field data to build a baseline of fish assemblage composition that can be used comparatively for future analyses of the impact of human actions in the region. A basic network of 68 sampling stations was defined for the entire region (4 050 km2. Fish assemblage species and size composition was estimated using visual census methods at three different spatial scales: a entire region, b inside the main reef area and c along a human impact coastal gradient. Multivariate numerical analyses revealed habitat type as the main factor inducing spatial variability of fish community composition, while the level of human impact appears to play the main role in fish assemblage composition changes along the coast. A trend of decreasing fish size toward the east supports the theory of more severe human impact due to overfishing and higher urban pollution in that direction. This is the first detailed study along the northwest coast of Cuba that focuses on fish community structure and the natural and human-induced variations at different spatial scales for the entire NW shelf. This research also provides input for a more comprehensive understanding of coastal marine fish communities’ status in the Gulf of Mexico basin. Rev. Biol. Trop. 57 (3: 721-740. Epub 2009 September 30.Se obtuvieron datos de campo para una línea base de la composición de la ictiofauna que pueda ser usada comparativamente para el análisis de impactos humanos futuros en la región. Se estableció una red básica de 68 estaciones de muestreo para la región completa (4 050 km2. La composición por especies y por tallas de la ictiofauna fue estimada utilizando métodos de censo visual en tres escalas espaciales diferentes: a La región completa, b dentro del área principal de arrecifes y c a lo largo de un gradiente costero de impacto humano. El tipo de hábitat es el factor principal que induce la variación espacial en la composición de la

  9. Characterizing lentic freshwater fish assemblages using multiple sampling methods

    Science.gov (United States)

    Fischer, Jesse R.; Quist, Michael C.

    2014-01-01

    Characterizing fish assemblages in lentic ecosystems is difficult, and multiple sampling methods are almost always necessary to gain reliable estimates of indices such as species richness. However, most research focused on lentic fish sampling methodology has targeted recreationally important species, and little to no information is available regarding the influence of multiple methods and timing (i.e., temporal variation) on characterizing entire fish assemblages. Therefore, six lakes and impoundments (48–1,557 ha surface area) were sampled seasonally with seven gear types to evaluate the combined influence of sampling methods and timing on the number of species and individuals sampled. Probabilities of detection for species indicated strong selectivities and seasonal trends that provide guidance on optimal seasons to use gears when targeting multiple species. The evaluation of species richness and number of individuals sampled using multiple gear combinations demonstrated that appreciable benefits over relatively few gears (e.g., to four) used in optimal seasons were not present. Specifically, over 90 % of the species encountered with all gear types and season combinations (N = 19) from six lakes and reservoirs were sampled with nighttime boat electrofishing in the fall and benthic trawling, modified-fyke, and mini-fyke netting during the summer. Our results indicated that the characterization of lentic fish assemblages was highly influenced by the selection of sampling gears and seasons, but did not appear to be influenced by waterbody type (i.e., natural lake, impoundment). The standardization of data collected with multiple methods and seasons to account for bias is imperative to monitoring of lentic ecosystems and will provide researchers with increased reliability in their interpretations and decisions made using information on lentic fish assemblages.

  10. [Effects of different soil and water loss control measures on the dung beetle assemblages in Huangfuchuan watershed, Inner Mongolia of North China].

    Science.gov (United States)

    Liu, Wei; Wang, Run-Run; Liu, Xin-Min

    2013-03-01

    By using pitfall trap method, and taking the croplands and natural grasslands under different soil and water loss control measures as sampling plots, an investigation was conducted on the dung beetle assemblages in the Huangfuchuan watershed of Inner Mongolia from September 2007 to September 2008, aimed to understand the effects of different soil and water loss control measures on the dung beetle assemblages in the watershed. A total of 6169 dung beetles were captured, belonging to 15 species, 5 genus, and 2 families. The dominant species were Aphodius rectus and Onthophagus gibbulus, accounting for 66. 54% and 13. 26% of the total captured beetles, respectively. A lack of the species suitable for living in woodland habitats was the basic feature of the dung beetle assemblages. As compared with the control, all test soil and water loss control measures did not cause an obvious increase of species richness, biomass, and abundance of the dung beetle assemblages. The biomass and species richness of the assemblages as well as the abundance of the functional groups II and III had a significant negative correlation with the average tree (grass) height. Under the effects of long-term agricultural cultivation and the lack of large herbivores, the species richness and abundance of the functional group I (larger paracoprids and telocoprids) were lower than those of the functional groups II (relatively smaller paracoprids) and II (endocoprids), the main components of the dung beetle assemblages in the watershed. The faeces of the residents and livestock in the study region provided abundant foods for the dung beetle assemblages, inducing the relatively high abundance and spices richness of the assemblages occurred in the croplands nearby the villages. Our results suggested that natural grasslands were the suitable habitats for the dung beetles in Huangfuchuan watershed. At regional scale, to popularize the successful experiences of comprehensive soil and water loss control

  11. Non-indigenous macroinvertebrate species in Lithuanian fresh waters, Part 2: Macroinvertebrate assemblage deviation from naturalness in lotic systems and the consequent potential impacts on ecological quality assessment

    Directory of Open Access Journals (Sweden)

    Arbačiauskas K.

    2011-12-01

    Full Text Available The biological pressure represented by non-indigenous macroinvertebrate species (NIMS should be addressed in the implementation of EU Water Framework Directive as this can have a direct impact on the ’naturalness’ of the invaded macroinvertebrate assemblage. The biocontamination concept allows assessment of this deviation from naturalness, by evaluation of abundance and disparity contamination of an assemblage. This study aimed to assess the biocontamination of macroinvertebrate assemblages in Lithuanian rivers, thereby revealing the most high-impact non-indigenous species, and to explore the relationship between biocontamination and conventional metrics of ecological quality. Most of the studied rivers appeared to be impacted by NIMS. The amphipods Pontogammarus robustoides, Chelicorophium curvispinum and snail Litoglyphus naticoides were revealed as high-impact NIMS for Lithuanian lotic systems. Metrics of ecological quality which largely depend upon the richness of indicator taxa, such as the biological monitoring working party (BMWP score and Ephemeroptera/Plecoptera/Trichoptera (EPT taxa number, were negatively correlated with biocontamination, implying they could provide unreliable ecological quality estimates when NIMS are present. Routine macroinvertebrate water quality monitoring data are sufficient for generation of the biocontamination assessment and thus can provide supplementary information, with minimal extra expense or effort. We therefore recommend that biocontamination assessment is included alongside established methods for gauging biological and chemical water quality.

  12. Altered vegetative assemblage trajectories within an urban brownfield

    International Nuclear Information System (INIS)

    Gallagher, Frank J.; Pechmann, Ildiko; Holzapfel, Claus; Grabosky, Jason

    2011-01-01

    Recognizing the growing importance of both structure (maintenance of biodiversity) and function (fostering natural cycles) of urban ecologies, we examine coarse scale (herbaceous, shrub and forest) beta guild trajectory in an urban brownfield. The distribution of the pioneer forest assemblage dominated by Betula populifolia Marsh. and Populus spp. could be correlated positively with total soil metal load (arsenic, cadmium, chromium, copper, lead, zinc, lead and vanadium),whereas herbaceous and shrub guilds were negatively correlated. Distinct assemblage development trajectories above and below a critical soil metal threshold are demonstrated. In addition, we postulate that the translocation of metals into the plant tissue of several dominant species may provide a positive feedback loop, maintaining relatively high concentrations of metals in the litter and soil. Therefore assembly theory, which allows for the development of alternate stable states, may provide a better model for the establishment of restoration objectives on degraded urban sites. - Highlights: → Forest distribution and total soil metal load yield strong positive correlations. → Shrub and herbaceous guild distribution and TML are negative and weaker. → Below a critical TML threshold transition between guilds exhibit a standard trajectory. → Above the critical TML threshold the shrub guild is virtually absent. → Metal cycling has the potential to lead to an alternative steady state. - High concentrationsof soil metals, impact the trajectory of vegetative assemblages in an urban brownfield leading to the speculation of an alternate stable state.

  13. Temporal distribution of intertidal macrozoobenthic assemblages in a Nanozostera noltii-dominated area (Lagoon of Venice).

    Science.gov (United States)

    Tagliapietra, D; Pessa, G; Cornello, M; Zitelli, A; Magni, P

    2016-03-01

    We describe the temporal distribution of intertidal macrozoobenthic assemblages in a small marsh pond of the Lagoon of Venice colonized by the seagrass Nanozostera noltii (Hornemman) Tomlinson et Posluzny. Three stations ranging in the degree of N. noltii cover were selected about 100 m apart and sampled 9 times at regular intervals from March 1996 to March 1997. We applied the concepts of resistance and resilience to "natural stress" (e.g. extent of protection from seagrass meadows, exposure of macrozoobenthic assemblages to high temperatures in summer) with the aim to assess the stability of a community along a gradient of seagrass coverage. Results showed that the most structured and taxa-rich macrozoobenthic assemblage occurred at the station covered by a continuous stand of N. noltii, where permanent taxa (i.e. found in 100% of samples) were almost double than those found at the other stations. During the annual cycle, the macrozoobenthic assemblages showed a cyclical pattern, with temporal fluctuations increasing as they moved further away from the seagrass beds. We propose the role of N. noltii offering structural complexity and stability as the more probable explanation to the observed differences between stations in the intertidal assemblages. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Large-scale spatial distribution patterns of gastropod assemblages in rocky shores.

    Directory of Open Access Journals (Sweden)

    Patricia Miloslavich

    Full Text Available Gastropod assemblages from nearshore rocky habitats were studied over large spatial scales to (1 describe broad-scale patterns in assemblage composition, including patterns by feeding modes, (2 identify latitudinal pattern of biodiversity, i.e., richness and abundance of gastropods and/or regional hotspots, and (3 identify potential environmental and anthropogenic drivers of these assemblages. Gastropods were sampled from 45 sites distributed within 12 Large Marine Ecosystem regions (LME following the NaGISA (Natural Geography in Shore Areas standard protocol (www.nagisa.coml.org. A total of 393 gastropod taxa from 87 families were collected. Eight of these families (9.2% appeared in four or more different LMEs. Among these, the Littorinidae was the most widely distributed (8 LMEs followed by the Trochidae and the Columbellidae (6 LMEs. In all regions, assemblages were dominated by few species, the most diverse and abundant of which were herbivores. No latitudinal gradients were evident in relation to species richness or densities among sampling sites. Highest diversity was found in the Mediterranean and in the Gulf of Alaska, while highest densities were found at different latitudes and represented by few species within one genus (e.g. Afrolittorina in the Agulhas Current, Littorina in the Scotian Shelf, and Lacuna in the Gulf of Alaska. No significant correlation was found between species composition and environmental variables (r≤0.355, p>0.05. Contributing variables to this low correlation included invasive species, inorganic pollution, SST anomalies, and chlorophyll-a anomalies. Despite data limitations in this study which restrict conclusions in a global context, this work represents the first effort to sample gastropod biodiversity on rocky shores using a standardized protocol across a wide scale. Our results will generate more work to build global databases allowing for large-scale diversity comparisons of rocky intertidal assemblages.

  15. Ecosystem productivity is associated with bacterial phylogenetic distance in surface marine waters.

    Science.gov (United States)

    Galand, Pierre E; Salter, Ian; Kalenitchenko, Dimitri

    2015-12-01

    Understanding the link between community diversity and ecosystem function is a fundamental aspect of ecology. Systematic losses in biodiversity are widely acknowledged but the impact this may exert on ecosystem functioning remains ambiguous. There is growing evidence of a positive relationship between species richness and ecosystem productivity for terrestrial macro-organisms, but similar links for marine micro-organisms, which help drive global climate, are unclear. Community manipulation experiments show both positive and negative relationships for microbes. These previous studies rely, however, on artificial communities and any links between the full diversity of active bacterial communities in the environment, their phylogenetic relatedness and ecosystem function remain hitherto unexplored. Here, we test the hypothesis that productivity is associated with diversity in the metabolically active fraction of microbial communities. We show in natural assemblages of active bacteria that communities containing more distantly related members were associated with higher bacterial production. The positive phylogenetic diversity-productivity relationship was independent of community diversity calculated as the Shannon index. From our long-term (7-year) survey of surface marine bacterial communities, we also found that similarly, productive communities had greater phylogenetic similarity to each other, further suggesting that the traits of active bacteria are an important predictor of ecosystem productivity. Our findings demonstrate that the evolutionary history of the active fraction of a microbial community is critical for understanding their role in ecosystem functioning. © 2015 John Wiley & Sons Ltd.

  16. Influence of Uranium on Bacterial Communities: A Comparison of Natural Uranium-Rich Soils with Controls

    Science.gov (United States)

    Mondani, Laure; Benzerara, Karim; Carrière, Marie; Christen, Richard; Mamindy-Pajany, Yannick; Février, Laureline; Marmier, Nicolas; Achouak, Wafa; Nardoux, Pascal; Berthomieu, Catherine; Chapon, Virginie

    2011-01-01

    This study investigated the influence of uranium on the indigenous bacterial community structure in natural soils with high uranium content. Radioactive soil samples exhibiting 0.26% - 25.5% U in mass were analyzed and compared with nearby control soils containing trace uranium. EXAFS and XRD analyses of soils revealed the presence of U(VI) and uranium-phosphate mineral phases, identified as sabugalite and meta-autunite. A comparative analysis of bacterial community fingerprints using denaturing gradient gel electrophoresis (DGGE) revealed the presence of a complex population in both control and uranium-rich samples. However, bacterial communities inhabiting uraniferous soils exhibited specific fingerprints that were remarkably stable over time, in contrast to populations from nearby control samples. Representatives of Acidobacteria, Proteobacteria, and seven others phyla were detected in DGGE bands specific to uraniferous samples. In particular, sequences related to iron-reducing bacteria such as Geobacter and Geothrix were identified concomitantly with iron-oxidizing species such as Gallionella and Sideroxydans. All together, our results demonstrate that uranium exerts a permanent high pressure on soil bacterial communities and suggest the existence of a uranium redox cycle mediated by bacteria in the soil. PMID:21998695

  17. Are grazer-induced adaptations of bacterial abundance and morphology timedependent?

    Directory of Open Access Journals (Sweden)

    Gianluca CORNO

    2006-02-01

    Full Text Available Predation by protists is a well known force that shapes bacterial communities and can lead to filamentous forms and aggregations of large cell clusters. These classic resistance strategies were observed as a direct consequence of predation by heteroand mixotrophic flagellates (the main group of bacteria predators in water on natural assemblages of bacteria and on single plastic strains. Recently it was shown that a long time exposure (about 30 days of a bacterial strain, characterized by high degree of phenotypic plasticity, to flagellates, without direct predation, enhanced the formation of resistant forms (filaments in a continuous culture system. Target prey populations and predators were separated by a dialysis membrane. Moreover, the positive impact on bacterial growth, due to the chemical excretes released by flagellates was demonstrated for exudates of photosynthetic activity. The same positive impact may also be seen in response to exudates related to grazing. In this study, two short-term experiments (<100 hours were conducted to test for modifications in the morphology and productivity of three different bacterial strains that were induced by the presence of active predators, but without direct predation. The growth and morphological distribution of each of the selected strains was tested separately using batch cultures. Cultures were either enriched with carbon in the presence or absence of flagellate predators, or included pre-filtered exudates from flagellate activity. In a second experiment, bottles were provided with a central dialysis bag that contained active flagellates, and were inoculated with the selected bacterial strains. In this way, bacteria were exposed to the presence of predators without direct predation. The bacterial strains used in this experience were characterised by a high degree of phenotypic plasticity and exhibited different successful strategies of resistance against grazing. The flagellates selected as

  18. Fish assemblages

    Science.gov (United States)

    McGarvey, Daniel J.; Falke, Jeffrey A.; Li, Hiram W.; Li, Judith; Hauer, F. Richard; Lamberti, G.A.

    2017-01-01

    Methods to sample fishes in stream ecosystems and to analyze the raw data, focusing primarily on assemblage-level (all fish species combined) analyses, are presented in this chapter. We begin with guidance on sample site selection, permitting for fish collection, and information-gathering steps to be completed prior to conducting fieldwork. Basic sampling methods (visual surveying, electrofishing, and seining) are presented with specific instructions for estimating population sizes via visual, capture-recapture, and depletion surveys, in addition to new guidance on environmental DNA (eDNA) methods. Steps to process fish specimens in the field including the use of anesthesia and preservation of whole specimens or tissue samples (for genetic or stable isotope analysis) are also presented. Data analysis methods include characterization of size-structure within populations, estimation of species richness and diversity, and application of fish functional traits. We conclude with three advanced topics in assemblage-level analysis: multidimensional scaling (MDS), ecological networks, and loop analysis.

  19. Plant-associated bacterial populations on native and invasive plant species: comparisons between 2 freshwater environments.

    Science.gov (United States)

    Olapade, Ola A; Pung, Kayleigh

    2012-06-01

    Plant-microbial interactions have been well studied because of the ecological importance of such relationships in aquatic systems. However, general knowledge regarding the composition of these biofilm communities is still evolving, partly as a result of several confounding factors that are attributable to plant host properties and to hydrodynamic conditions in aquatic environments. In this study, the occurrences of various bacterial phylogenetic taxa on 2 native plants, i.e., mayapple (Podophyllum peltatum L.) and cow parsnip (Heracleum maximum Bartram), and on an invasive species, i.e., garlic mustard (Alliaria petiolata (M. Bieb.) Cavara & Grande), were quantitatively examined using nucleic acid staining and fluorescence in situ hybridization. The plants were incubated in triplicates for about a week within the Kalamazoo River and Pierce Cedar Creek as well as in microcosms. The bacterial groups targeted for enumeration are known to globally occur in relatively high abundance and are also ubiquitously distributed in freshwater environments. Fluorescence in situ hybridization analyses of the bacterioplankton assemblages revealed that the majority of bacterial cells that hybridized with the different probes were similar between the 2 sites. In contrast, the plant-associated populations while similar on the 3 plants incubated in Kalamazoo River, their representations were highest on the 2 native plants relative to the invasive species in Pierce Cedar Creek. Overall, our results further suggested that epiphytic bacterial assemblages are probably under the influences of and probably subsequently respond to multiple variables and conditions in aquatic milieus.

  20. Demersal and larval fish assemblages in the Chukchi Sea

    Science.gov (United States)

    Norcross, Brenda L.; Holladay, Brenda A.; Busby, Morgan S.; Mier, Kathryn L.

    2010-01-01

    A multidisciplinary research cruise was conducted in the Chukchi Sea in summer 2004 during which we investigated assemblages of small demersal fishes and ichthyoplankton and the water masses associated with these assemblages. This study establishes a baseline of 30 demersal fish and 25 ichthyoplankton taxa in US and Russian waters of the Chukchi Sea. Presence/absence of small demersal fish clustered into four assemblages: Coastal Fishes, Western Chukchi Fishes, South Central Chukchi Fishes, and North Central Chukchi Fishes. Habitats occupied by small demersal fishes were characterized by sediment type, bottom salinity, and bottom temperature. Abundance of ichthyoplankton grouped into three assemblages with geographical extent similar to that of the bottom assemblages, except that there was a single assemblage for Central Chukchi Fishes. Water-column temperature and salinity characterized ichthyoplankton habitats. Three water masses, Alaska Coastal Water, Bering Sea Water, and Winter Water, were identified from both bottom and depth-averaged water-column temperature and salinity. A fourth water mass, Resident Chukchi Water, was identified only in the bottom water. The water mass and habitat characteristics with which demersal and larval fish assemblages were associated create a baseline to measure anticipated effects of climate change that are expected to be most severe at high latitudes. Monitoring fish assemblages could be a tool for assessing the effects of climate change. Climate-induced changes in distributions of species would result in a restructuring of fish assemblages in the Chukchi Sea.

  1. Effects of pulsed nutrient inputs on phytoplankton assemblage structure and blooms in an enclosed coastal area

    Science.gov (United States)

    Spatharis, Sofie; Tsirtsis, George; Danielidis, Daniel B.; Chi, Thang Do; Mouillot, David

    2007-07-01

    The response of phytoplankton assemblage structure to terrestrial nutrient inputs was examined for the Gulf of Kalloni in the Northern Aegean Sea, a productive semi-enclosed coastal marine ecosystem. The study was focused on a typical annual cycle, and emphasis was placed on the comparative analysis between blooms developing after significant nutrient inputs from the watershed, and naturally occurring blooms. Baseline information was collected on a monthly basis from a network of stations located in the oligotrophic open sea and the interior and more productive part of the embayment. Intensive sampling was also carried out along a gradient in the vicinity of a river which was the most important source of freshwater and nutrient input for the Gulf. Phytoplankton assemblage structure was analyzed from 188 samples using diversity indices (Shannon and Average Taxonomic Distinctness), multivariate plotting methods (NMDS), multivariate statistics (PERMANOVA), and canonical correspondence analysis (CCA). Three characteristic assemblages were recognized: (1) an autumn assemblage developed under nutrient depleted conditions, having low diversity due to the dominance of two small diatoms, (2) a winter bloom of the potentially toxic species Pseudo-nitzschia calliantha occurring immediately after a nutrient peak and characterized by very low diversity, and (3) a naturally occurring early summer bloom of centric diatoms with relatively high diversity. The results of the study support the view that moderate nutrient inputs may have a beneficial effect on the functioning of coastal ecosystems, stimulating the taxonomic diversity through the growth of different taxonomic groups and taxa. On the other hand, a sudden pulse of high nutrient concentrations may greatly affect the natural succession of organisms, have a negative effect on the diversity through the dominance of a single species, and can increase the possibility of a harmful algal bloom development.

  2. Seagrass epiphytic assemblages are strong indicators of agricultural discharge but weak indicators of host features

    Science.gov (United States)

    Prado, Patricia

    2018-05-01

    Wastewater pulses from rice agriculture are persistently discharged into the northern shore of the Alfacs Bay (Ebro Delta, NW Mediterranean) from April to November. The bay also receives water from coastal lagoons which are subjected to freshwater inputs from the Ebro River mixed to an unknown extent with agricultural wastewater during the same period. This paper compares epiphyte assemblages growing on leaves of Cymodocea nodosa in sites exposed to agricultural drainage channels, lagoon connection channels, and control sites in the Ebro Delta Natural Park (southern shore of the bay). Leaf epiphytic assemblages of Zostera noltii patches in the northern shore of the bay were also compared with those of adjacent beds of C. nodosa. Drainage channel sites had consistently distinctive assemblages (higher species richness, biomass load, and taxa composition) than control sites. Assemblages from lagoon channel sites were more variable, with three sites showing particularly high covers of epiphytic algae and two sites more similar to controls. Epiphyte patterns clearly matched in situ measures of nutrient availability, and were consistent with decreased shoot densities in discharge sites. In contrast, differences in epiphyte assemblages between seagrass species were minor, and mostly a result of higher epiphytic loads on C. nodosa than on Z. noltii, which features thinner leaves. Further research is needed to investigate the consequences of these plant and epiphyte alterations in important ecosystem processes such as decomposition and export rates, as well as overall effects of nutrients and salinity in secondary producers such as associated macroinvertebrate assemblages supporting locally important marine fisheries.

  3. Nestedness and successional trajectories of macroinvertebrate assemblages in man-made wetlands.

    Science.gov (United States)

    Ruhí, Albert; Boix, Dani; Gascón, Stéphanie; Sala, Jordi; Quintana, Xavier D

    2013-02-01

    Current successional models, primarily those based on floral succession, propose several distinct trajectories based on the integration of two key hypotheses from succession theory: convergence versus divergence in species composition among successional sites, and progression towards versus deviation from a desired reference state. We applied this framework to faunal succession, including differential colonization between active and passive dispersers, and the nested patterns generated as a consequence of this peculiarity. Nine man-made wetlands located in three different areas, from 0-3 years from wetland creation, were assessed. In addition, 91 wetlands distributed throughout the region were used as references for natural macroinvertebrate communities. We predicted the following: (1) highly nested structures in pioneering assemblages will decrease to lower mid-term values due to a shift from active pioneering taxa to passive disperser ones; (2) passive idiosyncratic taxa will elicit divergent successional trajectories among areas; (3) the divergent trajectories will provoke lower local and higher regional diversity values in the mid-term assemblages than in pioneer assemblages. Our results were largely congruent with hypotheses (1) and (2), diverging from the anticipated patterns only in the case of the temporary wetlands area. However, overall diversity trends based on hypothesis (3) did not follow the expected pattern. The divergent successional trajectories did not compensate for regional biodiversity losses that occurred as a consequence of pioneering colonizer decline over time. Consequently, we suggest reconsidering wetland construction for mitigation purposes within mid-term time frames (≤ 3 years). Wetlands may not offset, within this temporal scenario, regional biodiversity loss because the ecosystem may not support idiosyncratic taxa from natural wetlands.

  4. Bacterial inactivation in water by means of a combined process of pulsed dielectric barrier discharge and silver-modified natural zeolite

    International Nuclear Information System (INIS)

    Rodríguez-Méndez, B G; López-Callejas, R; Olguín, M T; Valencia-Alvarado, R; Peña-Eguiluz, R; Mercado-Cabrera, A; Alcántara-Díaz, D; Muñoz-Castro, A E; Hernández-Arias, A N; De la Piedad-Beneitez, A

    2014-01-01

    We propose a novel combined system of pulsed dielectric barrier discharges (PDBDs) and silver-modified natural zeolite (Ag–zeolite) in liquid in bubbles. The system was tested with the Escherichia coli bacteria immersed in water. In order to evaluate the efficiency of the system in bacterial inactivation a microbiological analysis was carried out; 9.82-ln of bacterial reduction was obtained using the combined system, whereas 0.43-ln of bacterial reduction was obtained using Ag–zeolite alone, and 6.26-ln with PDBD. The elapsed time was 10 minutes for the three treatments. (paper)

  5. Acoustic and temporal partitioning of cicada assemblages in city and mountain environments.

    Directory of Open Access Journals (Sweden)

    Bao-Sen Shieh

    Full Text Available Comparing adaptations to noisy city environments with those to natural mountain environments on the community level can provide significant insights that allow an understanding of the impact of anthropogenic noise on invertebrates that employ loud calling songs for mate attraction, especially when each species has its distinct song, as in the case of cicadas. In this study, we investigated the partitioning strategy of cicada assemblages in city and mountain environments by comparing the acoustic features and calling activity patterns of each species, recorded using automated digital recording systems. Our comparison of activity patterns of seasonal and diel calling revealed that there was no significant temporal partitioning of cicada assemblages in either environment. In addition, there was no correlation between the acoustic distance based on spectral features and temporal segregation. Heterospecific spectral overlap was low in both city and mountain environments, although city and mountain cicada assemblages were subject to significantly different levels of anthropogenic or interspecific noise. Furthermore, for the common species found in both environments, the calling activity patterns at both seasonal and diel time scales were significantly consistent across sites and across environments. We suggest that the temporal calling activity is constrained by endogenous factors for each species and is less flexible in response to external factors, such as anthropogenic noise. As a result, cicada assemblages in city environments with low species diversity do not demonstrate a more significant temporal partitioning than those in mountain environments with high species diversity.

  6. Spectral and physical properties of metal in meteorite assemblages - implications of asteroid surface materials

    International Nuclear Information System (INIS)

    Gaffey, M.J.

    1986-01-01

    One of the objectives of the present paper is related to a definition of the spectral contribution of the nickel-iron metal component in meteoritic assemblages. Another objective is the elucidation of the chemical, physical, and petrographic properties of the metal grains which affect the spectral signature in asteroid surface materials. It is pointed out that an improved understanding of the spectral and physical properties of metal in asteroid regoliths should permit an improved characterization of these objects, and, in particular, a better evaluation of the differentiated or undifferentiated nature of the S-type and M-type asteroids. Attention is given to the spectra of iron and nickel-iron metals, the spectral effects of metal in chondritic assemblages, the spectral reflectance of metal grains in ordinary chondrites, the nature of the surfaces of chondritic metal grains, the origin of coats on chondritic metal grains, and the fragmentation of metal on asteroid surfaces. 57 references

  7. Laboratory-Cultured Strains of the Sea Anemone Exaiptasia Reveal Distinct Bacterial Communities

    KAUST Repository

    Herrera Sarrias, Marcela; Ziegler, Maren; Voolstra, Christian R.; Aranda, Manuel

    2017-01-01

    Exaiptasia is a laboratory sea anemone model system for stony corals. Two clonal strains are commonly used, referred to as H2 and CC7, that originate from two genetically distinct lineages and that differ in their Symbiodinium specificity. However, little is known about their other microbial associations. Here, we examined and compared the taxonomic composition of the bacterial assemblages of these two symbiotic Exaiptasia strains, both of which have been cultured in the laboratory long-term under identical conditions. We found distinct bacterial microbiota for each strain, indicating the presence of host-specific microbial consortia. Putative differences in the bacterial functional profiles (i.e., enrichment and depletion of various metabolic processes) based on taxonomic inference were also detected, further suggesting functional differences of the microbiomes associated with these lineages. Our study contributes to the current knowledge of the Exaiptasia holobiont by comparing the bacterial diversity of two commonly used strains as models for coral research.

  8. Laboratory-Cultured Strains of the Sea Anemone Exaiptasia Reveal Distinct Bacterial Communities

    KAUST Repository

    Herrera Sarrias, Marcela

    2017-05-02

    Exaiptasia is a laboratory sea anemone model system for stony corals. Two clonal strains are commonly used, referred to as H2 and CC7, that originate from two genetically distinct lineages and that differ in their Symbiodinium specificity. However, little is known about their other microbial associations. Here, we examined and compared the taxonomic composition of the bacterial assemblages of these two symbiotic Exaiptasia strains, both of which have been cultured in the laboratory long-term under identical conditions. We found distinct bacterial microbiota for each strain, indicating the presence of host-specific microbial consortia. Putative differences in the bacterial functional profiles (i.e., enrichment and depletion of various metabolic processes) based on taxonomic inference were also detected, further suggesting functional differences of the microbiomes associated with these lineages. Our study contributes to the current knowledge of the Exaiptasia holobiont by comparing the bacterial diversity of two commonly used strains as models for coral research.

  9. Using Natural Products to Treat Resistant and Persistent Bacterial Infections

    Science.gov (United States)

    Deering, Robert W.

    Antimicrobial resistance is a growing threat to human health both worldwide and in the United States. Most concerning is the emergence of multi-drug resistant (MDR) bacterial pathogens, especially the 'ESKAPE' pathogens for which treatment options are dwindling. To complicate the problem, approvals of antibiotic drugs are extremely low and many research and development efforts in the pharmaceutical industry have ceased, leaving little certainty that critical new antibiotics are nearing the clinic. New antibiotics are needed to continue treating these evolving infections. In addition to antibiotics, approaches that aim to inhibit or prevent antimicrobial resistance could be useful. Also, studies that improve our understanding of bacterial pathophysiology could lead to new therapies for infectious disease. Natural products, especially those from the microbial world, have been invaluable as resources for new antibacterial compounds and as insights into bacterial physiology. The goal of this dissertation is to find new ways to treat resistant bacterial infections and learn more about the pathophysiology of these bacteria. Investigations of natural products to find molecules able to be used as new antibiotics or to modulate resistance and other parts of bacterial physiology are crucial aspects of the included studies. The first included study, which is reported in chapter two, details a chemical investigation of a marine Pseudoalteromonas sp. Purification efforts of the microbial metabolites were guided by testing against a resistance nodulation of cell division model of efflux pumps expressed in E. coli. These pumps play an important role in the resistance of MDR Gram negative pathogens such as Pseudomonas aeruginosa and Enterobacteriaceae. Through this process, 3,4-dibromopyrrole-2,5-dione was identified as a potent inhibitor of the RND efflux pumps and showed synergistic effects against the E. coli strain with common antibiotics including fluoroquinolones, beta

  10. Assessing effects of stocked trout on nongame fish assemblages in southern Appalachian Mountain streams

    Science.gov (United States)

    Weaver, D.; Kwak, Thomas J.

    2013-01-01

    Fisheries managers are faced with the challenge of balancing the management of recreational fisheries with that of conserving native species and preserving ecological integrity. The negative effects that nonnative trout species exert on native trout are well documented and include alteration of competitive interactions, habitat use, and production. However, the effects that nonnative trout may exert on nongame fish assemblages are poorly understood. Our objectives were to quantify the effects of trout stocking on native nongame fish assemblages intensively on one newly stocked river, the North Toe River, North Carolina, and extensively on other southern Appalachian Mountain streams that are annually stocked with trout. In the intensive study, we adopted a before-after, control-impact (BACI) experimental design to detect short-term effects on the nongame fish assemblage and found no significant differences in fish density, species richness, species diversity, or fish microhabitat use associated with trout stocking. We observed differences in fish microhabitat use between years, however, which suggests there is a response to environmental changes, such as the flow regime, which influence available habitat. In the extensive study, we sampled paired stocked and unstocked stream reaches to detect long-term effects from trout stocking; however, we detected no differences in nongame fish density, species richness, species diversity, or population size structure between paired sites. Our results revealed high inherent system variation caused by natural and anthropogenic factors that appear to overwhelm any acute or chronic effect of stocked trout. Furthermore, hatchery-reared trout may be poor competitors in a natural setting and exert a minimal or undetectable impact on native fish assemblages in these streams. These findings provide quantitative results necessary to assist agencies in strategic planning and decision making associated with trout fisheries, stream

  11. Characterization of the Bacterial Community Naturally Present on Commercially Grown Basil Leaves: Evaluation of Sample Preparation Prior to Culture-Independent Techniques

    Directory of Open Access Journals (Sweden)

    Siele Ceuppens

    2015-08-01

    Full Text Available Fresh herbs such as basil constitute an important food commodity worldwide. Basil provides considerable culinary and health benefits, but has also been implicated in foodborne illnesses. The naturally occurring bacterial community on basil leaves is currently unknown, so the epiphytic bacterial community was investigated using the culture-independent techniques denaturing gradient gel electrophoresis (DGGE and next-generation sequencing (NGS. Sample preparation had a major influence on the results from DGGE and NGS: Novosphingobium was the dominant genus for three different basil batches obtained by maceration of basil leaves, while washing of the leaves yielded lower numbers but more variable dominant bacterial genera including Klebsiella, Pantoea, Flavobacterium, Sphingobacterium and Pseudomonas. During storage of basil, bacterial growth and shifts in the bacterial community were observed with DGGE and NGS. Spoilage was not associated with specific bacterial groups and presumably caused by physiological tissue deterioration and visual defects, rather than by bacterial growth.

  12. Replacing Natural Gas by Biogas — Determining the Bacterial Contamination of Biogas by PCR

    Directory of Open Access Journals (Sweden)

    Jiřina Čermáková

    2012-01-01

    Full Text Available A promising way of using biogas is to upgrade it to natural gas, which is referred to as Substitute Natural Gas (SNG or biomethane. Biomethane, or biogas, is produced by biological processes of harnessing the ability of microorganisms to degrade organic material to methane. Some of the microorganisms are aerosolized from the digester into the biogas; afterwards a bio-film is formed that attaches to the surfaces of the distribution pipes, and can find it was to the place where the end use of biogas takes place. This paper deals with the detection of microbial species in biogas, their influenceon corrosion and the potential risk that diseases can be spread via biogas using molecular techniques. Using molecular methods, we found that raw biogas contains about 8 million microorganisms per m3, which is most likely the result of microbial transmission from the anaerobic digestion process. Some bacterial species may contribute to the corrosion of pipelines and equipment; others are opportunistic pathogens that can cause toxic reactions. However, most bacterial species, more than 40 % in biogas, are still unknown, as is their influence on the digestion process and on human health. Further studies are needed to better understand the behavior of microorganisms in anaerobic digestion and to preventmicrobial-influenced corrosion and microbial dissemination.

  13. Testing the effect of habitat structure and complexity on nekton assemblages using experimental oyster reefs

    Science.gov (United States)

    Humphries, Austin T.; LaPeyre, Megan K.; Kimball, Matthew E.; Rozas, Lawrence P.

    2011-01-01

    Structurally complex habitats are often associated with more diverse and abundant species assemblages in both aquatic and terrestrial ecosystems. Biogenic reefs formed by the eastern oyster (Crassostrea virginica) are complex in nature and are recognized for their potential habitat value in estuarine systems along the US Atlantic and Gulf of Mexico coasts. Few studies, however, have examined the response of nekton to structural complexity within oyster reefs. We used a quantitative sampling technique to examine how the presence and complexity of experimental oyster reefs influence the abundance, biomass, and distribution of nekton by sampling reefs 4 months and 16 months post-construction. Experimental oyster reefs were colonized immediately by resident fishes and decapod crustaceans, and reefs supported a distinct nekton assemblage compared to mud-bottom habitat. Neither increased reef complexity, nor age of the experimental reef resulted in further changes in nekton assemblages or increases in nekton abundance or diversity. The presence of oyster reefs per se was the most important factor determining nekton usage.

  14. Sediment bacterial community structures and their predicted functions implied the impacts from natural processes and anthropogenic activities in coastal area.

    Science.gov (United States)

    Su, Zhiguo; Dai, Tianjiao; Tang, Yushi; Tao, Yile; Huang, Bei; Mu, Qinglin; Wen, Donghui

    2018-06-01

    Coastal ecosystem structures and functions are changing under natural and anthropogenic influences. In this study, surface sediment samples were collected from disturbed zone (DZ), near estuary zone (NEZ), and far estuary zone (FEZ) of Hangzhou Bay, one of the most seriously polluted bays in China. The bacterial community structures and predicted functions varied significantly in different zones. Firmicutes were found most abundantly in DZ, highlighting the impacts of anthropogenic activities. Sediment total phosphorus was most influential on the bacterial community structures. Predicted by PICRUSt analysis, DZ significantly exceeded FEZ and NEZ in the subcategory of Xenobiotics Biodegradation and Metabolism; and DZ enriched all the nitrate reduction related genes, except nrfA gene. Seawater salinity and inorganic nitrogen, respectively as the representative natural and anthropogenic factor, performed exact-oppositely in nitrogen metabolism functions. The changes of bacterial community compositions and predicted functions provide a new insight into human-induced pollution impacts on coastal ecosystem. Copyright © 2018 Elsevier Ltd. All rights reserved.

  15. Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach

    Directory of Open Access Journals (Sweden)

    Román eZapién-Campos

    2015-05-01

    Full Text Available Most of the studies in Ecology have been devoted to analyzing the effects the environment has on individuals, populations, and communities, thus neglecting the effects of biotic interactions on the system dynamics. In the present work we study the structure of bacterial communities in the oligotrophic shallow water system of Churince, Cuatro Cienegas, Mexico. Since the physicochemical conditions of this water system are homogeneous and quite stable in time, it is an excellent candidate to study how biotic factors influence the structure of bacterial communities. In a previous study, the binary antagonistic interactions of 78 bacterial strains, isolated from Churince, were experimentally determined. We employ these data to develop a computer algorithm to simulate growth experiments in a cellular grid representing the pond. Remarkably, in our model, the dynamics of all the simulated bacterial populations is determined solely by antagonistic interactions. Our results indicate that all bacterial strains (even those that are antagonized by many other bacteria survive in the long term, and that the underlying mechanism is the formation of bacterial community patches. Patches corresponding to less antagonistic and highly susceptible strains are consistently isolated from the highly-antagonistic bacterial colonies by patches of neutral strains. These results concur with the observed features of the bacterial community structure previously reported. Finally, we study how our findings depend on factors like initial population size, differential population growth rates, homogeneous population death rates, and enhanced bacterial diffusion.

  16. Bacterial Biogeography across the Amazon River-Ocean Continuum

    Directory of Open Access Journals (Sweden)

    Mary Doherty

    2017-05-01

    Full Text Available Spatial and temporal patterns in microbial biodiversity across the Amazon river-ocean continuum were investigated along ∼675 km of the lower Amazon River mainstem, in the Tapajós River tributary, and in the plume and coastal ocean during low and high river discharge using amplicon sequencing of 16S rRNA genes in whole water and size-fractionated samples (0.2–2.0 μm and >2.0 μm. River communities varied among tributaries, but mainstem communities were spatially homogeneous and tracked seasonal changes in river discharge and co-varying factors. Co-occurrence network analysis identified strongly interconnected river assemblages during high (May and low (December discharge periods, and weakly interconnected transitional assemblages in September, suggesting that this system supports two seasonal microbial communities linked to river discharge. In contrast, plume communities showed little seasonal differences and instead varied spatially tracking salinity. However, salinity explained only a small fraction of community variability, and plume communities in blooms of diatom-diazotroph assemblages were strikingly different than those in other high salinity plume samples. This suggests that while salinity physically structures plumes through buoyancy and mixing, the composition of plume-specific communities is controlled by other factors including nutrients, phytoplankton community composition, and dissolved organic matter chemistry. Co-occurrence networks identified interconnected assemblages associated with the highly productive low salinity near-shore region, diatom-diazotroph blooms, and the plume edge region, and weakly interconnected assemblages in high salinity regions. This suggests that the plume supports a transitional community influenced by immigration of ocean bacteria from the plume edge, and by species sorting as these communities adapt to local environmental conditions. Few studies have explored patterns of microbial diversity in

  17. Does Nature and Persistence of Substrate at a Mesohabitat Scale Matter for Chironomidae Assemblages? a Study of Two Perennial Mountain Streams in Patagonia, Argentina

    Science.gov (United States)

    Epele, Luis Beltrán; Miserendino, María Laura; Brand, Cecilia

    2012-01-01

    Chironomid substrate—specific associations regarding the nature (organic—inorganic) and stability (stable—unstable) of different habitats were investigated at two low order Patagonian streams, during high and low water periods. Nant y Fall and Glyn rivers were visited twice (October 2007 and March 2008) and seven different habitat types were identified. A total of 60 samples were collected using a Surber sampler (0.09 m -2 and 250 µm) and a set of 23 environmental descriptors including physicochemical parameters and different fractions of particulate organic matter were assessed. 35 Chironomidae taxa were recorded with Orthocladiinae (20), Chironominae (7), and Podonominae (4) being the most well—represented subfamilies. Paratrichocladius sp. 1, Parapsectrocladius sp. 2, Parametriocnemus sp. 1, Pseudochironomus sp., and Rheotanytarsus sp. were the most abundant taxa. According to the relative preference index, at least 14 taxa showed strong affinity for a particular substrate. The structurally complex macrophyte Myriophyllum quitense supported 11 taxa compared with only five taxa found on the less complex Isoetes savatieri. Generally, stable substrates (boulders, cobbles, and rooted plants) supported significantly higher chironomids richness, abundance, and diversity than unstable ones (gravel—sand). Canonical correspondence analysis revealed that detritus (leaves, seeds, and biomass), macrophyte biomass, and secondarily hydraulic variables had high explanatory power on chironomids species composition and structure. This work suggests that more complex substrates showing persistence in the temporal dimension supported a diverse array of chironomids, meaning that the maintenance of natural habitat heterogeneity is essential for the community. Land—use practices having significant effects on ecological stream attributes such as increased turbidity, sediment deposition, and runoff patterns will alter assemblages. Understanding environmental associations

  18. Does nature and persistence of substrate at a mesohabitat scale matter for Chironomidae assemblages? A study of two perennial mountain streams in Patagonia, Argentina.

    Science.gov (United States)

    Epele, Luis Beltrán; Miserendino, María Laura; Brand, Cecilia

    2012-01-01

    Chironomid substrate-specific associations regarding the nature (organic-inorganic) and stability (stable-unstable) of different habitats were investigated at two low order Patagonian streams, during high and low water periods. Nant y Fall and Glyn rivers were visited twice (October 2007 and March 2008) and seven different habitat types were identified. A total of 60 samples were collected using a Surber sampler (0.09 m(-2) and 250 µm) and a set of 23 environmental descriptors including physicochemical parameters and different fractions of particulate organic matter were assessed. 35 Chironomidae taxa were recorded with Orthocladiinae (20), Chironominae (7), and Podonominae (4) being the most well-represented subfamilies. Paratrichocladius sp. 1, Parapsectrocladius sp. 2, Parametriocnemus sp. 1, Pseudochironomus sp., and Rheotanytarsus sp. were the most abundant taxa. According to the relative preference index, at least 14 taxa showed strong affinity for a particular substrate. The structurally complex macrophyte Myriophyllum quitense supported 11 taxa compared with only five taxa found on the less complex Isoetes savatieri. Generally, stable substrates (boulders, cobbles, and rooted plants) supported significantly higher chironomids richness, abundance, and diversity than unstable ones (gravel-sand). Canonical correspondence analysis revealed that detritus (leaves, seeds, and biomass), macrophyte biomass, and secondarily hydraulic variables had high explanatory power on chironomids species composition and structure. This work suggests that more complex substrates showing persistence in the temporal dimension supported a diverse array of chironomids, meaning that the maintenance of natural habitat heterogeneity is essential for the community. Land-use practices having significant effects on ecological stream attributes such as increased turbidity, sediment deposition, and runoff patterns will alter assemblages. Understanding environmental associations of the

  19. Bacterial anoxygenic photosynthesis on plant leaf surfaces.

    Science.gov (United States)

    Atamna-Ismaeel, Nof; Finkel, Omri; Glaser, Fabian; von Mering, Christian; Vorholt, Julia A; Koblížek, Michal; Belkin, Shimshon; Béjà, Oded

    2012-04-01

    The aerial surface of plants, the phyllosphere, is colonized by numerous bacteria displaying diverse metabolic properties that enable their survival in this specific habitat. Recently, we reported on the presence of microbial rhodopsin harbouring bacteria on the top of leaf surfaces. Here, we report on the presence of additional bacterial populations capable of harvesting light as a means of supplementing their metabolic requirements. An analysis of six phyllosphere metagenomes revealed the presence of a diverse community of anoxygenic phototrophic bacteria, including the previously reported methylobacteria, as well as other known and unknown phototrophs. The presence of anoxygenic phototrophic bacteria was also confirmed in situ by infrared epifluorescence microscopy. The microscopic enumeration correlated with estimates based on metagenomic analyses, confirming both the presence and high abundance of these microorganisms in the phyllosphere. Our data suggest that the phyllosphere contains a phylogenetically diverse assemblage of phototrophic species, including some yet undescribed bacterial clades that appear to be phyllosphere-unique. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  20. Streamflow characteristics and benthic invertebrate assemblages in streams across the western United States

    Science.gov (United States)

    Brasher, Anne M.D.; Konrad, Chris P.; May, Jason T.; Edmiston, C. Scott; Close, Rebecca N.

    2010-01-01

    Hydrographic characteristics of streamflow, such as high-flow pulses, base flow (background discharge between floods), extreme low flows, and floods, significantly influence aquatic organisms. Streamflow can be described in terms of magnitude, timing, duration, frequency, and variation (hydrologic regime). These characteristics have broad effects on ecosystem productivity, habitat structure, and ultimately on resident fish, invertebrate, and algae communities. Increasing human use of limited water resources has modified hydrologic regimes worldwide. Identifying the most ecologically significant hydrographic characteristics would facilitate the development of water-management strategies.Benthic invertebrates include insects, mollusks (snails and clams), worms, and crustaceans (shrimp) that live on the streambed. Invertebrates play an important role in the food web, consuming other invertebrates and algae and being consumed by fish and birds. Hydrologic alteration associated with land and water use can change the natural hydrologic regime and may affect benthic invertebrate assemblage composition and structure through changes in density of invertebrates or taxa richness (number of different species).This study examined associations between the hydrologic regime and characteristics of benthic invertebrate assemblages across the western United States and developed tools to identify streamflow characteristics that are likely to affect benthic invertebrate assemblages.

  1. TNT Biodegradation by Natural Microbial Assemblages at Estuarine Frontal Boundaries

    Science.gov (United States)

    2012-07-02

    St- Jean . 2007. The use of wet chemical oxidation with high-amplification isotope ratio mass spectrometry (WCO-IRMS) to measure stable isotope ...dissolved oxygen concentration (DO, mL L-1), bacterial production and mineralization rate of TNT, naphthalene (NAH) and phenanthrene (PHE) (water...m) in the Charleston Harbor system (26 June 2011) and measured for salinity (PSU), temperature (oC), dissolved oxygen concentration (DO, mL L-1

  2. Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia.

    Science.gov (United States)

    Rosa, Bruce A; Supali, Taniawati; Gankpala, Lincoln; Djuardi, Yenny; Sartono, Erliyani; Zhou, Yanjiao; Fischer, Kerstin; Martin, John; Tyagi, Rahul; Bolay, Fatorma K; Fischer, Peter U; Yazdanbakhsh, Maria; Mitreva, Makedonka

    2018-02-28

    The human intestine and its microbiota is the most common infection site for soil-transmitted helminths (STHs), which affect the well-being of ~ 1.5 billion people worldwide. The complex cross-kingdom interactions are not well understood. A cross-sectional analysis identified conserved microbial signatures positively or negatively associated with STH infections across Liberia and Indonesia, and longitudinal samples analysis from a double-blind randomized trial showed that the gut microbiota responds to deworming but does not transition closer to the uninfected state. The microbiomes of individuals able to self-clear the infection had more alike microbiome assemblages compared to individuals who remained infected. One bacterial taxon (Lachnospiracae) was negatively associated with infection in both countries, and 12 bacterial taxa were significantly associated with STH infection in both countries, including Olsenella (associated with reduced gut inflammation), which also significantly reduced in abundance following clearance of infection. Microbial community gene abundances were also affected by deworming. Functional categories identified as associated with STH infection included arachidonic acid metabolism; arachidonic acid is the precursor for pro-inflammatory leukotrienes that threaten helminth survival, and our findings suggest that some modulation of arachidonic acid activity in the STH-infected gut may occur through the increase of arachidonic acid metabolizing bacteria. For the first time, we identify specific members of the gut microbiome that discriminate between moderately/heavily STH-infected and non-infected states across very diverse geographical regions using two different statistical methods. We also identify microbiome-encoded biological functions associated with the STH infections, which are associated potentially with STH survival strategies, and changes in the host environment. These results provide a novel insight of the cross

  3. Denaturing gradient gel electrophoresis profiling of bacterial communities composition in Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Singh, S.K.; Ramaiah, N.

    of Environmental Biology circleshadowdwnMay 2011circleshadowdwn Introduction The bacteria play a major role in carbon dynamics of marine ecosystems and, the importance of heterotrophic bacteria in marine ecosystem functioning is very well recognized (Azam et al..., 2008). Denaturing gradient gel-electrophoressis (DGGE) based fingerprinting helps estimate the numbers of dominant phylotype in a given sample (Muyzer et al., 1993). Very diverse bacterial assemblages such as those in the soils present many bands...

  4. Autumn ichthyoplankton assemblage in the Yangtze Estuary shaped by environmental factors.

    Science.gov (United States)

    Zhang, Hui; Xian, Weiwei; Liu, Shude

    2016-01-01

    This study investigated the response of the ichthyoplankton community to environmental changes in the Yangtze Estuary using canonical correspondence analysis. Ichthyoplankton community and environmental data were recorded during the autumns of 1998, 2000, 2002, 2003, 2004, 2007 and 2009. Among the ichthyoplankton, the dominant larval and juvenile families were the Engraulidae, Gobiidae and Salangidae, and the most common eggs were from Trichiurus lepturus. The ichthyoplankton was identified via canonical correspondence analysis to three assemblages: an estuary assemblage dominated by Chaeturichthys stigmatias, a coastal assemblage dominated by Engraulis japonicus and Stolephorus commersonii, and an offshore assemblage dominated by Trichiurus lepturus. Regarding environmental factors in the Yangtze Estuary, suspended matter and surface seawater salinity were the main factors influencing the distributions of the different assemblages, while sediment from the Yangtze River during the rainy season and chlorophyll a were the principle drivers of the annual variances in the distribution of ichthyoplankton assemblages. Our aims in this study were to provide detailed characterizations of the ichthyoplankton assemblage in the autumns of seven years, examine the long-term dynamics of autumn ichthyoplankton assemblages, and evaluate the influence of environmental factors on the spatial distribution and inter-annual variations of ichthyoplankton assemblages associated with the Yangtze Estuary.

  5. Autumn ichthyoplankton assemblage in the Yangtze Estuary shaped by environmental factors

    Directory of Open Access Journals (Sweden)

    Hui Zhang

    2016-04-01

    Full Text Available This study investigated the response of the ichthyoplankton community to environmental changes in the Yangtze Estuary using canonical correspondence analysis. Ichthyoplankton community and environmental data were recorded during the autumns of 1998, 2000, 2002, 2003, 2004, 2007 and 2009. Among the ichthyoplankton, the dominant larval and juvenile families were the Engraulidae, Gobiidae and Salangidae, and the most common eggs were from Trichiurus lepturus. The ichthyoplankton was identified via canonical correspondence analysis to three assemblages: an estuary assemblage dominated by Chaeturichthys stigmatias, a coastal assemblage dominated by Engraulis japonicus and Stolephorus commersonii, and an offshore assemblage dominated by Trichiurus lepturus. Regarding environmental factors in the Yangtze Estuary, suspended matter and surface seawater salinity were the main factors influencing the distributions of the different assemblages, while sediment from the Yangtze River during the rainy season and chlorophyll a were the principle drivers of the annual variances in the distribution of ichthyoplankton assemblages. Our aims in this study were to provide detailed characterizations of the ichthyoplankton assemblage in the autumns of seven years, examine the long-term dynamics of autumn ichthyoplankton assemblages, and evaluate the influence of environmental factors on the spatial distribution and inter-annual variations of ichthyoplankton assemblages associated with the Yangtze Estuary.

  6. Environmental Quality Assessment of Bizerte Lagoon (Tunisia) Using Living Foraminifera Assemblages and a Multiproxy Approach

    Science.gov (United States)

    Alves Martins, Maria Virgínia; Zaaboub, Noureddine; Aleya, Lotfi; Frontalini, Fabrizio; Pereira, Egberto; Miranda, Paulo; Mane, Miguel; Rocha, Fernando; Laut, Lazaro; El Bour, Monia

    2015-01-01

    This study investigated the environmental quality of the Bizerte Lagoon (Tunisia) through an integrated approach that combined environmental, biogeochemical, and living benthic foraminiferal analyses. Specifically, we analyzed the physicochemical parameters of the water and sediment. The textural, mineralogical, and geochemical characteristics of the sediment, including total organic carbon, total nitrogen, simultaneously extracted metals (SEM), acid volatile sulfides (AVS), chlorophyll a, CaCO3, and changes in bacterial populations and carbon isotopes were measured. The SEM/AVS values indicated the presence of relatively high concentrations of toxic metals in only some areas. Foraminiferal assemblages were dominated by species such as A. parkinsoniana (20–91%), Bolivina striatula (coastal lagoons both in Mediterranean and northeast Atlantic regions. The results of this work suggest that Bizerte Lagoon is a unique setting. This lagoon is populated by typical marine species that invaded this ecosystem, attracted not only by the prevailing favorable environmental conditions but also by the abundance and quality of food. The results indicate that the metal pollution found in some areas have a negative impact on the assemblages of foraminifera. At present, however, this negative impact is not highly alarming. PMID:26372655

  7. Role of environmental factors for the vertical distribution (0–1000 m of marine bacterial communities in the NW Mediterranean Sea

    Directory of Open Access Journals (Sweden)

    J. F. Ghiglione

    2008-12-01

    Full Text Available Bacterioplankton plays a central role in energy and matter fluxes in the sea, yet the factors that constrain its variation in marine systems are still poorly understood. Here we use the explanatory power of direct multivariate gradient analysis to evaluate the driving forces exerted by environmental parameters on bacterial community distribution in the water column. We gathered and analysed data from a one month sampling period from the surface to 1000 m depth at the JGOFS-DYFAMED station (NW Mediterranean Sea. This station is characterized by very poor horizontal advection currents which makes it an ideal model to test hypotheses on the causes of vertical stratification of bacterial communities. Capillary electrophoresis single strand conformation polymorphism (CE-SSCP fingerprinting profiles analyzed using multivariate statistical methods demonstrated a vertical zonation of bacterial assemblages in three layers, above, in or just below the chlorophyll maximum and deeper, that remained stable during the entire sampling period. Through the use of direct gradient multivariate ordination analyses we demonstrate that a complex array of biogeochemical parameters is the driving force behind bacterial community structure shifts in the water column. Physico-chemical parameters such as phosphate, nitrate, salinity and to a lesser extent temperature, oxygen, dissolved organic carbon and photosynthetically active radiation acted in synergy to explain bacterial assemblages changes with depth. Analysis of lipid biomarkers of organic matter sources and fates suggested that bacterial community structure in the surface layers was in part explained by lipids of chloroplast origin. Further detailed analysis of pigment-based phytoplankton diversity gave evidence of a compartmentalized influence of several phytoplankton groups on bacterial community structure in the first 150 m depth.

  8. Soil arthropod fauna from natural ecosites and reclaimed oil sands soils in northern Alberta

    Energy Technology Data Exchange (ETDEWEB)

    Battigelli, J.P.; Leskiw, L.A. [Paragon Soil and Environmental Consulting Inc., Edmonton, AB (Canada)

    2006-07-01

    An understanding of soil invertebrates may facilitate current reclamation activities in the oil sands region of Alberta. This paper presented the results of a study investigating the density, diversity, and structure of soil arthropod assemblages in natural habitats and reclaimed sites. The purpose of the study was to establish a baseline inventory of soil arthropod assemblages in order to enable long-term monitoring of soil arthropod recolonization in disturbed sites. Nine natural ecosites were sampled for the study, including peat mix over secondary material over tailing sand; direct placement over tailing sand; peat mix over secondary over overburden; direct placement over overburden; peat mix over tailing sand; and peat mix over overburden. Samples were collected from previously established long-term soil and vegetation treatment plots in both natural ecosites and reclaimed soil sites located near Fort McMurray, Alberta. Results showed that densities of mesofauna were significantly higher in samples collected from natural ecosites. Acari and Collembola represented approximately 97 to 98 per cent of the fauna collected. It was also noted that the overall structure of the soil mesofauna community differed between natural soils and reclaimed soils. A significant reduction in the abundance of oribatid mites was observed in soils that had been reclaimed for over 34 years. Changes in the soil mesofauna community structure suggested that reclaimed soils continue to represent disturbed ecosites, as was indicated by higher proportions of prostigmatid mites and some collembolan families. Differences in community structure may influence soil ecosystem functions, including decomposition rates; nutrient recycling; soil structure; and fungal and bacterial biomass. It was concluded that further research is needed to examine oribatid mites and collembolan species diversity and community structure in reclaimed soils. 18 refs., 6 figs.

  9. Rapid bacterial mineralization of organic carbon produced during a phytoplankton bloom induced by natural iron fertilization in the Southern Ocean

    Science.gov (United States)

    Obernosterer, Ingrid; Christaki, Urania; Lefèvre, Dominique; Catala, Philippe; Van Wambeke, France; Lebaron, Philippe

    2008-03-01

    The response of heterotrophic bacteria ( Bacteria and Archaea) to the spring phytoplankton bloom that occurs annually above the Kerguelen Plateau (Southern Ocean) due to natural iron fertilization was investigated during the KErguelen Ocean and Plateau compared Study (KEOPS) cruise in January-February 2005. In surface waters (upper 100 m) in the core of the phytoplankton bloom, heterotrophic bacteria were, on an average, 3-fold more abundant and revealed rates of production ([ 3H] leucine incorporation) and respiration (bacterial metabolic activities were attributable to high-nucleic-acid-containing cells that dominated (≈80% of total cell abundance) the heterotrophic bacterial community associated with the phytoplankton bloom. Bacterial growth efficiencies varied between 14% and 20% inside the bloom and were bacterial activity, due to the stimulation by phytoplankton-derived dissolved organic matter. Within the Kerguelen bloom, bacterial carbon demand accounted for roughly 45% of gross community production. These results indicate that heterotrophic bacteria processed a significant portion of primary production, with most of it being rapidly respired.

  10. Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima.

    Science.gov (United States)

    Herfort, Lydie; Crump, Byron C; Fortunato, Caroline S; McCue, Lee Ann; Campbell, Victoria; Simon, Holly M; Baptista, António M; Zuber, Peter

    2017-12-01

    Estuarine turbidity maxima (ETM) function as hotspots of microbial activity and diversity in estuaries, yet, little is known about the temporal and spatial variability in ETM bacterial community composition. To determine which environmental factors affect ETM bacterial populations in the Columbia River estuary, we analyzed ETM bacterial community composition (Sanger sequencing and amplicon pyrosequencing of 16S rRNA gene) and bulk heterotrophic production ( 3 H-leucine incorporation rates). We collected water 20 times to cover five ETM events and obtained 42 samples characterized by different salinities, turbidities, seasons, coastal regimes (upwelling vs. downwelling), locations, and particle size. Spring and summer populations were distinct. All May samples had similar bacterial community composition despite having different salinities (1-24 PSU), but summer non-ETM bacteria separated into marine, freshwater, and brackish assemblages. Summer ETM bacterial communities varied depending on coastal upwelling or downwelling conditions and on the sampling site location with respect to tidal intrusion during the previous neap tide. In contrast to ETM, whole (>0.2 μm) and free-living (0.2-3 μm) assemblages of non-ETM waters were similar to each other, indicating that particle-attached (>3 μm) non-ETM bacteria do not develop a distinct community. Brackish water type (ETM or non-ETM) is thus a major factor affecting particle-attached bacterial communities. Heterotrophic production was higher in particle-attached than free-living fractions in all brackish waters collected throughout the water column during the rise to decline of turbidity through an ETM event (i.e., ETM-impacted waters). However, free-living communities showed higher productivity prior to or after an ETM event (i.e., non-ETM-impacted waters). This study has thus found that Columbia River ETM bacterial communities vary based on seasons, salinity, sampling location, and particle size, with the

  11. Global assemblages and structural models of International Relations

    DEFF Research Database (Denmark)

    Corry, Olaf

    2014-01-01

    -category of assemblages – those constructed as malleable and governable which I call ‘governance-objects’ – is central to structure in international relations. The chapter begins with standard definitions of what structures are – patterns of interaction between elements – and briefly covers the range of models currently...... used to simplify different structures. Next the chapter points to the blindness of most structural theories of IR to the role of assemblages in general and governance-objects in particular. Thirdly, the idea that a polity is constituted precisely by the assemblage of a governance...

  12. Hydrologic linkages drive spatial structuring of bacterial assemblages and functioning in alpine floodplains

    OpenAIRE

    Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart E.G.; Robinson, Christopher T.

    2015-01-01

    Microbial community assembly and microbial functions are affected by a number of different but coupled drivers such as local habitat characteristics, dispersal rates, and species interactions. In groundwater systems, hydrological flow can introduce spatial structure and directional dependencies among these drivers. We examined the importance of hydrology in structuring bacterial communities and their function within two alpine floodplains during different hydrological states. Piezometers were...

  13. Meiofaunal assemblages associated with native and non-indigenous macroalgae

    Science.gov (United States)

    Veiga, Puri; Sousa-Pinto, Isabel; Rubal, Marcos

    2016-07-01

    Meiofauna is a useful tool to detect effects of different disturbances; however, its relevance in the frame of biological invasions has been almost fully neglected. Meiofaunal assemblages associated with the invasive macroalga Sargassum muticum were studied and compared with those associated with two native macroalgae (Bifurcaria bifurcata and Chondrus crispus). We used a linear mixed model to determine the influence of habitat size (i.e. macroalgal biomass) in shaping meiofaunal assemblages. Results showed that habitat size (i.e. macroalgal biomass) shaped meiofaunal assemblages influencing its abundance, richness and structure. However, the identity of macroalga (i.e. species) appears also to play a significant role, particularly the differences of complexity among the studied species may shape their meiofaunal assemblages. Finally, the invasive macroalga appears to influence positively species richness. Our results highlight the need of including different faunal components to achieve a comprehensive knowledge on effects of invasive macroalgae and that meiofaunal assemblages may be a valuable tool to examine them.

  14. The nature of water within bacterial spores: protecting life in extreme environments

    Science.gov (United States)

    Rice, Charles V.; Friedline, Anthony; Johnson, Karen; Zachariah, Malcolm M.; Thomas, Kieth J., III

    2011-10-01

    The bacterial spore is a formidable container of life, protecting the vital contents from chemical attack, antimicrobial agents, heat damage, UV light degradation, and water dehydration. The exact role of the spore components remains in dispute. Nevertheless, water molecules are important in each of these processes. The physical state of water within the bacterial spore has been investigated since the early 1930's. The water is found two states, free or bound, in two different areas, core and non-core. It is established that free water is accessible to diffuse and exchange with deuterated water and that the diffusible water can access all areas of the spore. The presence of bound water has come under recent scrutiny and has been suggested the water within the core is mobile, rather than bound, based on the analysis of deuterium relaxation rates. Using an alternate method, deuterium quadrupole-echo spectroscopy, we are able to distinguish between mobile and immobile water molecules. In the absence of rapid motion, the deuterium spectrum of D2O is dominated by a broad line, whose line shape is used as a characteristic descriptor of molecular motion. The deuterium spectrum of bacterial spores reveals three distinct features: the broad peak of immobilized water, a narrow line of water in rapid motion, and a signal of intermediate width. This third signal is assigned this peak from partially deuterated proteins with the spore in which N-H groups have undergone exchange with water deuterons to form N-D species. As a result of these observations, the nature of water within the spore requires additional explanation to understand how the spore and its water preserve life.

  15. Pampean lizard assemblage from subtropical Brazil: a temporal analysis

    Directory of Open Access Journals (Sweden)

    Gisele R. Winck

    2011-12-01

    Full Text Available The increasing human occupation of natural environments is one of the greatest threats to biodiversity. To mitigate the negative anthropogenic effects, it is necessary to understand the characteristics of natural populations and the natural history of species. A study was conducted with an assemblage of lizards from a disturbed area of the Pampa biome, from February 2001 to January 2004. The assemblage showed a unimodal seasonal pattern, with the recruitment period occurring during the warmer months. The captures were seasonal for two of the three monitored years, and concentrated within warmer months. The minimum temperature explained the number of catches for the assemblage as a whole. However, when the species were analyzed individually, the temperature only explained the seasonal occurrence of Teius oculatus. The abundance of species was significantly different in the third year of study for Cercosaura schreibersii and Ophiodes striatus. This latter species was no longer registered in the study area from May 2003 until the end of the study. Therefore, O. striatus may be more sensitive to environmental changes, considering the events of change in vegetation during the study. With frequent and increasing environmental disturbances, it is necessary to take conservation measures and encourage the increase of knowledge on Pampean lizards.O crescimento da ocupação humana sobre ambientes naturais é uma das maiores ameaças à biodiversidade. Para amenizar os efeitos negativos antropogênicos, é necessário entender as características das populações naturais, e a história natural das espécies. Um estudo foi conduzido com uma assembeia de lagartos de uma área perturbada do Pampa, de fevereiro de 2002 a janeiro de 2004. A assembleia apresentou padrão sazonal unimodal, com recrutamento ocorrendo durante os meses mais quentes. As capturas foram sazonais durante dois dos três anos monitorados, e concentradas nos meses mais quentes. A

  16. Microbiological quality and bacterial diversity of the tropical oyster Crassostrea rhizophorae in a monitored farming system and from natural stocks.

    Science.gov (United States)

    Silva Neta, M T; Maciel, B M; Lopes, A T S; Marques, E L S; Rezende, R P; Boehs, G

    2015-12-02

    Microbiological evaluation is one of the most important parameters for analyzing the viability of an oyster farming system, which addresses public health and ecological concerns. Here, the microbiological quality of the oyster Crassostrea rhizophorae cultivated in a monitored environment and from natural beds in Bahia, northeastern Brazil, was determined. Bacterial diversity in oysters was measured by polymerase chain reaction-denaturing gradient gel electrophoresis. Sequence analysis revealed that most bacterial species showed similarity with uncultured or unidentified bacteria from environmental samples, and were clustered into the phylum Proteobacteria. Diverse bacteria from cultivated (monitored) oyster samples were grouped in the same cluster with a high similarity index (above 79%). Microbiological analyses revealed that these oysters did not contain pathogens. These results reflect the natural balance of the microbial communities essential to the maintenance of health and in inhibiting pathogen colonization in the oyster. On the other hand, bacterial diversity of samples from native stocks in extractive areas displayed a similarity index varying between 55 and 77%, and all samples were clustered separately from each other and from the cluster of samples derived from the cultivation area. Microbiological analyses showed that oysters from the extractive area were not fit for human consumption. This reflected a different composition of the microbial community in this area, probably resulting from anthropic impact. Our study also demonstrated that low temperatures and high rainfall limits the bacterial concentration in tropical oysters. This is the first study analyzing the total bacterial community profiles of the oyster C. rhizophorae.

  17. [Characteristics of ichthyoplankton assemblages in Yangtze Estuary and adjacent waters in spring].

    Science.gov (United States)

    Liu, Shu-De; Xian, Wei-Wei; Liu, Dong

    2008-10-01

    Based on the investigation data of ichthyoplankton assemblages and environmental factors in Yangtze Estuary and adjacent waters in May 1999 and 2001, the characteristics of ichthyoplankton assemblages in these areas in spring were studied by using TWINSPAN (two-way indicator species analysis) and CCA (canonical correspondence analysis). A total of 11 540 ichthyoplankton individuals were taxonomically identified, belonging to 11 orders, 18 families and 32 species, of which, Coilia mystus, Engraulis japonicus, Chaeturichthys hexanema, Allanetta bleekeri, and Trachidermis fasciatus were the dominant species. The ichthyoplankton communities were classified into three assemblages by using TWINSPAN, i.e., estuarine assemblage dominated by C. mystus, coastal assemblage dominated by A. bleekeri and T. fasciatus; and shelf assemblage featured by E. japonicus and C. hexanema. The CCA ordination of the interrelations among the three assemblages and their correlations to the environmental variables revealed that salinity, depth, dissolved oxygen, and total suspended particulate matter were the major factors affecting the ichthyoplankton assemblages in the study areas.

  18. Faunistic assemblages of a sublittoral coarse sand habitat of the northwestern Mediterranean

    Directory of Open Access Journals (Sweden)

    Eva Pubill

    2011-02-01

    Full Text Available The sublittoral megabenthic assemblages of a northwestern Mediterranean coarse sandy beach exploited for the bivalve Callista chione were studied. The spatial and bathymetric variability of its distinctive faunal assemblages was characterised by quantitative sampling performed with a clam dredge. The taxa studied were Mollusca Bivalvia and Gastropoda, Crustacea Decapoda, Echinodermata and Pisces, which accounted for over 99% of the total biomass. Three well-differentiated species assemblages were identified: (1 assemblage MSS (Medium Sand Shallow in medium sand (D50=0.37 mm and shallow waters (mean depth =6.5 m, (2 assemblage CSS (Coarse Sand Shallow in coarse sand (D50=0.62 mm in shallow waters (mean depth =6.7 m, and (3 assemblage CSD (Coarse Sand Deep in coarse sand (D50=0.64 mm in deeper waters (mean depth =16.2 m. Assemblage MSS was characterised by the codominance of the bivalves Mactra stultorum and Acanthocardia tuberculata. C. chione was dominant in both density and biomass in assemblages CSS and CSD. The occurrence of the crab Thia scutellata also characterised assemblage CSS, whereas the occurrence of the sea urchin Echinocardium mediterraneum characterised assemblage CSD. A depth breaking point of around 10 m determined the discontinuity between assemblages CSS and CSD, which was related to the closure depth of the beaches in the study area. Species richness was highest in the coarse sand communities; however, Shannon-Wiener diversity and Pielou equitability indexes were higher in the shallow fine sand community.

  19. Moral assemblages of volunteer tourism development in Cusco, Peru

    OpenAIRE

    Burrai, Elisa.; Mostafanezhad, Mary.; Hannam, Kevin.

    2016-01-01

    In this paper, we develop a conceptual approach from which to examine the moral landscape of volunteer tourism development in Cusco, Peru. Drawing from recent work on assemblage theory in geography and tourism studies, we explore how assemblage thinking can facilitate new understandings of volunteer tourism development. Using assemblage as an analytical framework allows us to understand volunteer tourism as a series of relational, processual, unequal and mobile practices. These practices, we ...

  20. Fish assemblages and diversity in three tributaries of the Irrawaddy River in China: changes, threats and conservation perspectives

    Directory of Open Access Journals (Sweden)

    Yang M.-L.

    2016-01-01

    Full Text Available Incompletely known fish assemblages and species diversity are substantial obstacles in fish conservation, particularly when their aquatic habitats are under threat due to rapid human-induced changes. Fish assemblages and diversity in three tributaries of the upper Irrawaddy River in China (the Dulong, Daying and Ruili rivers were examined based on field collections and literature resources. The newly compiled fish assemblage recorded 85 species (in 8 orders, 20 families and 51 genera distributed in the upper Irrawaddy. The fish compositions in the Daying (67 species, 44 genera, 19 families, 7 orders and Ruili rivers (65 species, 44 genera, 19 families, 8 orders were more similar to each other and more speciose than that in the Dulong River (14 species, 10 genera, 4 families, 3 orders. Two indices of taxonomic diversity (the average taxonomic distinctness (Δ+, and the variation in taxonomic distinctness (Λ+ were used to discriminate four collections spanning a ten-year period. A decrease in taxonomic diversity and an increase in unevenness of the fish assemblages were found in both the Daying River and Ruili rivers, which indicated that the impacts were accumulated gradually during this decade, when dams and the spread of non-native species were major threats. Comparatively speaking, the Dulong River is still in a near-natural state, and thus the fish community has experienced less disturbance. In situ conservation (nature reserves and tributary protection and ex situ conservation (artificial propagation and release should be combined and managed to promote fish conservation in the future.

  1. Reservoir floodplains support distinct fish assemblages

    Science.gov (United States)

    Miranda, Leandro E.; Wigen, S. L.; Dagel, Jonah D.

    2014-01-01

    Reservoirs constructed on floodplain rivers are unique because the upper reaches of the impoundment may include extensive floodplain environments. Moreover, reservoirs that experience large periodic water level fluctuations as part of their operational objectives seasonally inundate and dewater floodplains in their upper reaches, partly mimicking natural inundations of river floodplains. In four flood control reservoirs in Mississippi, USA, we explored the dynamics of connectivity between reservoirs and adjacent floodplains and the characteristics of fish assemblages that develop in reservoir floodplains relative to those that develop in reservoir bays. Although fish species richness in floodplains and bays were similar, species composition differed. Floodplains emphasized fish species largely associated with backwater shallow environments, often resistant to harsh environmental conditions. Conversely, dominant species in bays represented mainly generalists that benefit from the continuous connectivity between the bay and the main reservoir. Floodplains in the study reservoirs provided desirable vegetated habitats at lower water level elevations, earlier in the year, and more frequently than in bays. Inundating dense vegetation in bays requires raising reservoir water levels above the levels required to reach floodplains. Therefore, aside from promoting distinct fish assemblages within reservoirs and helping promote diversity in regulated rivers, reservoir floodplains are valued because they can provide suitable vegetated habitats for fish species at elevations below the normal pool, precluding the need to annually flood upland vegetation that would inevitably be impaired by regular flooding. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.

  2. Land use structures fish assemblages in reservoirs of the Tennessee River

    Science.gov (United States)

    Miranda, Leandro E.; Bies, J. M.; Hann, D. A.

    2015-01-01

    Inputs of nutrients, sediments and detritus from catchments can promote selected components of reservoir fish assemblages, while hindering others. However, investigations linking these catchment subsidies to fish assemblages have generally focussed on one or a handful of species. Considering this paucity of community-level awareness, we sought to explore the association between land use and fish assemblage composition in reservoirs. To this end, we compared fish assemblages in reservoirs of two sub-basins of the Tennessee River representing differing intensities of agricultural development, and hypothesised that fish assemblage structure indicated by species percentage composition would differ among reservoirs in the two sub-basins. Using multivariate statistical analysis, we documented inter-basin differences in land use, reservoir productivity and fish assemblages, but no differences in reservoir morphometry or water regime. Basins were separated along a gradient of forested and non-forested catchment land cover, which was directly related to total nitrogen, total phosphorous and chlorophyll-a concentrations. Considering the extensive body of knowledge linking land use to aquatic systems, it is reasonable to postulate a hierarchical model in which productivity has direct links to terrestrial inputs, and fish assemblages have direct links to both land use and productivity. We observed a shift from an invertivore-based fish assemblage in forested catchments to a detritivore-based fish assemblage in agricultural catchments that may be a widespread pattern among reservoirs and other aquatic ecosystems.

  3. The influence of fire on the assemblage structure of foraging birds in grasslands of the Serra da Canastra National Park, Brazil

    Directory of Open Access Journals (Sweden)

    Matheus G. Reis

    2016-06-01

    Full Text Available Grasslands are the most threatened physiognomies of the Cerrado biome (Brazilian savanna, a biodiversity hotspot with conservation as a priority. The Serra da Canastra National Park protects the most important remnants of the Cerrado's southern grasslands, which are under strong anthropogenic pressure. The present study describes the structure of bird assemblages that directly use food resources in burned areas, comparing areas affected by natural fire to the areas where controlled fires were set (a management strategy to combat arson. The tested null hypothesis was that different bird assemblages are structured in a similar manner, regardless of the post-fire period or assessed area. Between December/2012 and January/2015, 92 species were recorded foraging in the study areas. The results indicate that both types of burnings triggered profound and immediate changes in bird assemblages, increasing the number of species and individuals. Natural fires exhibited a more significant influence on the structure (diversity and dominance than prescribed burnings. Nevertheless, all the differences were no longer noticeable after a relatively short time interval of 2-3 months after prescribed burnings and 3-4 after natural fires. The findings may help the understanding of prescribed burnings as a management strategy for bird conservation in grasslands.

  4. Analysis and exploitation of bacterial population from natural uranium-rich soils: selection of a model specie

    International Nuclear Information System (INIS)

    Mondani, L.

    2010-01-01

    It is well known that soils play a key role in controlling the mobility of toxic metals and this property is greatly influenced by indigenous bacterial communities. This study has been conducted on radioactive and controls soils, collected in natural uraniferous areas (Limousin). A physico-chemical and mineralogical analysis of soils samples was carried out.The structure of bacterial communities was estimated by Denaturing Gradient Gel Electrophoresis (DGGE). The community structure is remarkably more stable in the uranium-rich soils than in the control ones, indicating that uranium exerts a high selection from the soils was constructed and screened for uranium resistance in order to study bacteria-uranium interactions. Scanning electron microscopy revealed that a phylo-genetically diverse set of uranium-resistant species ware able to chelate uranium at the cell surface. (author) [fr

  5. Benthic assemblages of rock pools in northern Portugal: seasonal and between-pool variability

    Directory of Open Access Journals (Sweden)

    Iacopo Bertocci

    2012-11-01

    Full Text Available We investigated the seasonal (winter vs summer and within season and spatial (between-pool variability of benthic assemblages of rock pools at mid-intertidal level along the shore of Viana do Castelo (North Portugal. Physical traits of rock pools, including size, depth and position along the shore, were also compared between pools. While pools did not differ for any of the examined physical traits, results indicated a clear seasonal difference in the structure of assemblages, including a total of 49 macroalgal and 13 animal taxa. This finding was driven by six taxa that are more abundant in winter (the reef-forming polychaete Sabellaria alveolata, the articulated coralline algae Corallina spp., the brown alga Bifurcaria bifurcata, the encrusting coralline alga Lithophyllum incrustans, the red alga Chondracanthus acicularis and the grazing snails Gibbula spp. and four algal taxa that are more abundant in summer (the invasive brown Sargassum muticum, the green Ulva spp., the kelp Laminaria ochroleuca and the filamentous red Ceramium spp.. These data provide a new contribution to the knowledge of rock pool systems and have potential implications for monitoring programmes aimed at assessing ecological modifications related to natural and anthropogenic disturbances and for identifying processes responsible for the variability of rock pool assemblages.

  6. Bacterioplankton assemblages in coastal ponds reflect the influence of hydrology and geomorphological setting.

    Science.gov (United States)

    Huggett, Megan J; Kavazos, Christopher R J; Bernasconi, Rachele; Czarnik, Robert; Horwitz, Pierre

    2017-06-01

    The factors that shape microbial community assembly in aquatic ecosystems have been widely studied; yet it is still unclear how distinct communities within a connected landscape influence one another. Coastal lakes are recipients of, and thus are connected to, both marine and terrestrial environments. Thus, they may host microbial assemblages that reflect the relative degree of influence by, and connectivity to, either system. In order to address this idea, we interrogated microbial community diversity at 49 sites in seven ponds in two seasons in the Lake MacLeod basin, a system fed by seawater flowing inland through underground karst. Environmental and spatial variation within ponds explain <9% of the community structure, while identity of the pond that samples were taken from explains 50% of community variation. That is, ponds each host distinct assemblages despite similarities in size, environment and position in the landscape, indicating a dominant role for local species sorting. The ponds contain a substantial amount of previously unknown microbial taxa, reflecting the unusual nature of this inland system. Rare marine taxa, possibly dispersed from seawater assemblages via the underground karst connection, are abundant within the inland system, suggesting an important role for regional dispersal within the metacommunities. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. Diversity and abundance of invertebrate epifaunal assemblages associated with gorgonians are driven by colony attributes

    KAUST Repository

    Curdia, Joao

    2015-03-20

    The present study aimed to explicitly quantify the link between the attributes of shallow-water gorgonian colonies (Octocorallia: Alcyonacea) and the ecological patterns of associated non-colonial epifaunal invertebrates. Based on multiple regression analysis, we tested the contribution of several attributes (colony height, width, and area, fractal dimension as a measure of colony complexity, lacunarity as a measure of the heterogeneity, and “colonial” epibiont cover) to abundance and taxonomic richness of associated assemblages. The results highlight the variation in the response of epifaunal assemblages to the gorgonian colony characteristics. The nature and intensity of the relationships were gorgonian species-dependent and varied from one taxonomic group to another. For both gorgonian species analyzed, the strongest predictor of species richness and abundance of the epifaunal assemblages was “colonial” epibiont cover, possibly due to a trophic effect (direct or indirect enhancement of food availability) combined with the surface available for colonization (species–area effect). Although structural complexity is usually indicated as the main driver for rich and abundant coral-associated assemblages, no significant relationship was observed between fractal dimension and the community descriptors; lacunarity, which reflects the sizes of the inter-branch spaces, was only linked to taxonomic richness in the assemblages associated with Leptogorgia lusitanica. The validity of the paradigm that structural complexity enhances biodiversity may be scale-dependent. In the case of gorgonians, the effect of complexity at the “garden” level may be more relevant than at the individual colony level. This reinforces the need for the conservation of gorgonian aggregation areas as a whole in order to preserve host diversity and size structure. © 2015 Springer-Verlag Berlin Heidelberg

  8. Bacterial acquisition in juveniles of several broadcast spawning coral species.

    Science.gov (United States)

    Sharp, Koty H; Ritchie, Kim B; Schupp, Peter J; Ritson-Williams, Raphael; Paul, Valerie J

    2010-05-28

    Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and zooxanthellae. The extent to which coral-bacterial associations are specific and the mechanisms for their maintenance across generations in the environment are unknown. The high diversity of bacteria in adult coral colonies has made it challenging to identify species-specific patterns. Localization of bacteria in gametes and larvae of corals presents an opportunity for determining when bacterial-coral associations are initiated and whether they are dynamic throughout early development. This study focuses on the early onset of bacterial associations in the mass spawning corals Montastraea annularis, M. franksi, M. faveolata, Acropora palmata, A. cervicornis, Diploria strigosa, and A. humilis. The presence of bacteria and timing of bacterial colonization was evaluated in gametes, swimming planulae, and newly settled polyps by fluorescence in situ hybridization (FISH) using general eubacterial probes and laser-scanning confocal microscopy. The coral species investigated in this study do not appear to transmit bacteria via their gametes, and bacteria are not detectable in or on the corals until after settlement and metamorphosis. This study suggests that mass-spawning corals do not acquire, or are not colonized by, detectable numbers of bacteria until after larval settlement and development of the juvenile polyp. This timing lays the groundwork for developing and testing new hypotheses regarding general regulatory mechanisms that control bacterial colonization and infection of corals, and how interactions among bacteria and juvenile polyps influence the structure of bacterial assemblages in corals.

  9. Effects of anthropogenic impacts on benthic macroinvertebrates assemblages in subtropical mountain streams

    Directory of Open Access Journals (Sweden)

    Leticia M. Mesa

    2013-12-01

    Full Text Available The nature of the riparian and surrounding landscape has been modified by anthropogenic activities, which may subsequently alter the composition and functional structure of macroinvertebrate assemblages. The effect of these changes on function of benthic fauna is difficult to assess due to the scarce knowledge on functional structures in tropical streams. In this study we evaluate whether sites impacted and unimpacted by anthropogenic alterations differed in assemblage composition and density, richness and diversity of each functional feeding group. The selection of the sites was related to their distinct riparian characteristics, following the QBRy riparian quality index. Collector-gatherer was the dominant functional feeding group, comprising 91% of total density, whereas the proportion of shredders was very low, representing less of 0.5% of total density. Asemblage composition of macroinvertebrates differed between impacted and unimpacted sites. Predators were dominant in taxa number, representing about 60% of total taxa richness. In addition, the diversity and richness of collector-gatherers differed significantly between degraded and unimpacted sites, reflecting the sensitivity of this group to environmental changes and the utility to be used in the assessment of anthropogenic modifications. The results of this study reinforce the idea that riparian corridor management is critical for the distribution of macroinvertebrate assemblages as well as functional organization of lotic streams.

  10. Effects of remediation on the bacterial community of an acid mine drainage impacted stream.

    Science.gov (United States)

    Ghosh, Suchismita; Moitra, Moumita; Woolverton, Christopher J; Leff, Laura G

    2012-11-01

    Acid mine drainage (AMD) represents a global threat to water resources, and as such, remediation of AMD-impacted streams is a common practice. During this study, we examined bacterial community structure and environmental conditions in a low-order AMD-impacted stream before, during, and after remediation. Bacterial community structure was examined via polymerase chain reaction amplification of 16S rRNA genes followed by denaturing gradient gel electrophoresis. Also, bacterial abundance and physicochemical data (including metal concentrations) were collected and relationships to bacterial community structure were determined using BIO-ENV analysis. Remediation of the study stream altered environmental conditions, including pH and concentrations of some metals, and consequently, the bacterial community changed. However, remediation did not necessarily restore the stream to conditions found in the unimpacted reference stream; for example, bacterial abundances and concentrations of some elements, such as sulfur, magnesium, and manganese, were different in the remediated stream than in the reference stream. BIO-ENV analysis revealed that changes in pH and iron concentration, associated with remediation, primarily explained temporal alterations in bacterial community structure. Although the sites sampled in the remediated stream were in relatively close proximity to each other, spatial variation in community composition suggests that differences in local environmental conditions may have large impacts on the microbial assemblage.

  11. How does conversion of natural tropical rainforest ecosystems affect soil bacterial and fungal communities in the Nile river watershed of Uganda?

    OpenAIRE

    Alele, Peter O; Sheil, Douglas; Surget-Groba, Yann; Lingling, Shi; Cannon, Charles H

    2014-01-01

    Uganda's forests are globally important for their conservation values but are under pressure from increasing human population and consumption. In this study, we examine how conversion of natural forest affects soil bacterial and fungal communities. Comparisons in paired natural forest and human-converted sites among four locations indicated that natural forest soils consistently had higher pH, organic carbon, nitrogen, and calcium, although variation among sites was large. Despite these diffe...

  12. Bacterial computing: a form of natural computing and its applications.

    Science.gov (United States)

    Lahoz-Beltra, Rafael; Navarro, Jorge; Marijuán, Pedro C

    2014-01-01

    The capability to establish adaptive relationships with the environment is an essential characteristic of living cells. Both bacterial computing and bacterial intelligence are two general traits manifested along adaptive behaviors that respond to surrounding environmental conditions. These two traits have generated a variety of theoretical and applied approaches. Since the different systems of bacterial signaling and the different ways of genetic change are better known and more carefully explored, the whole adaptive possibilities of bacteria may be studied under new angles. For instance, there appear instances of molecular "learning" along the mechanisms of evolution. More in concrete, and looking specifically at the time dimension, the bacterial mechanisms of learning and evolution appear as two different and related mechanisms for adaptation to the environment; in somatic time the former and in evolutionary time the latter. In the present chapter it will be reviewed the possible application of both kinds of mechanisms to prokaryotic molecular computing schemes as well as to the solution of real world problems.

  13. Determinants of fish assemblage structure in Northwestern Great Plains streams

    Science.gov (United States)

    Mullen, J.A.; Bramblett, R.G.; Guy, C.S.; Zale, A.V.; Roberts, D.W.

    2011-01-01

    Prairie streams are known for their harsh and stochastic physical conditions, and the fish assemblages therein have been shown to be temporally variable. We assessed the spatial and temporal variation in fish assemblage structure in five intermittent, adventitious northwestern Great Plains streams representing a gradient of watershed areas. Fish assemblages and abiotic conditions varied more spatially than temporally. The most important variables explaining fish assemblage structure were longitudinal position and the proportion of fine substrates. The proportion of fine substrates increased proceeding upstream, approaching 100% in all five streams, and species richness declined upstream with increasing fine substrates. High levels of fine substrate in the upper reaches appeared to limit the distribution of obligate lithophilic fish species to reaches further downstream. Species richness and substrates were similar among all five streams at the lowermost and uppermost sites. However, in the middle reaches, species richness increased, the amount of fine substrate decreased, and connectivity increased as watershed area increased. Season and some dimensions of habitat (including thalweg depth, absolute distance to the main-stem river, and watershed size) were not essential in explaining the variation in fish assemblages. Fish species richness varied more temporally than overall fish assemblage structure did because common species were consistently abundant across seasons, whereas rare species were sometimes absent or perhaps not detected by sampling. The similarity in our results among five streams varying in watershed size and those from other studies supports the generalization that spatial variation exceeds temporal variation in the fish assemblages of prairie and warmwater streams. Furthermore, given longitudinal position, substrate, and stream size, general predictions regarding fish assemblage structure and function in prairie streams are possible. ?? American

  14. Patterns at Multi-Spatial Scales on Tropical Island Stream Insect Assemblages: Gorgona Island Natural National Park, Colombia, Tropical Eastern Pacific

    Directory of Open Access Journals (Sweden)

    Magnolia Longo

    2014-02-01

    Full Text Available Tropical Eastern Pacific island streams (TEPis differ from other neotropical streams in their rainy climate, mixed sedimentary-volcanic geology and faunal composition. Yet, their relationships between environmental characteristics and stream biota remain unexplored. We analyzed the environmental subject at three spatial scales using a fully nested sampling design (6 streams, 2 reaches within each stream, 2 habitats within each reach, and 4 replicates per habitat on Gorgona Island (Colombia. Sampling was carried out in two months with contrasting rainfall during early 2009. We studied the spatial variation of assemblage composition and density along with 27 independent variables within two contrasting rainfall conditions. Five stream-scale variables, two reach-scale variables, and five habitat-scale variables were selected using a Canonical Correspondence Analysis (CCA. A partial CCA showed that the total variance explained was 13.98%, while stream- and habitat-scale variables explained the highest proportion of the variance (5.74 and 5.01%, respectively. Dissolved oxygen (as affected by rainfall, high-density use zone (a management category, and sedimentary geology were the best descriptors of insect assemblages. The two latter descriptors affected fine-scale variables such as total benthic organic matter and gravel substratum, respectively. A Nested ANOVA showed significant differences in total density and richness among streams and habitats, and significant differences between the two sampling months regardless of the spatial scale. The evenness showed a significant stream- and habitat-dependent temporal variability. These results suggested that rainfall regime in Gorgona Island might be a driver of insect assemblage dynamics mediated by water chemistry and substratum properties. Spatial assemblage variability here is greater within habitats (among samples, and a minor fraction occurs at habitat- and stream-scales, while no longitudinal

  15. Consumer–brand assemblages in advertising

    DEFF Research Database (Denmark)

    Bjerrisgaard, Sofie Møller; Kjeldgaard, Dannie; Bengtson, Anders

    2013-01-01

    This paper discusses how the use of tattoos in advertising renders diverse brand–consumer assemblages visible. In considering advertising practitioners as professionals of entanglement, the paper emphasizes the embeddedness of practitioners’ use of tattoo symbolism in institutionalized marketing...... systems and in the cultural history of tattooing. In accordance with recent emphasis on the importance of material devices for understanding contemporary sociality, this paper presents a semiotic analysis of a convenience sample of advertisements depicting tattoos. Tattoos are productive for the study...... potency. This analysis demonstrates how the emergence of brand tattoos in advertising challenges the dominant consumer centrism in consumer research and suggests a networked, emerging understanding of the subject in which agency is distributed in socio-technical assemblages....

  16. Environmental Quality Assessment of Bizerte Lagoon (Tunisia Using Living Foraminifera Assemblages and a Multiproxy Approach.

    Directory of Open Access Journals (Sweden)

    Maria Virgínia Alves Martins

    Full Text Available This study investigated the environmental quality of the Bizerte Lagoon (Tunisia through an integrated approach that combined environmental, biogeochemical, and living benthic foraminiferal analyses. Specifically, we analyzed the physicochemical parameters of the water and sediment. The textural, mineralogical, and geochemical characteristics of the sediment, including total organic carbon, total nitrogen, simultaneously extracted metals (SEM, acid volatile sulfides (AVS, chlorophyll a, CaCO3, and changes in bacterial populations and carbon isotopes were measured. The SEM/AVS values indicated the presence of relatively high concentrations of toxic metals in only some areas. Foraminiferal assemblages were dominated by species such as A. parkinsoniana (20-91%, Bolivina striatula (<40%, Hopkinsina atlantica (<17%, and Bolivina ordinaria (<15% that cannot be considered typical of impacted coastal lagoons both in Mediterranean and northeast Atlantic regions. The results of this work suggest that Bizerte Lagoon is a unique setting. This lagoon is populated by typical marine species that invaded this ecosystem, attracted not only by the prevailing favorable environmental conditions but also by the abundance and quality of food. The results indicate that the metal pollution found in some areas have a negative impact on the assemblages of foraminifera. At present, however, this negative impact is not highly alarming.

  17. Ichthyoplankton assemblages of coastal west-central Lake Erie and associated habitat characteristics

    Science.gov (United States)

    McKenna, J.E.; Hunter, R. Douglas; Fabrizio, M.C.; Savino, J.F.; Todd, T.N.; Bur, M.

    2008-01-01

    Early life stage survival often determines fish cohort strength and that survival is affected by habitat conditions. The structure and dynamics of ichthyoplankton assemblages can tell us much about biodiversity and fish population dynamics, but are poorly understood in nearshore areas of the Great Lakes, where most spawning and nursery habitats exist. Ichthyoplankton samples were collected with a neuston net in waters 2-13 m deep weekly or biweekly from mid-April through August, during 3 years (2000-2002) as part of a study of fish assemblages in west-central Lake Erie. A suite of abiotic variables was simultaneously measured to characterize habitat. Cluster and ordination analyses revealed several distinct ichthyoplankton assemblages that changed seasonally. A lake whitefish (Coregonus clupeaformis) dominated assemblage appeared first in April. In May, assemblages were dominated by several percid species. Summer assemblages were overwhelmingly dominated by emerald shiner (Notropis atherinoides), with large gizzard shad (Dorosoma cepedianum) and alewife (Alosa pseudoharengus) components. This seasonal trend in species assemblages was also associated with increasing temperature and water clarity. Water depth and drift processes may also play a role in structuring these assemblages. The most common and widely distributed assemblages were not associated with substratum type, which we characterized as either hard or soft. The timing of hatch and larval growth separated the major groups in time and may have adaptive significance for the members of each major assemblage. The quality and locations (with reference to lake circulation) of spawning and nursery grounds may determine larval success and affect year class strength.

  18. Individual variation in habitat use in two stream fish assemblages

    Directory of Open Access Journals (Sweden)

    Luisa Resende Manna

    2015-12-01

    Full Text Available The habitat use is an individual choice that is influenced by physical conditions such as substrate type, food resources availability and adequate depth. However, habitat use is often measured only through interspecific variability because intraspecific variability is supposed to be low. Here, the differences in habitat use by two stream fish assemblages in two different environments (Brazilian rainforest and semiarid were investigated at both interspecific and intraspecific levels. We performed 55 hours of underwater observation in a 200 meters long stretch in each stream and quantified the following habitat descriptors: (i water velocity, (ii distance from the stream bank, (iii substratum, (iv water column depth, (v aquatic cover, and (vi canopy percentage. To compare intra and interspecific variability we summarized the multivariate habitat use databases using Principal Components Analysis (PCA on Euclidean distance. An Analysis of Similarity (ANOSIM was performed to test the differences in habitat use by the two assemblages. Besides, in each fish community we did an Analysis of Variance (ANOVA to test within vs between species variability for individual position on each PCA axes. To go further than these univariate tests, the differences among the species and assemblages were tested with Permutational Multivariate Analysis of Variance (PERMANOVA. The habitat use between assemblages was significantly different (ANOSIM – R=0.14; p<0.001. PERMANOVA revealed significant differences among species in both assemblages (Rainforest - F=7.25; p<0.001; semiarid - F=4.84; p<0.001. Lower F values in the semiarid assemblage revealed a higher level of intraspecific variability for this assemblage. Our findings showed high intra and interspecific variability in both stream fish assemblages and highlight the importance of measuring individual’s differences for this feature of fish biodiversity. Additionally, the versatility described for tropical

  19. Bacterial Glycosyltransferases: Challenges and opportunities of a highly diverse enzyme class toward tailoring natural products

    Directory of Open Access Journals (Sweden)

    Jochen eSchmid

    2016-02-01

    Full Text Available The enzyme subclass of glycosyltransferases (EC 2.4 currently comprises 97 families as specified by CAZy classification. One of their important roles is in the biosynthesis of disaccharides, oligosaccharides and polysaccharides by catalyzing the transfer of sugar moieties from activated donor molecules to other sugar molecules. In addition glycosyltransferases also catalyze the transfer of sugar moieties onto aglycons, which is of great relevance for the synthesis of many high value natural products. Bacterial glycosyltransferases show a higher sequence similarity in comparison to mammalian ones. Even when most glycosyltransferases are poorly explored, state of the art technologies, such as protein engineering, domain swapping or computational analysis strongly enhance our understanding and utilization of these very promising classes of proteins. This perspective article will focus on bacterial glycosyltransferases, especially on classification, screening and engineering strategies to alter substrate specificity. The future development in these fields as well as obstacles and challenges will be highlighted and discussed.

  20. Bacterial computing: a form of natural computing and its applications

    Directory of Open Access Journals (Sweden)

    Rafael eLahoz-Beltra

    2014-03-01

    Full Text Available The capability to establish adaptive relationships with the environment is an essential characteristic of living cells. Both bacterial computing and bacterial intelligence are two general traits manifested along adaptive behaviors that respond to surrounding environmental conditions. These two traits have generated a variety of theoretical and applied approaches. Since the different systems of bacterial signaling and the different ways of genetic change are better known and more carefully explored, the whole adaptive possibilities of bacteria may be studied under new angles. For instance, there appear instances of molecular learning along the mechanisms of evolution. More in concrete, and looking specifically at the time dimension, the bacterial mechanisms of learning and evolution appear as two different and related mechanisms for adaptation to the environment; in somatic time the former and in evolutionary time the latter. In the present chapter it will be reviewed the possible application of both kinds of mechanisms to prokaryotic molecular computing schemes as well as to the solution of real world problems.

  1. Natural Sunlight Shapes Crude Oil-Degrading Bacterial Communities in Northern Gulf of Mexico Surface Waters

    OpenAIRE

    Bacosa, Hernando P.; Liu, Zhanfei; Erdner, Deana L.

    2015-01-01

    Following the Deepwater Horizon (DWH) spill in 2010, an enormous amount of oil was observed in the deep and surface waters of the northern Gulf of Mexico. Surface waters are characterized by intense sunlight and high temperature during summer. While the oil-degrading bacterial communities in the deep-sea plume have been widely investigated, the effect of natural sunlight on those in oil polluted surface waters remains unexplored to date. In this study, we incubated surface water from the DWH ...

  2. Assemblaged by desire: Potterheads’ productive consumption

    Directory of Open Access Journals (Sweden)

    André Luiz Maranhão de Souza Leão

    2018-02-01

    Full Text Available The Harry Potter saga became one of the cultural products with a major impact on the twenty-first century. Its fans, called potterheads, relate in a social space known as fandom. Their practices are based on the appropriation of the cultural text in a productive consumption process within a context of participatory culture. Assuming desire from the perspective of Deleuzian assemblage theory, which presents this concept as a flow of productive energy that is articulated through a collective force, this study aimed to understand how potterheads’ productive consumption is assemblaged by desire. We therefore explored multifocal data concerning practices of potterheads available on digital platforms using Foucauldian Discourse Analysis. Our results revealed that potterheads’ desire assemblage maintains their bond with the canonical universe of the saga, as a way of maintaining identity and security in the transition to adult life, through relationships in the fandom and in pursuit of broader social legitimacy. The study contributes theoretically by adopting the Deleuzian notion of desire as a lens to understand the collective action of consumers in cultural contexts of practice.

  3. Bleaching response of coral species in the context of assemblage response

    Science.gov (United States)

    Swain, Timothy D.; DuBois, Emily; Goldberg, Scott J.; Backman, Vadim; Marcelino, Luisa A.

    2017-06-01

    Caribbean coral reefs are declining due to a mosaic of local and global stresses, including climate change-induced thermal stress. Species and assemblage responses differ due to factors that are not easily identifiable or quantifiable. We calculated a novel species-specific metric of coral bleaching response, taxon- α and - β, which relates the response of a species to that of its assemblages for 16 species over 18 assemblages. By contextualizing species responses within the response of their assemblages, the effects of environmental factors are removed and intrinsic differences among taxa are revealed. Most corals experience either a saturation response, overly sensitive to weak stress ( α > 0) but under-responsive compared to assemblage bleaching ( β bleaching ( β > 1). This metric may help reveal key factors of bleaching susceptibility and identify species as targets for conservation.

  4. Variation in Symbiodinium ITS2 sequence assemblages among coral colonies.

    Science.gov (United States)

    Stat, Michael; Bird, Christopher E; Pochon, Xavier; Chasqui, Luis; Chauka, Leonard J; Concepcion, Gregory T; Logan, Dan; Takabayashi, Misaki; Toonen, Robert J; Gates, Ruth D

    2011-01-05

    Endosymbiotic dinoflagellates in the genus Symbiodinium are fundamentally important to the biology of scleractinian corals, as well as to a variety of other marine organisms. The genus Symbiodinium is genetically and functionally diverse and the taxonomic nature of the union between Symbiodinium and corals is implicated as a key trait determining the environmental tolerance of the symbiosis. Surprisingly, the question of how Symbiodinium diversity partitions within a species across spatial scales of meters to kilometers has received little attention, but is important to understanding the intrinsic biological scope of a given coral population and adaptations to the local environment. Here we address this gap by describing the Symbiodinium ITS2 sequence assemblages recovered from colonies of the reef building coral Montipora capitata sampled across Kāne'ohe Bay, Hawai'i. A total of 52 corals were sampled in a nested design of Coral Colony(Site(Region)) reflecting spatial scales of meters to kilometers. A diversity of Symbiodinium ITS2 sequences was recovered with the majority of variance partitioning at the level of the Coral Colony. To confirm this result, the Symbiodinium ITS2 sequence diversity in six M. capitata colonies were analyzed in much greater depth with 35 to 55 clones per colony. The ITS2 sequences and quantitative composition recovered from these colonies varied significantly, indicating that each coral hosted a different assemblage of Symbiodinium. The diversity of Symbiodinium ITS2 sequence assemblages retrieved from individual colonies of M. capitata here highlights the problems inherent in interpreting multi-copy and intra-genomically variable molecular markers, and serves as a context for discussing the utility and biological relevance of assigning species names based on Symbiodinium ITS2 genotyping.

  5. Exploring coral microbiome assemblages in the South China Sea.

    Science.gov (United States)

    Cai, Lin; Tian, Ren-Mao; Zhou, Guowei; Tong, Haoya; Wong, Yue Him; Zhang, Weipeng; Chui, Apple Pui Yi; Xie, James Y; Qiu, Jian-Wen; Ang, Put O; Liu, Sheng; Huang, Hui; Qian, Pei-Yuan

    2018-02-05

    Coral reefs are significant ecosystems. The ecological success of coral reefs relies on not only coral-algal symbiosis but also coral-microbial partnership. However, microbiome assemblages in the South China Sea corals remain largely unexplored. Here, we compared the microbiome assemblages of reef-building corals Galaxea (G. fascicularis) and Montipora (M. venosa, M. peltiformis, M. monasteriata) collected from five different locations in the South China Sea using massively-parallel sequencing of 16S rRNA gene and multivariate analysis. The results indicated that microbiome assemblages for each coral species were unique regardless of location and were different from the corresponding seawater. Host type appeared to drive the coral microbiome assemblages rather than location and seawater. Network analysis was employed to explore coral microbiome co-occurrence patterns, which revealed 61 and 80 co-occurring microbial species assembling the Galaxea and Montipora microbiomes, respectively. Most of these co-occurring microbial species were commonly found in corals and were inferred to play potential roles in host nutrient metabolism; carbon, nitrogen, sulfur cycles; host detoxification; and climate change. These findings suggest that the co-occurring microbial species explored might be essential to maintain the critical coral-microbial partnership. The present study provides new insights into coral microbiome assemblages in the South China Sea.

  6. Bacterial acquisition in juveniles of several broadcast spawning coral species.

    Directory of Open Access Journals (Sweden)

    Koty H Sharp

    Full Text Available Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and zooxanthellae. The extent to which coral-bacterial associations are specific and the mechanisms for their maintenance across generations in the environment are unknown. The high diversity of bacteria in adult coral colonies has made it challenging to identify species-specific patterns. Localization of bacteria in gametes and larvae of corals presents an opportunity for determining when bacterial-coral associations are initiated and whether they are dynamic throughout early development. This study focuses on the early onset of bacterial associations in the mass spawning corals Montastraea annularis, M. franksi, M. faveolata, Acropora palmata, A. cervicornis, Diploria strigosa, and A. humilis. The presence of bacteria and timing of bacterial colonization was evaluated in gametes, swimming planulae, and newly settled polyps by fluorescence in situ hybridization (FISH using general eubacterial probes and laser-scanning confocal microscopy. The coral species investigated in this study do not appear to transmit bacteria via their gametes, and bacteria are not detectable in or on the corals until after settlement and metamorphosis. This study suggests that mass-spawning corals do not acquire, or are not colonized by, detectable numbers of bacteria until after larval settlement and development of the juvenile polyp. This timing lays the groundwork for developing and testing new hypotheses regarding general regulatory mechanisms that control bacterial colonization and infection of corals, and how interactions among bacteria and juvenile polyps influence the structure of bacterial assemblages in corals.

  7. The sexuality-assemblages of young men: a new materialist analysis

    OpenAIRE

    Alldred, P; Fox, N

    2015-01-01

    This paper presents a new materialist exploration of young men and sexuality that shifts the focus away from bodies and individuals, toward the affective flow within assemblages of bodies, things, ideas and social institutions, and the sexual capacities this flow produces. Using data from two empirical studies, we explore the sexuality assemblages of teen boys and young men, and the micropolitics of these assemblages. We find that the sexuality produced in the bodies of young men is highly te...

  8. Environmental gradients structure gorgonian assemblages on coral reefs in SE Sulawesi, Indonesia

    Science.gov (United States)

    Rowley, Sonia J.

    2018-06-01

    Indonesian coral reefs are the epicenter of marine biodiversity, yet are under rapid anthropogenically induced decline. Therefore, ecological monitoring of high diversity taxa is paramount to facilitate effective management and conservation. This study presents an initial report from a comprehensive survey of shallow-water (0-15 m) gorgonian assemblage composition and structure across sites with varying habitat quality within the Wakatobi Marine National Park (WMNP), SE Sulawesi, Indonesia. Current estimates of over 90 morphospecies from 38 genera and 12 families within the calcaxonian, holaxonian and scleraxonian groups are reported. This extensive survey confirms high local gorgonian abundance, diversity and species richness in the absence of anthropogenic influence and increasing with depth. Notably, morphological variants of the zooxanthellate species Isis hippuris Linnaeus, 1758, and Briareum Blainville, 1830, drive site and habitat assemblage differences across environmental gradients. Azooxanthellate taxa, particularly within the Plexauridae, drive species richness and diversity with depth. Of the 14 predictor variables measured, benthic characteristics, water flow and natural light explained just 30% of gorgonian assemblage structure. Furthermore, zooxanthellate and azooxanthellate taxa partitioned distinct gorgonian communities into two trophic groups—autotrophs and heterotrophs, respectively—with contrasting diversity and abundance patterns within and between study sites. This study strongly supports the WMNP as an area of high regional gorgonian abundance and diversity. Varying ecological patterns across environmental clines can provide the foundation for future research and conservation management strategies in some of the most biodiverse marine ecosystems in the world.

  9. Reptile assemblage response to restoration of fire-suppressed longleaf pine sandhills.

    Science.gov (United States)

    Steen, David A; Smith, Lora L; Conner, L M; Litt, Andrea R; Provencher, Louis; Hiers, J Kevin; Pokswinski, Scott; Guyer, Craig

    2013-01-01

    Measuring the effects of ecological restoration on wildlife assemblages requires study on broad temporal and spatial scales. Longleaf pine (Pinus palustris) forests are imperiled due to fire suppression and subsequent invasion by hardwood trees. We employed a landscape-scale, randomized-block design to identify how reptile assemblages initially responded to restoration treatments including removal of hardwood trees via mechanical methods (felling and girdling), application of herbicides, or prescribed burning alone. Then, we examined reptile assemblages after all sites experienced more than a decade of prescribed burning at two- to thee-year return intervals. Data were collected concurrently at reference sites chosen to represent target conditions for restoration. Reptile assemblages changed most rapidly in response to prescribed burning, but reptile assemblages at all sites, including reference sites, were generally indistinguishable by the end of the study. Thus, we suggest that prescribed burning in longleaf pine forests over long time periods is an effective strategy for restoring reptile assemblages to the reference condition. Application of herbicides or mechanical removal of hardwood trees provided no apparent benefit to reptiles beyond what was achieved by prescribed fire alone.

  10. Rapid biotic homogenization of marine fish assemblages

    Science.gov (United States)

    Magurran, Anne E.; Dornelas, Maria; Moyes, Faye; Gotelli, Nicholas J.; McGill, Brian

    2015-01-01

    The role human activities play in reshaping biodiversity is increasingly apparent in terrestrial ecosystems. However, the responses of entire marine assemblages are not well-understood, in part, because few monitoring programs incorporate both spatial and temporal replication. Here, we analyse an exceptionally comprehensive 29-year time series of North Atlantic groundfish assemblages monitored over 5° latitude to the west of Scotland. These fish assemblages show no systematic change in species richness through time, but steady change in species composition, leading to an increase in spatial homogenization: the species identity of colder northern localities increasingly resembles that of warmer southern localities. This biotic homogenization mirrors the spatial pattern of unevenly rising ocean temperatures over the same time period suggesting that climate change is primarily responsible for the spatial homogenization we observe. In this and other ecosystems, apparent constancy in species richness may mask major changes in species composition driven by anthropogenic change. PMID:26400102

  11. paleoenvironmental settings and assemblage changes

    African Journals Online (AJOL)

    Kasanzu

    shallow borehole drilled in the southern coastal basin of Tanzania with the aim of characterizing foraminifera and palynomorphs assemblage changes aiming at reconstructing ..... decline in temperature at EOT which caused the extinction of ...

  12. Phytoplankton Assemblage Patterns in the Southern Mid-Atlantic Bight

    Science.gov (United States)

    Makinen, Carla; Moisan, Tiffany A. (Editor)

    2012-01-01

    As part of the Wallops Coastal Oceans Observing Laboratory (Wa-COOL) Project, we sampled a time-series transect in the southern Mid-Atlantic Bight (MAB) biweekly. Our 2-year time-series data included physical parameters, nutrient concentrations, and chlorophyll a concentrations. A detailed phytoplankton assemblage structure was examined in the second year. During the 2-year study, chlorophyll a concentration (and ocean color satellite imagery) indicated that phytoplankton blooms occurred in January/February during mixing conditions and in early autumn under stratified conditions. The chlorophyll a concentrations ranged from 0.25 microgram 1(exp -1) to 15.49 microgram 1(exp -1) during the 2-year period. We were able to discriminate approximately 116 different species under phase contrast microscopy. Dominant phytoplankton included Skeletonema costatum, Rhizosolenia spp., and Pseudo-nitzschia pungens. In an attempt to determine phytoplankton species competition/succession within the assemblage, we calculated a Shannon Weaver diversity index for our diatom microscopy data. Diatom diversity was greatest during the winter and minimal during the spring. Diatom diversity was also greater at nearshore stations than at offshore stations. Individual genera appeared patchy, with surface and subsurface patches appearing abruptly and persisting for only 1-2 months at a time. The distribution of individual species differed significantly from bulk variables of the assemblage (chlorophyll a ) and total phytoplankton assemblage (cells), which indicates that phytoplankton species may be limited in growth in ways that differ from those of the total assemblage. Our study demonstrated a highly diverse phytoplankton assemblage throughout the year, with opportunistic species dominating during spring and fall in response to seasonal changes in temperature and nutrients in the southern MAB.

  13. Public Sphere as Digital Assemblage

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    the 1990s onwards digitalization brought concepts of network and complexity into the theoretical discourse. This relational turn changed the social ontology of the public sphere into a dynamic and complex system, erasing the division between the fields of reality (the world), representation (discourse......Normative theories of public sphere have struggled with the topic of materiality. The historical narrative of the ‘public sphere’ situated the phenomenon in specific spaces, where practices (public deliberation) and language (discourse) constructed political agencies, and further publics. From......), and subjectivity (agency). This changed the public sphere into an assemblage consisting of both human and non-human actors interactingin a highly dynamic, networked environment. This paper proposes a framework for considering this new materiality in the field of the public sphere: the assemblage and complexity...

  14. Vertebrate assemblages from the early Late Cretaceous of southeastern Morocco: An overview

    Science.gov (United States)

    Cavin, L.; Tong, H.; Boudad, L.; Meister, C.; Piuz, A.; Tabouelle, J.; Aarab, M.; Amiot, R.; Buffetaut, E.; Dyke, G.; Hua, S.; Le Loeuff, J.

    2010-07-01

    Fossils of vertebrates have been found in great abundance in the continental and marine early Late Cretaceous sediments of Southeastern Morocco for more than 50 years. About 80 vertebrate taxa have so far been recorded from this region, many of which were recognised and diagnosed for the first time based on specimens recovered from these sediments. In this paper, we use published data together with new field data to present an updated overview of Moroccan early Late Cretaceous vertebrate assemblages. The Cretaceous series we have studied encompasses three Formations, the Ifezouane and Aoufous Formations, which are continental and deltaic in origin and are often grouped under the name "Kem Kem beds", and the Akrabou Formation which is marine in origin. New field observations allow us to place four recognised vertebrate clusters, corresponding to one compound assemblage and three assemblages, within a general temporal framework. In particular, two ammonite bioevents characterise the lower part of the Upper Cenomanian ( Calycoceras guerangeri Zone) at the base of the Akrabou Formation and the upper part of the Lower Turonian ( Mammites nodosoides Zone), that may extend into the Middle Turonian within the Akrabou Formation, and allow for more accurate dating of the marine sequence in the study area. We are not yet able to distinguish a specific assemblage that characterises the Ifezouane Formation when compared to the similar Aoufous Formation, and as a result we regard the oldest of the four vertebrate "assemblages" in this region to be the compound assemblage of the "Kem Kem beds". This well-known vertebrate assemblage comprises a mixture of terrestrial (and aerial), freshwater and brackish vertebrates. The archosaur component of this fauna appears to show an intriguingly high proportion of large-bodied carnivorous taxa, which may indicate a peculiar trophic chain, although collecting biases alter this palaeontological signal. A small and restricted assemblage, the

  15. Effect of oil palm on the Plecoptera and Trichoptera (Insecta) assemblages in streams of eastern Amazon.

    Science.gov (United States)

    de Paiva, Carina Kaory Sasahara; de Faria, Ana Paula Justino; Calvão, Lenize Batista; Juen, Leandro

    2017-08-01

    The production of oil palm is expected to increase in the Amazon region. However, expansion of oil palm plantation leads to significant changes in the physical structure of aquatic ecosystems, mainly through the reduction of riparian vegetation that is essential for aquatic biodiversity. Here, we evaluated the effects of oil palm on the physical habitat structure of Amazonian stream environments and assemblages of Plecoptera and Trichoptera (PT), ​both found in these streams. We compared streams sampled in oil palm plantations (n = 13) with natural forest areas ("reference" streams, n = 8), located in the eastern Amazon, Brazil. Our results showed that oil palm streams were more likely to be in close proximity to roads, had higher pH values, and higher amounts of fine substrate deposited in the channel than reference streams. Further, these environmental changes had important effects on the aquatic invertebrate assemblages, reducing the abundance and richness of PT. Nevertheless, the genera composition of the assemblages did not differ between reference and oil palm (PERMANOVA, pseudo-F (1,19)  = 1.891; p = 0.111). We conclude that oil palm production has clear negative impacts on aquatic environments and PT assemblages in Amazonian streams. We recommend that oil palm producers invest more in planning of road networks to avoid the construction of roads near to the riparian vegetation. This planning can minimize impacts of oil palm production on aquatic systems in the Amazon.

  16. The regulation of bacterial production in the Chesapeake Bay

    International Nuclear Information System (INIS)

    Chin-Leo, G.

    1988-01-01

    In this study, the possibility that periods when the rates of macromolecule syntheses become uncoupled occur in natural assemblages of bacteria was examined by comparing rates of bacterial DNA and protein synthesis. A dual-label method which measures incorporation rates of [ 3 H]thymidine (TdR) into macromolecules (DNA) and of [ 14 C]leucine (Leu) into protein was developed to facilitate simultaneous estimation of these cellular activities in a single incubation. Under controlled conditions, changes in rates of Leu incorporation preceded fluctuations in TdR incorporation and the Leu:TdR ratio varied prior to shifts in growth rate indicating the uncoupling of protein and DNA synthesis which occurs during unbalanced growth. The delay between this uncoupling and a change in growth rate was always shorter than the generation time. In Chesapeake Bay, during October 1986, the Leu:TdR ratio was quite constant over a diel cycle and with depth, but during July 1987, the magnitude of this ratio and its variation through time increased with depth. Growth conditions for heterotrophic bacteria in Chesapeake Bay during summer in surface waters and throughout the water column in fall may be relatively constant leading to balanced growth. In contrast, fluctuating growth conditions in subsurface waters during summer may lead to unbalanced growth

  17. Human impacts on functional and taxonomic homogenization of plateau fish assemblages in Yunnan, China

    Directory of Open Access Journals (Sweden)

    Guohuan Su

    2015-07-01

    Full Text Available Human activities and the consequent extinctions of native species and invasions of non-native species have been changing the composition of species assemblages worldwide. These anthropogenic impacts alter not only the richness of assemblages but also the biological dissimilarity among them. However, much of the research effort to date has focused on changes in taxonomic dissimilarity (i.e. accounting for species composition whether assessments of functional dissimilarity (i.e. accounting for the diversity of biological traits are much more scarce, despite revealing important complimentary information by accounting for changes in the diversity of biological traits. Here, we assess the temporal (1950s against 2000s changes in both taxonomic and functional dissimilarities of freshwater fish assemblages across lakes from the Yunnan Plateau in China. The Jaccard index to quantify the changes in both taxonomic and functional dissimilarity. We then partitioned dissimilarity to extract its turnover component and measured the changes in the contribution of turnover to dissimilarity. We found that functional and taxonomic homogenization occurred simultaneously. However, patterns between these two processes differed for some lakes. Taxonomic and functional homogenizations were stronger when the historical level of taxonomic dissimilarity among assemblages was high. The impact of extinctions of native species and invasions of non-native species on homogenization was otherwise complex to disentangle with no significant effect of any of the studied environmental factors. In agreement with other studies, our study proved that change in taxonomic dissimilarity cannot be used to predict changes in functional dissimilarity and, as an indicator of ecosystem functioning, functional dissimilarity should be used together with taxonomic dissimilarity to attain a more holistic understanding of human impacts on natural ecosystems.

  18. Assemblages of Patient Safety

    DEFF Research Database (Denmark)

    Balatsas Lekkas, Angelos

    2016-01-01

    This thesis identifies how design processes emerge during the use of devices in healthcare, by attending to assemblages where contingencies of risk and harm co-exist with the contribution of healthcare professionals to the safe care of patients. With support from the field of Science and Technology...... practices of interdisciplinary care....

  19. Temporal changes in taxonomic and functional diversity of fish assemblages downstream from mountaintop mining

    Science.gov (United States)

    Hitt, Nathaniel P.; Chambers, Douglas B.

    2014-01-01

    Mountaintop mining (MTM) affects chemical, physical, and hydrological properties of receiving streams, but the long-term consequences for fish-assemblage structure and function are poorly understood. We sampled stream fish assemblages using electrofishing techniques in MTM exposure sites and reference sites within the Guyandotte River basin, USA, during 2010–2011. We calculated indices of taxonomic diversity (species richness, abundance, Shannon diversity) and functional diversity (functional richness, functional evenness, functional divergence) to compare exposure and reference assemblages between seasons (spring and autumn) and across years (1999–2011). We based temporal comparisons on 2 sites that were sampled during 1999–2001 by Stauffer and Ferreri (2002). Exposure assemblages had lower taxonomic and functional diversity than reference assemblages or simulated assemblages that accounted for random variation. Differences in taxonomic composition between reference and exposure assemblages were associated with conductivity and aqueous Se concentrations. Exposure assemblages had fewer species, lower abundances, and less biomass than reference assemblages across years and seasons. Green Sunfish (Lepomis cyanellus) and Creek Chub (Semotilus atromaculatus) became numerically dominant in exposure assemblages over time because of their persistence and losses of other taxa. In contrast, species richness increased over time in reference assemblages, a result that may indicate recovery from drought. Mean individual biomass increased as fish density decreased and most obligate invertivores were apparently extirpated at MTM exposure sites. Effects of MTM were not related to physical-habitat conditions but were associated with water-quality variables, which may limit quality and availability of benthic macroinvertebrate prey. Simulations revealed effects of MTM that could not be attributed to random variation in fish assemblage structure.

  20. Combining projected changes in species richness and composition reveals climate change impacts on coastal Mediterranean fish assemblages

    DEFF Research Database (Denmark)

    Albouy, Camille; Guilhaumon, François; Bastos Araujo, Miguel

    2012-01-01

    future climatic niches of 288 coastal Mediterranean fish species based on a global warming scenario. We then aggregated geographically the species-level projections to analyse the projected changes in species richness and composition. Our results show that projected changes in assemblage composition....... nestedness), separately. We also present a mapping strategy to simultaneously visualize changes in species richness and assemblage composition. To illustrate our approach, we used the Mediterranean coastal fish fauna as a case study. Using Bioclimatic Envelope Models (BEMs) we first projected the potential......, the joint exploration of changes in species richness and composition coupled with the distinction between species replacement and nestedness bears important information for understanding the nature of climate change impacts on biodiversity. These methodological advances should help decision...

  1. Can data from disparate long-term fish monitoring programs be used to increase our understanding of regional and continental trends in large river assemblages?

    Science.gov (United States)

    Waite, Ian R.; Casper, Andrew F.; Ward, David L.; Sauer, Jennifer S.; Irwin, Elise R.; Chapman, Colin G.; Ickes, Brian S.; Paukert, Craig P.; Kosovich, John J.; Bayer, Jennifer M.

    2018-01-01

    Understanding trends in the diverse resources provided by large rivers will help balance tradeoffs among stakeholders and inform strategies to mitigate the effects of landscape scale stressors such as climate change and invasive species. Absent a cohesive coordinated effort to assess trends in important large river resources, a logical starting point is to assess our ability to draw inferences from existing efforts. In this paper, we use a common analytical framework to analyze data from five disparate fish monitoring programs to better understand the nature of spatial and temporal trends in large river fish assemblages. We evaluated data from programs that monitor fishes in the Colorado, Columbia, Illinois, Mississippi, and Tallapoosa rivers using non-metric dimensional scaling ordinations and associated tests to evaluate trends in fish assemblage structure and native fish biodiversity. Our results indicate that fish assemblages exhibited significant spatial and temporal trends in all five of the rivers. We also document native species diversity trends that were variable within and between rivers and generally more evident in rivers with higher species richness and programs of longer duration. We discuss shared and basin-specific landscape level stressors. Having a basic understanding of the nature and extent of trends in fish assemblages is a necessary first step towards understanding factors affecting biodiversity and fisheries in large rivers. PMID:29364953

  2. Can data from disparate long-term fish monitoring programs be used to increase our understanding of regional and continental trends in large river assemblages?

    Science.gov (United States)

    Counihan, Timothy D.; Waite, Ian R.; Casper, Andrew F.; Ward, David L.; Sauer, Jennifer S.; Irwin, Elise R.; Chapman, Colin G.; Ickes, Brian; Paukert, Craig P.; Kosovich, John J.; Bayer, Jennifer M.

    2018-01-01

    Understanding trends in the diverse resources provided by large rivers will help balance tradeoffs among stakeholders and inform strategies to mitigate the effects of landscape scale stressors such as climate change and invasive species. Absent a cohesive coordinated effort to assess trends in important large river resources, a logical starting point is to assess our ability to draw inferences from existing efforts. In this paper, we use a common analytical framework to analyze data from five disparate fish monitoring programs to better understand the nature of spatial and temporal trends in large river fish assemblages. We evaluated data from programs that monitor fishes in the Colorado, Columbia, Illinois, Mississippi, and Tallapoosa rivers using non-metric dimensional scaling ordinations and associated tests to evaluate trends in fish assemblage structure and native fish biodiversity. Our results indicate that fish assemblages exhibited significant spatial and temporal trends in all five of the rivers. We also document native species diversity trends that were variable within and between rivers and generally more evident in rivers with higher species richness and programs of longer duration. We discuss shared and basin-specific landscape level stressors. Having a basic understanding of the nature and extent of trends in fish assemblages is a necessary first step towards understanding factors affecting biodiversity and fisheries in large rivers.

  3. Rare symbionts may contribute to the resilience of coral–algal assemblages

    KAUST Repository

    Ziegler, Maren

    2017-12-01

    The association between corals and photosynthetic dinoflagellates (Symbiodinium spp.) is the key to the success of reef ecosystems in highly oligotrophic environments, but it is also their Achilles‘ heel due to its vulnerability to local stressors and the effects of climate change. Research during the last two decades has shaped a view that coral host–Symbiodinium pairings are diverse, but largely exclusive. Deep sequencing has now revealed the existence of a rare diversity of cryptic Symbiodinium assemblages within the coral holobiont, in addition to one or a few abundant algal members. While the contribution of the most abundant resident Symbiodinium species to coral physiology is widely recognized, the significance of the rare and low abundant background Symbiodinium remains a matter of debate. In this study, we assessed how coral–Symbiodinium communities assemble and how rare and abundant components together constitute the Symbiodinium community by analyzing 892 coral samples comprising >110 000 unique Symbiodinium ITS2 marker gene sequences. Using network modeling, we show that host–Symbiodinium communities assemble in non-random ‘clusters‘ of abundant and rare symbionts. Symbiodinium community structure follows the same principles as bacterial communities, for which the functional significance of rare members (the ‘rare bacterial biosphere’) has long been recognized. Importantly, the inclusion of rare Symbiodinium taxa in robustness analyses revealed a significant contribution to the stability of the host–symbiont community overall. As such, it highlights the potential functions rare symbionts may provide to environmental resilience of the coral holobiont.

  4. Differences in biological traits composition of benthic assemblages between unimpacted habitats

    DEFF Research Database (Denmark)

    Bolam, S.G.; Garcia, C.; Eggleton, J.

    2017-01-01

    of unimpacted benthic assemblages vary between different sedimentary habitats. Assemblages in deep, muddy environments unaffected by anthropogenic disturbance show increased proportions of downward conveyors and surface deposit-feeders, while burrowing, diffusive mixing, scavenging and predation traits assume...... greater numerical proportions in shallower habitats. Deep, coarser sediments are numerically more dominated by sessile, upward conveyors and suspension feeders. In contrast, unimpacted assemblages of coarse sediments in shallower regions are proportionally dominated by the diffusive mixers, burrowers......, scavengers and predators. Finally, assemblages of gravelly sediments exhibit a relatively greater numerical dominance of non-bioturbators and asexual reproducers. These findings may be used to form the basis of ranking habitats along a functional sensitivity gradient...

  5. Habitat specialization in tropical continental shelf demersal fish assemblages.

    Directory of Open Access Journals (Sweden)

    Ben M Fitzpatrick

    Full Text Available The implications of shallow water impacts such as fishing and climate change on fish assemblages are generally considered in isolation from the distribution and abundance of these fish assemblages in adjacent deeper waters. We investigate the abundance and length of demersal fish assemblages across a section of tropical continental shelf at Ningaloo Reef, Western Australia, to identify fish and fish habitat relationships across steep gradients in depth and in different benthic habitat types. The assemblage composition of demersal fish were assessed from baited remote underwater stereo-video samples (n = 304 collected from 16 depth and habitat combinations. Samples were collected across a depth range poorly represented in the literature from the fringing reef lagoon (1-10 m depth, down the fore reef slope to the reef base (10-30 m depth then across the adjacent continental shelf (30-110 m depth. Multivariate analyses showed that there were distinctive fish assemblages and different sized fish were associated with each habitat/depth category. Species richness, MaxN and diversity declined with depth, while average length and trophic level increased. The assemblage structure, diversity, size and trophic structure of demersal fishes changes from shallow inshore habitats to deeper water habitats. More habitat specialists (unique species per habitat/depth category were associated with the reef slope and reef base than other habitats, but offshore sponge-dominated habitats and inshore coral-dominated reef also supported unique species. This suggests that marine protected areas in shallow coral-dominated reef habitats may not adequately protect those species whose depth distribution extends beyond shallow habitats, or other significant elements of demersal fish biodiversity. The ontogenetic habitat partitioning which is characteristic of many species, suggests that to maintain entire species life histories it is necessary to protect corridors of

  6. Improving the energy efficiency of mine fan assemblages

    International Nuclear Information System (INIS)

    De Souza, Euler

    2015-01-01

    Energy associated with ventilating an underground operation comprises a significant portion of a mine operation's base energy demand and is consequently responsible for a large percentage of the total operating costs. Ventilation systems may account from 25 to 40% of the total energy costs and 40–50% of the energy consumption of a mine operation. Fans are the most important mechanical devices used to ventilate underground mines and the total fan power installed in a single mine operation can easily exceed 10,000 kW. Investigations of a number of mine main fan installations have determined their assemblage to be, in general, very energy inefficient. The author has found that 40–80% of the energy consumed by a main fan is used to overcome the resistance of fan assemblage components. This paper presents how engineering design principles can be applied to improve the performance and efficiency of fan installations, resulting in substantial reductions in power consumption, operating cost and greenhouse gas emissions. A detailed case study is presented to demonstrate that, by designing fan assemblages using proper engineering concepts of fluid physics and industrial ventilation design, main fan systems will operate at efficiencies well above 80–90% (compared to common operating efficiencies of between 20 and 65%), resulting in a drastic reduction in a mine's overall costs and base electrical and energy loads. - Highlights: • Increases in fan assemblage efficiencies with minimum capital investment. • Improved designs for substantial fan power and operating cost savings. • General solutions and tactics for improving existing main fan installations. • Case study presented to demonstrate proper design of fan assemblages.

  7. Bacterial Community Succession in Pine-Wood Decomposition.

    Science.gov (United States)

    Kielak, Anna M; Scheublin, Tanja R; Mendes, Lucas W; van Veen, Johannes A; Kuramae, Eiko E

    2016-01-01

    Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

  8. High-throughput sequencing for the detection of the bacterial and fungal diversity in Mongolian naturally fermented cow's milk in Russia.

    Science.gov (United States)

    Liu, Wenjun; Zheng, Yi; Kwok, Lai-Yu; Sun, Zhihong; Zhang, Jiachao; Guo, Zhuang; Hou, Qiangchuan; Menhe, Bilige; Zhang, Heping

    2015-02-22

    Traditional fermented dairy products are major components of the typical Mongolian diet since ancient times. However, almost all the previous studies on the microbial composition of traditional Mongolian fermented dairy products analyzed food samples from the Chinese Mongolian region and Mongolia but not the Russian Mongolian region. In this study, the bacterial and fungal community diversity of nineteen naturally fermented cow's milk (NFCM) samples from local Mongolian families residing in Kalmykia and Chita of Russia was investigated with pyrosequencing. Firmicutes and Ascomycota were the predominant phyla respectively for bacteria and fungi. The abundance of the bacterial phylum Acidobacteria was considerably different between the samples from the two regions. At genus level, Lactobacillus and Pichia were the predominating bacterial and fungal genera, respectively, while six bacterial genera significantly differed between the Kalmykia (enrichment of Aeromonas, Bacillus, Clostridium, Streptococcus, Vogesella) and Chita (enrichment of Lactococcus) samples. The results of principal coordinate analysis (PCoA) based on the bacterial or fungal composition of the Kalmykia and Chita samples revealed a different microbiota structure between the samples collected in these two locations. The redundancy analysis (RDA) identified 60 bacterial and 21 fungal OTUs as the key variables responsible for such microbiota structural difference. Our results suggest that structural differences existed in the microbiota of NFCM between Kalmykia and Chita. The difference in geographic environment may be an important factor influencing the microbial diversity of NFCM made by the Mongolians in Russia.

  9. Mass transfer of therapeutics through natural human plaque biofilms: a model for therapeutic delivery to pathological bacterial biofilms.

    Science.gov (United States)

    Robinson, Colin

    2011-09-01

    Bacterial biofilms in the mouth are prime mediators of the destruction of the dental and oral tissues. This brief review summarises recent work using a device for generating intact plaque in the mouth on natural enamel surfaces such that quantitative studies of mass transfer through natural plaque biofilms could be carried out in relation to plaque architecture. This data is discussed against the background of existing information. The device revealed complex plaque architecture with high a surface area to mass ratio decreasing from the exterior of the biofilm towards the tissue surface. Fluoride, a potent inhibitor of caries was concentrated in the outer regions of the biofilm. This implies some restriction of diffusion and possibly binding to the high surface area of the outer biofilm. Whilst all components examined conformed to this distribution pattern, some relatively uncharged materials penetrated the bacterial biomass whilst other, more highly charged materials tended to be restricted to the channels or biomass surface. Plaque architecture was robust but could be altered using detergent indicating that biomass architecture and chemistry could be manipulated as a possible means of facilitating mass transport of therapeutics. Copyright © 2011 Elsevier Ltd. All rights reserved.

  10. Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

    Science.gov (United States)

    Comte, J.; Lovejoy, C.; Crevecoeur, S.; Vincent, W. F.

    2016-01-01

    Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a north-south permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa (operational taxonomic units, OTUs), and then analyzed these results relative to environmental variables to identify variables controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley; however, the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial "keystone species". These highly connected nodes (OTUs) in the network were not merely the numerically dominant taxa, and their loss would alter the organization of microbial consortia and ultimately the food web structure and functioning of these aquatic ecosystems.

  11. Translanguaging and Semiotic Assemblages

    Science.gov (United States)

    Pennycook, Alastair

    2017-01-01

    This paper asks what translanguaging could start to look like if it incorporated an expanded version of language and questioned not only to the borders between languages but also the borders between semiotic modes. Developing the idea of spatial repertoires and assemblages, and looking at data from a Bangladeshi-owned corner shop, this paper…

  12. How does conversion of natural tropical rainforest ecosystems affect soil bacterial and fungal communities in the Nile river watershed of Uganda?

    Directory of Open Access Journals (Sweden)

    Peter O Alele

    Full Text Available Uganda's forests are globally important for their conservation values but are under pressure from increasing human population and consumption. In this study, we examine how conversion of natural forest affects soil bacterial and fungal communities. Comparisons in paired natural forest and human-converted sites among four locations indicated that natural forest soils consistently had higher pH, organic carbon, nitrogen, and calcium, although variation among sites was large. Despite these differences, no effect on the diversity of dominant taxa for either bacterial or fungal communities was detected, using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE. Composition of fungal communities did generally appear different in converted sites, but surprisingly, we did not observe a consistent pattern among sites. The spatial distribution of some taxa and community composition was associated with soil pH, organic carbon, phosphorus and sodium, suggesting that changes in soil communities were nuanced and require more robust metagenomic methods to understand the various components of the community. Given the close geographic proximity of the paired sampling sites, the similarity between natural and converted sites might be due to continued dispersal between treatments. Fungal communities showed greater environmental differentiation than bacterial communities, particularly according to soil pH. We detected biotic homogenization in converted ecosystems and substantial contribution of β-diversity to total diversity, indicating considerable geographic structure in soil biota in these forest communities. Overall, our results suggest that soil microbial communities are relatively resilient to forest conversion and despite a substantial and consistent change in the soil environment, the effects of conversion differed widely among sites. The substantial difference in soil chemistry, with generally lower nutrient quantity in converted

  13. Characterization of the rate and temperature sensitivities of bacterial remineralization of dissolved organic phosphorus by natural populations

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    Angelicque E. White

    2012-08-01

    Full Text Available Production, transformation, and degradation are the principal components of the cycling of dissolved organic matter (DOM in marine systems. Heterotrophic Bacteria (and Archaea play a large part in this cycling via enzymatic decomposition and intracellular transformations of organic material to inorganic carbon (C, nitrogen (N , and phosphorus (P. The rate and magnitude of inorganic nutrient regeneration from DOM is related to the elemental composition and lability of DOM substrates as well as the nutritional needs of the mediating organisms. While many previous efforts have focused on C and N cycling of DOM, less is known in regards to the controls of organic P utilization and remineralization by natural populations of bacteria. In order to constrain the relative time scales and degradation of select dissolved organic P (DOP compounds we have conducted a series of experiments focused on (1 assessment of the short-term lability of a range of DOP compounds, (2 characterization of labile DOP remineralization rates and (3 examination of temperature sensitivities of labile DOP remineralization for varying bacterial populations. Results reinforce previous findings of monoester and polyphosphate lability and the relative recalcitrance of a model phosphonate: 2-aminoethylphosphonate. High resolution time-series of P monoester remineralization indicates decay constants on the order of 0.67-7.04 d-1 for bacterial populations isolated from coastal and open ocean surface waters. The variability of these rates is predictably related to incubation temperature and initial concentrations of heterotrophic bacteria. Additional controls on DOP hydrolysis included seasonal shifts in bacterial populations and the physiological state of bacteria at the initiation of DOP addition experiments. Composite results indicate that bacterial hydrolysis of P-monoesters exceeds bacterial P demand and thus DOP remineralization efficiency may control P availability to autotrophs.

  14. Mangrove clearing impacts on macrofaunal assemblages and benthic food webs in a tropical estuary.

    Science.gov (United States)

    Bernardino, Angelo Fraga; Gomes, Luiz Eduardo de Oliveira; Hadlich, Heliatrice Louise; Andrades, Ryan; Correa, Lucas Barreto

    2018-01-01

    Despite over 21,000ha of mangrove forests being removed per year in Brazil, ecological changes following mangrove deforestation have been overlooked. Here we evaluated changes in benthic macrofaunal assemblages and food-webs at a mangrove removal and natural sites in a tropical estuary in Eastern Brazil. The impacted site had coarser sediment particle sizes suggesting significant changes in sedimentation processes after forest clearing. Spatial differences in macrofaunal abundance, biomass and diversity were not directly associated with the removal of mangrove forests, supporting recolonization of impacted areas by estuarine fauna. However, benthic assemblage composition, infaunal δ 13 C signatures and food-web diversity markedly differed at the impacted site being strongly related to sedimentary changes. The loss of infaunal trophic diversity that followed mangrove removal suggests that large-scale forest clearing may impact estuarine food webs, with potential consequences to nearby coastal ecosystems given the high clearing rate of mangrove forests in Brazil. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species.

    Science.gov (United States)

    Desgarennes, Damaris; Garrido, Etzel; Torres-Gomez, Miryam J; Peña-Cabriales, Juan J; Partida-Martinez, Laila P

    2014-12-01

    Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  16. Mass coral bleaching causes biotic homogenization of reef fish assemblages.

    Science.gov (United States)

    Richardson, Laura E; Graham, Nicholas A J; Pratchett, Morgan S; Eurich, Jacob G; Hoey, Andrew S

    2018-04-06

    Global climate change is altering community composition across many ecosystems due to nonrandom species turnover, typically characterized by the loss of specialist species and increasing similarity of biological communities across spatial scales. As anthropogenic disturbances continue to alter species composition globally, there is a growing need to identify how species responses influence the establishment of distinct assemblages, such that management actions may be appropriately assigned. Here, we use trait-based analyses to compare temporal changes in five complementary indices of reef fish assemblage structure among six taxonomically distinct coral reef habitats exposed to a system-wide thermal stress event. Our results revealed increased taxonomic and functional similarity of previously distinct reef fish assemblages following mass coral bleaching, with changes characterized by subtle, but significant, shifts toward predominance of small-bodied, algal-farming habitat generalists. Furthermore, while the taxonomic or functional richness of fish assemblages did not change across all habitats, an increase in functional originality indicated an overall loss of functional redundancy. We also found that prebleaching coral composition better predicted changes in fish assemblage structure than the magnitude of coral loss. These results emphasize how measures of alpha diversity can mask important changes in the structure and functioning of ecosystems as assemblages reorganize. Our findings also highlight the role of coral species composition in structuring communities and influencing the diversity of responses of reef fishes to disturbance. As new coral species configurations emerge, their desirability will hinge upon the composition of associated species and their capacity to maintain key ecological processes in spite of ongoing disturbances. © 2018 John Wiley & Sons Ltd.

  17. Aquatic insect assemblages associated with subalpine stream segment types in relict glaciated headwaters

    Science.gov (United States)

    Kubo, Joshua S.; Torgersen, Christian E.; Bolton, Susan M.; Weekes, Anne A.; Gara, Robert I.

    2013-01-01

    1. Aquatic habitats and biotic assemblages in subalpine headwaters are sensitive to climate and human impacts. Understanding biotic responses to such perturbations and the contribution of high-elevation headwaters to riverine biodiversity requires the assessment of assemblage composition among habitat types. We compared aquatic insect assemblages among headwater stream segment types in relict glaciated subalpine basins in Mt. Rainier National Park, Washington, USA. 2. Aquatic insects were collected during summer and autumn in three headwater basins. In each basin, three different stream segment types were sampled: colluvial groundwater sources, alluvial lake inlets, and cascade-bedrock lake outlets. Ward's hierarchical cluster analysis revealed high β diversity in aquatic insect assemblages, and non-metric multidimensional scaling indicated that spatial and temporal patterns in assemblage composition differed among headwater stream segment types. Aquatic insect assemblages showed more fidelity to stream segment types than to individual basins, and the principal environmental variables associated with assemblage structure were temperature and substrate. 3. Indicator species analyses identified specific aquatic insects associated with each stream segment type. Several rare and potentially endemic aquatic insect taxa were present, including the recently described species, Lednia borealis (Baumann and Kondratieff). 4. Our results indicate that aquatic insect assemblages in relict glaciated subalpine headwaters were strongly differentiated among stream segment types. These results illustrate the contribution of headwaters to riverine biodiversity and emphasise the importance of these habitats for monitoring biotic responses to climate change. Monitoring biotic assemblages in high-elevation headwaters is needed to prevent the potential loss of unique and sensitive biota.

  18. Demersal Assemblages on the Soft Bottoms off the Catalan-Levante Coast of the Spanish Mediterranean

    Directory of Open Access Journals (Sweden)

    Mariano García-Rodríguez

    2011-01-01

    Full Text Available The analysis of 255 bottom trawl samples obtained in annual experimental surveys (2007–2010 along the western Mediterranean shows the existence of five well-defined demersal assemblages that follow a depth distribution: (a upper shelf assemblages, including two assemblages differentiated by the type of substrate (sand-muddy and terrigenous muddy bottoms; (b a middle shelf assemblage; (c an upper slope assemblage; (d a middle slope assemblage. Faunally, they are dominated by fish (37% of 452 total species, followed by crustaceans (22%, molluscs (17%, echinoderms (9%, and other invertebrates (15%. The assemblages identified showed major alterations on the shelf and shelf edge and less pronounced ones on the upper and middle slope. The average diversity values were more or less high, evidencing the high species richness in the western Mediterranean. The identified assemblages may facilitate future multispecies fisheries management based on an ecosystem approach.

  19. Bacterial Community Structure in a Mollisol Under Long-Term Natural Restoration, Cropping, and Bare Fallow History Estimated by PCR-DGGE

    Institute of Scientific and Technical Information of China (English)

    WANG Guang-Hua; JIN Jian; LIU Jun-Jie; CHEN Xue-Li; LIU Ju-Dong; LIU Xiao-Bing

    2009-01-01

    Soil microbial biomass and community structures are commonly used as indicators for soil quality and fertility.A investigation was performed to study the effects of long-term natural restoration,cropping,and bare fallow managements on the soil microbial biomass and bacterial community structures in depths of 0-10,20-30,and 40-50 cm in a black soil (Mollisol).Microbial biomass was estimated from chloroform fumigation-extraction,and bacterial community structures were determined by analysis of 16S rDNA using polymerase chain reaction-denaturing gradient gel electrophoresis (PCRDGGE).Experimental results showed that microbial biomass significantly declined with soil depth in the managements of restoration and cropping,but not in the bare fallow.DGGE profiles indicated that the band number in top 0-10 cm soils was less than that in depth of 20-30 or 40-50 cm.These suggested that the microbial population was high but the bacterial community structure was simple in the topsoil.Cluster and principle component analysis based on DGGE banding patterns showed that the bacterial community structure was affected by soil depth more primarily than by managements,and the succession of bacterial community as increase of soil depth has a similar tendency in the three managements.Fourteen predominating DGGE bands were excised and sequenced,in which 6 bands were identified as the taxa of Verrucomicrobia,2 bands as Actinobacteria,2 bands as α-Proteobacteria,and the other 4 bands as δ-Proteobacteria,Acidobacteria,Nitrospira,and unclassified bacteria.In addition,the sequences of 11 DGGE bands were closely related to uncultured bacteria.Thus,the bacterial community structure in black soil was stable,and the predominating bacterial groups were uncultured.

  20. Characterization of a subtropical hawksbill sea turtle (Eretmocheyles imbricata assemblage utilizing shallow water natural and artificial habitats in the Florida Keys.

    Directory of Open Access Journals (Sweden)

    Jonathan C Gorham

    Full Text Available In order to provide information to better inform management decisions and direct further research, vessel-based visual transects, snorkel transects, and in-water capture techniques were used to characterize hawksbill sea turtles in the shallow marine habitats of a Marine Protected Area (MPA, the Key West National Wildlife Refuge in the Florida Keys. Hawksbills were found in hardbottom and seagrass dominated habitats throughout the Refuge, and on man-made rubble structures in the Northwest Channel near Cottrell Key. Hawksbills captured (N = 82 were exclusively juveniles and subadults with a straight standard carapace length (SSCL ranging from 21.4 to 69.0cm with a mean of 44.1 cm (SD = 10.8. Somatic growth rates were calculated from 15 recaptured turtles with periods at large ranging from 51 to 1188 days. Mean SSCL growth rate was 7.7 cm/year (SD = 4.6. Juvenile hawksbills (<50 cm SSCL showed a significantly higher growth rate (9.2 cm/year, SD = 4.5, N = 11 than subadult hawksbills (50-70 cm SSCL, 3.6 cm/year, SD = 0.9, N = 4. Analysis of 740 base pair mitochondrial control region sequences from 50 sampled turtles yielded 12 haplotypes. Haplotype frequencies were significantly different compared to four other Caribbean juvenile foraging aggregations, including one off the Atlantic coast of Florida. Many-to-one mixed stock analysis indicated Mexico as the primary source of juveniles in the region and also suggested that the Refuge may serve as important developmental habitat for the Cuban nesting aggregation. Serum testosterone radioimmunoassay results from 33 individuals indicated a female biased sex ratio of 3.3 females: 1 male for hawksbills in the Refuge. This assemblage of hawksbills is near the northern limit of the species range, and is one of only two such assemblages described in the waters of the continental United States. Since this assemblage resides in an MPA with intensive human use, basic information on

  1. Recovery of macrobenthic assemblages following experimental sand burial

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    José J. Barrón

    2008-09-01

    Full Text Available This research was supported by a fund provided by the Instituto de Ciencias del Mar y Limnología (UNAM and a fund provided to Celia Olabarria in 2004 and 2005 by the University of Vigo for overseas short stays.AbstractPeriodic inundation by sand is a very common feature of rocky coasts throughout the world. Even so, there have been few direct observations or experiments to investigate the role of sediments on intertidal rocky shores. We designed a field experiment in Mazatlán Bay, Mexico, to test the initial impact and subsequent recovery of intertidal macrobenthic assemblages exposed to sand burial at two sites of varying wave exposure. Both sites supported different natural assemblages. Treatment plots for the addition of sediment and control plots (50 × 50 cm, separated by at least 1.5 m, were randomly placed across the mid-water tidal level. The initial response of the resident macrobenthos and the subsequent recolonization was monitored over a period of 95 days. The main effect of sediment deposition at both sites was mortality and removal of biota due to smothering. The recovery process was rapid and may in part have been the result of the mechanism by which the small, disturbed patches were recolonized. Most of the invertebrates colonized the patches as adults; several seaweeds exhibited vegetative growth as the major mechanism of colonization (e.g., Ulva lactuca Linnaeus, 1753, Amphiroa valonioides Yendo, 1902 and Chaetomorpha antennina (Borgensen Kutzing, 1849. The rate of recovery varied between the sites, however. Recovery of species numbers proceeded quickly at the sheltered site (day 7, but took 95 days at the exposed site. In contrast, biomass reached control levels by day 45 at the sheltered site, but already by day 15 at the exposed site. By day 95, the assemblages recovered to 83.5% and 81% similarity with the controls at the sheltered and exposed sites respectively. Although differences in wave exposure could be very

  2. Elucidating Duramycin’s Bacterial Selectivity and Mode of Action on the Bacterial Cell Envelope

    Directory of Open Access Journals (Sweden)

    Sahar Hasim

    2018-02-01

    Full Text Available The use of naturally occurring antimicrobial peptides provides a promising route to selectively target pathogenic agents and to shape microbiome structure. Lantibiotics, such as duramycin, are one class of bacterially produced peptidic natural products that can selectively inhibit the growth of other bacteria. However, despite longstanding characterization efforts, the microbial selectivity and mode of action of duramycin are still obscure. We describe here a suite of biological, chemical, and physical characterizations that shed new light on the selective and mechanistic aspects of duramycin activity. Bacterial screening assays have been performed using duramycin and Populus-derived bacterial isolates to determine species selectivity. Lipidomic profiles of selected resistant and sensitive strains show that the sensitivity of Gram-positive bacteria depends on the presence of phosphatidylethanolamine (PE in the cell membrane. Further the surface and interface morphology were studied by high resolution atomic force microscopy and showed a progression of cellular changes in the cell envelope after treatment with duramycin for the susceptible bacterial strains. Together, these molecular and cellular level analyses provide insight into duramycin’s mode of action and a better understanding of its selectivity.

  3. Juvenile bottlenecks and salinity shape grey mullet assemblages in Mediterranean estuaries

    Science.gov (United States)

    Cardona, Luis; Hereu, Bernat; Torras, Xavier

    2008-05-01

    Previous research has suggested that competitive bottlenecks may exist for the Mediterranean grey mullets (Osteichthyes, Mugilidae) at the fry stage with the exotic Cyprinus carpio (Osteichthyes, Cyprinidae) playing a central role. As a consequence, the structure of grey mullet assemblages at later stages is thought to reflect previous competition as well as differences in osmoregulatory skills. This paper tests that hypothesis by examining four predictions about the relative abundance of five grey mullet species in 42 Western Mediterranean estuary sites from three areas (Aiguamolls de l'Empordà, Ebro Delta and Minorca) differing in the salinity level and occurrence of C. carpio. Field data confirmed the predictions as: (1) Liza aurata and Mugil cephalus were scarce everywhere and never dominated the assemblage; (2) Liza saliens dominated the assemblage where the salinity level was higher than 13; (3) Liza ramado always dominated the assemblage where the salinity level was lower than 13 and C. carpio was present; and (4) Chelon labrosus dominated the assemblage only where the salinity level was lower than 13 and C. carpio was absent. The catch per unit effort of C. labrosus of any size was smaller in the presence of C. carpio than where it had not been introduced, which is in agreement with the juvenile competitive bottleneck hypothesis. Discriminant analysis confirmed that the assemblage structure was linked to the salinity level and the occurrence of C. carpio for both early juveniles and late juveniles as well as adults. The data reported here reveal that the structure of grey mullet assemblages inhabiting Mediterranean estuaries is determined by salinity and competitive interactions at the fry stage.

  4. THE INFLUENCE OF SUBMERGED MACROPHYTES ON SEDIMENTARY DIATOM ASSEMBLAGES(1).

    Science.gov (United States)

    Vermaire, Jesse C; Prairie, Yves T; Gregory-Eaves, Irene

    2011-12-01

    Submerged macrophytes are a central component of lake ecosystems; however, little is known regarding their long-term response to environmental change. We have examined the potential of diatoms as indicators of past macrophyte biomass. We first sampled periphyton to determine whether habitat was a predictor of diatom assemblage. We then sampled 41 lakes in Quebec, Canada, to evaluate whether whole-lake submerged macrophyte biomass (BiomEpiV) influenced surface sediment diatom assemblages. A multivariate regression tree (MRT) was used to construct a semiquantitative model to reconstruct past macrophyte biomass. We determined that periphytic diatom assemblages on macrophytes were significantly different from those on wood and rocks (ANOSIM R = 0.63, P macrophyte, nutrient-limited lakes (BiomEpiV ≥525 μg · L(-1) ; total phosphorus [TP] macrophyte, nutrient-limited lakes (BiomEpiV macrophytes have a significant influence on diatom community structure and that sedimentary diatom assemblages can be used to infer past macrophyte abundance. © 2011 Phycological Society of America.

  5. Detecting carbon uptake and cellular allocation by individual algae in multispecies assemblages: Tracking carbon into single algal cells

    Energy Technology Data Exchange (ETDEWEB)

    Murdock, Justin N. [USDA Agricultural Research Service, National Sedimentation Laboratory, Oxford Mississippi; Department of Biology, Tennessee Technological University, Cookeville Tennessee

    2015-11-03

    Algal species vary in carbon (C) need and uptake rates. Understanding differences in C uptake and cellular allocation among species from natural communities will bring new insight into many ecosystem process questions including how species changes will alter energy availability and C sequestration in aquatic ecosystems. A major limitation of current methods that measure algal C incorporation is the inability to separate the response of individual species from mixed-species assemblages. I used Fourier-transform infrared microspectroscopy to qualitatively measure inorganic 13C isotope incorporation into individual algal cells in single species, two species, and natural phytoplankton assemblages. Lateral shifts in spectral peaks from 13C treatments were observed in all species. Comparison of peaks associated with carbohydrates, proteins, and lipids allowed for the detection of which individuals took in C, and which macromolecules the C was used to make. For example, shifts in Spirogyra spectral peaks showed substantial C incorporation in carbohydrates. Further, shifts in peaks at 1160 cm-1, 1108 cm-1, 1080 cm-1, 1048 cm-1, and 1030 cm-1 suggested C was being allocated into cellulose. The natural phytoplankton assemblage demonstrated how C could be tracked into co-occurring species. A diatom had large shifts in protein and carbohydrate peaks, while a green alga and euglenoid had only a few shifts in protein related peaks. Fourier-transform infrared microspectroscopy is an established, label free method for measuring the chemical composition of algal cells. However, adding a label such as 13C isotope can greatly expand the technique's capabilities by qualitatively tracking C movement between inorganic and organic states within single cells.

  6. Exogenous indirect photoinactivation of bacterial pathogens and indicators in water with natural and synthetic photosensitizers in simulated sunlight with reduced UVB.

    Science.gov (United States)

    Maraccini, P A; Wenk, J; Boehm, A B

    2016-08-01

    To investigate the UVB-independent and exogenous indirect photoinactivation of eight human health-relevant bacterial species in the presence of photosensitizers. Eight bacterial species were exposed to simulated sunlight with greatly reduced UVB light intensity in the presence of three synthetic photosensitizers and two natural photosensitizers. Inactivation curves were fit with shoulder log-linear or first-order kinetic models, from which the presence of a shoulder and magnitude of inactivation rate constants were compared. Eighty-four percent reduction in the UVB light intensity roughly matched a 72-95% reduction in the overall bacterial photoinactivation rate constants in sensitizer-free water. With the UVB light mostly reduced, the exogenous indirect mechanism contribution was evident for most bacteria and photosensitizers tested, although most prominently with the Gram-positive bacteria. Results confirm the importance of UVB light in bacterial photoinactivation and, with the reduction of the UVB light intensity, that the Gram-positive bacteria are more vulnerable to the exogenous indirect mechanism than Gram-negative bacteria. UVB is the most important range of the sunlight spectrum for bacterial photoinactivation. In aquatic environments where photosensitizers are present and there is high UVB light attenuation, UVA and visible wavelengths can contribute to exogenous indirect photoinactivation. © 2016 The Society for Applied Microbiology.

  7. Assemblages of micronektonic fishes and invertebrates in a gradient of regional warming along the Western Antarctic Peninsula

    Science.gov (United States)

    Parker, Melanie L.; Fraser, William R.; Ashford, Julian; Patarnello, Tomaso; Zane, Lorenzo; Torres, Joseph J.

    2015-12-01

    Micronektonic fishes and invertebrates were sampled with 32 midwater trawls at nine sites along the Western Antarctic Peninsula (WAP) in the austral fall (March-April) of 2010. Study sites were located within four hypothesized hydrographic regions: near Joinville Island in Region I, at Croker Passage, near Anvers Island, and near Renaud Island in Region II, within Marguerite Bay and the Marguerite Trough in Region III, and near Charcot Island in Region IV. A total of 62 taxa representing 12 taxonomic groups of pelagic invertebrates and 9 families of fish were captured, but assemblages were dominated by only a few species. The most numerically abundant taxa were the euphausiids, Thysanoessa macrura, Euphausia superba, and E. crystallorophias, combining to contribute nearly 79% of the total catch. Biomass dominants included E. superba, which contributed more than 44% of the total catch, the notothenioid Pleuragramma antarctica, and the salp, Salpa thompsoni. A comparison of total catches among sites revealed that the largest volumetric abundances and biomasses were captured at the Marguerite Bay site. Cluster analysis of abundance data identified distinct multispecies assemblages at Joinville Island in Region I, Croker Passage in Region II, Marguerite Bay in Region III, and Charcot Island in Region IV. A fifth distinct assemblage included samples from sites near Anvers and Renaud Island in Region II, and from the Marguerite Trough in Region III. Assemblages at Joinville Island and Croker Passage were both dominated by E. superba and S. thompsoni, but hydrographic conditions at Joinville Island favored a neritic assemblage, underscored by substantial numbers of P. antarctica. The assemblage at Croker Passage was more oceanic in nature with major inputs from the myctophid, Electrona antarctica and the hyperiid amphipod, Themisto gaudichaudii. Marguerite Bay and Charcot Island were well-mixed assemblages with strong representation by both neritic and oceanic fauna. The

  8. Removing forest canopy cover restores a reptile assemblage.

    Science.gov (United States)

    Pike, David A; Webb, Jonathan K; Shine, Richard

    2011-01-01

    Humans are rapidly altering natural systems, leading to changes in the distribution and abundance of species. However, so many changes are occurring simultaneously (e.g., climate change, habitat fragmentation) that it is difficult to determine the cause of population fluctuations from correlational studies. We used a manipulative field experiment to determine whether forest canopy cover directly influences reptile assemblages on rock outcrops in southeastern Australia. Our experimental design consisted of three types of rock outcrops: (1) shady sites in which overgrown vegetation was manually removed (n = 25); (2) overgrown controls (n = 30); and (3) sun-exposed controls (n = 20). Following canopy removal, we monitored reptile responses over 30 months. Canopy removal increased reptile species richness, the proportion of shelter sites used by reptiles, and relative abundances of five species that prefer sun-exposed habitats. Our manipulation also decreased the abundances of two shade-tolerant species. Canopy cover thus directly influences this reptile assemblage, with the effects of canopy removal being dependent on each species' habitat preferences (i.e., selection or avoidance of sun-exposed habitat). Our study suggests that increases in canopy cover can cause declines of open-habitat specialists, as previously suggested by correlative studies from a wide range of taxa. Given that reptile colonization of manipulated outcrops occurred rapidly, artificially opening the canopy in ecologically informed ways could help to conserve imperiled species with patchy distributions and low vagility that are threatened by vegetation overgrowth. One such species is Australia's most endangered snake, the broadheaded snake (Hoplocephalus bungaroides).

  9. Downstream impacts of dams: shifts in benthic invertivorous fish assemblages

    Science.gov (United States)

    Granzotti, Rafaela Vendrametto; Miranda, Leandro E.; Agostinho, Angelo A.; Gomes, Luiz Carlos

    2018-01-01

    Impoundments alter connectivity, sediment transport and water discharge in rivers and floodplains, affecting recruitment, habitat and resource availability for fish including benthic invertivorous fish, which represent an important link between primary producers and higher trophic levels in tropical aquatic ecosystems. We investigated long-term changes to water regime, water quality, and invertivorous fish assemblages pre and post impoundment in three rivers downstream of Porto Primavera Reservoir in south Brazil: Paraná, Baía and Ivinhema rivers. Impacts were distinct in the Paraná River, which is fully obstructed by the dam, less evident in the Baía River which is partially obstructed by the dam, but absent in the unimpounded Ivinhema River. Changes in water regime were reflected mainly as changes in water-level fluctuation with little effect on timing. Water transparency increased in the Paraná River post impoundment but did not change in the Baía and Ivinhema rivers. Changes in fish assemblages included a decrease in benthic invertivorous fish in the Paraná River and a shift in invertivorous fish assemblage structure in the Baía and Paraná rivers but not in the unimpounded Ivinhema River. Changes in water regime and water transparency, caused by impoundment, directly or indirectly impacted invertivorous fish assemblages. Alterations of fish assemblages following environmental changes have consequences over the entire ecosystem, including a potential decrease in the diversity of mechanisms for energy flow. We suggest that keeping existing unimpounded tributaries free of dams, engineering artificial floods, and intensive management of fish habitat within the floodplain may preserve native fish assemblages and help maintain functionality and ecosystem services in highly impounded rivers.

  10. Ichthyoplankton assemblage structure of springs in the Yangtze Estuary revealed by biological and environmental visions.

    Science.gov (United States)

    Zhang, Hui; Xian, Weiwei; Liu, Shude

    2015-01-01

    The ichthyoplankton assemblage structure in the Yangtze Estuary was analyzed based on four springs in 1999, 2001, 2004 and 2007 in order to provide detailed characterizations of the ichthyoplankton assemblage in springs, examine the long-term dynamics of spring ichthyoplankton assemblages, and evaluate the influence of environmental factors on the spatial distribution and inter-annual variations of ichthyoplankton assemblages associated with the Yangtze Estuary. Forty-two ichthyoplankton species belonging to 23 families were collected. Engraulidae was the most abundant family, including six species and comprising 67.91% of the total catch. Only four species (Coilia mystus, Engraulis japonicus, Trachidermis fasciatus and Allanetta bleekeri) could be considered dominant, accounting for 88.70% of total abundance. The structure of the ichthyoplankton spring assemblage persisted on an annual basis, with the dominant species reappearing consistently even though their abundance fluctuated from year to year. This inter-annual variation probably reflects variable environmental conditions influenced by jellyfish blooms, declining river flow, and overfishing. Canonical correspondence analysis indicated aspatial structure of the ichthyoplankton assemblage in three areas: (1) an inner assemblage dominated by C. mystus; (2) a central assemblage dominated by A. bleekeri and T. fasciatus; and (3) a shelf assemblage featuring E. japonicus. The observed ichthyoplankton assemblage structure appears to be strongly influenced by depth, salinity and suspended particulate matter gradients.

  11. Natural habitats matter: Determinants of spatial pattern in the composition of animal assemblages of the Czech Republic

    Czech Academy of Sciences Publication Activity Database

    Divíšek, Jan; Zelený, D.; Culek, M.; Šťastný, K.

    2014-01-01

    Roč. 59, August 2014 (2014), s. 7-17 ISSN 1146-609X Institutional support: RVO:68145535 Keywords : animal assemblages * habitat mapping * spatial autocorrelation * CORINE Land Cover * Moran's eigenvector maps Subject RIV: DE - Earth Magnetism, Geodesy, Geography Impact factor: 1.617, year: 2014 http://ac.els-cdn.com/S1146609X14000617/1-s2.0-S1146609X14000617-main.pdf?_tid=209d34aa-3809-11e4-832a-00000aab0f01&acdnat=1410257438_9d3ff4b5ec62fd44054f111493753231

  12. Bacterial community succession in pine-wood decomposition

    Directory of Open Access Journals (Sweden)

    Anna eKielak

    2016-03-01

    Full Text Available Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

  13. Benthic Macroinvertebrate Assemblages in the Near Coastal Zone of Lake Erie

    Science.gov (United States)

    Benthic macroinvertebrate assemblages have been used as indicators of ecological condition because their responses integrate localized environmental conditions of the sediments and overlying water. Assemblages of benthic invertebrates in the near coastal region are of particular...

  14. Changing bee and hoverfly pollinator assemblages along an urban-rural gradient.

    Directory of Open Access Journals (Sweden)

    Adam J Bates

    Full Text Available The potential for reduced pollination ecosystem service due to global declines of bees and other pollinators is cause for considerable concern. Habitat degradation, destruction and fragmentation due to agricultural intensification have historically been the main causes of this pollinator decline. However, despite increasing and accelerating levels of global urbanization, very little research has investigated the effects of urbanization on pollinator assemblages. We assessed changes in the diversity, abundance and species composition of bee and hoverfly pollinator assemblages in urban, suburban, and rural sites across a UK city.Bees and hoverflies were trapped and netted at 24 sites of similar habitat character (churchyards and cemeteries that varied in position along a gradient of urbanization. Local habitat quality (altitude, shelter from wind, diversity and abundance of flowers, and the broader-scale degree of urbanization (e.g. percentage of built landscape and gardens within 100 m, 250 m, 500 m, 1 km, and 2.5 km of the site were assessed for each study site. The diversity and abundance of pollinators were both significantly negatively associated with higher levels of urbanization. Assemblage composition changed along the urbanization gradient with some species positively associated with urban and suburban land-use, but more species negatively so. Pollinator assemblages were positively affected by good site habitat quality, in particular the availability of flowering plants.Our results show that urban areas can support diverse pollinator assemblages, but that this capacity is strongly affected by local habitat quality. Nonetheless, in both urban and suburban areas of the city the assemblages had fewer individuals and lower diversity than similar rural habitats. The unique development histories of different urban areas, and the difficulty of assessing mobile pollinator assemblages in just part of their range, mean that complementary studies in

  15. The Liana assemblage of a Congolian rainforest : diversity, structure and dynamics

    NARCIS (Netherlands)

    Ewango Ekokinya, Corneille

    2010-01-01

    Key words: Liana assemblage, species composition, community, dynamics, canopy openness, Manniophyton fulvum, functional traits, population density, pervasive change.

    This study analyzes the diversity, composition, and dynamics of the liana assemblage of the Ituri rain forest in

  16. Growh performance, nitrogen balance and urinary purine derivatives in growing-furring mink (Mustela vison) fed bacterial protein produced from natural gas

    DEFF Research Database (Denmark)

    Ahlstrøm, Ø.; Tauson, Anne-Helene; Hellwing, Anne Louise Frydendahl

    2006-01-01

    A bacterial protein meal (BPM), containing 70% crude protein and produced on natural gas, was evaluated versus fish meal as protein source for mink in the growing-furring period (June 29-November 26). BPM, rich in nucleic acids, accounted for 0 (control), 20 and 40% of dietary crude protein...

  17. Settlement performance of the Mediterranean reef-builders Dendropoma cristatum (Biondi 1859) in response to natural bacterial films.

    Science.gov (United States)

    La Marca, Emanuela Claudia; Catania, Valentina; Quatrini, Paola; Milazzo, Marco; Chemello, Renato

    2018-06-01

    The gastropod Dendropoma cristatum is a biogenic engineer of the central Mediterranean, forming reefs along the lower rocky intertidal fringe with a remarkable ecological role. To understand whether reef-associated biofilm cultivable bacterial and biofilm ageing may trigger the settlement of the juvenile snails, a combination of laboratory techniques and field experiments was used. Reef-associated biofilm cultivable bacteria were isolated, and a settlement-choice experiment was performed in situ on artificial biofilms composed of i) a mixture of six biofilm-forming selected isolates, ii) all the cultivable bacteria, and iii) 13-, 23-, 32-day old biofilms formed under natural conditions. Overall, settlement rate significantly differed among biofilm treatments (p < 0.0001). A significant positive correlation between biofilm ageing and juvenile D. cristatum settlement was assessed (r = 0.69 (p < 0.001), whereas the biofilm bacterial composition (relatively to the cultivable fraction) did not show any effect on the vermetid's settlement rate. Copyright © 2018. Published by Elsevier Ltd.

  18. Growth performance and carcase quality in broiler chickens fed on bacterial protein grown on natural gas.

    Science.gov (United States)

    Øverland, M; Schøyen, H F; Skrede, A

    2010-10-01

    1. The effects of increasing concentrations (0, 40, 80 or 120 g/kg) of bacterial protein meal (BPM) and bacterial protein autolysate (BPA) grown on natural gas on growth performance and carcase quality in broiler chickens were examined. 2. Adding BPM to diets reduced feed intake and improved gain: feed from 0 to 21 d and overall to 35 d, but did not significantly affect weight gain compared to the soybean meal based control diet. 3. Increasing concentrations of BPA significantly reduced growth rate, feed intake, gain: feed, carcase weight and dressing percentage, but significantly increased carcase dry matter, fat and energy content. 4. Adding BPM to diets had no effect on viscosity of diets and jejunal digesta, and minor effects on litter quality, whereas BPA increased the viscosity of diets and jejunal digesta, improved litter quality at 21 d, but decreased litter quality at 32 d. 5. To conclude, broiler chickens performed better on a BPM product with intact proteins than on an autolysate with ruptured cell walls and a high content of free amino acids and low molecular-weight peptides.

  19. Microhabitat influence on larval fish assemblages within ...

    Science.gov (United States)

    We examined larval and juvenile fish assemblage structure in relation to microhabitat variables within the St. Louis River estuary, a drowned river mouth of Lake Superior. Fish were sampled in vegetated beds throughout the estuary, across a gradient of vegetation types and densities (including disturbed, preserved and post-restoration sites). Canonical correspondence analysis, relating species abundances to environmental variables revealed that plant species richness, turbidity and aquatic plant cover were most influential in structuring assemblages. Results from this microhabitat analysis at this crucial life stage has potential to inform wetland restoration efforts within the St. Louis River and other Great Lake coastal wetlands. not applicable

  20. Groundwater declines are linked to changes in Great Plains stream fish assemblages.

    Science.gov (United States)

    Perkin, Joshuah S; Gido, Keith B; Falke, Jeffrey A; Fausch, Kurt D; Crockett, Harry; Johnson, Eric R; Sanderson, John

    2017-07-11

    Groundwater pumping for agriculture is a major driver causing declines of global freshwater ecosystems, yet the ecological consequences for stream fish assemblages are rarely quantified. We combined retrospective (1950-2010) and prospective (2011-2060) modeling approaches within a multiscale framework to predict change in Great Plains stream fish assemblages associated with groundwater pumping from the United States High Plains Aquifer. We modeled the relationship between the length of stream receiving water from the High Plains Aquifer and the occurrence of fishes characteristic of small and large streams in the western Great Plains at a regional scale and for six subwatersheds nested within the region. Water development at the regional scale was associated with construction of 154 barriers that fragment stream habitats, increased depth to groundwater and loss of 558 km of stream, and transformation of fish assemblage structure from dominance by large-stream to small-stream fishes. Scaling down to subwatersheds revealed consistent transformations in fish assemblage structure among western subwatersheds with increasing depths to groundwater. Although transformations occurred in the absence of barriers, barriers along mainstem rivers isolate depauperate western fish assemblages from relatively intact eastern fish assemblages. Projections to 2060 indicate loss of an additional 286 km of stream across the region, as well as continued replacement of large-stream fishes by small-stream fishes where groundwater pumping has increased depth to groundwater. Our work illustrates the shrinking of streams and homogenization of Great Plains stream fish assemblages related to groundwater pumping, and we predict similar transformations worldwide where local and regional aquifer depletions occur.

  1. A kinetic study of cation release from a mixed mineral assemblage: implications for determination of uranium uptake

    International Nuclear Information System (INIS)

    Fenton, B.R.; Waite, T.D.

    1996-01-01

    The uptake of U(VI) as UO 2+ 2 on a natural complex mineral assemblage has been studied using batch selective chemical extraction techniques and secondary ion mass spectroscopy (SIMS). Sediments used in the study consisted of a quartz/mica schist collected from the locale of the Koongarra Uranium ore body, Alligator Rivers Uranium Province, Northern Territory, Australia. The bulk sediment was gravity separated into four size fractions, with attention focused on the nominally <25 μm and 250-1000 μm fractions of the bulk sample, in order to assess the effects of particle size on uranium uptake. Investigation of the kinetics of elemental release in the presence of selective extractants show that uranium is bound largely within the iron and aluminium oxyhydroxides of the assemblage, with a highly mobile fraction of this associated with aluminol sites. SIMS analysis of the natural substrate confirms that significant quantities of aluminium are present in surface layers. The effect of particle size on the uptake of uranium indicates very little change with respect to particle size. This finding may be attributed to the presence of highly porous surface coatings. (orig.)

  2. Effects of energy related activities on the plankton of the Chesapeake Bay. Section I. Work in progress. Progress report, 1 August 1975--31 July 1976

    International Nuclear Information System (INIS)

    Taft, J.L.

    1976-01-01

    Progress is reported on the following research projects: release of dissolved organic carbon by phytoplankton; plankton respiration and nutrient regeneration; bacterial utilization of labeled compounds; effects of heat and chlorine on natural assemblages of Chesapeake Bay phytoplankton; and nutrient flux between sediment and water

  3. Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages

    KAUST Repository

    Lescot, Magali

    2015-11-27

    Genes encoding reverse transcriptases (RTs) are found in most eukaryotes, often as a component of retrotransposons, as well as in retroviruses and in prokaryotic retroelements. We investigated the abundance, classification and transcriptional status of RTs based on Tara Oceans marine metagenomes and metatranscriptomes encompassing a wide organism size range. Our analyses revealed that RTs predominate large-size fraction metagenomes (>5 μm), where they reached a maximum of 13.5% of the total gene abundance. Metagenomic RTs were widely distributed across the phylogeny of known RTs, but many belonged to previously uncharacterized clades. Metatranscriptomic RTs showed distinct abundance patterns across samples compared with metagenomic RTs. The relative abundances of viral and bacterial RTs among identified RT sequences were higher in metatranscriptomes than in metagenomes and these sequences were detected in all metatranscriptome size fractions. Overall, these observations suggest an active proliferation of various RT-assisted elements, which could be involved in genome evolution or adaptive processes of plankton assemblage.

  4. Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages

    KAUST Repository

    Lescot, Magali; Hingamp, Pascal; Kojima, Kenji K; Villar, Emilie; Romac, Sarah; Veluchamy, Alaguraj; Boccara, Martine; Jaillon, Olivier; Ludicone, Daniele; Bowler, Chris; Wincker, Patrick; Claverie, Jean-Michel; Ogata, Hiroyuki

    2015-01-01

    Genes encoding reverse transcriptases (RTs) are found in most eukaryotes, often as a component of retrotransposons, as well as in retroviruses and in prokaryotic retroelements. We investigated the abundance, classification and transcriptional status of RTs based on Tara Oceans marine metagenomes and metatranscriptomes encompassing a wide organism size range. Our analyses revealed that RTs predominate large-size fraction metagenomes (>5 μm), where they reached a maximum of 13.5% of the total gene abundance. Metagenomic RTs were widely distributed across the phylogeny of known RTs, but many belonged to previously uncharacterized clades. Metatranscriptomic RTs showed distinct abundance patterns across samples compared with metagenomic RTs. The relative abundances of viral and bacterial RTs among identified RT sequences were higher in metatranscriptomes than in metagenomes and these sequences were detected in all metatranscriptome size fractions. Overall, these observations suggest an active proliferation of various RT-assisted elements, which could be involved in genome evolution or adaptive processes of plankton assemblage.

  5. Benthic foraminifera baseline assemblages from a coastal nearshore reef complex on the central Great Barrier Reef

    Science.gov (United States)

    Johnson, Jamie; Perry, Chris; Smithers, Scott; Morgan, Kyle

    2016-04-01

    Declining water quality due to river catchment modification since European settlement (c. 1850 A.D.) represents a major threat to the health of coral reefs on Australia's Great Barrier Reef (GBR), particularly for those located in the coastal waters of the GBR's inner-shelf. These nearshore reefs are widely perceived to be most susceptible to declining water quality owing to their close proximity to river point sources. Despite this, nearshore reefs have been relatively poorly studied with the impacts and magnitudes of environmental degradation still remaining unclear. This is largely due to ongoing debates concerning the significance of increased sediment yields against naturally high background sedimentary regimes. Benthic foraminifera are increasingly used as tools for monitoring environmental and ecological change on coral reefs. On the GBR, the majority of studies have focussed on the spatial distributions of contemporary benthic foraminiferal assemblages. While baseline assemblages from other environments (e.g. inshore reefs and mangroves) have been described, very few records exist for nearshore reefs. Here, we present preliminary results from the first palaeoecological study of foraminiferal assemblages of nearshore reefs on the central GBR. Cores were recovered from the nearshore reef complex at Paluma Shoals using percussion techniques. Recovery was 100%, capturing the entire Holocene reef sequence of the selected reef structures. Radiocarbon dating and subsequent age-depth modelling techniques were used to identify reef sequences pre-dating European settlement. Benthic foraminifera assemblages were reconstructed from the identified sequences to establish pre-European ecological baselines with the aim of providing a record of foraminiferal distribution during vertical reef accretion and against which contemporary ecological change may be assessed.

  6. Time-averaged molluscan death assemblages: Palimpsests of richness, snapshots of abundance

    Science.gov (United States)

    Kidwell, Susan M.

    2002-09-01

    Field tests that compare living communities to associated dead remains are the primary means of estimating the reliability of biological information in the fossil record; such tests also provide insights into the dynamics of skeletal accumulation. Contrary to expectations, molluscan death assemblages capture a strong signal of living species' rank-order abundances. This finding, combined with independent evidence for exponential postmortem destruction of dead cohorts, argues that, although the species richness of a death assemblage may be a time-averaged palimpsest of the habitat (molluscan death assemblages contain, on average, ˜25% more species than any single census of the local live community, after sample-size standardization), species' relative-abundance data from the same assemblage probably constitute a much higher acuity record dominated by the most recent dead cohorts (e.g., from the past few hundred years or so, rather than the several thousand years recorded by the total assemblage and usually taken as the acuity of species-richness information). The pervasive excess species richness of molluscan death assemblages requires further analysis and modeling to discriminate among possible sources. However, time averaging alone cannot be responsible unless rare species (species with low rates of dead-shell production) are collectively more durable (have longer taphonomic half-lives) than abundant species. Species richness and abundance data thus appear to present fundamentally different taphonomic qualities for paleobiological analysis. Relative- abundance information is more snapshot-like and thus taphonomically more straightforward than expected, especially compared to the complex origins of dead-species richness.

  7. Long-Term Bird Assemblage Trends in Areas of High and Low Human Population Density

    International Nuclear Information System (INIS)

    Barrett, K.; Romagosa, C.M.; Williams, M.I.

    2008-01-01

    Urban areas are expanding globally, and the impact of high human population density (HHPD) on bird species richness remains unresolved. Studies primarily focus on species richness along an urban-to-rural gradient; however, some studies have analyzed larger-scale patterns and found results that contrast with those obtained at smaller scales. To move the discussion beyond static species richness patterns, we analyzed the effect of HHPD on bird assemblage dynamics (year-to-year extinction probability, turnover, changes in species richness) across the United States over a 25-year period. We found that bird assemblages in both high and low human population density areas changed significantly over the period of record. Specifically, bird assemblages increased in species richness on average. Assemblage change in areas of HHPD was not significantly different from assemblage change in areas with LHPD. These results suggest that human population density alone does not alter the persistence of avian assemblage patterns.

  8. Public sphere as assemblage: the cultural politics of roadside memorialization.

    Science.gov (United States)

    Campbell, Elaine

    2013-09-01

    This paper investigates contemporary academic accounts of the public sphere. In particular, it takes stock of post-Habermasian public sphere scholarship, and acknowledges a lively and variegated debate concerning the multiple ways in which individuals engage in contemporary political affairs. A critical eye is cast over a range of key insights which have come to establish the parameters of what 'counts' as a/the public sphere, who can be involved, and where and how communicative networks are established. This opens up the conceptual space for re-imagining a/the public sphere as an assemblage. Making use of recent developments in Deleuzian-inspired assemblage theory - most especially drawn from DeLanda's (2006) 'new philosophy of society' - the paper sets out an alternative perspective on the notion of the public sphere, and regards it as a space of connectivity brought into being through a contingent and heterogeneous assemblage of discursive, visual and performative practices. This is mapped out with reference to the cultural politics of roadside memorialization. However, a/the public sphere as an assemblage is not simply a 'social construction' brought into being through a logic of connectivity, but is an emergent and ephemeral space which reflexively nurtures and assembles the cultural politics (and political cultures) of which it is an integral part. The discussion concludes, then, with a consideration of the contribution of assemblage theory to public sphere studies. (Also see Campbell 2009a). © London School of Economics and Political Science 2013.

  9. Hydrogen limitation and syntrophic growth among natural assemblages of thermophilic methanogens at deep-sea hydrothermal vents

    Directory of Open Access Journals (Sweden)

    Begüm D. Topçuoğlu

    2016-08-01

    Full Text Available Thermophilic methanogens are common autotrophs at hydrothermal vents, but their growth constraints and dependence on H2 syntrophy in situ are poorly understood. Between 2012 and 2015, methanogens and H2-producing heterotrophs were detected by growth at 80°C and 55°C at most diffuse (7-40°C hydrothermal vent sites at Axial Seamount. Microcosm incubations of diffuse hydrothermal fluids at 80°C and 55°C demonstrated that growth of thermophilic and hyperthermophilic methanogens is primarily limited by H2 availability. Amendment of microcosms with NH4+ generally had no effect on CH4 production. However, annual variations in abundance and CH4 production were observed in relation to the eruption cycle of the seamount. Microcosm incubations of hydrothermal fluids at 80°C and 55°C supplemented with tryptone and no added H2 showed CH4 production indicating the capacity in situ for methanogenic H2 syntrophy. 16S rRNA genes were found in 80°C microcosms from H2-producing archaea and H2-consuming methanogens, but not for any bacteria. In 55°C microcosms, sequences were found from the H2-producing bacteria and H2-consuming methanogens and sulfate-reducing bacteria. A co-culture of representative organisms showed that Thermococcus paralvinellae supported the syntrophic growth of Methanocaldococcus bathoardescens at 82°C and Methanothermococcus sp. strain BW11 at 60°C. The results demonstrate that modeling of subseafloor methanogenesis should focus primarily on H2 availability and temperature, and that thermophilic H2 syntrophy can support methanogenesis within natural microbial assemblages and may be an important energy source for thermophilic autotrophs in marine geothermal environments.

  10. Rare species contribute disproportionately to the functional structure of species assemblages.

    Science.gov (United States)

    Leitão, Rafael P; Zuanon, Jansen; Villéger, Sébastien; Williams, Stephen E; Baraloto, Christopher; Fortunel, Claire; Mendonça, Fernando P; Mouillot, David

    2016-04-13

    There is broad consensus that the diversity of functional traits within species assemblages drives several ecological processes. It is also widely recognized that rare species are the first to become extinct following human-induced disturbances. Surprisingly, however, the functional importance of rare species is still poorly understood, particularly in tropical species-rich assemblages where the majority of species are rare, and the rate of species extinction can be high. Here, we investigated the consequences of local and regional extinctions on the functional structure of species assemblages. We used three extensive datasets (stream fish from the Brazilian Amazon, rainforest trees from French Guiana, and birds from the Australian Wet Tropics) and built an integrative measure of species rarity versus commonness, combining local abundance, geographical range, and habitat breadth. Using different scenarios of species loss, we found a disproportionate impact of rare species extinction for the three groups, with significant reductions in levels of functional richness, specialization, and originality of assemblages, which may severely undermine the integrity of ecological processes. The whole breadth of functional abilities within species assemblages, which is disproportionately supported by rare species, is certainly critical in maintaining ecosystems particularly under the ongoing rapid environmental transitions. © 2016 The Author(s).

  11. Fish assemblage structure and relations with environmental conditions in a Rocky Mountain watershed

    Science.gov (United States)

    Quist, M.C.; Hubert, W.A.; Isaak, D.J.

    2004-01-01

    Fish and habitat were sampled from 110 reaches in the Salt River basin (Idaho and Wyoming) during 1996 and 1997 to assess patterns in fish assemblage structure across a Rocky Mountain watershed. We identified four distinct fish assemblages using cluster analysis: (1) allopatric cutthroat trout (Oncorhynchus clarki (Richardson, 1836)); (2) cutthroat trout - brook trout (Salvelinus fontinalis (Mitchell, 1814)) - Paiute sculpin (Cottus beldingi Eigenmann and Eigenmann, 1891); (3) cutthroat trout - brown trout (Salmo trutta L., 1758) - mottled sculpin (Cottus bairdi Girard, 1850); and (4) Cyprinidae-Catostomidae. The distribution of fish assemblages was explained by thermal characteristics, stream geomorphology, and local habitat features. Reaches with allopatric cutthroat trout and the cutthroat trout - brook trout - Paiute sculpin assemblage were located in high-elevation, high-gradient streams. The other two fish assemblages were generally located in low-elevation streams. Associations between habitat gradients, locations of reaches in the watershed, and occurrence of species were further examined using canonical correspondence analysis. The results suggest that stream geomorphology, thermal conditions, and local habitat characteristics influence fish assemblage structure across a Rocky Mountain watershed, and they provide information on the ecology of individual species that can guide conservation activities. ?? 2004 NRC Canada.

  12. Determinism in fish assemblages of floodplain lakes of the vastly disturbed Mississippi Alluvial Valley

    Science.gov (United States)

    Miranda, L.E.; Lucas, G.M.

    2004-01-01

    The Mississippi Alluvial Valley between southern Illinois and southern Louisiana contains hundreds of floodplain lakes, most of which have been adversely affected by landscape modifications used to control flooding and support agriculture. We examined fish assemblages in lakes of this region to determine whether deterministic patterns developed in relation to prominent abiotic lake characteristics and to explore whether relevant abiotic factors could be linked to specific assemblage structuring mechanisms. The distributions of 14 taxa in 29 lakes were governed primarily by two gradients that contrasted assemblages in terms of lake area, lake elongation, and water clarity. The knowledge of whether a lake was clear or turbid, large or small, and long or short helped determine fish assemblage characteristics. Abiotic factors influenced fish assemblage structures, plausibly through limitations on foraging and physiological tolerances. Determinism in assemblage organization of floodplain lakes relative to recurrence in physicochemical features has been documented for unaltered rivers. Whereas the Mississippi Alluvial Valley has been subjected to vast anthropogenic disturbances and is not a fully functional floodplain river, fish assemblages in its floodplain lakes remain deterministic and organized by the underlying factors that also dictate assemblages in unaltered rivers. In advanced stages of lake aging, fish assemblages in these lakes are expected to largely include species that thrive in turbid, shallow systems with few predators and low oxygen concentrations. The observed patterns related to physical characteristics of these lakes suggest three general conservation foci, including (1) watershed management to control erosion, (2) removal of sediments or increases in water level to alleviate depth reductions and derived detriments to water physicochemistry, and (3) management of fish populations through stockings, removals, and harvest regulations.

  13. TNT Degradation by Natural Microbial Assemblages at Frontal Boundaries Between Water Masses in Coastal Ecosystems (ER-2124 Interim Report)

    Science.gov (United States)

    2014-06-26

    Tuominen, L. 1995. Comparison of leucine uptake methods and a thymidine incorporation method for measuring bacterial activity in sediment. J...measuring TNT incorporation rates into bacterial DNA using sediment samples. By seasonally repeating these survey measurements and mixing experiments...of days to months (e.g., PAHs; Boyd et al. 2008). TNT ring carbon is incorporated into bacterial macromolecules at rates in water that are 10-100

  14. Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea

    Science.gov (United States)

    Zhang, Yao; Zhao, Zihao; Dai, Minhan; Jiao, Nianzhi; Herndl, Gerhard J

    2014-01-01

    To test the hypothesis that different drivers shape the diversity and biogeography of the total and active bacterial community, we examined the bacterial community composition along two transects, one from the inner Pearl River estuary to the open waters of the South China Sea (SCS) and the other from the Luzon Strait to the SCS basin, using 454 pyrosequencing of the 16S rRNA and 16S rRNA gene (V1-3 regions) and thereby characterizing the active and total bacterial community, respectively. The diversity and biogeographic patterns differed substantially between the active and total bacterial communities. Although the composition of both the total and active bacterial community was strongly correlated with environmental factors and weakly correlated with geographic distance, the active bacterial community displayed higher environmental sensitivity than the total community and particularly a greater distance effect largely caused by the active assemblage from deep waters. The 16S rRNA vs. rDNA relationships indicated that the active bacteria were low in relative abundance in the SCS. This might be due to a high competition between active bacterial taxa as indicated by our community network models. Based on these analyses, we speculate that high competition could cause some dispersal limitation of the active bacterial community resulting in a distinct distance-decay relationship. Altogether, our results indicated that the biogeographic distribution of bacteria in the SCS is the result of both environmental control and distance decay. PMID:24684298

  15. Mangrove removal in the belize cays: effects on mangrove-associated fish assemblages in the intertidal and subtidal

    Science.gov (United States)

    Taylor, D.S.; Reyier, E.A.; Davis, W.P.; McIvor, C.C.

    2007-01-01

    We investigated the effects of mangrove cutting on fish assemblages in Twin Cays, Belize, in two habitat types. We conducted visual censuses at two sites in adjoining undisturbed/disturbed (30%–70% of shoreline fringe removed) sub-tidal fringing Rhizophora mangle Linnaeus, 1753. Observers recorded significantly more species and individuals in undisturbed sites, especially among smaller, schooling species (e.g., atherinids, clupeids), where densities were up to 200 times greater in undisturbed habitat. Multivariate analyses showed distinct species assemblages between habitats at both sites. In addition, extensive trapping with wire minnow traps within the intertidal zone in both undisturbed and disturbed fringing and transition (landward) mangrove forests was conducted. Catch rates were low: 638 individuals from 24 species over 563 trap-nights. Trap data, however, indicated that mangrove disturbance had minimal effect on species composition in either forest type (fringe/transition). Different results from the two methods (and habitat types) may be explained by two factors: (1) a larger and more detectable species pool in the subtidal habitat, with visual "access" to all species, and (2) the selective nature of trapping. Our data indicate that even partial clearing of shoreline and more landward mangroves can have a significant impact on local fish assemblages.

  16. Assessment of bacterial diversity in the cattle tick Rhipicephalus (Boophilus microplus through tag-encoded pyrosequencing

    Directory of Open Access Journals (Sweden)

    Bendele Kylie G

    2011-01-01

    Full Text Available Abstract Background Ticks are regarded as the most relevant vectors of disease-causing pathogens in domestic and wild animals. The cattle tick, Rhipicephalus (Boophilus microplus, hinders livestock production in tropical and subtropical parts of the world where it is endemic. Tick microbiomes remain largely unexplored. The objective of this study was to explore the R. microplus microbiome by applying the bacterial 16S tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP technique to characterize its bacterial diversity. Pyrosequencing was performed on adult males and females, eggs, and gut and ovary tissues from adult females derived from samples of R. microplus collected during outbreaks in southern Texas. Results Raw data from bTEFAP were screened and trimmed based upon quality scores and binned into individual sample collections. Bacteria identified to the species level include Staphylococcus aureus, Staphylococcus chromogenes, Streptococcus dysgalactiae, Staphylococcus sciuri, Serratia marcescens, Corynebacterium glutamicum, and Finegoldia magna. One hundred twenty-one bacterial genera were detected in all the life stages and tissues sampled. The total number of genera identified by tick sample comprised: 53 in adult males, 61 in adult females, 11 in gut tissue, 7 in ovarian tissue, and 54 in the eggs. Notable genera detected in the cattle tick include Wolbachia, Coxiella, and Borrelia. The molecular approach applied in this study allowed us to assess the relative abundance of the microbiota associated with R. microplus. Conclusions This report represents the first survey of the bacteriome in the cattle tick using non-culture based molecular approaches. Comparisons of our results with previous bacterial surveys provide an indication of geographic variation in the assemblages of bacteria associated with R. microplus. Additional reports on the identification of new bacterial species maintained in nature by R. microplus that may be

  17. Assessment of bacterial diversity in the cattle tick Rhipicephalus (Boophilus) microplus through tag-encoded pyrosequencing

    Science.gov (United States)

    2011-01-01

    Background Ticks are regarded as the most relevant vectors of disease-causing pathogens in domestic and wild animals. The cattle tick, Rhipicephalus (Boophilus) microplus, hinders livestock production in tropical and subtropical parts of the world where it is endemic. Tick microbiomes remain largely unexplored. The objective of this study was to explore the R. microplus microbiome by applying the bacterial 16S tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP) technique to characterize its bacterial diversity. Pyrosequencing was performed on adult males and females, eggs, and gut and ovary tissues from adult females derived from samples of R. microplus collected during outbreaks in southern Texas. Results Raw data from bTEFAP were screened and trimmed based upon quality scores and binned into individual sample collections. Bacteria identified to the species level include Staphylococcus aureus, Staphylococcus chromogenes, Streptococcus dysgalactiae, Staphylococcus sciuri, Serratia marcescens, Corynebacterium glutamicum, and Finegoldia magna. One hundred twenty-one bacterial genera were detected in all the life stages and tissues sampled. The total number of genera identified by tick sample comprised: 53 in adult males, 61 in adult females, 11 in gut tissue, 7 in ovarian tissue, and 54 in the eggs. Notable genera detected in the cattle tick include Wolbachia, Coxiella, and Borrelia. The molecular approach applied in this study allowed us to assess the relative abundance of the microbiota associated with R. microplus. Conclusions This report represents the first survey of the bacteriome in the cattle tick using non-culture based molecular approaches. Comparisons of our results with previous bacterial surveys provide an indication of geographic variation in the assemblages of bacteria associated with R. microplus. Additional reports on the identification of new bacterial species maintained in nature by R. microplus that may be pathogenic to its vertebrate hosts

  18. Here Comes the Sun ... and I Say, "It' an Assemblage"

    Science.gov (United States)

    Skophammer, Karen

    2011-01-01

    In this article, the author discusses how she combines science lesson with a hands-on art project. She used the wonderfully creative suns shown on the Sunday edition of "The CBS Morning Show" to give the students fodder for thought. She describes how to create an assemblage. An assemblage is like a collage, but it moves past the two-dimensional…

  19. Mesh size effects on assessments of planktonic hydrozoan abundance and assemblage structure

    Science.gov (United States)

    Nogueira Júnior, Miodeli; Pukanski, Luis Eduardo de M.; Souza-Conceição, José M.

    2015-04-01

    The choice of appropriate mesh-size is paramount to accurately quantify planktonic assemblages, however there is no such information available for hydrozoans. Here planktonic hydrozoan abundance and assemblage structure were compared using 200 and 500 μm meshes at Babitonga estuary (S Brazil), throughout a year cycle. Species richness and Shannon-Wiener diversity were higher in the 200 μm mesh, while evenness was typically higher in the 500 μm. Assemblage structure was significantly different between meshes (PERMANOVA, P 8 mm in October. These results suggest that both meshes have their drawbacks and the best choice would depend on the objectives of each study. Nevertheless species richness, total abundances and most taxa were better represented by the 200 μm mesh, suggesting that it is more appropriate to quantitatively sample planktonic hydrozoan assemblages.

  20. Shaping up: a geometric morphometric approach to assemblage ecomorphology.

    Science.gov (United States)

    Bower, L M; Piller, K R

    2015-09-01

    This study adopts an ecomorphological approach to test the utility of body shape as a predictor of niche relationships among a stream fish assemblage of the Tickfaw River (Lake Pontchartrain Basin) in southeastern Louisiana, U.S.A. To examine the potential influence of evolutionary constraints, analyses were performed with and without the influence of phylogeny. Fish assemblages were sampled throughout the year, and ecological data (habitat and tropic guild) and body shape (geometric morphometric) data were collected for each fish specimen. Multivariate analyses were performed to examine relationships and differences between body shape and ecological data. Results indicate that a relationship exists between body shape and trophic guild as well as flow regime, but no significant correlation between body shape and substratum was found. Body shape was a reliable indicator of position within assemblage niche space. © 2015 The Fisheries Society of the British Isles.

  1. [Effects of cascading hydropower dams operation on the structure and distribution pattern of benthic macroinvertebrate assemblages in Manwan Reservoir, Southwest China].

    Science.gov (United States)

    Li, Jin Peng; Dong, Shi Kui; Peng, Ming Chun; Wu, Xuan; Zhou, Fang; Yu, Yin

    2017-12-01

    Benthic macroinvertebrate assemblages are one of the biological groups in aquatic ecosystem most sensitive to the habitat change and degradation, and can be a biological indicator for the aquatic ecosystem change and succession in cascading hydropower dam reservoir. The middle and lower reaches of the Lancang River are key spot for international biodiversity conservation and ecological studies on the effects of cascading hydropower dam exploitation. In this study, the reservoir of Manwan hydropower dam, the first dam in Lancang-Mekong river main stream, was selected as the study site. The benthic macroinvertebrate assemblages were sampled in 2011 and 2016 respectively. Meanwhile, the survey data before impounding (natural river, 1996) and early stage of single dam (1997) were collected to conduct the overall analysis for structure, distribution pattern and evolution of benthic macroinvertebrate assemblages. The results showed that the dominant biological group was gradually changed from the Oligochaeta and Insecta to the Mollusca. Along the longitudinal gradient, the density and biomass of the benthic macroinvertebrate assemblages were remarkably increased in reservoir, especially in the lacustrine zone. As for the functional feeding group, the predator and gatherer-collector changed into filter-collector predominantly in lacustrine zone. With the cascading dams operation, the biotic index indicated that the water quality of reservoir in 2016 was better than in 2011. The evolution of benthic macroinvertebrate assemblages in the Manwan Reservoir was related to the operation of Xiaowan dam in the upper reach, the hydrological regime and siltation in the reservoir, and would continue with dynamic changes with the operation of the cascading hydropower dam.

  2. C9.A/14 steelwork joints de poutres par plaque frontale : assemblages par gousset

    CERN Document Server

    2015-01-01

    Les Tables de résistances ultimes des assemblages boulonnés par plaque frontale et par gousset, complétées par une description des modèles de calcul et des exemples d’application, ont pour but de faciliter la tâche de l'ingénieur et du constructeur. Cette première partie C9.A/14 contient les chapitres suivants: - Joints de poutres par plaque frontale en acier S235 et S355 - Assemblages par gousset en acier S235 et S355 Les Tables contiennent des données relatives à la géométrie ainsi que les valeurs de calcul correspondantes des résistances ultimes des assemblages ; elles remplacent le chapitre « Assemblages par plaques frontales et boulons HR » des anciennes Tables C9.1 de 1983 / 2002. Le calcul de ces assemblages par plaque frontale est basé sur les hypothèses du modèle de la méthode des composants décrite dans la norme SN EN 1993-1-8. Les vérifications sont effectuées selon la norme SIA 263:2013. Les assemblages par gousset remplacent les assemblages par double cornière, (telle...

  3. SEXUAL DYSFUNCTION ASSOCIATION WITH THE CHRONIC BACTERIAL PROSTATITIS

    Directory of Open Access Journals (Sweden)

    H. S. Ibishev

    2013-01-01

    Full Text Available The study involved 230 patients aged 20 to 45 years with a diagnosis of chronic bacterial prostatitis. The study found that in patients with chronic bacterial prostatitis clinical picture, in addition to pain, is a lower urinary tract symptoms, neuro-vegetative and sexual dysfunction. In patients with chronic bacterial prostatitis, recorded various sexual disorders, most of which are normalized after antibiotic therapy. Erectile dysfunction, which are recorded in patients with chronic bacterial prostatitis is psychogenic in nature dysfunction.

  4. Climate mediates the effects of disturbance on ant assemblage structure

    Science.gov (United States)

    Gibb, Heloise; Sanders, Nathan J.; Dunn, Robert R.; Watson, Simon; Photakis, Manoli; Abril, Silvia; Andersen, Alan N.; Angulo, Elena; Armbrecht, Inge; Arnan, Xavier; Baccaro, Fabricio B.; Bishop, Tom R.; Boulay, Raphael; Castracani, Cristina; Del Toro, Israel; Delsinne, Thibaut; Diaz, Mireia; Donoso, David A.; Enríquez, Martha L.; Fayle, Tom M.; Feener, Donald H.; Fitzpatrick, Matthew C.; Gómez, Crisanto; Grasso, Donato A.; Groc, Sarah; Heterick, Brian; Hoffmann, Benjamin D.; Lach, Lori; Lattke, John; Leponce, Maurice; Lessard, Jean-Philippe; Longino, John; Lucky, Andrea; Majer, Jonathan; Menke, Sean B.; Mezger, Dirk; Mori, Alessandra; Munyai, Thinandavha C.; Paknia, Omid; Pearce-Duvet, Jessica; Pfeiffer, Martin; Philpott, Stacy M.; de Souza, Jorge L. P.; Tista, Melanie; Vasconcelos, Heraldo L.; Vonshak, Merav; Parr, Catherine L.

    2015-01-01

    Many studies have focused on the impacts of climate change on biological assemblages, yet little is known about how climate interacts with other major anthropogenic influences on biodiversity, such as habitat disturbance. Using a unique global database of 1128 local ant assemblages, we examined whether climate mediates the effects of habitat disturbance on assemblage structure at a global scale. Species richness and evenness were associated positively with temperature, and negatively with disturbance. However, the interaction among temperature, precipitation and disturbance shaped species richness and evenness. The effect was manifested through a failure of species richness to increase substantially with temperature in transformed habitats at low precipitation. At low precipitation levels, evenness increased with temperature in undisturbed sites, peaked at medium temperatures in disturbed sites and remained low in transformed sites. In warmer climates with lower rainfall, the effects of increasing disturbance on species richness and evenness were akin to decreases in temperature of up to 9°C. Anthropogenic disturbance and ongoing climate change may interact in complicated ways to shape the structure of assemblages, with hot, arid environments likely to be at greatest risk. PMID:25994675

  5. Relationships between structural complexity, coral traits, and reef fish assemblages

    Science.gov (United States)

    Darling, Emily S.; Graham, Nicholas A. J.; Januchowski-Hartley, Fraser A.; Nash, Kirsty L.; Pratchett, Morgan S.; Wilson, Shaun K.

    2017-06-01

    With the ongoing loss of coral cover and the associated flattening of reef architecture, understanding the links between coral habitat and reef fishes is of critical importance. Here, we investigate whether considering coral traits and functional diversity provides new insights into the relationship between structural complexity and reef fish communities, and whether coral traits and community composition can predict structural complexity. Across 157 sites in Seychelles, Maldives, the Chagos Archipelago, and Australia's Great Barrier Reef, we find that structural complexity and reef zone are the strongest and most consistent predictors of reef fish abundance, biomass, species richness, and trophic structure. However, coral traits, diversity, and life histories provided additional predictive power for models of reef fish assemblages, and were key drivers of structural complexity. Our findings highlight that reef complexity relies on living corals—with different traits and life histories—continuing to build carbonate skeletons, and that these nuanced relationships between coral assemblages and habitat complexity can affect the structure of reef fish assemblages. Seascape-level estimates of structural complexity are rapid and cost effective with important implications for the structure and function of fish assemblages, and should be incorporated into monitoring programs.

  6. Bacterial natural product biosynthetic domain composition in soil correlates with changes in latitude on a continent-wide scale.

    Science.gov (United States)

    Lemetre, Christophe; Maniko, Jeffrey; Charlop-Powers, Zachary; Sparrow, Ben; Lowe, Andrew J; Brady, Sean F

    2017-10-31

    Although bacterial bioactive metabolites have been one of the most prolific sources of lead structures for the development of small-molecule therapeutics, very little is known about the environmental factors associated with changes in secondary metabolism across natural environments. Large-scale sequencing of environmental microbiomes has the potential to shed light on the richness of bacterial biosynthetic diversity hidden in the environment, how it varies from one environment to the next, and what environmental factors correlate with changes in biosynthetic diversity. In this study, the sequencing of PCR amplicons generated using primers targeting either ketosynthase domains from polyketide biosynthesis or adenylation domains from nonribosomal peptide biosynthesis was used to assess biosynthetic domain composition and richness in soils collected across the Australian continent. Using environmental variables collected at each soil site, we looked for environmental factors that correlated with either high overall domain richness or changes in the domain composition. Among the environmental variables we measured, changes in biosynthetic domain composition correlate most closely with changes in latitude and to a lesser extent changes in pH. Although it is unclear at this time the exact mix of factors that may drive the relationship between biosynthetic domain composition and latitude, from a practical perspective the identification of a latitudinal basis for differences in soil metagenome biosynthetic domain compositions should help guide future natural product discovery efforts. Published under the PNAS license.

  7. [Bacterial biofilms as a natural form of existence of bacteria in the environment and host organism].

    Science.gov (United States)

    Romanova, Iu M; Gintsburg, A L

    2011-01-01

    Advances in microscopic analysis and molecular genetics research methods promoted the acquisition of evidence that natural bacteria populations exist predominately as substrate attached biofilms. Bacteria in biofilms are able to exchange signals and display coordinated activity that is inherent to multicellular organisms. Formation of biofilm communities turned out to be one of the main survival strategies of bacteria in their ecological niche. Bacteria in attached condition in biofilm are protected from the environmental damaging factors and effects of antibacterial substances in the environment and host organism during infection. According to contemporary conception, biofilm is a continuous layer of bacterial cells that are attached to a surface and each other, and contained in a biopolymer matrix. Such bacterial communities may be composed of bacteria of one or several species, and composed of actively functioning cells as well as latent and uncultured forms. Particular attention has recently been paid to the role of biofilms in the environment and host organism. Microorganisms form biofilm on any biotic and abiotic surfaces which creates serious problems in medicine and various areas of economic activity. Currently, it is established that biofilms are one of the pathogenetic factors of chronic inflection process formation. The review presents data on ubiquity of bacteria existence as biofilms, contemporary methods of microbial community analysis, structural-functional features of bacterial biofilms. Particular attention is paid to the role of biofilm in chronic infection process formation, heightened resistance to antibiotics of bacteria in biofilms and possible mechanisms of resistance. Screening approaches for agents against biofilms in chronic infections are discussed.

  8. Reef fish and coral assemblages at Maptaput, Rayong Province

    Directory of Open Access Journals (Sweden)

    Voravit Cheevaporn

    2007-06-01

    Full Text Available This study describes the structure of coral and fish assemblages of a group of small islands and pinnacles in the vicinity of Maptaput deep sea port, Rayong Province, Thailand during 2002. The coral and fish assemblages at Saket Island and nearby pinnacle, Hin-Yai, which are located less than 1 km from the deep sea port, had changed. Living coral cover in 2002 was 8% at Hin-Yai and 4% at Saket Island which decreased from 33% and 64%, respectively in the previous report in 1992. Numbers of coral species at Saket Island decreased from 41 species to 13 species. Acropora spp. that previously dominated the area had nearly disappeared. For fishes, a total of 40 species were found in 2002 the numbers decreased to only 6 species at Saket Island and 36 species at Hin-Yai. Fishes that dominated the area are small pomacentrids. After 1997, the conditions of coral and fish assemblages at Saket Island and Hin-Yai had markedly changed, whereas, the conditions found in the nearby area are much better. Sediment load from port construction was the primary cause of the degradation. This should indicate the adverse effect of sedimentation on coral and reef fish assemblages at Maptaput. Coral communities developed on rock pinnacles west of Maptaput deep-sea port are reported and described herein for the first time.

  9. Green and brown propolis: efficient natural biocides for the control of bacterial contamination of alcoholic fermentation of distilled beverage

    Directory of Open Access Journals (Sweden)

    Márcia Justino Rossini Mutton

    2014-12-01

    Full Text Available This study aimed to evaluate the efficiency of natural biocides, brown and green propolis, for the control of bacterial contamination in the production of sugarcane spirit. The treatments consisted of brown and green propolis extracts, ampicillin, and a control and were assessed at the beginning and end of harvest season in ten fermentation cycles. In the microbiological analyses, the lactic acid bacteria were quantified in the inoculum before and after the treatment with biocides, and the viability of yeast cells during fermentation was evaluated. The levels of acids, glycerol, total residual reducing sugars, and ethanol were analyzed for the wine resulting from each fermentation cycle. A reduction in the number of bacterial contaminants in the inoculum in the treatments with the natural biocides was observed, but it did not affect the viability of yeast cells. The control of the contaminants led to the production of higher levels of ethanol and reduced acidity in the wine produced. The results of the use of brown and green propolis to control the growth microorganisms in the fermentation of sugarcane spirit can be of great importance for using alternative strategies to synthetic antibacterials in fermentation processes including other distilled beverage or spirits.

  10. Petroleum Oxidation in Marine Microcosms by Natural Microbial Assemblages

    Science.gov (United States)

    Wardlaw, G. D.; Reddy, C. M.; Nelson, R. K.; Ehrhardt, C. J.; Valentine, D. L.

    2006-12-01

    Millions of gallons of petroleum are emitted into marine environments each year and the oxidation of this oil by microbes is an important mechanism for mediating toxicity. In terms of quantity, petroleum is the most abundant organic pollutant impacting marine environments today. Recent advances in chromatography have led to the development of comprehensive two-dimensional gas chromatography (GC &GC). The acronym, GC GC, is used because orthogonal gas chromatographic separations are achieved in both analytical dimensions by using stationary phases with varying partitioning abilities and selectivity. This novel method has greatly expanded the analytical window of petroleum hydrocarbons and was used to track the loss of petroleum hydrocarbons in aerobic marine microcosm experiments. Sediment microcosms were composed of seawater and sediment collected from the Coal Oil Point (COP) seep field off the coast of Santa Barbara, CA. Oil collected directly from the reservoir underlying the seep field was added to each microcosm, and samples were incubated for one year. Net metabolism was tracked by quantifying oxygen consumption and carbon dioxide production. The loss of petroleum components was tracked with GC GC, whereas the bacterial and archaeal community structures were tracked using T-RFLP. Results of these incubation studies will be presented.

  11. Spatial and seasonal patterns of ichthyoplankton assemblages in the Haizhou Bay and its adjacent waters of China

    Science.gov (United States)

    Li, Zengguang; Ye, Zhenjiang; Wan, Rong

    2015-12-01

    Surveys were conducted in five voyages in Haizhou Bay and its adjacent coastal area from March to December 2011 during full moon spring tides. The ichthyoplankton assemblages and the environmental factors that affect their spatial and seasonal patterns were determined. Totally 35 and 12 fish egg and larvae taxa were identified, respectively. Over the past several decades, the egg and larval species composition has significantly changed in Haizhou Bay and its adjacent waters, most likely corresponding with the alteration of fishery resources, which are strongly affected by anthropogenic activities and climate change. The Bray-Curtis dissimilarity index identified four assemblages: near-shore bay assemblage, middle bay assemblage and two closely related assemblages (near-shore/middle bay assemblage and middle/edge of bay assemblage). The primary species of each assemblage principally reflected the spawning strategies of adult fish. The near-shore bay assemblage generally occurred in near-shore bay, with depths measuring ichthyoplankton in each assemblage were determined by interactions between biological behavioral traits and oceanographic features, particularly the variation of local conditions within the constraint of a general reproductive strategy. The results of Spearman's rank correlation analysis indicated that both fish egg and larval abundance were positively correlated with depth, which is critical to the oceanographic features in Haizhou Bay.

  12. Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System

    Science.gov (United States)

    Bhatnagar, Srijak; Eisen, Jonathan A.; Kopp, Artyom

    2011-01-01

    Drosophila melanogaster is emerging as an important model of non-pathogenic host–microbe interactions. The genetic and experimental tractability of Drosophila has led to significant gains in our understanding of animal–microbial symbiosis. However, the full implications of these results cannot be appreciated without the knowledge of the microbial communities associated with natural Drosophila populations. In particular, it is not clear whether laboratory cultures can serve as an accurate model of host–microbe interactions that occur in the wild, or those that have occurred over evolutionary time. To fill this gap, we characterized natural bacterial communities associated with 14 species of Drosophila and related genera collected from distant geographic locations. To represent the ecological diversity of Drosophilids, examined species included fruit-, flower-, mushroom-, and cactus-feeders. In parallel, wild host populations were compared to laboratory strains, and controlled experiments were performed to assess the importance of host species and diet in shaping bacterial microbiome composition. We find that Drosophilid flies have taxonomically restricted bacterial communities, with 85% of the natural bacterial microbiome composed of only four bacterial families. The dominant bacterial taxa are widespread and found in many different host species despite the taxonomic, ecological, and geographic diversity of their hosts. Both natural surveys and laboratory experiments indicate that host diet plays a major role in shaping the Drosophila bacterial microbiome. Despite this, the internal bacterial microbiome represents only a highly reduced subset of the external bacterial communities, suggesting that the host exercises some level of control over the bacteria that inhabit its digestive tract. Finally, we show that laboratory strains provide only a limited model of natural host–microbe interactions. Bacterial taxa used in experimental studies are rare or absent in

  13. Drivers of larval fish assemblage shift during the spring-summer transition in the coastal Mediterranean

    Science.gov (United States)

    Álvarez, Itziar; Catalán, Ignacio A.; Jordi, Antoni; Palmer, Miquel; Sabatés, Ana; Basterretxea, Gotzon

    2012-01-01

    The influence of coastal environmental conditions from winter-spring to summer on fish larvae assemblages in a temperate area has suggested a seasonal shift in ecosystem-level variation through which trophic pathways shift from the pelagic to the benthic system. This variation may be related to marked effects in the reproductive strategies in the fishes inhabiting the area and indirectly affect ichthyoplankton assemblages. Larval fish assemblages were sampled fortnightly at three stations located in coastal waters off southern Mallorca (Western Mediterranean) from March to August 2007, covering the main spawning period for the resident coastal fish in this region. The larval fish assemblage showed clear seasonality with higher specific abundance but lower diversity in the spring. Two main assemblages were identified: a spring assemblage, occurring at surface seawater temperatures ichthyoplankton communities occurred in early June, coinciding with the onset of summer hydrographical conditions and the local benthic productivity peak.

  14. Impacts of Alterations of Organic Inputs on the Bacterial Community within the sediments of Wind Cave, South Dakota, USA

    Directory of Open Access Journals (Sweden)

    Chelius Marisa K.

    2009-01-01

    Full Text Available Wind Cave (WICA in the Black Hills of South Dakota, like many mostly dry caves in temperate regions is an energy-starved system.The biotic communities that reside in these systems are low in diversity and simple in structure, and sensitive to changes in externalinputs of organic matter. Caves open to tourist traffic offer an opportunity to study the impacts of organic matter amendments in theform of human and rodent hair and dander, clothing lint, material from rodent activity (nesting materials and feces, and algal growthin and around artificial lighting. This study reports on the impacts of carbon amendments from humans and rodents on the bacterialand archaeal communities within the sediments of WICA from annual surveys and from a manipulative study that added lint (‘L’;cellulose plus rodent dander and rodent hair, rodent feces (‘F’, and a combination of both (‘LF’. The survey confirmed that bacterialbiomass was higher in regions of the cave with the highest rates of lint (hair and natural clothing fibers input. The manipulative studyfound that organic amendments in the forms of lint (L and rodent feces (F altered the WICA bacterial community structure in bothabundance and diversity, with the combined lint and feces (LF amendment having the most significant response. The high similarityof the LF and L communities suggests that the cave bacterial community is more carbon than nitrogen limited. The implication ofcave development to management practices is immediate and practical. Even small amounts of lint and organic matter foreign tocave bacteria significantly compromise the integrity of the endemic community resulting in the replacement of undescribed speciesby assemblages with at best, unknown impacts to natural cave features.

  15. Changes in benthic fish assemblages as a consequence of coastal works in a coastal lagoon: The Mar Menor (Spain, Western Mediterranean).

    Science.gov (United States)

    Pérez-Ruzafa, A; García-Charton, J A; Barcala, E; Marcos, C

    2006-01-01

    The benthic fish assemblage of the Mar Menor consisted of 37 species. Dominant species are: Gobius cobitis, Lipophrys pavo and Tripterygion tripteronotus on infralittoral rocks; Pomatoschistus marmoratus, Callionymus pussillus, Callionymus risso and Solea vulgaris on sandy bottoms and Gobius niger, Syngnathus abaster, Hippocampus ramulosus and Symphodus cinereus on Cymodocea nodosa-Caulerpa prolifera mixed beds. From 1985 to 1989 tourist development has led to the creation of new beaches and the installation of artificial rocky structures for retaining sediments. Dredging for the extraction of sand and subsequent pumping altered sediment characteristics causing a real stress leading to the substitution of typical sandy bottoms communities with Cymodocea nodosa by Caulerpa prolifera communities on mud. Soft bottom fish assemblages responded to changes in vegetation cover and substratum characteristics mainly changing the species composition, while artificial hard substrata contain a similar fish community than natural ones, harbouring even richer and more diverse assemblages. This positive effect of breakwaters should not obscure their likely negative effects on hydrodynamics and the subsequent changes of sediment quality and vegetation cover on the breakwaters' area of influence.

  16. Social Equity and the Assemblage of Values in Australian Higher Education

    Science.gov (United States)

    Rizvi, Fazal; Lingard, Bob

    2011-01-01

    The paper argues that the policy concept of social equity cannot be adequately understood in a generalised abstract manner, but is better viewed as an assemblage that brings together a number of contrasting, and sometimes competing, values. Our use of assemblage is somewhat eclectic and is designed to underscore the performative character of…

  17. Species richness and trait composition of butterfly assemblages change along an altitudinal gradient.

    Science.gov (United States)

    Leingärtner, Annette; Krauss, Jochen; Steffan-Dewenter, Ingolf

    2014-06-01

    Species richness patterns along altitudinal gradients are well-documented ecological phenomena, yet very little data are available on how environmental filtering processes influence the composition and traits of butterfly assemblages at high altitudes. We have studied the diversity patterns of butterfly species at 34 sites along an altitudinal gradient ranging from 600 to 2,000 m a.s.l. in the National Park Berchtesgaden (Germany) and analysed traits of butterfly assemblages associated with dispersal capacity, reproductive strategies and developmental time from lowlands to highlands, including phylogenetic analyses. We found a linear decline in butterfly species richness along the altitudinal gradient, but the phylogenetic relatedness of the butterfly assemblages did not increase with altitude. Compared to butterfly assemblages at lower altitudes, those at higher altitudes were composed of species with larger wings (on average 9%) which laid an average of 68% more eggs. In contrast, egg maturation time in butterfly assemblages decreased by about 22% along the altitudinal gradient. Further, butterfly assemblages at higher altitudes were increasingly dominated by less widespread species. Based on our abundance data, but not on data in the literature, population density increased with altitude, suggesting a reversed density-distribution relationship, with higher population densities of habitat specialists in harsh environments. In conclusion, our data provide evidence for significant shifts in the composition of butterfly assemblages and for the dominance of different traits along the altitudinal gradient. In our study, these changes were mainly driven by environmental factors, whereas phylogenetic filtering played a minor role along the studied altitudinal range.

  18. Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

    Science.gov (United States)

    Brenkman, Samuel J.; Connolly, Patrick J.

    2008-01-01

    Rivers and streams that drain from Olympic, Mount Rainier, and North Cascades National Parks are among the most protected corridors in the lower 48 States, and represent some of the largest tracts of contiguous, undisturbed habitat throughout the range of several key fish species of the Pacific Northwest. These watersheds are of high regional importance as freshwater habitat sanctuaries for native fish, where habitat conditions are characterized as having little to no disturbance from development, channelization, impervious surfaces, roads, diversions, or hydroelectric projects. Fishery resources are of high ecological and cultural importance in Pacific Northwest National Parks, and significantly contribute to economically important recreational, commercial, and tribal fisheries. This protocol describes procedures to monitor trends in fish assemblages, fish abundance, and water temperature in eight rivers and five wadeable streams in Olympic National Park during summer months, and is based on 4 years of field testing. Fish assemblages link freshwater, marine, and terrestrial ecosystems. They also serve as focal resources of national parks and are excellent indicators of ecological conditions of rivers and streams. Despite the vital importance of native anadromous and resident fish populations, there is no existing monitoring program for fish assemblages in the North Coast and Cascades Network. Specific monitoring objectives of this protocol are to determine seasonal and annual trends in: (1) fish species composition, (2) timing of migration of adult fish, (3) relative abundance, (4) age and size structure, (5) extent of non-native and hatchery fish, and (6) water temperature. To detect seasonal and annual trends in fish assemblages in reference sites, we rely on repeated and consistent annual sampling at each monitoring site. The general rationale for the repeated sampling of reference sites is to ensure that we account for the high interannual variability in fish

  19. Life history theory predicts fish assemblage response to hydrologic regimes.

    Science.gov (United States)

    Mims, Meryl C; Olden, Julian D

    2012-01-01

    The hydrologic regime is regarded as the primary driver of freshwater ecosystems, structuring the physical habitat template, providing connectivity, framing biotic interactions, and ultimately selecting for specific life histories of aquatic organisms. In the present study, we tested ecological theory predicting directional relationships between major dimensions of the flow regime and life history composition of fish assemblages in perennial free-flowing rivers throughout the continental United States. Using long-term discharge records and fish trait and survey data for 109 stream locations, we found that 11 out of 18 relationships (61%) tested between the three life history strategies (opportunistic, periodic, and equilibrium) and six hydrologic metrics (two each describing flow variability, predictability, and seasonality) were statistically significant (P history strategies, with 82% of all significant relationships observed supporting predictions from life history theory. Specifically, we found that (1) opportunistic strategists were positively related to measures of flow variability and negatively related to predictability and seasonality, (2) periodic strategists were positively related to high flow seasonality and negatively related to variability, and (3) the equilibrium strategists were negatively related to flow variability and positively related to predictability. Our study provides important empirical evidence illustrating the value of using life history theory to understand both the patterns and processes by which fish assemblage structure is shaped by adaptation to natural regimes of variability, predictability, and seasonality of critical flow events over broad biogeographic scales.

  20. Case-Control Study of Risk Factors for Sporadic Giardiasis and Parasite Assemblages in North West England.

    Science.gov (United States)

    Minetti, Corrado; Lamden, Kenneth; Durband, Caroline; Cheesbrough, John; Platt, Katherine; Charlett, Andre; O'Brien, Sarah J; Fox, Andrew; Wastling, Jonathan M

    2015-10-01

    Giardia duodenalis is a major cause of infectious gastroenteritis worldwide, and it is diversified into eight genetic assemblages (A to H), which are distinguishable only by molecular typing. There is some evidence that the assemblages infecting humans (assemblages A and B) may have different transmission routes, but systematically acquired data, combining epidemiological and molecular findings, are required. We undertook a case-control study with Giardia genotyping in North West England, to determine general and parasite assemblage-specific risk factors. For people without a history of foreign travel, swimming in swimming pools and changing diapers were the most important risk factors for the disease. People infected with assemblage B reported a greater number of symptoms and higher frequencies of vomiting, abdominal pain, swollen stomach, and loss of appetite, compared with people infected with assemblage A. More importantly, keeping a dog was associated only with assemblage A infections, suggesting the presence of a potential zoonotic reservoir for this assemblage. This is the first case-control study to combine epidemiological data with Giardia genotyping, and it shows the importance of integrating these two levels of information for better understanding of the epidemiology of this pathogen. Copyright © 2015, Minetti et al.

  1. Effects of symbiotic bacteria and tree chemistry on the growth and reproduction of bark beetle fungal symbionts

    Science.gov (United States)

    A.S. Adams; C.R. Currie; Y. Cardoza; K.D. Klepzig; K.F. Raffa

    2009-01-01

    Bark beetles are associated with diverse assemblages of microorganisms, many of which affect their interactions with host plants and natural enemies. We tested how bacterial associates of three bark beetles with various types of host relationships affect growth and reproduction of their symbiotic fungi. Fungi were exposed to volatiles...

  2. Modelling of acid-base titration curves of mineral assemblages

    Directory of Open Access Journals (Sweden)

    Stamberg Karel

    2016-01-01

    Full Text Available The modelling of acid-base titration curves of mineral assemblages was studied with respect to basic parameters of their surface sites to be obtained. The known modelling approaches, component additivity (CA and generalized composite (GC, and three types of different assemblages (fucoidic sandstones, sedimentary rock-clay and bentonite-magnetite samples were used. In contrary to GC-approach, application of which was without difficulties, the problem of CA-one consisted in the credibility and accessibility of the parameters characterizing the individual mineralogical components.

  3. Dynamic succession of soil bacterial community during continuous cropping of peanut (Arachis hypogaea L..

    Directory of Open Access Journals (Sweden)

    Mingna Chen

    Full Text Available Plant health and soil fertility are affected by plant-microbial interactions in soils. Peanut is an important oil crop worldwide and shows considerable adaptability, but growth and yield are negatively affected by continuous cropping. In this study, 16S rRNA gene clone library analyses were used to study the succession of soil bacterial communities under continuous peanut cultivation. Six libraries were constructed for peanut over three continuous cropping cycles and during its seedling and pod-maturing growth stages. Cluster analyses indicated that soil bacterial assemblages obtained from the same peanut cropping cycle were similar, regardless of growth period. The diversity of bacterial sequences identified in each growth stage library of the three peanut cropping cycles was high and these sequences were affiliated with 21 bacterial groups. Eight phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia were dominant. The related bacterial phylotypes dynamic changed during continuous cropping progress of peanut. This study demonstrated that the bacterial populations especially the beneficial populations were positively selected. The simplification of the beneficial microbial communities such as the phylotypes of Alteromonadales, Burkholderiales, Flavobacteriales, Pseudomonadales, Rhizobiales and Rhodospirillales could be important factors contributing to the decline in peanut yield under continuous cropping. The microbial phylotypes that did not successively changed with continuous cropping, such as populations related to Rhizobiales and Rhodospirillales, could potentially resist stress due to continuous cropping and deserve attention. In addition, some phylotypes, such as Acidobacteriales, Chromatiales and Gemmatimonadales, showed a contrary tendency, their abundance or diversity increased with continuous peanut cropping progress. Some bacterial phylotypes including

  4. Multivariate and Spatial Visualisation of Archaeological Assemblages

    Directory of Open Access Journals (Sweden)

    Martin Sterry

    2018-05-01

    Full Text Available Multivariate analyses, in particular correspondence analysis (CA, have become a standard exploratory tool for analysing and interpreting variance in archaeological assemblages. While they have greatly helped analysts, they unfortunately remain abstract to the viewer, all the more so if the viewer has little or no experience with multivariate statistics. A second issue with these analyses can arise from the detachment of archaeological material from its geo-referenced location and typically considered only in terms of arbitrary classifications (e.g. North Europe, Central Europe, South Europe instead of the full range of local conditions (e.g. proximity to other assemblages, relationships with other spatial phenomena. This article addresses these issues by presenting a novel method for spatially visualising CA so that these analyses can be interpreted intuitively. The method works by transforming the resultant bi-plots of the CA into colour maps using the HSV colour model, in which the similarity and difference between assemblages directly corresponds to the similarity and difference of the colours used to display them. Utilising two datasets – ceramics from the excavations of the Roman fortress of Vetera I, and terra sigillata forms collected as part of 'The Samian Project' – the article demonstrates how the method is applied and how it can be used to draw out spatial and temporal trends.

  5. Demersal fish assemblages off southern New Zealand in relation to depth and temperature

    Science.gov (United States)

    Jacob, W.; McClatchie, S.; Probert, P. K.; Hurst, R. J.

    1998-12-01

    We examined the relationship between demersal fish assemblage and depth, temperature, latitude and longitude off southern New Zealand (46-54°S and 165-180°E) in water depths of 80-787 m. Catch weight data were analysed by two-way indicator analysis (TWIA), groupaverage agglomerative clustering (UPGMA) and Detrended Correspondence Analysis (DCA). The spatial pattern of demersal fish off southern New Zealand conforms to the concept of species groups or fish assemblages related to environmental gradients. Shallow-water assemblages were dominated by species from the families Gempylidae, Squalidae, Triakidae and Moridae, mainly represented by Thyrsites atun, Squalus acanthias, Galeorhinus australis, and Pseudophycis bachus. Deep water assemblages were dominated by Chimaeridae, Argentinidae, Merlucciidae and Macrouridae, mainly represented by Hydrolagus novaezelandiae, Argentina elongata, Macruronus novaezelandiae, and Lepidorhynchus denticulatus. Total catch weight was often dominated by Merlucciidae, Macrouridae and Gempylidae. Fish assemblages were related to discrete ranges of depth (300 m) and temperature (9.5°C), but the range of sediment types was too narrow to show any correlation.

  6. Molluscan assemblages on coral reefs and associated hard substrata in the northern Red Sea

    Science.gov (United States)

    Zuschin, M.; Hohenegger, J.; Steininger, F.

    2001-09-01

    Information on spatial variability and distribution patterns of organisms in coral reef environments is necessary to evaluate the increasing anthropogenic disturbance of marine environments (Richmond 1993; Wilkinson 1993; Dayton 1994). Therefore different types of subtidal, reef-associated hard substrata (reef flats, reef slopes, coral carpets, coral patches, rock grounds), each with different coral associations, were investigated to determine the distribution pattern of molluscs and their life habits (feeding strategies and substrate relations). The molluscs were strongly dominated by taxa with distinct relations to corals, and five assemblages were differentiated. The Dendropoma maxima assemblage on reef flats is a discrete entity, strongly dominated by this encrusting and suspension-feeding gastropod. All other assemblages are arranged along a substrate gradient of changing coral associations and potential molluscan habitats. The Coralliophila neritoidea- Barbatia foliata assemblage depends on the presence of Porites and shows a dominance of gastropods feeding on corals and of bivalves associated with living corals. The Chamoidea- Cerithium spp. assemblage on rock grounds is strongly dominated by encrusting bivalves. The Drupella cornus-Pteriidae assemblage occurs on Millepora- Acropora reef slopes and is strongly dominated by bivalves associated with living corals. The Barbatia setigera- Ctenoides annulata assemblage includes a broad variety of taxa, molluscan life habits and bottom types, but occurs mainly on faviid carpets and is transitional among the other three assemblages. A predicted degradation of coral coverage to rock bottoms due to increasing eutrophication and physical damage in the study area (Riegl and Piller 2000) will result in a loss of coral-associated molluscs in favor of bivalve crevice dwellers in dead coral heads and of encrusters on dead hard substrata.

  7. Effects of triclosan on bacterial community composition and 'Vibrio' populations in natural seawater microcosms

    Directory of Open Access Journals (Sweden)

    Keri Ann Lydon

    2017-05-01

    Full Text Available Pharmaceuticals and personal care products, including antimicrobials, can be found at trace levels in treated wastewater effluent. Impacts of chemical contaminants on coastal aquatic microbial community structure and pathogen abundance are unknown despite the potential for selection through antimicrobial resistance. In particular, 'Vibrio', a marine bacterial genus that includes several human pathogens, displays resistance to the ubiquitous antimicrobial compound triclosan. Here we demonstrated through use of natural seawater microcosms that triclosan (at a concentration of ~5 ppm can induce a significant 'Vibrio' growth response (68–1,700 fold increases in comparison with no treatment controls for three distinct coastal ecosystems: Looe Key Reef (Florida Keys National Marine Sanctuary, Doctors Arm Canal (Big Pine Key, FL, and Clam Bank Landing (North Inlet Estuary, Georgetown, SC. Additionally, microbial community analysis by 16 S rRNA gene sequencing for Looe Key Reef showed distinct changes in microbial community structure with exposure to 5 ppm triclosan, with increases observed in the relative abundance of 'Vibrio'naceae (17-fold, Pseudoalteromonadaceae (65-fold, Alteromonadaceae (108-fold, Colwelliaceae (430-fold, and Oceanospirillaceae (1,494-fold. While the triclosan doses tested were above concentrations typically observed in coastal surface waters, results identify bacterial families that are potentially resistant to triclosan and/or adapted to use triclosan as a carbon source. The results further suggest the potential for selection of 'Vibrio' in coastal environments, especially sediments, where triclosan may accumulate at high levels.

  8. Temporal variability in epifaunal assemblages associated with temperate gorgonian gardens

    KAUST Repository

    Dias, I.M.; Curdia, Joao; Cunha, M.R.; Santos, M.N.; Carvalho, Susana

    2015-01-01

    The present study is one of the few that investigate the temporal variability of epifaunal assemblages associated with coral species, particularly the octocorals Eunicella gazella and Leptogorgia lusitanica in south Portugal. The results suggest time rather than colony size as a primary driver of the ecological patterns of these assemblages, which were dominated by amphipods, molluscs and polychaetes. Temporal variability was linked to changes in environmental parameters, namely temperature, chlorophyll a and particulate organic carbon. Hence, temporal variability must be taken into account for the design of future biodiversity assessment studies, as different patterns may be observed depending on the sampling time. Associated epifaunal assemblages were consistently dominated by resident species (i.e. species present in all sampling periods) and a peak of rare species was observed in the transition from spring to summer following the increase of seawater temperature. Turnover was particularly high in the transition between the spring and summer periods. In both hosts, turnover was higher in the small sized colonies, which generally harboured less diverse and less abundant assemblages which also differed from those inhabiting larger size colonies. The high levels of diversity associated with gorgonian colonies highlights the need for the conservation of this priority habitat.

  9. Temporal variability in epifaunal assemblages associated with temperate gorgonian gardens

    KAUST Repository

    Dias, I.M.

    2015-10-19

    The present study is one of the few that investigate the temporal variability of epifaunal assemblages associated with coral species, particularly the octocorals Eunicella gazella and Leptogorgia lusitanica in south Portugal. The results suggest time rather than colony size as a primary driver of the ecological patterns of these assemblages, which were dominated by amphipods, molluscs and polychaetes. Temporal variability was linked to changes in environmental parameters, namely temperature, chlorophyll a and particulate organic carbon. Hence, temporal variability must be taken into account for the design of future biodiversity assessment studies, as different patterns may be observed depending on the sampling time. Associated epifaunal assemblages were consistently dominated by resident species (i.e. species present in all sampling periods) and a peak of rare species was observed in the transition from spring to summer following the increase of seawater temperature. Turnover was particularly high in the transition between the spring and summer periods. In both hosts, turnover was higher in the small sized colonies, which generally harboured less diverse and less abundant assemblages which also differed from those inhabiting larger size colonies. The high levels of diversity associated with gorgonian colonies highlights the need for the conservation of this priority habitat.

  10. Uniform functional structure across spatial scales in an intertidal benthic assemblage.

    Science.gov (United States)

    Barnes, R S K; Hamylton, Sarah

    2015-05-01

    To investigate the causes of the remarkable similarity of emergent assemblage properties that has been demonstrated across disparate intertidal seagrass sites and assemblages, this study examined whether their emergent functional-group metrics are scale related by testing the null hypothesis that functional diversity and the suite of dominant functional groups in seagrass-associated macrofauna are robust structural features of such assemblages and do not vary spatially across nested scales within a 0.4 ha area. This was carried out via a lattice of 64 spatially referenced stations. Although densities of individual components were patchily dispersed across the locality, rank orders of importance of the 14 functional groups present, their overall functional diversity and evenness, and the proportions of the total individuals contained within each showed, in contrast, statistically significant spatial uniformity, even at areal scales functional groups in their geospatial context also revealed weaker than expected levels of spatial autocorrelation, and then only at the smaller scales and amongst the most dominant groups, and only a small number of negative correlations occurred between the proportional importances of the individual groups. In effect, such patterning was a surface veneer overlying remarkable stability of assemblage functional composition across all spatial scales. Although assemblage species composition is known to be homogeneous in some soft-sediment marine systems over equivalent scales, this combination of patchy individual components yet basically constant functional-group structure seems as yet unreported. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Lions as Bone Accumulators? Paleontological and Ecological Implications of a Modern Bone Assemblage from Olduvai Gorge.

    Directory of Open Access Journals (Sweden)

    Mari Carmen Arriaza

    Full Text Available Analytic models have been developed to reconstruct early hominin behaviour, especially their subsistence patterns, revealed mainly through taphonomic analyses of archaeofaunal assemblages. Taphonomic research is used to discern which agents (carnivores, humans or both generate the bone assemblages recovered at archaeological sites. Taphonomic frameworks developed during the last decades show that the only large-sized carnivores in African biomes able to create bone assemblages are leopards and hyenas. A carnivore-made bone assemblage located in the short-grassland ecological unit of the Serengeti (within Olduvai Gorge was studied. Taphonomic analyses of this assemblage including skeletal part representation, bone density, breakage patterns and anatomical distribution of tooth marks, along with an ecological approach to the prey selection made by large carnivores of the Serengeti, were carried out. The results show that this bone assemblage may be the first lion-accumulated assemblage documented, although other carnivores (namely spotted hyenas may have also intervened through postdepositional ravaging. This first faunal assemblage potentially created by lions constitutes a new framework for neotaphonomic studies. Since lions may accumulate carcasses under exceptional circumstances, such as those documented at the site reported here, this finding may have important consequences for interpretations of early archaeological and paleontological sites, which provide key information about human evolution.

  12. Lions as Bone Accumulators? Paleontological and Ecological Implications of a Modern Bone Assemblage from Olduvai Gorge.

    Science.gov (United States)

    Arriaza, Mari Carmen; Domínguez-Rodrigo, Manuel; Yravedra, José; Baquedano, Enrique

    2016-01-01

    Analytic models have been developed to reconstruct early hominin behaviour, especially their subsistence patterns, revealed mainly through taphonomic analyses of archaeofaunal assemblages. Taphonomic research is used to discern which agents (carnivores, humans or both) generate the bone assemblages recovered at archaeological sites. Taphonomic frameworks developed during the last decades show that the only large-sized carnivores in African biomes able to create bone assemblages are leopards and hyenas. A carnivore-made bone assemblage located in the short-grassland ecological unit of the Serengeti (within Olduvai Gorge) was studied. Taphonomic analyses of this assemblage including skeletal part representation, bone density, breakage patterns and anatomical distribution of tooth marks, along with an ecological approach to the prey selection made by large carnivores of the Serengeti, were carried out. The results show that this bone assemblage may be the first lion-accumulated assemblage documented, although other carnivores (namely spotted hyenas) may have also intervened through postdepositional ravaging. This first faunal assemblage potentially created by lions constitutes a new framework for neotaphonomic studies. Since lions may accumulate carcasses under exceptional circumstances, such as those documented at the site reported here, this finding may have important consequences for interpretations of early archaeological and paleontological sites, which provide key information about human evolution.

  13. Lions as Bone Accumulators? Paleontological and Ecological Implications of a Modern Bone Assemblage from Olduvai Gorge

    Science.gov (United States)

    Arriaza, Mari Carmen; Domínguez-Rodrigo, Manuel; Yravedra, José; Baquedano, Enrique

    2016-01-01

    Analytic models have been developed to reconstruct early hominin behaviour, especially their subsistence patterns, revealed mainly through taphonomic analyses of archaeofaunal assemblages. Taphonomic research is used to discern which agents (carnivores, humans or both) generate the bone assemblages recovered at archaeological sites. Taphonomic frameworks developed during the last decades show that the only large-sized carnivores in African biomes able to create bone assemblages are leopards and hyenas. A carnivore-made bone assemblage located in the short-grassland ecological unit of the Serengeti (within Olduvai Gorge) was studied. Taphonomic analyses of this assemblage including skeletal part representation, bone density, breakage patterns and anatomical distribution of tooth marks, along with an ecological approach to the prey selection made by large carnivores of the Serengeti, were carried out. The results show that this bone assemblage may be the first lion-accumulated assemblage documented, although other carnivores (namely spotted hyenas) may have also intervened through postdepositional ravaging. This first faunal assemblage potentially created by lions constitutes a new framework for neotaphonomic studies. Since lions may accumulate carcasses under exceptional circumstances, such as those documented at the site reported here, this finding may have important consequences for interpretations of early archaeological and paleontological sites, which provide key information about human evolution. PMID:27144649

  14. Does species diversity limit productivity in natural grassland communities?

    NARCIS (Netherlands)

    Grace, James B.; Anderson, T. Michael; Smith, Melinda D.; Seabloom, Eric; Andelman, Sandy J.; Meche, Gayna; Weiher, Evan; Allain, Larry K.; Jutila, Heli; Sankaran, Mahesh; Knops, Johannes; Ritchie, Mark; Willig, Michael R.

    Theoretical analyses and experimental studies of synthesized assemblages indicate that under particular circumstances species diversity can enhance community productivity through niche complementarity. It remains unclear whether this process has important effects in mature natural ecosystems where

  15. Adaptive Bacterial Foraging Optimization

    Directory of Open Access Journals (Sweden)

    Hanning Chen

    2011-01-01

    Full Text Available Bacterial Foraging Optimization (BFO is a recently developed nature-inspired optimization algorithm, which is based on the foraging behavior of E. coli bacteria. Up to now, BFO has been applied successfully to some engineering problems due to its simplicity and ease of implementation. However, BFO possesses a poor convergence behavior over complex optimization problems as compared to other nature-inspired optimization techniques. This paper first analyzes how the run-length unit parameter of BFO controls the exploration of the whole search space and the exploitation of the promising areas. Then it presents a variation on the original BFO, called the adaptive bacterial foraging optimization (ABFO, employing the adaptive foraging strategies to improve the performance of the original BFO. This improvement is achieved by enabling the bacterial foraging algorithm to adjust the run-length unit parameter dynamically during algorithm execution in order to balance the exploration/exploitation tradeoff. The experiments compare the performance of two versions of ABFO with the original BFO, the standard particle swarm optimization (PSO and a real-coded genetic algorithm (GA on four widely-used benchmark functions. The proposed ABFO shows a marked improvement in performance over the original BFO and appears to be comparable with the PSO and GA.

  16. Effects of Management Legacies on Stream Fish and Aquatic Benthic Macroinvertebrate Assemblages

    Science.gov (United States)

    Quist, Michael C.; Schultz, Randall D.

    2014-09-01

    Fish and benthic macroinvertebrate assemblages often provide insight on ecological conditions for guiding management actions. Unfortunately, land use and management legacies can constrain the structure of biotic communities such that they fail to reflect habitat quality. The purpose of this study was to describe patterns in fish and benthic macroinvertebrate assemblage structure, and evaluate relationships between biota and habitat characteristics in the Chariton River system of south-central Iowa, a system likely influenced by various potential management legacies (e.g., dams, chemical removal of fishes). We sampled fishes, benthic macroinvertebrates, and physical habitat from a total of 38 stream reaches in the Chariton River watershed during 2002-2005. Fish and benthic macroinvertebrate assemblages were dominated by generalist species tolerant of poor habitat quality; assemblages failed to show any apparent patterns with regard to stream size or longitudinal location within the watershed. Metrics used to summarize fish assemblages and populations [e.g., presence-absence, relative abundance, Index of Biotic Integrity for fish (IBIF)] were not related to habitat characteristics, except that catch rates of piscivores were positively related to the depth and the amount of large wood. In contrast, family richness of benthic macroinvertebrates, richness of Ephemeroptera, Trichoptera, and Plecoptera taxa, and IBI values for benthic macroinvertebrates (IBIBM) were positively correlated with the amount of overhanging vegetation and inversely related to the percentage of fine substrate. A long history of habitat alteration by row-crop agriculture and management legacies associated with reservoir construction has likely resulted in a fish assemblage dominated by tolerant species. Intolerant and sensitive fish species have not recolonized streams due to downstream movement barriers (i.e., dams). In contrast, aquatic insect assemblages reflected aquatic habitat, particularly

  17. Fish-assemblage variation between geologically defined regions and across a longitudinal gradient in the Monkey River Basin, Belize

    Science.gov (United States)

    Esselman, P.C.; Freeman, Mary C.; Pringle, C.M.

    2006-01-01

    assemblage structure within each geologic type. The fauna showed weak compositional zonation into 3 groups (headwaters, coastal plain, and nearshore). Nearly 20% of the fish species collected have migratory life cycles (including Joturus pichardi, Agonostomus monticola, and Gobiomorus dormitor) that use freshwater and marine habitats. Some of these species probably rely on a natural flow regime and longitudinal connectivity for reproduction and dispersal of young, and natural flow regime and longitudinal connectivity are important factors for maintenance of functional linkages between the uplands and the coast in the ridge-to-reef corridor where the Monkey River is located. Therefore, we suggest that the viability of migratory fish populations may be a good biological indicator of upland-to-estuary connectivity important both to fishes and coastal ecosystem function. We recommend follow-up studies to substantiate the relative strengths of relationships between community structure and abiotic factors in contrasting geologies and to examine potential bottom-up responses of stream biota to the higher nutrient levels that were observed in stream waters draining the Santa Rosa Group geologic type.

  18. Seafloor massive sulfide deposits support unique megafaunal assemblages: Implications for seabed mining and conservation.

    Science.gov (United States)

    Boschen, Rachel E; Rowden, Ashley A; Clark, Malcolm R; Pallentin, Arne; Gardner, Jonathan P A

    2016-04-01

    Mining of seafloor massive sulfides (SMS) is imminent, but the ecology of assemblages at SMS deposits is poorly known. Proposed conservation strategies include protected areas to preserve biodiversity at risk from mining impacts. Determining site suitability requires biological characterisation of the mine site and protected area(s). Video survey of a proposed mine site and protected area off New Zealand revealed unique megafaunal assemblages at the mine site. Significant relationships were identified between assemblage structure and environmental conditions, including hydrothermal features. Unique assemblages occurred at both active and inactive chimneys and are particularly at risk from mining-related impacts. The occurrence of unique assemblages at the mine site suggests that the proposed protected area is insufficient alone and should instead form part of a network. These results provide support for including hydrothermally active and inactive features within networks of protected areas and emphasise the need for quantitative survey data of proposed sites. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  19. Variable responses of fish assemblages, habitat, and stability to natural-channel-design restoration in Catskill Mountain streams

    Science.gov (United States)

    Baldigo, Barry P.; Ernst, Anne G.; Warren, Dana R.; Miller, Sarah J.

    2010-01-01

    Natural-channel-design (NCD) restorations were recently implemented within large segments of five first- and second-order streams in the Catskill Mountains of New York in an attempt to increase channel stability, reduce bed and bank erosion, and sustain water quality. In conjunction with these efforts, 54 fish and habitat surveys were done from 1999 to 2007 at six restored reaches and five stable control reaches to evaluate the effects of NCD restoration on fish assemblages, habitat, and bank stability. A before–after–control–impact study design and two-factor analysis of variance were used to quantify the net changes in habitat and fish population and community indices at treatment reaches relative to those at unaltered control reaches. The density and biomass of fish communities were often dominated by one or two small prey species and no or few predator species before restoration and by one or more trout (Salmonidae) species after restoration. Significant increases in community richness (30%), diversity (40%), species or biomass equitability (32%), and total biomass (up to 52%) in at least four of the six restored reaches demonstrate that NCD restorations can improve the health and sustainability of fish communities in geomorphically unstable Catskill Mountain streams over the short to marginally long term. Bank stability, stream habitat, and trout habitat suitability indices (HSIs) generally improved significantly at the restored reaches, but key habitat features and trout HSIs did not change or decreased at two of them. Fish communities and trout populations at these two reaches were not positively affected by NCD restorations. Though NCD restorations often had a positive effect on habitat and fish communities, our results show that the initial habitat conditions limit the relative improvements than can be achieved, habitat quality and stability do not necessarily respond in unison, and biotic and abiotic responses cannot always be generalized.

  20. Tidal switch on metabolic activity: Salinity induced responses on bacterioplankton metabolic capabilities in a tropical estuary

    Digital Repository Service at National Institute of Oceanography (India)

    Thottathil, S.D.; Balachandran, K.K.; Jayalakshmy, K.V.; Gupta, G.V.M.; Nair, S.

    , P.A., 2002. Compositional change in free-living bacterial communities along a salinity gradient in two temperate estuaries. Limnology and Oceanography 47, 453e470. Cottrell, M.T., Kirchman, D.L., 2000. Natural assemblages of marine proteo- bacteria...) according to a salinity gradient. Estuarine, Coastal and Shelf Science 24, 95e108. Pullin, M.J., Bertilsson, S., Goldstone, J.V., Voelker, B.M., 2004. Effects of sunlight and hydroxyl radical on dissolved organic matter: bacterial growth efficiency...

  1. Climate change effects on North American inland fish populations and assemblages

    Science.gov (United States)

    Lynch, Abigail J.; Myers, Bonnie; Chu, Cindy; Eby, Lisa A.; Falke, Jeffrey A.; Kovach, Ryan P.; Krabbenhoft, Trevor J.; Kwak, Thomas J.; Lyons, John; Paukert, Craig P.; Whitney, James E.

    2016-01-01

    Climate is a critical driver of many fish populations, assemblages, and aquatic communities. However, direct observational studies of climate change impacts on North American inland fishes are rare. In this synthesis, we (1) summarize climate trends that may influence North American inland fish populations and assemblages, (2) compile 31 peer-reviewed studies of documented climate change effects on North American inland fish populations and assemblages, and (3) highlight four case studies representing a variety of observed responses ranging from warmwater systems in the southwestern and southeastern United States to coldwater systems along the Pacific Coast and Canadian Shield. We conclude by identifying key data gaps and research needs to inform adaptive, ecosystem-based approaches to managing North American inland fishes and fisheries in a changing climate.

  2. Last glacial megafaunal death assemblage and early human occupation at Lake Menindee, southeastern Australia

    Science.gov (United States)

    Cupper, Matthew L.; Duncan, Jacqui

    2006-09-01

    The Tedford subfossil locality at Lake Menindee preserves a diverse assemblage of marsupials, monotremes and placental rodents. Of the 38 mammal taxa recorded at the site, almost a third are of extinct megafauna. Some of the bones are articulated or semi-articulated and include almost complete skeletons, indicating that aeolian sediments rapidly buried the animals following death. New optical ages show the site dates to the early part of the last glacial (55,700 ± 1300 yr weighted mean age). This is close to the 51,200-39,800 yr Australia-wide extinction age for megafauna suggested by Roberts et al. [2001, Science 292:1888-1892], but like all previous researchers, we cannot conclusively determine whether humans were implicated in the deaths of the animals. Although an intrusive hearth at the site dating to 45,100 ± 1400 yr ago is the oldest evidence of human occupation of the Darling River, no artifacts were identified in situ within the sub-fossil-bearing unit. Non-anthropogenic causes, such as natural senescence or ecosystem stress due to climatic aridity, probably explain the mortality of the faunal assemblage at Lake Menindee.

  3. Seasonal variability of rocky reef fish assemblages: Detecting functional and structural changes due to fishing effects

    Science.gov (United States)

    Henriques, Sofia; Pais, Miguel Pessanha; Costa, Maria José; Cabral, Henrique Nogueira

    2013-05-01

    The present study analyzed the effects of seasonal variation on the stability of fish-based metrics and their capability to detect changes in fish assemblages, which is yet poorly understood despite the general idea that guilds are more resilient to natural variability than species abundances. Three zones subject to different levels of fishing pressure inside the Arrábida Marine Protected Area (MPA) were sampled seasonally. The results showed differences between warm (summer and autumn) and cold (winter and spring) seasons, with the autumn clearly standing out. In general, the values of the metrics density of juveniles, density of invertebrate feeders and density of omnivores increased in warm seasons, which can be attributed to differences in recruitment patterns, spawning migrations and feeding activity among seasons. The density of generalist/opportunistic individuals was sensitive to the effect of fishing, with higher values at zones with the lowest level of protection, while the density of individuals with high commercial value only responded to fishing in the autumn, due to a cumulative result of both juveniles and adults abundances during this season. Overall, this study showed that seasonal variability affects structural and functional features of the fish assemblage and that might influence the detection of changes as a result of anthropogenic pressures. The choice of a specific season, during warm sea conditions after the spawning period (July-October), seems to be more adequate to assess changes on rocky-reef fish assemblages.

  4. Effects of reconstruction of a pre-European vertebrate assemblage on ground-dwelling arachnids in arid Australia.

    Science.gov (United States)

    Silvey, Colin J; Hayward, Matthew W; Gibb, Heloise

    2015-06-01

    Species loss can result in changes in assemblage structure and ecosystem function through ecological cascades. Australian vertebrate assemblages changed significantly following European colonisation, which resulted in the establishment of invasive vertebrates and the loss of native marsupials, many of which consume invertebrates. Conservation focusses on the removal of invasive carnivores and the reintroduction of regionally extinct species to fenced sites, resulting in what could be considered a reconstruction of pre-European vertebrate assemblages. In semi-arid Australian spinifex mallee ecosystems, we asked: (1) what is the effect of reconstructed pre-European vertebrate assemblages on native arachnid assemblages? and (2) what direct or indirect mechanisms (predation, disturbance and/or competition) could plausibly be responsible for these effects? We compared sites with reconstructed vertebrate assemblages with paired control sites. Arachnids were sampled using pitfall trapping and direct searching. Hypotheses regarding mechanisms were tested using scat analysis (predation) and by comparing burrow depth (disturbance) and scorpion mass (competition) between control and reconstructed sites. The dominant dune scorpion, Urodacus yaschenkoi, was less abundant and a wolf spider (Lycosa gibsoni species group) more abundant in reconstructed sites. Differences in spider assemblage composition were marginally non-significant. Scat analysis confirmed native vertebrate predation on scorpions and we found no evidence that competition or disturbance affected scorpions. We, thus, suggest that changes in spider assemblages may have resulted from ecological cascades via decreases in dune scorpions. The loss of omnivorous mammals and other changes associated with the invasion of carnivores may, therefore, have had broad-reaching consequences for native arachnid assemblages in Australian ecosystems.

  5. Spatial and seasonal patterns in fish assemblage in Corrego Rico, upper Parana River basin

    Directory of Open Access Journals (Sweden)

    Erico L. H Takahashi

    Full Text Available The upper Paraná River basin drains areas of intensive industry and agriculture, suffering negative impacts. The Córrego Rico flows through sugar cane fields and receives urban wastewater. The aim of this work is to describe and to compare the fish assemblage structure in Córrego Rico. Six standardized bimonthly samples were collected between August 2008 and June 2009 in seven different stretches of Córrego Rico. Fishes were collected with an experimental seine and sieves, euthanized, fixed in formalin and preserved in ethanol for counting and identification. Data were recorded for water parameters, instream habitat and riparian features within each stretch. Non-metric multidimensional scaling, species richness and diversity analysis were performed to examine spatial and seasonal variation in assemblage structure. Fish assemblage structure was correlated with instream habitat and water parameters. The fish assemblage was divided in three groups: upper, middle and lower reaches. High values of richness and diversity were observed in the upper and lower stretches due to connectivity with a small lake and Mogi Guaçu River, respectively. Middle stretches showed low values of richness and diversity suggesting that a small dam in the middle stretch negatively impacts the fish assemblage. Seasonal differences in fish assemblage structure were observed only in the lower stretches.

  6. Coral assemblages are structured along a turbidity gradient on the Southwestern Gulf of Mexico, Veracruz

    Science.gov (United States)

    Jordán-Garza, A. G.; González-Gándara, C.; Salas-Pérez, J. J.; Morales-Barragan, A. M.

    2017-04-01

    Corals on the reef corridor of the southwestern Gulf of Mexico have evolved on a terrigenous shallow continental shelf under the influence of several natural river systems. As a result, water turbidity on these reefs can be high, with visibility as low as turbidity and chlorophyll-a, the coral species composition and environmental variables were analyzed for the three main reef systems of the reef corridor of the southwestern Gulf of Mexico. Completeness of the data set was assessed using species accumulation curves and non-parametric estimators of species richness. Differences in coral assemblages' composition between the reef systems were investigated using univariate (ANOVA) and multivariate (nMDS, ANOSIM, SIMPER) analyses and the relationship between the assemblages and environmental data was assessed using a forward selection process in canonical correspondence analysis (CCA) to eliminate non-significant environmental variables. The northern and central Veracruz reef systems share a similar number of coral species (p=0.78 mult. comp.) and both showed higher species richness than the southern system (pturbidity and productivity were significant on the final CCA configuration, which showed a gradient of increasing turbidity from north to south. Reef geomorphology and the effect of turbidity help explain differences in coral assemblages' composition. More studies are necessary to establish if turbidity could function as a refuge for future environmental stress. Each Veracruz reef system is at the same time unique and shares a pool of coral species. To protect these ecosystems it is necessary to effectively manage water quality and consider coral diversity on the reef corridor of the southwestern Gulf of Mexico.

  7. Spatial and temporal dynamics of drosophilid larval assemblages associated to fruits

    Directory of Open Access Journals (Sweden)

    Renata Alves da Mata

    2015-03-01

    Full Text Available The study of organisms and their resources is critical to further understanding population dynamics in space and time. Although drosophilids have been widely used as biological models, their relationship with breeding and feeding sites has received little attention. Here, we investigate drosophilids breeding in fruits in the Brazilian Savanna, in two contrasting vegetation types, throughout 16 months. Specifically, larval assemblages were compared between savannas and forests, as well as between rainy and dry seasons. The relationships between resource availability and drosophilid abundance and richness were also tested. The community (4,022 drosophilids of 23 species and 2,496 fruits of 57 plant taxa varied widely in space and time. Drosophilid assemblages experienced a strong bottleneck during the dry season, decreasing to only 0.5% of the abundance of the rainy season. Additionally, savannas displayed lower richness and higher abundance than the forests, and were dominated by exotic species. Both differences in larval assemblages throughout the year and between savannas and gallery forests are consistent with those previously seen in adults. Although the causes of this dynamic are clearly multifactorial, resource availability (richness and abundance of rotten fruits was a good predictor of the fly assemblage structure.

  8. Controls on bacterial and archaeal community structure and greenhouse gas production in natural, mined, and restored Canadian peatlands

    Directory of Open Access Journals (Sweden)

    Nathan eBasiliko

    2013-07-01

    Full Text Available Northern peatlands are important global C reservoirs, largely because of their slow rates of microbial C mineralization. Particularly in sites that are heavily influenced by anthropogenic disturbances, there is scant information about microbial ecology and whether or not microbial community structure influences greenhouse gas production. This work characterized communities of bacteria and archaea using terminal restriction fragment length polymorphism and sequence analysis of 16S rRNA and functional genes across eight natural, mined, or restored peatlands in two locations in eastern Canada. Correlations were explored among chemical properties of peat, bacterial and archaeal community structure, and carbon dioxide and methane production rates under oxic and anoxic conditions. Bacteria and archaea similar to those found in other peat soil environments were detected. In contrast to other reports, methanogen diversity was low in our study, with only 2 groups of known or suspected methanogens. Although mining and restoration affected substrate availability and microbial activity, these land-uses did not consistently affect bacterial or archaeal community composition. In fact, larger differences were observed between the two locations and between oxic and anoxic peat samples than between mined and restored sites, with anoxic samples characterized by less detectable bacterial diversity and stronger dominance by members of the phylum Acidobacteria. There were also no apparent strong linkages between prokaryote community structure and methane or carbon dioxide production, suggesting that different organisms exhibit functional redundancy and/or that the same taxa function at very different rates when exposed to different peat substrates. In contrast to other earlier work focusing on fungal communities across similar mined and restored peatlands, bacterial and archaeal communities appeared to be more resistant or resilient to peat substrate changes brought

  9. Interannual variation in the composition of the assemblages of medusae and ctenophores in St. Helena Bay, Southern Benguela Ecosystem

    Directory of Open Access Journals (Sweden)

    Emmanuelle Buecher

    2000-12-01

    Full Text Available The assemblages of medusae and ctenophores were examined from samples collected each winter from St Helena Bay, over the 10-year period 1988-1997. A total of 50 hydromedusae, 1 scyphozoan and 2 ctenophore species were identified from 243 samples. Although the data set is characterised by great interannual variability, two main assemblages could be identified each year. These were characterised by either holoplanktonic medusae (e.g. Liriope tetraphylla, Aglaura hemistoma or meroplanktonic medusae (e.g. Mitrocomella millardae, Chrysaora hysoscella and ctenophores (e.g. Pleurobrachia pileus. The holoplanktonic medusae were typical of samples at the southern edge of the Bay, and were positively associated with both depth and temperature. Their abundances tended to increase during warm years (1992, 1993 and 1997 as warm surface water flooded the Bay. The meroplanktonic medusae and ctenophores were typical of samples collected within the Bay, and the density of species tended to be negatively correlated with temperature and depth. In spite of the eurythermal nature of the meroplanktonic species, they were more common during cold years (1990 and 1995. This paper represents the first Bay-wide, interannual study of any zooplankton group, and contributes important base line information on the structure of regional pelagic assemblages.

  10. Environmental variables measured at multiple spatial scales exert uneven influence on fish assemblages of floodplain lakes

    Science.gov (United States)

    Dembkowski, Daniel J.; Miranda, Leandro E.

    2014-01-01

    We examined the interaction between environmental variables measured at three different scales (i.e., landscape, lake, and in-lake) and fish assemblage descriptors across a range of over 50 floodplain lakes in the Mississippi Alluvial Valley of Mississippi and Arkansas. Our goal was to identify important local- and landscape-level determinants of fish assemblage structure. Relationships between fish assemblage structure and variables measured at broader scales (i.e., landscape-level and lake-level) were hypothesized to be stronger than relationships with variables measured at finer scales (i.e., in-lake variables). Results suggest that fish assemblage structure in floodplain lakes was influenced by variables operating on three different scales. However, and contrary to expectations, canonical correlations between in-lake environmental characteristics and fish assemblage structure were generally stronger than correlations between landscape-level and lake-level variables and fish assemblage structure, suggesting a hierarchy of influence. From a resource management perspective, our study suggests that landscape-level and lake-level variables may be manipulated for conservation or restoration purposes, and in-lake variables and fish assemblage structure may be used to monitor the success of such efforts.

  11. Fish assemblage structure and habitat associations in a large western river system

    Science.gov (United States)

    Smith, C.D.; Quist, Michael C.; Hardy, R. S.

    2016-01-01

    Longitudinal gradients of fish assemblage and habitat structure were investigated in the Kootenai River of northern Idaho. A total of 43 500-m river reaches was sampled repeatedly with several techniques (boat-mounted electrofishing, hoop nets and benthic trawls) in the summers of 2012 and 2013. Differences in habitat and fish assemblage structure were apparent along the longitudinal gradient of the Kootenai River. Habitat characteristics (e.g. depth, substrate composition and water velocity) were related to fish assemblage structure in three different geomorphic river sections. Upper river sections were characterized by native salmonids (e.g. mountain whitefish Prosopium williamsoni), whereas native cyprinids (peamouth Mylocheilus caurinus, northern pikeminnow Ptychocheilus oregonensis) and non-native fishes (pumpkinseed Lepomis gibbosus, yellow perch Perca flavescens) were common in the downstream section. Overall, a general pattern of species addition from upstream to downstream sections was discovered and is likely related to increased habitat complexity and additions of non-native species in downstream sections. Assemblage structure of the upper sections were similar, but were both dissimilar to the lower section of the Kootenai River. Species-specific hurdle regressions indicated the relationships among habitat characteristics and the predicted probability of occurrence and relative abundance varied by species. Understanding fish assemblage structure in relation to habitat could improve conservation efforts of rare fishes and improve management of coldwater river systems.

  12. Shikarpur lithic assemblage: New questions regarding Rohri chert blade production

    Directory of Open Access Journals (Sweden)

    Charusmita Gadekar

    2014-03-01

    Full Text Available Recent excavations at Shikarpur, a fortified Harappan site situated near the Gulf of Kuchchh in Gujarat, Western India, brought to light a large collection of Rohri chert blades.  Chert found in the Rohri hill near Sukkur in Sindh, central Pakistan is distinctive and easily identifiable. The wide distribution of standardized Rohri chert blades is often regarded as a testimony to the Harappan efficiency in long distance trade and craft production.  The possibility of localized production of Rohri chert blades in Gujarat is often negated due to the constraints of raw-material availability.  The absence of Rohri chert working debitage from most of the sites in Gujarat, has lent support to this position. The Shikarpur Rohri blade assemblage however incorporates more than 650 blades, a large fluted blade-core and a few Rohri chert debitage.  These have led the excavators to suggest that some of the blades found at Shikarpur were locally produced from raw materials brought to the site from the Rohri hills.  Typo-technological features of the Rohri chert assemblage from Shikarpur have been analysed in this background. These along with metrical features of the assemblage are compared with Rohri chert assemblages from other major Harappan sites in the region to check the validity of the proposed ‘limited local production’.

  13. Archaeal and bacterial community analysis of several Yellowstone National Park hot springs

    Science.gov (United States)

    Colman, D. R.; Takacs-Vesbach, C. D.

    2012-12-01

    The hot springs of Yellowstone National Park (YNP) are home to a diverse assemblage of microorganisms. Culture-independent studies have significantly expanded our understanding of the diversity of both Bacteria and Archaea present in YNP springs as well as the geochemical and ecological controls on communities. While the ecological analysis of Bacteria among the physicochemically heterogenous springs of YNP has been previously conducted, less is known about the extent of diversity of Archaeal communities and the chemical and ecological controls on their populations. Here we report a culture-independent analysis of 31 hot spring archaeal and bacterial communities of YNP springs using next generation sequencing. We found the phylogenetic diversity of Archaea to be generally comparable to that of co-occurring bacterial communities although overall, in the springs we investigated, diversity was higher for Bacteria than Archaea. Chemical and physical controls were similar for both domains with pH correlating most strongly with community composition. Community differences reflected the partitioning of taxonomic groups in low or high pH springs for both domains. Results will be discussed in a geochemical and ecological context.

  14. Mollusc life and death assemblages on a tropical rocky shore as proxies for the taphonomic loss in a fossil counterpart

    DEFF Research Database (Denmark)

    Sørensen, Anne Mehlin; Surlyk, Finn

    2013-01-01

    a lower taxonomic agreement to the death assemblage than found in previous published studies. Rocky shore life and death assemblages thus appear to show lower taxonomic agreement compared to muddy or sandy shelf assemblages due to the mix after death with the sandy beach assemblage. A hypothetical fossil......Comparison of a modern rocky shore mollusc life assemblage from Thailand with the associated death assemblage, and interpretation of the fossilization potential of the latter, are used to investigate the fidelity in reconstruction of ancient analogues. The fauna from the death assemblage represents...... species from the rocky shore and the associated sandy pocket beaches, and only a few exotic species from other, completely different habitats are present. The environmental fidelity between the life and death assemblage is thus high, with the majority of species from the death assemblage representing...

  15. Environmental constraints on the compositional and phylogenetic beta-diversity of tropical forest snake assemblages.

    Science.gov (United States)

    Moura, Mario R; Costa, Henrique C; Argôlo, Antônio J S; Jetz, Walter

    2017-09-01

    The ongoing biodiversity crisis increases the importance and urgency of studies addressing the role of environmental variation on the composition and evolutionary history of species assemblages, but especially the tropics and ectotherms remain understudied. In regions with rainy summers, coexistence of tropical ectothermic species may be determined by the partitioning of the climatic niche, as ectotherms can rely on water availability and thermoregulatory behaviour to buffer constraints along their climatic niche. Conversely, tropical ectotherms facing dry summers would have fewer opportunities to climatic niche partitioning and other processes rather than environmental filtering would mediate species coexistence. We used 218 snake assemblages to quantify the compositional (CBD) and phylogenetic (PBD) beta-diversity of snakes in the Atlantic Forest (AF) hotspot, South America. We identify two AF regions with distinct climatological regimes: dry summers in the northern-AF and rainy summers in the southern-AF. While accounting for the influence of multiscale spatial processes, we disentangle the relative contribution of thermal, water-related and topographic conditions in structuring the CBD and PBD of snake assemblages, and determine the extent in which snake assemblages under distinct climatological regimes are affected by environmental filtering. Thermal conditions best explain CBD and PBD of snakes for the whole AF, whereas water-related factors best explain the structure of snake assemblages within a same climatological regime. CBD and PBD patterns are similarly explained by spatial factors but snake assemblages facing dry summers are more affected by spatial processes operating at fine to intermediate spatial scale, whereas those assemblages in regions with rainy summers have a stronger signature of coarse-scale processes. As expected, environmental filtering plays a stronger role in southern-AF than northern-AF, and the synergism between thermal and water

  16. Sublittoral seaweed communities on natural and artificial substrata ...

    African Journals Online (AJOL)

    We also compared algal communities colonising ceramic, marble and pretreated ceramic tiles placed on the reef for six months. We identified 95 algae (14 Chlorophyta, 11 Phaeophyceae, 69 Rhodophyta and one cyanobacterium). Assemblages on natural and artificial substrata were dominated by the brown alga ...

  17. Hydrologic alteration affects aquatic plant assemblages in an arid-land river

    Science.gov (United States)

    Vinson, Mark; Hestmark, Bennett; Barkworth, Mary E.

    2014-01-01

    We evaluated the effects of long-term flow alteration on primary-producer assemblages. In 1962, Flaming Gorge Dam was constructed on the Green River. The Yampa River has remained an unregulated hydrologically variable river that joins the Green River 100 km downstream from Flaming Gorge Dam. In the 1960s before dam construction only sparse occurrences of two macroalgae, Cladophora and Chara, and no submerged vascular plants were recorded in the Green and Yampa rivers. In 2009–2010, aquatic plants were abundant and widespread in the Green River from the dam downstream to the confluence with the Yampa River. The assemblage consisted of six vascular species, Elodea canadensis, Myriophyllum sibiricum, Nasturtium officinale,Potamogeton crispus, Potamogeton pectinatus, and Ranunculus aquatilis, the macroalgae Chara and Cladophora, and the bryophyte, Amblystegium riparium. In the Green River downstream from the Yampa River, and in the Yampa River, only sparse patches of Chara and Cladophora growing in the splash zone on boulders were collected. We attribute the observed changes in the Green River to an increase in water transparency and a reduction in suspended and bed-load sediment and high flow disturbances. The lack of hydrophyte colonization downstream from the confluence with the Yampa River has implications for understanding tributary amelioration of dam effects and for designing more natural flow-regime schedules downstream from large dams.

  18. Presence of riparian vegetation increases biotic condition of fish assemblages in two Brazilian reservoirs

    OpenAIRE

    Ferreira, Fabio Cop; Souza, Ursulla Pereira; Petrere Junior2, Miguel

    2015-01-01

    Abstract The riparian vegetation in lakes and reservoirs is source of course wood structures such as trunks and branches and is used as sheltering, spawning and foraging habitats for fishes. The reduction of these submerged structures can thus, affect the composition and structure of fish assemblages in reservoirs. Aim To evaluate the influence of riparian vegetation on the biotic condition of fish assemblage by adapting the Reservoir Fish Assemblage Index (RFAI) to two reservoirs in the Upp...

  19. Patterns and drivers of bacterial α- and β-diversity across vertical profiles from surface to subsurface sediments.

    Science.gov (United States)

    Luna, Gian Marco; Corinaldesi, Cinzia; Rastelli, Eugenio; Danovaro, Roberto

    2013-10-01

    We investigated the patterns and drivers of bacterial α- and β-diversity, along with viral and prokaryotic abundance and the carbon production rates, in marine surface and subsurface sediments (down to 1 m depth) in two habitats: vegetated sediments (seagrass meadow) and non-vegetated sediments. Prokaryotic abundance and production decreased with depth in the sediment, but cell-specific production rates and the virus-to-prokaryote ratio increased, highlighting unexpectedly high activity in the subsurface. The highest diversity was observed in vegetated sediments. Bacterial β-diversity between sediment horizons was high, and only a minor number of taxa was shared between surface and subsurface layers. Viruses significantly contributed to explain α- and β-diversity patterns. Despite potential limitations due to the only use of fingerprinting techniques, this study indicates that the coastal subsurface host highly active and diversified bacterial assemblages, that subsurface cells are more active than expected and that viruses promote β-diversity and stimulate bacterial metabolism in subsurface layers. The limited number of taxa shared between habitats, and between surface and subsurface sediment horizons, suggests that future investigations of the shallow subsurface will provide insights into the census of bacterial diversity, and the comprehension of the patterns and drivers of prokaryotic diversity in marine ecosystems. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

  20. Benthic macroinvertebrate assemblages in mangroves and open ...

    African Journals Online (AJOL)

    Benthic macroinvertebrate assemblages in mangroves and open intertidal areas on the Dar es Salaam coast, Tanzania. ... it is recommended that conservation efforts along the Tanzanian coast should focus here. Keywords: benthic macrofauna, community structure, littoral zone, Tanganyika, Western Indian Ocean ...

  1. Coastal fish assemblages reflect geological and oceanographic gradients within an Australian zootone.

    Directory of Open Access Journals (Sweden)

    Euan S Harvey

    Full Text Available Distributions of mobile animals have been shown to be heavily influenced by habitat and climate. We address the historical and contemporary context of fish habitats within a major zootone: the Recherche Archipelago, southern western Australia. Baited remote underwater video systems were set in nine habitat types within three regions to determine the species diversity and relative abundance of bony fishes, sharks and rays. Constrained ordinations and multivariate prediction and regression trees were used to examine the effects of gradients in longitude, depth, distance from islands and coast, and epibenthic habitat on fish assemblage composition. A total of 90 species from 43 families were recorded from a wide range of functional groups. Ordination accounted for 19% of the variation in the assemblage composition when constrained by spatial and epibenthic covariates, and identified redundancy in the use of distance from the nearest emergent island as a predictor. A spatial hierarchy of fourteen fish assemblages was identified using multivariate prediction and regression trees, with the primary split between assemblages on macroalgal reefs, and those on bare or sandy habitats supporting seagrass beds. The characterisation of indicator species for assemblages within the hierarchy revealed important faunal break in fish assemblages at 122.30 East at Cape Le Grand and subtle niche partitioning amongst species within the labrids and monacanthids. For example, some species of monacanthids were habitat specialists and predominantly found on seagrass (Acanthaluteres vittiger, Scobinichthys granulatus, reef (Meuschenia galii, Meuschenia hippocrepis or sand habitats (Nelusetta ayraudi. Predatory fish that consume molluscs, crustaceans and cephalopods were dominant with evidence of habitat generalisation in reef species to cope with local disturbances by wave action. Niche separation within major genera, and a sub-regional faunal break, indicate future

  2. Influence of the nano-micro structure of the surface on bacterial adhesion

    Directory of Open Access Journals (Sweden)

    Carolina Díaz

    2007-03-01

    Full Text Available Biomaterials failures are frequently associated to the formation of bacterial biofilms on the surface. The aim of this work is to study the adhesion of non motile bacteria streptococci consortium and motile Pseudomonas fluorescens. Substrates with micro and nanopatterned topography were used. The influence of surface characteristics on bacterial adhesion was investigated using optical and epifluorescence microscopy, scanning electron microscopy (SEM and atomic force microscopy (AFM. Results showed an important influence of the substratum nature. On microrough surfaces, initial bacterial adhesion was less significant than on smooth surfaces. In contrast, nanopatterned samples showed more bacterial attachment than the smooth control. It was also noted a remarkable difference in morphology, orientation and distribution of bacteria between the smooth and the nanostructured substrate. The results show the important effect of substratum nature and topography on bacterial adhesion which depended on the relation between roughness characteristics dimensions and bacterial size.

  3. Survival of ship biofouling assemblages during and after voyages to the Canadian Arctic.

    Science.gov (United States)

    Chan, Farrah T; MacIsaac, Hugh J; Bailey, Sarah A

    2016-01-01

    Human-mediated vectors often inadvertently translocate species assemblages to new environments. Examining the dynamics of entrained species assemblages during transport can provide insights into the introduction risk associated with these vectors. Ship biofouling is a major transport vector of nonindigenous species in coastal ecosystems globally, yet its magnitude in the Arctic is poorly understood. To determine whether biofouling organisms on ships can survive passages in Arctic waters, we examined how biofouling assemblage structure changed before, during, and after eight round-trip military voyages from temperate to Arctic ports in Canada. Species richness first decreased (~70% loss) and then recovered (~27% loss compared to the original assemblages), as ships travelled to and from the Arctic, respectively, whereas total abundance typically declined over time (~55% total loss). Biofouling community structure differed significantly before and during Arctic transits as well as between those sampled during and after voyages. Assemblage structure varied across different parts of the hull; however, temporal changes were independent of hull location, suggesting that niche areas did not provide protection for biofouling organisms against adverse conditions in the Arctic. Biofouling algae appear to be more tolerant of transport conditions during Arctic voyages than are mobile, sessile, and sedentary invertebrates. Our results suggest that biofouling assemblages on ships generally have poor survivorship during Arctic voyages. Nonetheless, some potential for transporting nonindigenous species to the Arctic via ship biofouling remains, as at least six taxa new to the Canadian Arctic, including a nonindigenous cirripede, appeared to have survived transits from temperate to Arctic ports.

  4. Origin of an Assemblage Massively Dominated by Carnivorans from the Miocene of Spain

    Science.gov (United States)

    Domingo, M. Soledad; Alberdi, M. Teresa; Azanza, Beatriz; Silva, Pablo G.; Morales, Jorge

    2013-01-01

    Carnivoran-dominated fossil sites provide precious insights into the diversity and ecology of species rarely recovered in the fossil record. The lower level assemblage of Batallones-1 fossil site (Late Miocene; Madrid Basin, Spain) has yielded one of the most abundant and diversified carnivoran assemblage ever known from the Cenozoic record of mammals. A comprehensive taphonomic study is carried out here in order to constrain the concentration mode of this remarkable assemblage. Another distinctive feature of Batallones-1 is that the accumulation of carnivoran remains took place in the context of a geomorphological landform (cavity formation through a piping process) practically unknown in the generation of fossil sites. Two characteristics of the assemblage highly restrict the probable causes for the accumulation of the remains: (1) the overwhelming number of carnivorans individuals; and (2) the mortality profiles estimated for the four most abundant taxa do not correspond to the classic mortality types but rather were the consequence of the behavior of the taxa. This evidence together with other taphonomic data supports the hypothesis that carnivoran individuals actively entered the cavity searching for resources (food or water) and were unable to exit. The scarcity of herbivores implies that the shaft was well visible and avoided by these taxa. Fossil bones exhibit a very good preservation state as a consequence of their deposition in the restricted and protective environment of the chamber. Batallones-1 had another assemblage (upper level assemblage) that was dominated by herbivore remains and that potentially corresponded to the final stages of the cavity filling. PMID:23650542

  5. Assemblage Organization in Stream Fishes: Effects of Enviromental Variation and Interspecific Interactions

    Science.gov (United States)

    Gary D. Grossman; Robert E. Ratajczak; Maurice Crawford; Mary C. Freeman

    1998-01-01

    We assessed the relative importance of environmental variation, interspecific competition for space, and predator abundance on assemblage structure and microhabitat use in a stream fish assemblage inhabiting Coweeta Creek, North Carolina, USA. Our study encompassed a l0-yr time span (1983-1992) and included some of the highest and lowest flows in the last 58 years. We...

  6. Effects of Water Level Increase on Phytoplankton Assemblages in a Drinking Water Reservoir

    Directory of Open Access Journals (Sweden)

    Yangdong Pan

    2018-03-01

    Full Text Available Excessive water level fluctuation may affect physico-chemical characteristics, and consequently ecosystem function, in lakes and reservoirs. In this study, we assessed the changes of phytoplankton assemblages in response to water level increase in Danjiangkou Reservoir, one of the largest drinking water reservoirs in Asia. The water level increased from a low of 137 m to 161 m in 2014 as a part of the South–North Water Diversion Project. Phytoplankton assemblages were sampled four times per year before, during and after the water level increase, at 10 sites. Environmental variables such as total nitrogen as well as phytoplankton biomass decreased after the water level increase. Non-metric multi-dimensional scaling analysis indicated that before the water level increase, phytoplankton assemblages showed distinct seasonal variation with diatom dominance in both early and late seasons while such seasonal variation was much less evident after the water level increase. Month and year (before and after explained 13% and 6% of variance in phytoplankton assemblages (PERMANOVA, p < 0.001 respectively, and phytoplankton assemblages were significantly different before and after the water level increase. Both chlorophytes and cyanobacteria became more abundant in 2015. Phytoplankton compositional change may largely reflect the environmental changes, such as hydrodynamics mediated by the water level increase.

  7. Effects of organic pollution on biological communities of marine biofilm on hard substrata

    International Nuclear Information System (INIS)

    Sanz-Lázaro, C.; Fodelianakis, S.; Guerrero-Meseguer, L.; Marín, A.; Karakassis, I.

    2015-01-01

    We examined the effect of organic enrichment on diatom and bacterial assemblages of marine epilithic biofilms on two locations in the Mediterranean, one situated in Spain and the other in Greece. Total organic carbon, total organic nitrogen, stable isotopes (δ 13 C and δ 15 N) and chlorophyll a indicated significant incorporation of organic wastes, increased primary production and trophic niche modifications on the biofilms close to the organic enrichment source. In Spain, where the organic load was higher than in Greece, diatom and, to some extent, bacterial assemblages varied following the organic enrichment gradient. The taxonomic richness of diatom and bacterial communities was not influenced by organic enrichment. Classical community parameters showed consistent patterns to organic pollution in both locations, whereas community assemblages were only influenced when organic pollution was greatest. The successional patterns of these communities were similar to other epilithic communities. The modification of community assemblages induced by organic pollution may affect ecological functions. - Highlights: • We examined the effect of organic enrichment on assemblages of marine biofilms. • Classical community parameters showed consistent patterns to organic pollution. • Diatom and bacterial assemblages were affected under high level of organic enrichment. • Successional patterns were similar to other communities inhabiting hard substrata. • Assemblage modifications induced by organic pollution may affect ecological functions. - Organic pollution modifies the assemblages of biofilm communities which may affect important ecological functions

  8. Activity and Phylogenetic Diversity of Bacterial Cells with High and Low Nucleic Acid Content and Electron Transport System Activity in an Upwelling Ecosystem

    OpenAIRE

    Longnecker, K.; Sherr, B. F.; Sherr, E. B.

    2005-01-01

    We evaluated whether bacteria with higher cell-specific nucleic acid content (HNA) or an active electron transport system, i.e., positive for reduction of 5-cyano-2,3-ditolyl tetrazolium chloride (CTC), were responsible for the bulk of bacterioplankton metabolic activity. We also examined whether the phylogenetic diversity of HNA and CTC-positive cells differed from the diversity of Bacteria with low nucleic acid content (LNA). Bacterial assemblages were sampled both in eutrophic shelf waters...

  9. Distribution patterns of fish assemblages in an Eastern Mediterranean intermittent river

    Directory of Open Access Journals (Sweden)

    Vardakas L.

    2015-01-01

    Full Text Available The distribution patterns of fish assemblages within streams can provide insights for river type classifications and may warrant specific conservation actions. However, there is limited knowledge of how fish assemblages assort along a longitudinal axis in Mediterranean intermittent streams. Patterns in spatial and temporal distribution of fish communities were analysed in a Mediterranean intermittent river (Evrotas River located in Southern Greece, hosting three endemic range restricted species of high conservation concern, during the period 2007−2009, with 80% of the river’s total length desiccating in the 2007 and 2008 droughts. The general trend was an increase in fish density and species richness along an upstream-downstream gradient. Fish assemblages from upstream to downstream were characterized by a decrease of the most rheophilic species (Squalius keadicus and an increase of the most stagnophilic species (Tropidophoxinellus spartiaticus. Three river segments, characterized by a high degree of homogeneity were delineated. Habitat and environmental preferences for the studied fish species were identified, with elevation and low flowing habitats being the most important environmental factors affecting fish distribution patterns. The current study provides evidence that even in an intermittent river an assemblage pattern following a longitudinal gradient can be identified, mainly due to the lack of instream barriers that allows recolonization after flow resumption.

  10. Impacts of discarded plastic bags on marine assemblages and ecosystem functioning.

    Science.gov (United States)

    Green, Dannielle Senga; Boots, Bas; Blockley, David James; Rocha, Carlos; Thompson, Richard

    2015-05-05

    The accumulation of plastic debris is a global environmental problem due to its durability, persistence, and abundance. Although effects of plastic debris on individual marine organisms, particularly mammals and birds, have been extensively documented (e.g., entanglement and choking), very little is known about effects on assemblages and consequences for ecosystem functioning. In Europe, around 40% of the plastic items produced are utilized as single-use packaging, which rapidly accumulate in waste management facilities and as litter in the environment. A range of biodegradable plastics have been developed with the aspiration of reducing the persistence of litter; however, their impacts on marine assemblages or ecosystem functioning have never been evaluated. A field experiment was conducted to assess the impact of conventional and biodegradable plastic carrier bags as litter on benthic macro- and meio-faunal assemblages and biogeochemical processes (primary productivity, redox condition, organic matter content, and pore-water nutrients) on an intertidal shore near Dublin, Ireland. After 9 weeks, the presence of either type of bag created anoxic conditions within the sediment along with reduced primary productivity and organic matter and significantly lower abundances of infaunal invertebrates. This indicates that both conventional and biodegradable bags can rapidly alter marine assemblages and the ecosystem services they provide.

  11. The Roman-Irish Bath: Medical/health history as therapeutic assemblage.

    Science.gov (United States)

    Foley, Ronan

    2014-04-01

    The invention of a new form of hot-air bath in Blarney, Ireland in 1856, variously known in its lifetime as the Roman-Irish or Turkish Bath, acted as the starting point for a the production of a globalised therapeutic landscape. Tracking the diffusion of the Roman-Irish bath template from its local invention in Ireland to a global reach across the Victorian world and recognizing its place within a wider hydrotherapeutic history, this paper frames that diffusion as a valuable empirical addition to assemblage theory. The specific empirical history of the spread of the Roman-Irish/Turkish bath idea is drawn from primary archival and secondary historical sources. It is then discussed and, drawing from work on assemblage theory, analyzed against three broad themes: mobile networks, socio-material practices and contested emergence. The emergent relational geographies of the Roman-Irish Bath identify important roles for the diffusion and transformation of specific medical settings, identities and functions. These were linked in turn to competing social-healing pathways wherein bodies were technologically and morally managed, to produce a more inhabited form of therapeutic assemblage. In all cases the differential diffusion of the bath idea, it's shifting and fractured material forms and multiple inhabitations and discourses were contested and mobile and spoke to an assemblage approach which has ripe potential for exploration across a range of medical/health geography settings. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Local and regional effects of reopening a tidal inlet on estuarine water quality, seagrass habitat, and fish assemblages

    Science.gov (United States)

    Milbrandt, Eric C.; Bartleson, Richard D.; Coen, Loren D.; Rybak, Olexandr; Thompson, Mark A.; DeAngelo, Jacquelyn A.; Stevens, Philip W.

    2012-06-01

    Blind Pass is an inlet that separates Sanibel and Captiva Islands in southwest Florida but has historically closed and opened by both anthropogenic and natural processes. In July 2010, a dredging project to open the small inlet between the two barrier islands was completed. The objective of this study was to use and supplement ongoing estuary-monitoring programs to examine the responses of water quality, seagrass habitat metrics, and fish assemblages both in the immediate vicinity of the inlet and at broader scales (up to 40 km2). As far as we are aware, there are no previous studies with this intensity of sampling, both before and after an inlet opening. Significant increases in salinity and turbidity were observed inside Blind Pass, with significant decreases in CDOM and chlorophyll a, however, the effects were not far-reaching and limited to less than 1.7 km from the inlet within Pine Island Sound. Seagrass habitat metrics were expected to respond rapidly after the inlet was opened given the reduced light attenuation. However, there were no changes in shoot densities, species composition, and epiphytic algae within the approximately one-year duration of the study. The reopening of the pass did not substantially change fish assemblage structure, except for those from deeper habitats. Although immediate increases in the abundances of estuarine-dependent species were predicted in shallow habitats post opening, this did not occur. In conclusion, the effects of reopening a relatively small ocean inlet on water quality were apparent in the immediate vicinity of the inlet (within 1.7 km), but far-reaching effects on water quality, seagrass metrics, and fish assemblages were not immediately apparent in this well-flushed estuary. If subtle changes in tidal exchange and circulation affect productivity of seagrasses or its fish assemblages at broad scales, it may take several years to reach a steady state.

  13. Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage.

    Science.gov (United States)

    Chaillou, Stéphane; Chaulot-Talmon, Aurélie; Caekebeke, Hélène; Cardinal, Mireille; Christieans, Souad; Denis, Catherine; Desmonts, Marie Hélène; Dousset, Xavier; Feurer, Carole; Hamon, Erwann; Joffraud, Jean-Jacques; La Carbona, Stéphanie; Leroi, Françoise; Leroy, Sabine; Lorre, Sylvie; Macé, Sabrina; Pilet, Marie-France; Prévost, Hervé; Rivollier, Marina; Roux, Dephine; Talon, Régine; Zagorec, Monique; Champomier-Vergès, Marie-Christine

    2015-05-01

    The microbial spoilage of meat and seafood products with short shelf lives is responsible for a significant amount of food waste. Food spoilage is a very heterogeneous process, involving the growth of various, poorly characterized bacterial communities. In this study, we conducted 16S ribosomal RNA gene pyrosequencing on 160 samples of fresh and spoiled foods to comparatively explore the bacterial communities associated with four meat products and four seafood products that are among the most consumed food items in Europe. We show that fresh products are contaminated in part by a microbiota similar to that found on the skin and in the gut of animals. However, this animal-derived microbiota was less prevalent and less abundant than a core microbiota, psychrotrophic in nature, mainly originated from the environment (water reservoirs). We clearly show that this core community found on meat and seafood products is the main reservoir of spoilage bacteria. We also show that storage conditions exert strong selective pressure on the initial microbiota: alpha diversity in fresh samples was 189±58 operational taxonomic units (OTUs) but dropped to 27±12 OTUs in spoiled samples. The OTU assemblage associated with spoilage was shaped by low storage temperatures, packaging and the nutritional value of the food matrix itself. These factors presumably act in tandem without any hierarchical pattern. Most notably, we were also able to identify putative new clades of dominant, previously undescribed bacteria occurring on spoiled seafood, a finding that emphasizes the importance of using culture-independent methods when studying food microbiota.

  14. Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage

    Science.gov (United States)

    Chaillou, Stéphane; Chaulot-Talmon, Aurélie; Caekebeke, Hélène; Cardinal, Mireille; Christieans, Souad; Denis, Catherine; Hélène Desmonts, Marie; Dousset, Xavier; Feurer, Carole; Hamon, Erwann; Joffraud, Jean-Jacques; La Carbona, Stéphanie; Leroi, Françoise; Leroy, Sabine; Lorre, Sylvie; Macé, Sabrina; Pilet, Marie-France; Prévost, Hervé; Rivollier, Marina; Roux, Dephine; Talon, Régine; Zagorec, Monique; Champomier-Vergès, Marie-Christine

    2015-01-01

    The microbial spoilage of meat and seafood products with short shelf lives is responsible for a significant amount of food waste. Food spoilage is a very heterogeneous process, involving the growth of various, poorly characterized bacterial communities. In this study, we conducted 16S ribosomal RNA gene pyrosequencing on 160 samples of fresh and spoiled foods to comparatively explore the bacterial communities associated with four meat products and four seafood products that are among the most consumed food items in Europe. We show that fresh products are contaminated in part by a microbiota similar to that found on the skin and in the gut of animals. However, this animal-derived microbiota was less prevalent and less abundant than a core microbiota, psychrotrophic in nature, mainly originated from the environment (water reservoirs). We clearly show that this core community found on meat and seafood products is the main reservoir of spoilage bacteria. We also show that storage conditions exert strong selective pressure on the initial microbiota: alpha diversity in fresh samples was 189±58 operational taxonomic units (OTUs) but dropped to 27±12 OTUs in spoiled samples. The OTU assemblage associated with spoilage was shaped by low storage temperatures, packaging and the nutritional value of the food matrix itself. These factors presumably act in tandem without any hierarchical pattern. Most notably, we were also able to identify putative new clades of dominant, previously undescribed bacteria occurring on spoiled seafood, a finding that emphasizes the importance of using culture-independent methods when studying food microbiota. PMID:25333463

  15. A classic Late Frasnian chondrichthyan assemblage from southern Belgium

    Science.gov (United States)

    Ginter, Michał; Gouwy, Sofie; Goolaerts, Stijn

    2017-09-01

    Samples from the Upper Frasnian (Devonian) of Lompret Quarry and Nismes railway section in Dinant Synclinorium, southern Belgium, yielded several chondrichthyan teeth and scales. The teeth belong to three genera: Phoebodus, Cladodoides and Protacrodus. The comparison with selected Late Frasnian chondrichthyan assemblages from the seas between Laurussia and Gondwana revealed substantial local differences of taxonomic composition due to palaeoenvironmental conditions, such as depth, distance to submarine platforms, oxygenation of water, and possibly also temperature. The assemblage from Belgium, with its high frequency of phoebodonts, is the most similar to that from the Ryauzyak section, South Urals, Russia, and the Horse Spring section, Canning Basin, Australia.

  16. ANALISIS PERMUKIMAN PEMULUNG SEBAGAI SEBUAH ASSEMBLAGE STUDI KASUS: PERMUKIMAN PEMULUNG DI WILAYAH JURANGMANGU, TANGERANG SELATAN

    Directory of Open Access Journals (Sweden)

    Eka Permanasari

    2017-01-01

    There are some research on social and economical condition of informal waste-picker settlements. However, the research on the urban assemblage of informal waste-picker settlements are not very common. Therefore, this research focus on how the social and economical condition shape the informal waste-picker settlements in terms of urban assemblage.   This research investigates the development and transformation of the informal waste-picker settlements in two prime locations in Jurangmangu, South Tangerang. The methods are through observation and interview to key persons (leaders on each settlement. The urban assemblage on these waste-picker settlements is heavily influenced by social and economical condition and activity of their users.   Key words: waste picker settlements, urban assemblage, informality

  17. Characteristics of microfossils assemblages of core SB-01 from Sanshui basin and discussion of paleocene-eocene boundary

    International Nuclear Information System (INIS)

    Chen Liang; Xie Yecai; Wang Zhengqing; Ma Chuang

    2011-01-01

    Characteristics of microfossils assemblages of core SB-01 from Sanshui Basin have been analysised in this paper. Based on micropaleontological study and data from carbon and oxygen isotopes of bulk carbonates, which depth of Paleocene-Eocene boundary from the core was discussed. Ostracode assemblages include the Sinocypris nitela-Cyprois buxinensis-Limnocythere honggangensis assemblage(89.0-73.38 m) with few species and low abundance and the Sinocypris nitela-Cyprois buxinensis-Limnocythere honggangensis assemblage (73.38-0 m) with few species and low abundance during early and middle the core deposition and relatively many species and abundance increasing quickly of the late time of the core deposition; Charophyte assemblages contain the Peckichara subspherica-Rhabdochara jiangduensis assemblage (89.0-73.38 m) with rich species, high abundance and large sizes of fossils and the Gyrogona qianjiangica-Obtusochara brevicylindrica assemblage (73.38-53.75 m) with few species,low abundance and small sizes of fossils. At 73.38 m core depth, the great changes of microfossils assemblages and carbon isotopes values (decrease by more than 3.0 per thousand) and oxygen isotopes values of bulk carbonates take place, which consist with the geological records of the Paleocene-Eocene Thermal Maximum (PETM). Hence, Paleocene-Eocene boundary of SanShui Basin should be roughly placed at 73.38 m core depth. (authors)

  18. Antibiotics promote aggregation within aquatic bacterial communities

    Directory of Open Access Journals (Sweden)

    Gianluca eCorno

    2014-07-01

    Full Text Available The release of antibiotics (AB into the environment poses several threats for human health due to potential development of ABresistant natural bacteria. Even though the use of low-dose antibiotics has been promoted in health care and farming, significant amounts of AB are observed in aquatic environments. Knowledge on the impact of AB on natural bacterial communities is missing both in terms of spread and evolution of resistance mechanisms, and of modifications of community composition and productivity. New approaches are required to study the response of microbial communities rather than individual resistance genes. In this study a chemostat-based experiment with 4 coexisting bacterial strains has been performed to mimicking the response of a freshwater bacterial community to the presence of antibiotics in low and high doses. Bacterial abundance rapidly decreased by 75% in the presence of AB, independently of their concentration, and remained constant until the end of the experiment. The bacterial community was mainly dominated by Aeromonas hydrophila and Brevundimonas intermedia while the other two strains, Micrococcus luteus and Rhodococcus sp. never exceed 10%. Interestingly, the bacterial strains, which were isolated at the end of the experiment, were not AB-resistant, while reassembled communities composed of the 4 strains, isolated from treatments under AB stress, significantly raised their performance (growth rate, abundance in the presence of AB compared to the communities reassembled with strains isolated from the treatment without AB. By investigating the phenotypic adaptations of the communities subjected to the different treatments, we found that the presence of AB significantly increased co-aggregation by 5-6 fold.These results represent the first observation of co-aggregation as a successful strategy of AB resistance based on phenotype in aquatic bacterial communities, and can represent a fundamental step in the understanding of

  19. Simplification of arboreal marsupial assemblages in response to increasing urbanization.

    Science.gov (United States)

    Isaac, Bronwyn; White, John; Ierodiaconou, Daniel; Cooke, Raylene

    2014-01-01

    Arboreal marsupials play an essential role in ecosystem function including regulating insect and plant populations, facilitating pollen and seed dispersal and acting as a prey source for higher-order carnivores in Australian environments. Primarily, research has focused on their biology, ecology and response to disturbance in forested and urban environments. We used presence-only species distribution modelling to understand the relationship between occurrences of arboreal marsupials and eco-geographical variables, and to infer habitat suitability across an urban gradient. We used post-proportional analysis to determine whether increasing urbanization affected potential habitat for arboreal marsupials. The key eco-geographical variables that influenced disturbance intolerant species and those with moderate tolerance to disturbance were natural features such as tree cover and proximity to rivers and to riparian vegetation, whereas variables for disturbance tolerant species were anthropogenic-based (e.g., road density) but also included some natural characteristics such as proximity to riparian vegetation, elevation and tree cover. Arboreal marsupial diversity was subject to substantial change along the gradient, with potential habitat for disturbance-tolerant marsupials distributed across the complete gradient and potential habitat for less tolerant species being restricted to the natural portion of the gradient. This resulted in highly-urbanized environments being inhabited by a few generalist arboreal marsupial species. Increasing urbanization therefore leads to functional simplification of arboreal marsupial assemblages, thus impacting on the ecosystem services they provide.

  20. Invasive carnivores alter ecological function and enhance complementarity in scavenger assemblages on ocean beaches.

    Science.gov (United States)

    Brown, Marion B; Schlacher, Thomas A; Schoeman, David S; Weston, Michael A; Huijbers, Chantal M; Olds, Andrew D; Connolly, Rod M

    2015-10-01

    Species composition is expected to alter ecological function in assemblages if species traits differ strongly. Such effects are often large and persistent for nonnative carnivores invading islands. Alternatively, high similarity in traits within assemblages creates a degree of functional redundancy in ecosystems. Here we tested whether species turnover results in functional ecological equivalence or complementarity, and whether invasive carnivores on islands significantly alter such ecological function. The model system consisted of vertebrate scavengers (dominated by raptors) foraging on animal carcasses on ocean beaches on two Australian islands, one with and one without invasive red foxes (Vulpes vulpes). Partitioning of scavenging events among species, carcass removal rates, and detection speeds were quantified using camera traps baited with fish carcasses at the dune-beach interface. Complete segregation of temporal foraging niches between mammals (nocturnal) and birds (diurnal) reflects complementarity in carrion utilization. Conversely, functional redundancy exists within the bird guild where several species of raptors dominate carrion removal in a broadly similar way. As predicted, effects of red foxes were large. They substantially changed the nature and rate of the scavenging process in the system: (1) foxes consumed over half (55%) of all carrion available at night, compared with negligible mammalian foraging at night on the fox-free island, and (2) significant shifts in the composition of the scavenger assemblages consuming beach-cast carrion are the consequence of fox invasion at one island. Arguably, in the absence of other mammalian apex predators, the addition of red foxes creates a new dimension of functional complementarity in beach food webs. However, this functional complementarity added by foxes is neither benign nor neutral, as marine carrion subsidies to coastal red fox populations are likely to facilitate their persistence as exotic

  1. Arthropod assemblages on native and nonnative plant species of a coastal reserve in California.

    Science.gov (United States)

    Fork, Susanne K

    2010-06-01

    Biological invasions by nonnative plant species are a widespread phenomenon. Many studies have shown strong ecological impacts of plant invasions on native plant communities and ecosystem processes. Far fewer studies have examined effects on associated animal communities. From the perspective of a reserve's land management, I addressed the question of whether arthropod assemblages on two nonnative plant species of concern were impoverished compared with those assemblages associated with two predominant native plant species of that reserve. If the nonnative plant species, Conium maculatum L., and Phalaris aquatica L., supported highly depauperate arthropod assemblages compared with the native plant species, Baccharis pilularis De Candolle and Leymus triticoides (Buckley) Pilger, this finding would provide additional support for prioritizing removal of nonnatives and restoration of natives. I assessed invertebrate assemblages at the taxonomic levels of arthropod orders, Coleoptera families, and Formicidae species, using univariate analyses to examine community attributes (richness and abundance) and multivariate techniques to assess arthropod assemblage community composition differences among plant species. Arthropod richness estimates by taxonomic level between native and nonnative vegetation showed varying results. Overall, arthropod richness of the selected nonnative plants, examined at higher taxonomic resolution, was not necessarily less diverse than two of common native plants found on the reserve, although differences were found among plant species. Impacts of certain nonnative plant species on arthropod assemblages may be more difficult to elucidate than those impacts shown on native plants and ecosystem processes.

  2. Algal-bacterial interactions in metal contaminated floodplain sediments

    International Nuclear Information System (INIS)

    Boivin, M.E.Y.; Greve, G.D.; Garcia-Meza, J.V.; Massieux, B.; Sprenger, W.; Kraak, M.H.S.; Breure, A.M.; Rutgers, M.; Admiraal, W.

    2007-01-01

    The aim of the present study was to investigate algal-bacterial interactions in a gradient of metal contaminated natural sediments. By means of multivariate techniques, we related the genetic structure (denaturing gradient gel electrophoresis, DGGE) and the physiological structure (community-level physiological profiling, CLPP) of the bacterial communities to the species composition of the algal communities and to the abiotic environmental variables, including metal contamination. The results revealed that genetic and physiological structure of the bacterial communities correlated with the species composition of the algal community, but hardly to the level of metal pollution. This must be interpreted as an indication for a strong and species-specific linkage of algal and bacterial species in floodplain sediments. Metals were, however, not proven to affect either the algal or the bacterial communities of the Dutch river floodplains. - Algal and bacterial communities in floodplain sediments are interlinked, but are not affected by metal pollution

  3. Dust Rains Deliver Diverse Assemblages of Microorganisms to the Eastern Mediterranean

    Science.gov (United States)

    Itani, Ghida Nouhad; Smith, Colin Andrew

    2016-03-01

    Dust rains may be particularly effective at delivering microorganisms, yet their biodiversities have been seldom examined. During 2011 and 2012 in Beirut, Lebanon, 16 of 21 collected rainfalls appeared dusty. Trajectory modelling of air mass origins was consistent with North African sources and at least one Southwest Asian source. As much as ~4 g particulate matter, ~20 μg DNA, and 50 million colony forming units were found deposited per square meter during rainfalls each lasting less than one day. Sequencing of 93 bacteria and 25 fungi cultured from rain samples revealed diverse bacterial phyla, both Gram positive and negative, and Ascomycota fungi. Denaturing Gradient Gel Electrophoresis of amplified 16S rDNA of 13 rains revealed distinct and diverse assemblages of bacteria. Dust rain 16S libraries yielded 131 sequences matching, in decreasing order of abundance, Betaproteobacteria, Alphaproteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Cyanobacteria, Epsilonproteobacteria, Gammaproteobacteria, and Deltaproteobacteria. Clean rain 16S libraries yielded 33 sequences matching only Betaproteobacteria family Oxalobacteraceae. Microbial composition varied between dust rains, and more diverse and different microbes were found in dust rains than clean rains. These results show that dust rains deliver diverse communities of microorganisms that may be complex products of revived desert soil species and fertilized cloud species.

  4. Spatiotemporal dynamics of the bacterial microbiota on lacustrine Cladophora glomerata (Chlorophyta).

    Science.gov (United States)

    Braus, Michael J; Graham, Linda E; Whitman, Thea L

    2017-12-01

    The branched periphytic green alga Cladophora glomerata, often abundant in nearshore waters of lakes and rivers worldwide, plays important ecosystem roles, some mediated by epibiotic microbiota that benefit from host-provided surface, organic C, and O 2 . Previous microscopy and high-throughput sequencing studies have indicated surprising epibiont taxonomic and functional diversity, but have not included adequate consideration of sample replication or the potential for spatial and temporal variation. Here, we report the results of 16S rRNA amplicon-based phylum-to-genus taxonomic analysis of Cladophora-associated bacterial epibiota sampled in replicate from three microsites and at six times during the open-water season of 2014, from the same lake locale (Picnic Point, Lake Mendota, Dane Co., WI, USA) explored by high-throughput sequencing studies in two previous years. Statistical methods were used to test null hypotheses that the bacterial community: (i) is homogeneous across microsites tested, and (ii) does not change over the course of a growth season or among successive years. Results indicated a dynamic microbial community that is more strongly influenced by sampling day during the growth season than by microsite variation. A surprising diversity of bacterial genera known to be associated with the key function of methane-oxidation (methanotrophy), including relatively high-abundance of Crenothrix, Methylomonas, Methylovulum, and Methylocaldum-showed intraseasonal and interannual variability possibly related to temperature differences, and microsite preferences possibly related to variation in methane abundance. By contrast, a core assemblage of bacterial genera seems to persist over a growth season and from year to year, possibly transmitted by a persistent attached host resting stage. © 2017 Phycological Society of America.

  5. Arsenic uptake in bacterial calcite

    Science.gov (United States)

    Catelani, Tiziano; Perito, Brunella; Bellucci, Francesco; Lee, Sang Soo; Fenter, Paul; Newville, Matthew; Rimondi, Valentina; Pratesi, Giovanni; Costagliola, Pilario

    2018-02-01

    Bio-mediated processes for arsenic (As) uptake in calcite were investigated by means of X-ray Diffraction (XRD) and X-ray Absorption Spectroscopy (XAS) coupled with X-ray Fluorescence measurements. The environmental bacterial strain Bacillus licheniformis BD5, sampled at the Bullicame Hot Springs (Viterbo, Central Italy), was used to synthesize calcite from As-enriched growth media. Both liquid and solid cultures were applied to simulate planktonic and biofilm community environments, respectively. Bacterial calcite samples cultured in liquid media had an As enrichment factor (Kd) 50 times higher than that from solid media. The XRD analysis revealed an elongation of the crystal lattice along the c axis (by 0.03 Å) for biogenic calcite, which likely resulted from the substitution of larger arsenate for carbonate in the crystal. The XAS data also showed a clear difference in the oxidation state of sorbed As between bacterial and abiotic calcite. Abiotic chemical processes yielded predominantly As(V) uptake whereas bacterial precipitation processes led to the uptake of both As(III) and As(V). The presence of As(III) in bacterial calcite is proposed to result from subsequent reduction of arsenate to arsenite by bacterial activities. To the best of our knowledge, this is the first experimental observation of the incorporation of As(III) in the calcite crystal lattice, revealing a critical role of biochemical processes for the As cycling in nature.

  6. Arsenic uptake in bacterial calcite

    Energy Technology Data Exchange (ETDEWEB)

    Catelani, Tiziano; Perito, Brunella; Bellucci, Francesco; Lee, Sang Soo; Fenter, Paul; Newville, Matthew G.; Rimondi, Valentina; Pratesi, Giovanni; Costagliola, Pilario

    2018-02-01

    Bio-mediated processes for arsenic (As) uptake in calcite were investigated by means of X-ray Diffraction (XRD) and Xray Absorption Spectroscopy (XAS) coupled with X-ray Fluorescence measurements. The environmental bacterial strain Bacillus licheniformis BD5, sampled at the Bullicame Hot Springs (Viterbo, Central Italy), was used to synthesize calcite from As-enriched growth media. Both liquid and solid cultures were applied to simulate planktonic and biofilm community environments, respectively. Bacterial calcite samples cultured in liquid media had an As enrichment factor (Kd) 50 times higher than that from solid media. The XRD analysis revealed an elongation of the crystal lattice along the c axis (by 0.03Å) for biogenic calcite, which likely resulted from the substitution of larger arsenate for carbonate in the crystal. The XAS data also showed a clear difference in the oxidation state of sorbed As between bacterial and abiotic calcite. Abiotic chemical processes yielded predominantly As(V) uptake whereas bacterial precipitation processes led to the uptake of both As(III) and As(V). The presence of As(III) in bacterial calcite is proposed to result from subsequent reduction of arsenate to arsenite by bacterial activities. To the best of our knowledge, this is the first experimental observation of the incorporation of As(III) in the calcite crystal lattice, revealing a critical role of biochemical processes for the As cycling in nature.

  7. Influence of land use on bacterial and archaeal diversity and community structures in three natural ecosystems and one agricultural soil.

    Science.gov (United States)

    Lynn, Tin Mar; Liu, Qiong; Hu, Yajun; Yuan, Hongzhao; Wu, Xiaohong; Khai, Aye Aye; Wu, Jinshui; Ge, Tida

    2017-07-01

    Studying shifts in microbial communities under different land use can help in determining the impact of land use on microbial diversity. In this study, we analyzed four different land-use types to determine their bacterial and archaeal diversity and abundance. Three natural ecosystems, that is, wetland (WL), grassland (GL), and forest (FR) soils, and one agricultural soil, that is, tea plantation (TP) soil, were investigated to determine how land use shapes bacterial and archaeal diversity. For this purpose, molecular analyses, such as quantitative polymerase chain reaction (Q-PCR), 16S rRNA gene sequencing, and terminal restriction fragment length polymorphism (T-RFLP), were used. Soil physicochemical properties were determined, and statistical analyses were performed to identify the key factors affecting microbial diversity in these soils. Phylogenetic affiliations determined using the Ribosomal Database Project (RDP) database and T-RFLP revealed that the soils had differing bacterial diversity. WL soil was rich in only Proteobacteria, whereas GR soil was rich in Proteobacteria, followed by Actinobacteria. FR soil had higher abundance of Chloroflexi species than these soils. TP soil was rich in Actinobacteria, followed by Chloroflexi, Acidobacteria, Proteobacteria, and Firmicutes. The archaeal diversity of GL and FR soils was similar in that most of their sequences were closely related to Nitrososphaerales (Thaumarchaeota phylum). In contrast, WL soil, followed by TP soil, had greater archaeal diversity than other soils. Eight different archaeal classes were found in WL soil, and Pacearchaeota class was the richest one. The abundance of bacterial and archaeal 16S rRNA gene copies in WL and GL soils was significantly higher than that in FR and TP soils. Redundancy analysis showed that bacterial diversity was influenced by abiotic factors, e.g., total organic carbon and pH, whereas total nitrogen, pH, and cation exchange capacity (CEC) significantly affected

  8. Testing for functional convergence of temperate rainforest tree assemblages in Chile and New Zealand

    NARCIS (Netherlands)

    Lusk, C.H.; Jimenez-Castillo, M.; Aragón, R.; Easdale, T.A.; Poorter, L.; Hinojosa, L.F.; Mason, N.W.H.W.H.

    2016-01-01

    An important tenet of biogeography and comparative ecology is that disjunct assemblages in similar physical environments are functionally more similar to each other than to assemblages from other environments. Temperate rainforests in South America, New Zealand and Australia share certain

  9. Holocene molluscan assemblages in the Magellan region

    Directory of Open Access Journals (Sweden)

    Sandra Gordillo

    1999-12-01

    Full Text Available In the Magellan region, much of the shoreline of the Beagle Channel coast (54°53´S; 67° - 68°W is bordered by Holocene raised beaches, which contain a large number of molluscs and other shelled taxa. The purpose of this work is to document the presence of various molluscan assemblages deposited with little or no postmortem transportation. An epifaunal Chlamys patagonica palaeocommunity (ca. 8,000 - 7,000 BP and three infaunal (Tawera gayi, Ameghinomya antiqua - Hiatella solida and Ameghinomya antiqua - Ensis macha palaeocommunities (ca. 4,400 - 4,000 BP were recognized. All the assemblages studied represent shallow, subtidal, cold-temperate environments. Based on comparisons with modern benthic communities in this region, these associations show that no remarkable ecologic and climatic changes occurred during the period ca. 8,000 - 4,000 BP. Thus, an apparent stability of modern marine communities over a period of several thousand years is suggested.

  10. High prevalence of biofilm synergy among bacterial soil isolates in cocultures indicates bacterial interspecific cooperation

    DEFF Research Database (Denmark)

    Ren, Dawei; Madsen, Jonas Stenløkke; Sørensen, Søren Johannes

    2015-01-01

    of single-species biofilms, indicating that all the individual strains benefit from inclusion in the multispecies community. Our results show a high prevalence of synergy in biofilm formation in multispecies consortia isolated from a natural bacterial habitat and suggest that interspecific cooperation...

  11. The effects of host age and spatial location on bacterial community composition in the English Oak tree (Quercus robur).

    Science.gov (United States)

    Meaden, S; Metcalf, C J E; Koskella, B

    2016-04-27

    Drivers of bacterial community assemblages associated with plants are diverse and include biotic factors, such as competitors and host traits, and abiotic factors, including environmental conditions and dispersal mechanisms. We examine the roles of spatial distribution and host size, as an approximation for age, in shaping the microbiome associated with Quercus robur woody tissue using culture-independent 16S rRNA gene amplicon sequencing. In addition to providing a baseline survey of the Q. robur microbiome, we screened for the pathogen of acute oak decline. Our results suggest that age is a predictor of bacterial community composition, demonstrating a surprising negative correlation between tree age and alpha diversity. We find no signature of dispersal limitation within the Wytham Woods plot sampled. Together, these results provide evidence for niche-based hypotheses of community assembly and the importance of tree age in bacterial community structure, as well as highlighting that caution must be applied when diagnosing dysbiosis in a long-lived plant host. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  12. Hybrid carbon nanostructure assemblage for high performance pseudo-capacitors

    Directory of Open Access Journals (Sweden)

    A. K. Mishra

    2012-06-01

    Full Text Available Investigation of novel nanocomposites for pseudo-capacitors with high capacitance and energy density is the spotlight of current energy research. In the present work, hybrid carbon nanostructure assemblage of graphene and multiwalled carbon nanotubes has been used as carbon support to nanostructured RuO2 and polyaniline for high energy supercapacitors. Maximum specific capacitances of 110, 235 and 440 F g−1 at the voltage sweep rate of 10 mV s−1 and maximum energy densities of 7, 12.5 and 20.5 Wh kg−1 were observed for carbon assemblage and its RuO2 and polyanilne decorated nanocomposites, respectively, with 1M H2SO4 as electrolyte.

  13. Sensitivity of metrics of phylogenetic structure to scale, source of data and species pool of hummingbird assemblages along elevational gradients.

    Directory of Open Access Journals (Sweden)

    Sebastián González-Caro

    Full Text Available Patterns of phylogenetic structure of assemblages are increasingly used to gain insight into the ecological and evolutionary processes involved in the assembly of co-occurring species. Metrics of phylogenetic structure can be sensitive to scaling issues and data availability. Here we empirically assess the sensitivity of four metrics of phylogenetic structure of assemblages to changes in (i the source of data, (ii the spatial grain at which assemblages are defined, and (iii the definition of species pools using hummingbird (Trochilidae assemblages along an elevational gradient in Colombia. We also discuss some of the implications in terms of the potential mechanisms driving these patterns. To explore how source of data influence phylogenetic structure we defined assemblages using three sources of data: field inventories, museum specimens, and range maps. Assemblages were defined at two spatial grains: coarse-grained (elevational bands of 800-m width and fine-grained (1-km(2 plots. We used three different species pools: all species contained in assemblages, all species within half-degree quadrats, and all species either above or below 2000 m elevation. Metrics considering phylogenetic relationships among all species within assemblages showed phylogenetic clustering at high elevations and phylogenetic evenness in the lowlands, whereas those metrics considering only the closest co-occurring relatives showed the opposite trend. This result suggests that using multiple metrics of phylogenetic structure should provide greater insight into the mechanisms shaping assemblage structure. The source and spatial grain of data had important influences on estimates of both richness and phylogenetic structure. Metrics considering the co-occurrence of close relatives were particularly sensitive to changes in the spatial grain. Assemblages based on range maps included more species and showed less phylogenetic structure than assemblages based on museum or field

  14. Dynamics of avian haemosporidian assemblages through millennial time scales inferred from insular biotas of the West Indies.

    Science.gov (United States)

    Soares, Leticia; Latta, Steven C; Ricklefs, Robert E

    2017-06-20

    Although introduced hemosporidian (malaria) parasites (Apicomplexa: Haemosporida) have hastened the extinction of endemic bird species in the Hawaiian Islands and perhaps elsewhere, little is known about the temporal dynamics of endemic malaria parasite populations. Haemosporidian parasites do not leave informative fossils, and records of population change are lacking beyond a few decades. Here, we take advantage of the isolation of West Indian land-bridge islands by rising postglacial sea levels to estimate rates of change in hemosporidian parasite assemblages over a millennial time frame. Several pairs of West Indian islands have been connected and separated by falling and rising sea levels associated with the advance and retreat of Pleistocene continental glaciers. We use island isolation following postglacial sea-level rise, ca. 2.5 ka, to characterize long-term change in insular assemblages of hemosporidian parasites. We find that assemblages on formerly connected islands are as differentiated as assemblages on islands that have never been connected, and both are more differentiated than local assemblages sampled up to two decades apart. Differentiation of parasite assemblages between formerly connected islands reflects variation in the prevalence of shared hemosporidian lineages, whereas differentiation between islands isolated by millions of years reflects replacement of hemosporidian lineages infecting similar assemblages of avian host species.

  15. Bottom fish assemblages at the shelf and continental slope off East Greenland

    DEFF Research Database (Denmark)

    Jørgensen, Ole A; Hvingel, Carsten; Møller, P.R.

    2015-01-01

    During 2006 and 2008 two bottom trawl surveys were conducted at East Greenland to 72°N covering depths down to 1500 m. In the 149 trawl hauls in total 113 fish species were recorded of which 37 were considered pelagic and excluded from the analyses. As a first step the abundance data for the 76...... benthic species were used for analyses of the fish fauna diversity and fish assemblages. Nine assemblages were found by a standard type of cluster analysis. A Bayesian multinomial logit model was then applied to calculate vectors of probabilities defining the likelihood of each haul belonging to each...... distribution, species composition, temperature and depth. Three of the assemblages were located in the cold Iceland Sea while six were found in the somewhat warmer Irminger Sea...

  16. Sponge assemblages on the deep Mediterranean continental shelf and slope (Menorca Channel, Western Mediterranean Sea)

    Science.gov (United States)

    Santín, Andreu; Grinyó, Jordi; Ambroso, Stefano; Uriz, Maria J.; Gori, Andrea; Dominguez-Carrió, Carlos; Gili, Josep-Maria

    2018-01-01

    Sponge assemblages on continental shelves and slopes around the world have been known about for centuries. However, due to limitations of the traditional sampling systems, data about individual sponge species rather than assemblages have been reported. This study characterizes sponge assemblages over a wide bathymetric range ( 50-350 m depth) and covering the entire continental shelf and the upper slope of the Menorca Channel, an area soon to be declared a Marine Protected Area (MPA) as part of the Natura 2000 Network. Quantitative analysis of 85 video-transects (a total linear distance of 75 km), together with representative collections to confirm species identifications, allowed us to discriminate six major assemblages. Differences in the assemblages mainly corresponded to differences in substrate type and depth. On the inner continental shelf, a semi-sciaphilous Axinellid assemblage dominated the rocky outcrops. Maërl beds on the inner continental shelf were dominated by Haliclona (Reniera) mediterranea, whereas the horny sponge Aplysina cavernicola and several other haliclonids mostly dominated maërl beds and rocky substrates of the outer shelf. Soft sediments on the shelf break hosted a monospecific Thenea muricata assemblage, whereas rocky substrates of the shelf break were characterized by a mixture of encrusting, columnar and fan-shaped sponges. Finally, the upper slope was dominated by Hamacantha (Vomerula) falcula and the hexactinellid Tretodictyum reiswigi. Overall, sponge diversity showed its highest values above the shelf break, plummeting severely on the upper slope. Despite this diversity decrease, we found very high densities (> 70 ind./m2) of sponges over vast areas of both the shelf break and the upper slope.

  17. Ecological release in lizard assemblages of neotropical savannas.

    Science.gov (United States)

    Mesquita, Daniel Oliveira; Colli, Guarino Rinaldi; Vitt, Laurie J

    2007-08-01

    We compare lizard assemblages of Cerrado and Amazonian savannas to test the ecological release hypothesis, which predicts that niche dimensions and abundance should be greater in species inhabiting isolated habitat patches with low species richness (Amazonian savannas and isolated Cerrado patches) when compared with nonisolated areas in central Cerrado with greater species richness. We calculated microhabitat and diet niche breadths with data from 14 isolated Cerrado patches and Amazon savanna areas and six central Cerrado populations. Morphological data were compared using average Euclidean distances, and lizard abundance was estimated using the number of lizards captured in pitfall traps over an extended time period. We found no evidence of ecological release with respect to microhabitat use, suggesting that historical factors are better microhabitat predictors than ecological factors. However, data from individual stomachs indicate that ecological release occurs in these areas for one species (Tropidurus) but not others (Ameiva ameiva, Anolis, Cnemidophorus, and Micrablepharus), suggesting that evolutionary lineages respond differently to environmental pressures, with tropidurids being more affected by ecological factors than polychrotids, teiids, and gymnophthalmids. We found no evidence that ecological release occurs in these areas using morphological data. Based on abundance data, our results indicate that the ecological release (density compensation) hypothesis is not supported: lizard species are not more abundant in isolated areas than in nonisolated areas. The ecology of species is highly conservative, varying little from assemblage to assemblage. Nevertheless, increases in niche breadth for some species indicate that ecological release occurs as well.

  18. Soil metal concentrations and vegetative assemblage structure in an urban brownfield

    International Nuclear Information System (INIS)

    Gallagher, Frank J.; Pechmann, Ildiko; Bogden, John D.; Grabosky, Jason; Weis, Peddrick

    2008-01-01

    Anthropogenic sources of toxic elements have had serious ecological and human health impacts. Analysis of the soil samples from a brownfield within Liberty State Park, Jersey City, NJ, USA, showed that arsenic, chromium, lead, zinc and vanadium exist at concentrations above those considered ambient for the area. Accumulation and translocation features were characterized for the dominant plant species of four vegetative assemblages. The trees Betula populifolia and Populus deltoides were found to be accumulating Zn in leaf tissue at extremely high levels. B. populifolia, P. deltoides and Rhus copallinum accumulated Cr primarily in the root tissue. A comparison of soil metal maps and vegetative assemblage maps indicates that areas of increasing total soil metal load were dominated by successional northern hardwoods while semi-emergent marshes consisting mostly of endemic species were restricted primarily to areas of low soil metal load. - The study yields insight into the impact of metal contaminates soils on vegetative assemblage structure and development

  19. Impacts of fishing and environmental factors driving changes on littoral fish assemblages in a subtropical oceanic island

    Science.gov (United States)

    Sangil, Carlos; Martín-García, Laura; Hernández, José Carlos; Concepción, Laura; Fernández, Raúl; Clemente, Sabrina

    2013-08-01

    The structure of demersal fish assemblages of commercial interest was studied at 51 sites on La Palma Island (Canary Islands, northeastern Atlantic). On this island, demersal fish populations are limited and independent from other islands. As deep water separates the islands and the shallow sublittoral platforms are not continuous, adult inter-island migrations are not possible except between the islands of Lanzarote and Fuerteventura. Otherwise, each island functions as a closed system, and the status of an island fish assemblage depends on local environmental conditions and activities performed in situ by the islanders. These circumstances provide a unique opportunity to test the intrainsular variability of fish assemblages. With this background, environmental parameters, fishing pressure and distance to the MPA were considered to identify the main factors explaining the spatial variation of fish assemblages off La Palma Island. Twenty-six fish species were recorded, but 60% of the total fish biomass was represented by only five species (Sparisoma cretense, Pomadasys incisus, Canthidermis sufflamen, Diplodus cervinus cervinus and Bodianus scrofa). However, the structure of assemblages was heterogeneous in response to different variables and showed substantial spatial variation. The assemblages were strongly modified by the presence of upright seaweed cover, fishing activities, and certain environmental variables. Differences were more pronounced in species that occupied the higher trophic levels. The most disturbed assemblages were those located in areas with lower upright seaweed cover and with higher fishing pressure, whereas the best-preserved assemblages corresponded to sites with controlled fishing activities, located within the MPA.

  20. The intrinsic resistome of bacterial pathogens.

    Science.gov (United States)

    Olivares, Jorge; Bernardini, Alejandra; Garcia-Leon, Guillermo; Corona, Fernando; B Sanchez, Maria; Martinez, Jose L

    2013-01-01

    Intrinsically resistant bacteria have emerged as a relevant health problem in the last years. Those bacterial species, several of them with an environmental origin, present naturally low-level susceptibility to several drugs. It has been proposed that intrinsic resistance is mainly the consequence of the impermeability of cellular envelopes, the activity of multidrug efflux pumps or the lack of appropriate targets for a given family of drugs. However, recently published articles indicate that the characteristic phenotype of susceptibility to antibiotics of a given bacterial species depends on the concerted activity of several elements, what has been named as intrinsic resistome. These determinants comprise not just classical resistance genes. Other elements, several of them involved in basic bacterial metabolic processes, are of relevance for the intrinsic resistance of bacterial pathogens. In the present review we analyze recent publications on the intrinsic resistomes of Escherichia coli and Pseudomonas aeruginosa. We present as well information on the role that global regulators of bacterial metabolism, as Crc from P. aeruginosa, may have on modulating bacterial susceptibility to antibiotics. Finally, we discuss the possibility of searching inhibitors of the intrinsic resistome in the aim of improving the activity of drugs currently in use for clinical practice.

  1. The intrinsic resistome of bacterial pathogens

    Directory of Open Access Journals (Sweden)

    Jorge Andrés Olivares Pacheco

    2013-04-01

    Full Text Available Intrinsically resistant bacteria have emerged as a relevant health problem in the last years. Those bacterial species, several of them with an environmental origin, present naturally a low-level susceptibility to several drugs. It has been proposed that intrinsic resistance is mainly the consequence of the impermeability of cellular envelopes, the activity of multidrug efflux pumps or the lack of appropriate targets for a given family of drugs. However, recently published articles indicate that the characteristic phenotype of susceptibility to antibiotics of a given bacterial species depends on the concerted activity of several elements, what has been named as intrinsic resistome. These determinants comprise not just classical resistance genes. Other elements, several of them involved in basic bacterial metabolic processes, are of relevance for the intrinsic resistance of bacterial pathogens. In the present review we analyse recent publications on the intrinsic resistomes of Escherichia coli and Pseudomonas aeruginosa. We present as well information on the role that global regulators of bacterial metabolism, as Crc from P. aeruginosa, may have on modulating bacterial susceptibility to antibiotics. Finally, we discuss the possibility of searching inhibitors of the intrinsic resistome in the aim of improving the activity of drugs currently in use for clinical practice.

  2. Stabilization of bacterially expressed erythropoietin by single site-specific introduction of short branched PEG chains at naturally occurring glycosylation sites.

    Science.gov (United States)

    Hoffmann, E; Streichert, K; Nischan, N; Seitz, C; Brunner, T; Schwagerus, S; Hackenberger, C P R; Rubini, M

    2016-05-24

    The covalent attachment of polyethylene glycol (PEG) to therapeutic proteins can improve their physicochemical properties. In this work we utilized the non-natural amino acid p-azidophenylalanine (pAzF) in combination with the chemoselective Staudinger-phosphite reaction to install branched PEG chains to recombinant unglycosylated erythropoietin (EPO) at each single naturally occurring glycosylation site. PEGylation with two short 750 or 2000 Da PEG units at positions 24, 38, or 83 significantly decreased unspecific aggregation and proteolytic degradation while biological activity in vitro was preserved or even increased in comparison to full-glycosylated EPO. This site-specific bioconjugation approach permits to analyse the impact of PEGylation at single positions. These results represent an important step towards the engineering of site-specifically modified EPO variants from bacterial expression with increased therapeutic efficacy.

  3. Application of bacterial cytological profiling to crude natural product extracts reveals the antibacterial arsenal of Bacillus subtilis.

    Science.gov (United States)

    Nonejuie, Poochit; Trial, Rachelle M; Newton, Gerald L; Lamsa, Anne; Ranmali Perera, Varahenage; Aguilar, Julieta; Liu, Wei-Ting; Dorrestein, Pieter C; Pogliano, Joe; Pogliano, Kit

    2016-05-01

    Although most clinically used antibiotics are derived from natural products, identifying new antibacterial molecules from natural product extracts is difficult due to the complexity of these extracts and the limited tools to correlate biological activity with specific molecules. Here, we show that bacterial cytological profiling (BCP) provides a rapid method for mechanism of action determination on plates and in complex natural product extracts and for activity-guided purification. We prepared an extract from Bacillus subtilis 3610 that killed the Escherichia coli lptD mutant and used BCP to observe two types of bioactivities in the unfractionated extract: inhibition of translation and permeablization of the cytoplasmic membrane. We used BCP to guide purification of the molecules responsible for each activity, identifying the translation inhibitors bacillaene and bacillaene B (glycosylated bacillaene) and demonstrating that two molecules contribute to cell permeabilitization, the bacteriocin subtilosin and the cyclic peptide sporulation killing factor. Our results suggest that bacillaene mediates translational arrest, and show that bacillaene B has a minimum inhibitory concentration 10 × higher than unmodified bacillaene. Finally, we show that BCP can be used to screen strains on an agar plate without the need for extract preparation, greatly saving time and improving throughput. Thus, BCP simplifies the isolation of novel natural products, by identifying strains, crude extracts and fractions with interesting bioactivities even when multiple activities are present, allowing investigators to focus labor-intensive steps on those with desired activities.

  4. The influence of finfish aquaculture on benthic fish and crustacean assemblages in Fitzgerald Bay, South Australia

    Directory of Open Access Journals (Sweden)

    Jason E. Tanner

    2015-09-01

    Full Text Available The influence of sea-cage aquaculture on wildfish assemblages has received little attention outside of Europe. Sea-cage aquaculture of finfish is a major focus in South Australia, and while the main species farmed is southern bluefin tuna (Thunnus maccoyii, there is also an important yellowtail kingfish (Seriola lalandi industry. Yellowtail kingfish aquaculture did not appear to have any local or regional effects on demersal assemblages (primarily fish, but also some crustaceans surveyed by baited remote underwater video (BRUV in Fitzgerald Bay. We did, however, detect small scale spatial variations in assemblages within the bay. The type of bait used strongly influenced the assemblage recorded, with significantly greater numbers of fish attracted to deployments where sardines were used as the bait to compared to those with no bait. The pelleted feed used by the aquaculture industry was just as attractive as sardines at one site, and intermediate between sardines and no bait at the other. There was significant temporal variability in assemblages at both farm sites and one control site, while the second control site was temporally stable (over the 9 weeks of the study. Overall, the results suggested that aquaculture was having little if any impact on the abundance and assemblage structure of the demersal macrofauna in Fitzgerald Bay.

  5. Differences in the structure of copepod assemblages in four tropical estuaries: Importance of pollution and the estuary hydrodynamics.

    Science.gov (United States)

    Araujo, Adriana V; Dias, Cristina O; Bonecker, Sérgio L C

    2017-02-15

    We examined the relationship between pollution and structure of copepod assemblages in estuaries, using sampling standardization of salinity range to reduce the effects of "Estuarine Quality Paradox". Copepod assemblages were analyzed in four Southeast Brazilian estuaries with different water quality levels and different hydrodynamic characteristics. The pollution negatively impacted the descriptors of the assemblage structure. The distribution of structure of copepod assemblages also showed a main separation trend between the most polluted estuaries and those less polluted. Temperature was the main factor affecting the assemblage structuring in the four estuaries. This factor acted in synergism with the effects of pollution impact and physical characteristics of the estuaries on the structure of copepod assemblages, supporting the potential vulnerability of coastal environments due to nutrient enrichment associated with climate change. Our study demonstrated the importance of sampling standardization of the salinity range in estuaries for reliable analysis of pollution effects on biota. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Intra-Diegetic Cameras as Cinematic Actor Assemblages in Found Footage Horror Cinema

    DEFF Research Database (Denmark)

    Rødje, Kjetil

    2017-01-01

    that comprises what is commonly known as human actors as well as material entities that play an active part in motion picture images. The use of intra-diegetic cameras in contemporary found footage horror films constitutes a particular case of such cinematic actor assemblages. Through a dynamic relational...... performance, cameras here take on roles as active agents with the potential to affect other elements within the images as well as the films’ audiences. In found footage horror the assemblage mode of operation creates suspense, since the vulnerability of the camera threatens the viewer's access to the depicted...... events. While human characters and individual entities making up the camera assemblage are disposable, the recording is not. Found footage horror crucially hinges upon the survival of the footage. I will further suggest that these films allow filmmakers to experiment with the acting capabilities of intra...

  7. Carbon nanotubes as anti-bacterial agents.

    Science.gov (United States)

    Mocan, Teodora; Matea, Cristian T; Pop, Teodora; Mosteanu, Ofelia; Buzoianu, Anca Dana; Suciu, Soimita; Puia, Cosmin; Zdrehus, Claudiu; Iancu, Cornel; Mocan, Lucian

    2017-10-01

    Multidrug-resistant bacterial infections that have evolved via natural selection have increased alarmingly at a global level. Thus, there is a strong need for the development of novel antibiotics for the treatment of these infections. Functionalized carbon nanotubes through their unique properties hold great promise in the fight against multidrug-resistant bacterial infections. This new family of nanovectors for therapeutic delivery proved to be innovative and efficient for the transport and cellular translocation of therapeutic molecules. The current review examines the latest progress in the antibacterial activity of carbon nanotubes and their composites.

  8. Megabenthic assemblages in the continental shelf edge and upper slope of the Menorca Channel, Western Mediterranean Sea

    Science.gov (United States)

    Grinyó, Jordi; Gori, Andrea; Greenacre, Michael; Requena, Susana; Canepa, Antonio; Lo Iacono, Claudio; Ambroso, Stefano; Purroy, Ariadna; Gili, Josep-Maria

    2018-03-01

    Highly diverse megabenthic assemblages dominated by passive and active suspension feeders have been recently reported in shelf edge environments of the Mediterranean Sea. Due to their frequent association with species of commercial interest, these assemblages have been heavily impacted by fishing. The vulnerability and low resilience of these assemblages, composed mainly by long-living and slow-growing species, have motivated the implementation of management measures such as the restriction of bottom trawling, and the establishment of large protected areas embracing these environments. The Menorca Channel is one of such areas recently included in the European Union Natura 2000 network. Quantitative analysis of video transects recorded at 95-360 m depth by manned submersible and remotely operated vehicles were used to characterize megabenthic assemblages and to assess their geographical and bathymetric distribution. Six different assemblages were identified, mainly segregated by substrate type and depth. Hard substrates hosted coral gardens and sponge grounds, whereas soft sediments were mainly characterized by large extensions of the crinoid Leptometra phalangium and the brachiopod Gryphus vitreus. The good preservation of most of the observed assemblages is probably related to a low bottom trawling pressure, which mainly concentrates deeper on the adjacent continental slope. Because of their biological and ecological value, management and conservation measures need to be established to preserve these benthic assemblages.

  9. Fouling assemblages associated with estuarine artificial reefs in new South Wales, Australia

    Directory of Open Access Journals (Sweden)

    Rob Mckenzie

    2011-01-01

    Full Text Available Previous studies examining the dynamics of succession on artificial reefs have predominantly focussed on fish communities and largely ignored the role of fouling assemblages in explaining the patterns of community structure associated with artificial reefs. The objective of this study was to record the development of epibiotic assemblages on three "design specific" (Reef Ball® estuarine artificial reefs systems located in Lake Macquarie, Botany Bay and St Georges Basin in New South Wales, Australia. Recruitment to the artificial reefs was relatively rapid with the majority of taxa identified over the two-year study period observed within the first year post-deployment. The artificial reefs in Lake Macquarie and St Georges Basin were characterised by low diversity with four and nine taxa recorded respectively in contrast to the sixteen taxa observed on the Botany Bay reefs. Results indicated no significant differences in percentage cover of taxa among reefs in either St Georges Basin or Lake Macquarie. In contrast, comparisons between individual Botany Bay reefs identified significant differences in the percentage cover of species between artificial reefs. Analysis of assemblage structure with reef age indicated discrete patterns among estuaries with an overall reduction in the percentage cover of filamentous turfing algae (FTA identified for all reef systems with an increase in reef age. Variations in environmental and physical conditions (turbidity, water flow, wave action and proximity to naturally occurring reef may have contributed to the observed differences in fouling assemblages between estuaries and between artificial reefs within Botany Bay.Estudos prévios que examinaram a dinâmica de sucessão em recifes artificiais foram focalizados nas comunidades de peixes, e sempre ignoraram o papel exercido pelos organismos incrustantes sobre a estruturação das comunidades associadas aos recifes artificiais. O presente estudo tem por objetivo

  10. Patterns of Assemblage Structure Indicate a Broader Conservation Potential of Focal Amphibians for Pond Management.

    Directory of Open Access Journals (Sweden)

    Elin Soomets

    Full Text Available Small freshwater ponds host diverse and vulnerable biotic assemblages but relatively few conspicuous, specially protected taxa. In Europe, the amphibians Triturus cristatus and Pelobates fuscus are among a few species whose populations have been successfully restored using pond restoration and management activities at the landscape scale. In this study, we explored whether the ponds constructed for those two target species have wider conservation significance, particularly for other species of conservation concern. We recorded the occurrence of amphibians and selected aquatic macro-invertebrates (dragonflies; damselflies; diving beetles; water scavenger beetles in 66 ponds specially constructed for amphibians (up to 8 years post construction and, for comparison, in 100 man-made ponds (created by local people for cattle or garden watering, peat excavation, etc. and 65 natural ponds in Estonia. We analysed nestedness of the species assemblages and its dependence on the environment, and described the co-occurrence patterns between the target amphibians and other aquatic species. The assemblages in all ponds were significantly nested, but the environmental determinants of nestedness and co-occurrence of particular species differed among pond types. Constructed ponds were most species-rich irrespective of the presence of the target species; however, T. cristatus was frequent in those ponds and rare elsewhere, and it showed nested patterns in every type of pond. We thus conclude that pond construction for the protected amphibians can serve broader habitat conservation aims in the short term. However, the heterogeneity and inconsistent presence of species of conservation concern observed in other types of ponds implies that long-term perspectives on pond management require more explicit consideration of different habitat and biodiversity values. We also highlight nestedness analysis as a tool that can be used for the practical task of selecting focal

  11. Thermal and hydrologic responses to climate change predict marked alterations in boreal stream invertebrate assemblages.

    Science.gov (United States)

    Mustonen, Kaisa-Riikka; Mykrä, Heikki; Marttila, Hannu; Sarremejane, Romain; Veijalainen, Noora; Sippel, Kalle; Muotka, Timo; Hawkins, Charles P

    2018-06-01

    Air temperature at the northernmost latitudes is predicted to increase steeply and precipitation to become more variable by the end of the 21st century, resulting in altered thermal and hydrological regimes. We applied five climate scenarios to predict the future (2070-2100) benthic macroinvertebrate assemblages at 239 near-pristine sites across Finland (ca. 1200 km latitudinal span). We used a multitaxon distribution model with air temperature and modeled daily flow as predictors. As expected, projected air temperature increased the most in northernmost Finland. Predicted taxonomic richness also increased the most in northern Finland, congruent with the predicted northwards shift of many species' distributions. Compositional changes were predicted to be high even without changes in richness, suggesting that species replacement may be the main mechanism causing climate-induced changes in macroinvertebrate assemblages. Northern streams were predicted to lose much of the seasonality of their flow regimes, causing potentially marked changes in stream benthic assemblages. Sites with the highest loss of seasonality were predicted to support future assemblages that deviate most in compositional similarity from the present-day assemblages. Macroinvertebrate assemblages were also predicted to change more in headwaters than in larger streams, as headwaters were particularly sensitive to changes in flow patterns. Our results emphasize the importance of focusing protection and mitigation on headwater streams with high-flow seasonality because of their vulnerability to climate change. © 2018 John Wiley & Sons Ltd.

  12. Coral-Associated Bacterial Diversity is Conserved Across Two Deep-Sea Anthothela Species

    Directory of Open Access Journals (Sweden)

    Stephanie Nichole Lawler

    2016-04-01

    Full Text Available Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12 and Baltimore Canyons (n = 11 from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp. and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp. had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

  13. The scales of variability of stream fish assemblage at tributary confluences

    Directory of Open Access Journals (Sweden)

    István Czeglédi

    2015-12-01

    Full Text Available Tributary confluences play an important role in the dispersal of organisms, and consequently, in shaping regional scale diversity in stream networks. Despite their importance in dispersal processes, little is known about how ecological assemblages are organized in these habitats. We studied the scales of variability of stream fish assemblages over three seasons using a hierarchical sampling design, which incorporated three tributaries, three sites at the mouth of each tributary and using four sampling units at each site. We found strong scale dependent variability in species richness, composition and relative abundance. Most of the variation was accounted for by the interactive effect of season, between stream and between site effects, while habitat structure of the sampling units had a relatively minor role. Species richness showed a continuous decrease from the mainstem river in most cases, while species composition and relative abundance changed less consistently along the longitudinal profile. Consequently, we found that not only the junctions presented a strong filter on the species pool, but some species were filtered out if they passed this critical habitat bottleneck. Spatial position of the tributaries along the river also contributed to assemblage variability in the confluences. Overall, our results suggest high variability in fish assemblages across multiple scales at tributary confluences. Environmental management should take a more critical care on the filtering role of tributary confluences in species dispersal, for better understanding patterns and processes in the branches of dendritic stream networks.

  14. Differential response of fish assemblages to coral reef-based seaweed farming.

    Directory of Open Access Journals (Sweden)

    E James Hehre

    Full Text Available As the global demand for seaweed-derived products drives the expansion of seaweed farming onto shallow coral ecosystems, the effects of farms on fish assemblages remain largely unexplored. Shallow coral reefs provide food and shelter for highly diverse fish assemblages but are increasingly modified by anthropogenic activities. We hypothesized that the introduction of seaweed farms into degraded shallow coral reefs had potential to generate ecological benefits for fish by adding structural complexity and a possible food source. We conducted 210 transects at 14 locations, with sampling stratified across seaweed farms and sites adjacent to and distant from farms. At a seascape scale, locations were classified by their level of exposure to human disturbance. We compared sites where (1 marine protected areas (MPAs were established, (2 neither MPAs nor blast fishing was present (hence "unprotected", and (3 blast fishing occurred. We observed 80,186 fish representing 148 species from 38 families. The negative effects of seaweed farms on fish assemblages appeared stronger in the absence of blast fishing and were strongest when MPAs were present, likely reflecting the positive influence of the MPAs on fish within them. Species differentiating fish assemblages with respect to seaweed farming and disturbance were typically small but also included two key target species. The propensity for seaweed farms to increase fish diversity, abundance, and biomass is limited and may reduce MPA benefits. We suggest that careful consideration be given to the placement of seaweed farms relative to MPAs.

  15. Differential response of fish assemblages to coral reef-based seaweed farming.

    Science.gov (United States)

    Hehre, E James; Meeuwig, J J

    2015-01-01

    As the global demand for seaweed-derived products drives the expansion of seaweed farming onto shallow coral ecosystems, the effects of farms on fish assemblages remain largely unexplored. Shallow coral reefs provide food and shelter for highly diverse fish assemblages but are increasingly modified by anthropogenic activities. We hypothesized that the introduction of seaweed farms into degraded shallow coral reefs had potential to generate ecological benefits for fish by adding structural complexity and a possible food source. We conducted 210 transects at 14 locations, with sampling stratified across seaweed farms and sites adjacent to and distant from farms. At a seascape scale, locations were classified by their level of exposure to human disturbance. We compared sites where (1) marine protected areas (MPAs) were established, (2) neither MPAs nor blast fishing was present (hence "unprotected"), and (3) blast fishing occurred. We observed 80,186 fish representing 148 species from 38 families. The negative effects of seaweed farms on fish assemblages appeared stronger in the absence of blast fishing and were strongest when MPAs were present, likely reflecting the positive influence of the MPAs on fish within them. Species differentiating fish assemblages with respect to seaweed farming and disturbance were typically small but also included two key target species. The propensity for seaweed farms to increase fish diversity, abundance, and biomass is limited and may reduce MPA benefits. We suggest that careful consideration be given to the placement of seaweed farms relative to MPAs.

  16. Functional redundancy patterns reveal non-random assembly rules in a species-rich marine assemblage.

    Directory of Open Access Journals (Sweden)

    Nicolas Guillemot

    Full Text Available The relationship between species and the functional diversity of assemblages is fundamental in ecology because it contains key information on functional redundancy, and functionally redundant ecosystems are thought to be more resilient, resistant and stable. However, this relationship is poorly understood and undocumented for species-rich coastal marine ecosystems. Here, we used underwater visual censuses to examine the patterns of functional redundancy for one of the most diverse vertebrate assemblages, the coral reef fishes of New Caledonia, South Pacific. First, we found that the relationship between functional and species diversity displayed a non-asymptotic power-shaped curve, implying that rare functions and species mainly occur in highly diverse assemblages. Second, we showed that the distribution of species amongst possible functions was significantly different from a random distribution up to a threshold of ∼90 species/transect. Redundancy patterns for each function further revealed that some functions displayed fast rates of increase in redundancy at low species diversity, whereas others were only becoming redundant past a certain threshold. This suggested non-random assembly rules and the existence of some primordial functions that would need to be fulfilled in priority so that coral reef fish assemblages can gain a basic ecological structure. Last, we found little effect of habitat on the shape of the functional-species diversity relationship and on the redundancy of functions, although habitat is known to largely determine assemblage characteristics such as species composition, biomass, and abundance. Our study shows that low functional redundancy is characteristic of this highly diverse fish assemblage, and, therefore, that even species-rich ecosystems such as coral reefs may be vulnerable to the removal of a few keystone species.

  17. Freshwater processing of terrestrial dissolved organic matter: What governs lability?

    Science.gov (United States)

    D'Andrilli, J.; Smith, H. J.; Junker, J. R.; Scholl, E. A.; Foreman, C. M.

    2016-12-01

    Aquatic and terrestrial ecosystems are linked through the transfer of energy and materials. Allochthonous organic matter (OM) is central to freshwater ecosystem function, influencing local food webs, trophic state, and nutrient availability. In order to understand the nature and fate of OM from inland headwaters to the open ocean, it is imperative to understand the links between OM lability and ecosystem function. Thus, biological, chemical, and physical factors need to be evaluated together to inform our understanding of environmental lability. We performed a laboratory processing experiment on naturally occurring OM leachates from riparian leaves, grasses, and pine needles. Measures of water chemistry, OM optical and molecular characterization, bacterial abundances, microbial assemblage composition, respiration, and C:N:P were integrated to discern the nature and fate of labile and recalcitrant OM in a freshwater stream. Peak processing of all OM sources in the stream water occurred after two days, with spikes in bacterial cell abundances, respiration rates, microbial assemblage shifts, and maximum C utilization. Respiration rates and microbial assemblages were dependent on the degree of lability of the OM molecular composition. Within the first few days, no differences in respiration rates were observed between leachate sources, however, beyond day five, the rates diverged with C processing efficiency correlated with OM lability. Originally comprised of amino acid-like, labile fluorescent species, the inoculated stream water OM became more recalcitrant after 16 days, indicating humification processing over time. Our study highlights the importance of interdisciplinary approaches for understanding the processing and fate of OM in aquatic ecosystems.

  18. Simplification of arboreal marsupial assemblages in response to increasing urbanization.

    Directory of Open Access Journals (Sweden)

    Bronwyn Isaac

    Full Text Available Arboreal marsupials play an essential role in ecosystem function including regulating insect and plant populations, facilitating pollen and seed dispersal and acting as a prey source for higher-order carnivores in Australian environments. Primarily, research has focused on their biology, ecology and response to disturbance in forested and urban environments. We used presence-only species distribution modelling to understand the relationship between occurrences of arboreal marsupials and eco-geographical variables, and to infer habitat suitability across an urban gradient. We used post-proportional analysis to determine whether increasing urbanization affected potential habitat for arboreal marsupials. The key eco-geographical variables that influenced disturbance intolerant species and those with moderate tolerance to disturbance were natural features such as tree cover and proximity to rivers and to riparian vegetation, whereas variables for disturbance tolerant species were anthropogenic-based (e.g., road density but also included some natural characteristics such as proximity to riparian vegetation, elevation and tree cover. Arboreal marsupial diversity was subject to substantial change along the gradient, with potential habitat for disturbance-tolerant marsupials distributed across the complete gradient and potential habitat for less tolerant species being restricted to the natural portion of the gradient. This resulted in highly-urbanized environments being inhabited by a few generalist arboreal marsupial species. Increasing urbanization therefore leads to functional simplification of arboreal marsupial assemblages, thus impacting on the ecosystem services they provide.

  19. Recent benthic foraminifera assemblages from mangrove swamp and channels of Abu Dhabi (UAE)

    Science.gov (United States)

    Fiorini, Flavia; Lokier, Stephen W.; Odeh, Weaam A. S. Al; Paul, Andreas; Song, Jianfeng; Freeman, Mark; Michel, Françoise

    2017-04-01

    Zonation of Recent mangrove environments can be defined using benthic foraminifera, however, little is known about foraminifera from mangrove environments of the Persian/Arabian Gulf. The objective of this study is to produce a detailed micropaleontological and sedimentological analysis to identify foraminiferal associations from mangrove swamps and channels located on the eastern side of Abu Dhabi Island (UAE). Detailed sediment sampling collection in mangal environments of Eastern Abu Dhabi was carried out to assess the distribution of benthic foraminifera in different sedimentary facies in the mangal and in the surrounding natural environments of the upper and lower intertidal area (mud flats and channels). A 100 m transect across a natural channel in a mangal on the eastern side of Abu Dhabi Island was sampled in detail for sedimentological and foraminiferal analysis. Forty-seven samples were collected at 2 meter intervals along the transect in a number of different sedimentary facies including; fine sediment in areas exposed during low tide and close to mangrove trees (Avicennia marina), fine sediment rich in leaf material, coarse sediment in channels, and coarse sediments with a shell lag. At each sampling location environmental parameters were recorded, including water depth, salinity, temperature and pH. Samples collected for foraminiferal analysis were stained in rose Bengal in order to identify living specimens. Samples collected on the mud flat at the margin of the channel show a living foraminiferal assemblage characterised by abundant foraminifera belonging to the genera Ammonia, Elphidium, Cribroelphidium, Triloculina, Quinqueloculina, Sigmoilinita, Spiroloculina, Peneroplis and Spirolina. Samples collected in the lower (wet) intertidal area close to Avicennia marina roots, presented a low-diversity assemblage mostly comprising small-sized opportunistic foraminifera of the genera Ammonia and Cribroelphidium along with rare Triloculina and

  20. Suprabenthic assemblages from the Capbreton area (SE Bay of Biscay). Faunal recovery after a canyon turbidity disturbance

    Science.gov (United States)

    Frutos, Inmaculada; Sorbe, Jean Claude

    2017-12-01

    In the Capbreton area, suprabenthic assemblages were sampled with a sledge towed over the bottom, at different sites located within the upper part of a 'gouf-type' canyon (8 hauls between 642 m and 797 m, on the axis of the thalweg or on flat perched flank terraces such as site K), on the northern adjacent open slope (2 hauls between 500 and 567 m) and on the northern adjacent shelf margin (2 hauls between 151 m and 158 m). A multivariate analysis carried on the faunal data discriminated different assemblages in this area: a near-canyon shelf assemblage (55 species, mainly amphipods and decapods; 3496 ind./100 m2, 40% mysids; dominant species: Nyctiphanes couchii, Leptomysis gracilis, Weswoodilla rectirostris, Anchialina agilis, Scopelocheirus hopei and Philocheras bispinosus); an open slope assemblage (111 species, mainly amphipods and isopods; 249 ind./100 m2, 36% amphipods; dominant species: Disconectes phalangium, Munnopsurus atlanticus and Boreomysis arctica); a canyon E assemblage (129 species, mainly amphipods, mysids and cumaceans; 1172 ind./100 m2, 58% amphipods; dominant species: Melphidippa sp. B, Chelator insignis); a canyon E' assemblage (107 species, mainly amphipods and mysids; 507 ind./100 m2, 73% amphipods; dominant species: Cleonardopsis carinata, Bonnierella abyssorum, Rhachotropis caeca and Arcturopsis giardi); and a temporary canyon assemblage at site K (34 species, mainly amphipods and mysids; 899 ind./100 m2, 85% amphipods; dominant species: Tmetomyx similis, Caeconyx caeculus, Nebalia sp. A and Cleonardopsis carinata). Site K was sampled only four months after a turbidity event, detected on sediment cores (18 cm thick Bouma sequence) taken during the same cruise and triggered by the violent storm ('ouragan Martin', wind up to 200 km/h) which affected the French Atlantic coast on 27 December 1999. The corresponding suprabenthic assemblage showed evidence of deep structural changes after this catastrophic event, characterized by relative low

  1. Self-assemblage and post-radiation recovery of cell supramolecular structures

    International Nuclear Information System (INIS)

    Grodzinskij, D.M.; Kolomiets, K.D.

    1979-01-01

    The role of the molecular equation and self-assemblage in post-radiation chromatin recovery of meristematic cells of pea rootlets is shown. Found are the two repair types at the chromatin level by fractionating of the radiation dose. The first type comprises transient processes including DNA repair, the second type comprises processes including biosynthesis of the chromatin components and proteins, in the first place. The role of protein biosynthesis in the process of recovery of the chromatin supramolecular structure is shown. The improved radiostability of chromatin self-assemblage is characteristic for the level of its subunits. The supramolecular chromatin structure of the other levels has less radiostability

  2. Do landscape factors affect brownfield carabid assemblages?

    International Nuclear Information System (INIS)

    Small, Emma; Sadler, Jon P.; Telfer, Mark

    2006-01-01

    The carabid fauna of 28 derelict sites in the West Midlands (England) were sampled over the course of one growing season (April-October, 1999). The study aimed to investigate the relationship between carabid assemblages and five measures of landscape structure pertinent to derelict habitat. At each site measurements of landscape features pertinent to derelict habitat were made: (i) the proximity of habitat corridors; (ii) the density of surrounding derelict land; (iii) the distance between the site and the rural fringe; and (iv) the size of the site. Concurrent surveys of the soil characteristics, vegetation type, and land use history were conducted. The data were analysed using a combination of ordination (DCA, RDA), variance partitioning (using pRDA) and binary linear regression. The results suggest that:1.There is very little evidence that the carabid assemblages of derelict sites were affected by landscape structure, with assemblages instead being principally related to within-site habitat variables, such as site age (since last disturbance), substrate type and vegetation community. 2.No evidence was found to support the hypothesis that sites away from railway corridors are more impoverished in their carabid fauna than sites on corridors. 3.There are some suggestions from this study that rarer and non-flying specialist species may be affected by isolation, taking longer to reach sites. We infer from this that older sites with retarded succession, and sites in higher densities of surrounding derelict land may eventually become more species rich and that these sites may be important for maintaining populations of rarer and flightless species. 4.Conservation efforts to maintain populations of these species should focus principally on habitat quality issues, such as maintaining early successional habitats that have a diversity of seed producing annuals and perennial plants and enhancing substrate variability rather than landscape issues

  3. Experimental test of postfire management in pine forests: impact of salvage logging versus partial cutting and nonintervention on bird-species assemblages.

    Science.gov (United States)

    Castro, Jorge; Moreno-Rueda, Gregorio; Hódar, José A

    2010-06-01

    There is an intense debate about the effects of postfire salvage logging versus nonintervention policies on regeneration of forest communities, but scant information from experimental studies is available. We manipulated a burned forest area on a Mediterranean mountain to experimentally analyze the effect of salvage logging on bird-species abundance, diversity, and assemblage composition. We used a randomized block design with three plots of approximately 25 ha each, established along an elevational gradient in a recently burned area in Sierra Nevada Natural and National Park (southeastern Spain). Three replicates of three treatments differing in postfire burned wood management were established per plot: salvage logging, nonintervention, and an intermediate degree of intervention (felling and lopping most of the trees but leaving all the biomass). Starting 1 year after the fire, we used point sampling to monitor bird abundance in each treatment for 2 consecutive years during the breeding and winter seasons (720 censuses total). Postfire burned-wood management altered species assemblages. Salvage logged areas had species typical of open- and early-successional habitats. Bird species that inhabit forests were still present in the unsalvaged treatments even though trees were burned, but were almost absent in salvage-logged areas. Indeed, the main dispersers of mid- and late-successional shrubs and trees, such as thrushes (Turdus spp.) and the European Jay (Garrulus glandarius) were almost restricted to unsalvaged treatments. Salvage logging might thus hamper the natural regeneration of the forest through its impact on assemblages of bird species. Moreover, salvage logging reduced species abundance by 50% and richness by 40%, approximately. The highest diversity at the landscape level (gamma diversity) resulted from a combination of all treatments. Salvage logging may be positive for bird conservation if combined in a mosaic with other, less-aggressive postfire

  4. Ambiguous taxa: Effects on the characterization and interpretation of invertebrate assemblages

    Science.gov (United States)

    Cuffney, T.F.; Bilger, Michael D.; Haigler, A.M.

    2007-01-01

    Damaged and immature specimens often result in macroinvertebrate data that contain ambiguous parent-child pairs (i.e., abundances associated with multiple related levels of the taxonomic hierarchy such as Baetis pluto and the associated ambiguous parent Baetis sp.). The choice of method used to resolve ambiguous parent-child pairs may have a very large effect on the characterization of invertebrate assemblages and the interpretation of responses to environmental change because very large proportions of taxa richness (73-78%) and abundance (79-91%) can be associated with ambiguous parents. To address this issue, we examined 16 variations of 4 basic methods for resolving ambiguous taxa: RPKC (remove parent, keep child), MCWP (merge child with parent), RPMC (remove parent or merge child with parent depending on their abundances), and DPAC (distribute parents among children). The choice of method strongly affected assemblage structure, assemblage characteristics (e.g., metrics), and the ability to detect responses along environmental (urbanization) gradients. All methods except MCWP produced acceptable results when used consistently within a study. However, the assemblage characteristics (e.g., values of assemblage metrics) differed widely depending on the method used, and data should not be combined unless the methods used to resolve ambiguous taxa are well documented and are known to be comparable. The suitability of the methods was evaluated and compared on the basis of 13 criteria that considered conservation of taxa richness and abundance, consistency among samples, methods, and studies, and effects on the interpretation of the data. Methods RPMC and DPAC had the highest suitability scores regardless of whether ambiguous taxa were resolved for each sample separately or for a group of samples. Method MCWP gave consistently poor results. Methods MCWP and DPAC approximate the use of family-level identifications and operational taxonomic units (OTU), respectively. Our

  5. Seagrass Parameter Affect the Fish Assemblages in Karimunjawa Archipelago

    Science.gov (United States)

    Sri Susilo, Endang; Nugroho Sugianto, Denny; Munasik; Nirwani; Adhi Suryono, Chrisna

    2018-02-01

    Seagrass beds promote high species diversity, abundance and biomass, and become important habitats for some economically important fishes. Plants of seagrasses result in structurally highly complex habitats and offering feeding grounds, shelter from predation as well as nursery areas for diverse fish assemblages. However, research on fish communities in Southeast Asian seagrass bed is rarely conducted. In the present study fish assemblages in seagrass beds with different parameters (cover, diversity and similarity indices, domination) was investigated in the Karimunjawa Islands, Indonesia. The purpose of this study were to assess whether fish assemblages differ concerning on the abundance and the species number. This study was conducted on the seagrass bed on Karimunjawa Islands in Java Sea, particularly in the water of Menjangan Besar and Menjangan Kecil Island. Line-quadrant transect was used to assess seagrass data, while the occurrence and individual number of fish harboured in the selected seagrass bed was counted by using underwater visual census in the stationary point count transects. Seagrass cover in Menjangan Kecil Island (41%) with various canopy included both upper and lower canopy was considerable higher than those in Menjangan Besar Island (5%). Fish diversity, species composition and abundance are considerably different between the two study sites. This study revealed that seagrass density or cover and canopy structure affected the fish abundance and species number harboured.

  6. Bacterial Diversity and Bioremediation Potential of the Highly Contaminated Marine Sediments at El-Max District (Egypt, Mediterranean Sea)

    KAUST Repository

    Amer, Ranya A.

    2015-02-01

    Coastal environments worldwide are threatened by the effects of pollution, a risk particularly high in semienclosed basins like the Mediterranean Sea that is poorly studied from bioremediation potential perspective especially in the Southern coast. Here, we investigated the physical, chemical, and microbiological features of hydrocarbon and heavy metals contaminated sediments collected at El-Max bay (Egypt). Molecular and statistical approaches assessing the structure of the sediment-dwelling bacterial communities showed correlations between the composition of bacterial assemblages and the associated environmental parameters. Fifty strains were isolated on mineral media supplemented by 1% crude oil and identified as a diverse range of hydrocarbon-degrading bacteria involved in different successional stages of biodegradation. We screened the collection for biotechnological potential studying biosurfactant production, biofilm formation, and the capability to utilize different hydrocarbons. Some strains were able to grow on multiple hydrocarbons as unique carbon source and presented biosurfactant-like activities and/or capacity to form biofilm and owned genes involved in different detoxification/degradation processes. El-Max sediments represent a promising reservoir of novel bacterial strains adapted to high hydrocarbon contamination loads. The potential of the strains for exploitation for in situ intervention to combat pollution in coastal areas is discussed.

  7. Effect of copper on multiple successional stages of a marine fouling assemblage.

    Science.gov (United States)

    McElroy, David J; Hochuli, Dieter F; Doblin, Martina A; Murphy, Richard J; Blackburn, Robert J; Coleman, Ross A

    2017-11-01

    Copper based paints are used to prevent fouling on the hulls of ships. The widely documented effect of copper on hull assemblages may be primarily due to direct effects on the invertebrates themselves or indirect effects from copper absorbed into the microbial biofilm before settlement has commenced. Artificial units of habitat were exposed to varied regimes of copper to examine (1) the photosynthetic efficiency and pigments of early-colonising biofilms, and (2) subsequent macroinvertebrate assemblage change in response to the different regimes of copper. Macroinvertebrate assemblages were found to be less sensitive to the direct effects of copper than indirect effects as delivered through biofilms that have been historically exposed to copper, with some species more tolerant than others. This raises further concern for the efficacy of copper as a universal antifoulant on the hulls of ships, which may continue to assist the invasion of copper-tolerant invertebrate species.

  8. Influence of Interspecific Competition and Landscape Structure on Spatial Homogenization of Avian Assemblages

    Science.gov (United States)

    Robertson, Oliver J.; McAlpine, Clive; House, Alan; Maron, Martine

    2013-01-01

    Human-induced biotic homogenization resulting from landscape change and increased competition from widespread generalists or ‘winners’, is widely recognized as a global threat to biodiversity. However, it remains unclear what aspects of landscape structure influence homogenization. This paper tests the importance of interspecific competition and landscape structure, for the spatial homogeneity of avian assemblages within a fragmented agricultural landscape of eastern Australia. We used field observations of the density of 128 diurnal bird species to calculate taxonomic and functional similarity among assemblages. We then examined whether taxonomic and functional similarity varied with patch type, the extent of woodland habitat, land-use intensity, habitat subdivision, and the presence of Manorina colonies (a competitive genus of honeyeaters). We found the presence of a Manorina colony was the most significant factor positively influencing both taxonomic and functional similarity of bird assemblages. Competition from members of this widespread genus of native honeyeater, rather than landscape structure, was the main cause of both taxonomic and functional homogenization. These species have not recently expanded their range, but rather have increased in density in response to agricultural landscape change. The negative impacts of Manorina honeyeaters on assemblage similarity were most pronounced in landscapes of moderate land-use intensity. We conclude that in these human-modified landscapes, increased competition from dominant native species, or ‘winners’, can result in homogeneous avian assemblages and the loss of specialist species. These interacting processes make biotic homogenization resulting from land-use change a global threat to biodiversity in modified agro-ecosystems. PMID:23724136

  9. Two-stage recovery of amphibian assemblages following selective logging of tropical forests.

    Science.gov (United States)

    Adum, Gilbert Baase; Eichhorn, Markus Peter; Oduro, William; Ofori-Boateng, Caleb; Rödel, Mark-Oliver

    2013-04-01

    There is a lack of quantitative information on the effectiveness of selective-logging practices in ameliorating effects of logging on faunal communities. We conducted a large-scale replicated field study in 3 selectively logged moist semideciduous forests in West Africa at varying times after timber extraction to assess post logging effects on amphibian assemblages. Specifically, we assessed whether the diversity, abundance, and assemblage composition of amphibians changed over time for forest-dependent species and those tolerant of forest disturbance. In 2009, we sampled amphibians in 3 forests (total of 48 study plots, each 2 ha) in southwestern Ghana. In each forest, we established plots in undisturbed forest, recently logged forest, and forest logged 10 and 20 years previously. Logging intensity was constant across sites with 3 trees/ha removed. Recently logged forests supported substantially more species than unlogged forests. This was due to an influx of disturbance-tolerant species after logging. Simultaneously Simpson's index decreased, with increased in dominance of a few species. As time since logging increased richness of disturbance-tolerant species decreased until 10 years after logging when their composition was indistinguishable from unlogged forests. Simpson's index increased with time since logging and was indistinguishable from unlogged forest 20 years after logging. Forest specialists decreased after logging and recovered slowly. However, after 20 years amphibian assemblages had returned to a state indistinguishable from that of undisturbed forest in both abundance and composition. These results demonstrate that even with low-intensity logging (≤3 trees/ha) a minimum 20-year rotation of logging is required for effective conservation of amphibian assemblages in moist semideciduous forests. Furthermore, remnant patches of intact forests retained in the landscape and the presence of permanent brooks may aid in the effective recovery of amphibian

  10. Coral reef fish assemblages at Clipperton Atoll (Eastern Tropical Pacific and their relationship with coral cover

    Directory of Open Access Journals (Sweden)

    Aurora M. Ricart

    2016-11-01

    Full Text Available Clipperton Atoll, one of the most isolated coral reefs worldwide, is of great scientific interest due to its geomorphology and high levels of endemism. This study explored the reef fish assemblage structure of Clipperton Atoll and its relationship with live coral cover. Nine stations were sampled at three sites and three depths (6, 12 and 20 m around the reef, measuring fish species richness and biomass and hermatypic coral cover (at genus level. We evaluated variation in species richness, biomass and diversity of fish assemblages among sites and depths, as well as the relationship between the entire fish assemblage composition and live coral cover. The results showed that species richness and biomass were similar among sites, but differed across depths, increasing with depth. In contrast, diversity differed among sites but not among depths. Multivariate analyses indicated that fish assemblage composition differed among sites and depths in relation to changes in cover of coral of the genera Pocillopora, Porites, Pavona and Leptoseris, which dominate at different depths. The results showed that fish species richness and diversity were low at Clipperton Atoll and that, in isolated coral reefs with a low habitat heterogeneity and low human disturbance, live coral cover has a significant influence on the spatial variation of the reef fish assemblages. This study highlights the importance of coral habitat structure in shaping coral reef fish assemblages.

  11. Environmental and Anthropogenic Impacts on Avifaunal Assemblages in an Urban Parkland, 1976 to 2007

    Directory of Open Access Journals (Sweden)

    Sara Elizabeth Ormond

    2014-03-01

    Full Text Available Urban environments are unique, rapidly changing habitats in which almost half of the world’s human population resides. The effects of urbanisation, such as habitat (vegetation removal, pollution and modification of natural areas, commonly cause biodiversity loss. Long-term ecological monitoring of urban environments is vital to determine the composition and long-term trends of faunal communities. This paper provides a detailed view of long-term changes in avifaunal assemblages of the Adelaide City parklands and discusses the anthropogenic and environmental factors that contributed to the changes between 1976 and 2007. The Adelaide City parklands (ACP comprise 760 ha of land surrounding Adelaide’s central business district. Naturalist Robert Whatmough completed a 32-year survey of the ACP to determine the structure of the urban bird community residing there. Annual species richness and the abundance of birds in March and September months were analysed. Linear regression analysis was applied to species richness and abundance data of each assemblage. Resident parkland birds demonstrated significant declines in abundance. Native and introduced species also exhibited long-term declines in species richness and abundance throughout the 32-year period. Cycles of varying time periods indicated fluctuations in avian biodiversity demonstrating the need for future monitoring and statistical analyses on bird communities in the Adelaide City parklands.

  12. Techniques de formage et d'assemblage

    CERN Document Server

    Favre, G; CERN. Geneva. TS Department

    2004-01-01

    Les sections Techniques d'Assemblage du groupe EST/MF et Brasage du groupe EST/SM ont été groupées en un seul service dans un but de rationalisation accrue des ressources et méthodes. Ce service dispose de nombreux moyens : soudure et découpe LASER (YAG, 350 W), soudure par faisceau d'électrons (deux installations, 35 et 7.5 kW), équipements TIG orbital, jet line, MIG, soudure plasma, boîte à gants, portique de soudage trois axes multiprocédés, presses plieuses, rouleuses, moyens de repoussage, alimentation à induction 12 kW et divers fours sous vide et à air. Le service est composé de 17 personnes dont la polyvalence est encouragée. Les activités de la section seront décrites à travers quelques exemples significatifs récents, notamment : l'assemblage des amenées de courant HTS, la réalisation des chambres LSS, des tubes HET, d'enveloppes céramiques pour détecteurs PET-HPD, le brasage de RFQ, la soudure du Barrel d'ATLAS ou encore le soudage des lignes de thermalisation du toroïde d'AT...

  13. Megabenthic assemblages at the Hudson Canyon head (NW Atlantic margin): Habitat-faunal relationships

    Science.gov (United States)

    Pierdomenico, Martina; Gori, Andrea; Guida, Vincent G.; Gili, Josep-Maria

    2017-09-01

    The distribution of megabenthic communities at the head of Hudson Canyon and adjacent continental shelf was studied by means of underwater video transects and still photo imagery collected using a towed camera system. The goal was to explore the relationships between faunal distribution and physical seafloor conditions and to test the hypothesis that increased seafloor heterogeneity in the Hudson Canyon supports a larger diversity of benthic communities, compared with the adjacent continental shelf. Hierarchical cluster analysis was performed to identify benthic assemblages as defined in imagery. The BIO-ENV procedure and the Canonical Correspondence Analysis were carried out to elucidate species groupings in relation to terrain variables extracted from bathymetric data. Species accumulation curves were generated to evaluate species turn over in and out of Hudson Canyon. The results indicate that seafloor morphology is the main physical factor related to benthic community composition and distribution. Assemblages dominated by sponges, zoanthids and cup corals colonized the canyon margins and flanks, and were associated with coarse-grained sediments, while sea pen assemblages were observed along muddy seafloor within the thalweg. An assemblage dominated by sea stars occurred on the shelf, associated with a sandy seafloor. Some assemblages were exclusively observed in the canyon area, suggesting that the increased variability of seafloor composition, together with the oceanographic processes specific to the canyon area, enhance beta diversity. The colonization by benthic suspension feeders within the canyon, in contrast to shelf assemblages, mainly composed of carnivores and detritus feeders could be favored the intense hydrodynamics at the canyon head that increase the availability of suspended organic matter. From the perspective of management and conservation of marine resources, the results obtained support the relevance of Hudson Canyon as a biodiversity hotspot

  14. Fish assemblage dynamics in a Neotropical floodplain relative to aquatic macrophytes and the homogenizing effect of a flood pulse

    Science.gov (United States)

    Gomes, L.C.; Bulla, C. K.; Agostinho, A. A.; Vasconcelos, L. P.; Miranda, Leandro E.

    2012-01-01

    The presence of aquatic macrophytes is a key factor in the selection of habitats by fish in floodplain lakes because these plants enhance the physical and biological complexities of aquatic habitats. The seasonal flood pulse may influence this interaction, but there is no information in the literature about the effects that flood events may have on macrophytes assemblages and its associated effects on fish assemblages. Thus, this article aimed to investigate whether species richness, evenness and similarities in fish assemblage composition differed between littoral areas vegetated with macrophytes and unvegetated areas, before and after a flood. We sampled three lakes in the floodplain of the upper Paraná River basin. Sampling was conducted before (December 2004 and January 2005) and after (early March, late March and May 2005) a flood event. Overall, species richness and evenness were higher in macrophytes-covered areas. Before the flood, the composition of fish assemblages was distinct when comparing vegetated and unvegetated areas. After the flood, the similarity in fish assemblage composition was higher, indicating a homogenization effect of floods for fish inhabiting littoral areas of floodplain lakes. After the flood, opportunistic species dominated the fish assemblages in aquatic macrophytes, apparently restructuring assemblages in the littoral, restarting a succession process. Thus, the observed homogenization effect of the flood could minimize biological interactions and could induce fish assemblages to begin a new process of structurization.

  15. Determining light stress responses for a tropical multi-species seagrass assemblage.

    Science.gov (United States)

    Statton, John; McMahon, Kathryn; Lavery, Paul; Kendrick, Gary A

    2018-03-01

    Existing mitigations to address deterioration in water clarity associated with human activities are based on responses from single seagrass species but may not be appropriate for diverse seagrass assemblages common to tropical waters. We present findings from a light experiment designed to determine the effects of magnitude and duration of low light on a mixed tropical seagrass assemblage. Mixed assemblages of three commonly co-occurring Indo-West Pacific seagrasses, Cymodocea serrulata, Halodule uninervis and Halophila ovalis were grown in climate-controlled tanks, where replicate pots were subjected to a gradient in light availability (0.9-21.6 mols PAR m -2 day -1 ) for 12 weeks. Increased shading resulted in declines in growth and changes in cellular and photosynthesis responses for all species, although time-scale and magnitude of response were species-specific. Applying management criteria (e.g. thresholds) relevant to one species may under- or over-estimate potential for impact on other species and the meadow as a whole. Copyright © 2018 Elsevier Ltd. All rights reserved.

  16. Larval assemblages of large and medium-sized pelagic species in the Straits of Florida

    Science.gov (United States)

    Richardson, David E.; Llopiz, Joel K.; Guigand, Cedric M.; Cowen, Robert K.

    2010-07-01

    Critical gaps in our understanding of the distributions, interactions, life histories and preferred habitats of large and medium-size pelagic fishes severely constrain the implementation of ecosystem-based, spatially structured fisheries management approaches. In particular, spawning distributions and the environmental characteristics associated with the early life stages are poorly documented. In this study, we consider the diversity, assemblages, and associated habitat of the larvae of large and medium-sized pelagic species collected during 2 years of monthly surveys across the Straits of Florida. In total, 36 taxa and 14,295 individuals were collected, with the highest diversity occurring during the summer and in the western, frontal region of the Florida Current. Only a few species (e.g. Thunnus obesus, T. alalunga, Tetrapturus pfluegeri) considered for this study were absent. Small scombrids (e.g. T. atlanticus, Katsuwonus pelamis, Auxis spp.) and gempylids dominated the catch and were orders of magnitude more abundant than many of the rare species (e.g. Thunnus thynnus,Kajikia albida). Both constrained (CCA) and unconstrained (NMDS) multivariate analyses revealed a number of species groupings including: (1) a summer Florida edge assemblage (e.g. Auxis spp., Euthynnus alleterattus, Istiophorus platypterus); (2) a summer offshore assemblage (e.g. Makaira nigricans, T. atlanticus, Ruvettus pretiosus, Lampris guttatus); (3) an ubiquitous assemblage (e.g. K. pelamis, Coryphaena hippurus, Xiphias gladius); and (4) a spring/winter assemblage that was widely dispersed in space (e.g. trachipterids). The primary environmental factors associated with these assemblages were sea-surface temperature (highest in summer-early fall), day length (highest in early summer), thermocline depth (shallowest on the Florida side) and fluorescence (highest on the Florida side). Overall, the results of this study provide insights into how a remarkable diversity of pelagic species

  17. Diversity of non-biting midge larvae assemblages in the Jacuí River basin, Brazil.

    Science.gov (United States)

    Floss, Elzira Cecília Serafini; Kotzian, Carla Bender; Spies, Márcia Regina; Secretti, Elisangela

    2012-01-01

    The richness and composition of a mountain-river chironomid larvae assemblage in the Jacuí River basin, Brazil were studied, and compared with other riverine non-biting midge larvae assemblages previously studied in the country. Additionally, the influence of some regional-scale environmental characteristics on the spatial distribution of these assemblages was tested. The specimens were collected at 12 sites in the middle course of the Jacuí River basin (in the state of Rio Grande do Sul) between April 2000 and May 2002. Around 100 taxa were recorded. The dominant taxa belonged to the genera Rheotanytarsus, Cricotopus, Polypedilum, and Pseudochironomus. Twenty-two rare taxa were found, representing 22% of the total of taxa inventoried. Fourteen genera (Aedokritus, Axarus, Endotribelos, Kiefferulus, Manoa, Oukuriella, Phaenopsectra, Stenochironomus, Xenochironomus, Xestochironomus, Cardiocladius, Metriocnemus, Paracladius, and Rheocricotopus) represent new occurrences in Rio Grande do Sul. The similarity analysis of the chironomid larvae assemblages inventoried in 32 regions of Brazil indicated five groups with similarity higher than 50%. The groups, when the effects of spatial autocorrelation were removed, displayed a weak positive correlation between the assemblage composition and the aquatic system or hydraulic conditions and the hydrographic basin, and a weak negative correlation in relation to the biome. The altitude showed no correlation with the composition of the assemblage. The relatively high richness of the region surveyed in relation to other Brazilian regions corroborates some tendencies already noted in other parts of the world, such as: i) lotic systems may constitute an exception to the rule that diversity is greater in tropical regions, ii) regions of transitional relief may contain the greatest richness of Chironomidae, and iii) in rivers, the group might have its spatial distribution influenced to a greater extent by local environmental

  18. Multi-scale sampling to evaluate assemblage dynamics in an oceanic marine reserve.

    Science.gov (United States)

    Thompson, Andrew R; Watson, William; McClatchie, Sam; Weber, Edward D

    2012-01-01

    To resolve the capacity of Marine Protected Areas (MPA) to enhance fish productivity it is first necessary to understand how environmental conditions affect the distribution and abundance of fishes independent of potential reserve effects. Baseline fish production was examined from 2002-2004 through ichthyoplankton sampling in a large (10,878 km(2)) Southern Californian oceanic marine reserve, the Cowcod Conservation Area (CCA) that was established in 2001, and the Southern California Bight as a whole (238,000 km(2) CalCOFI sampling domain). The CCA assemblage changed through time as the importance of oceanic-pelagic species decreased between 2002 (La Niña) and 2003 (El Niño) and then increased in 2004 (El Niño), while oceanic species and rockfishes displayed the opposite pattern. By contrast, the CalCOFI assemblage was relatively stable through time. Depth, temperature, and zooplankton explained more of the variability in assemblage structure at the CalCOFI scale than they did at the CCA scale. CalCOFI sampling revealed that oceanic species impinged upon the CCA between 2002 and 2003 in association with warmer offshore waters, thus explaining the increased influence of these species in the CCA during the El Nino years. Multi-scale, spatially explicit sampling and analysis was necessary to interpret assemblage dynamics in the CCA and likely will be needed to evaluate other focal oceanic marine reserves throughout the world.

  19. Sediment and carbon deposition vary among vegetation assemblages in a coastal salt marsh

    Directory of Open Access Journals (Sweden)

    J. J. Kelleway

    2017-08-01

    Full Text Available Coastal salt marshes are dynamic, intertidal ecosystems that are increasingly being recognised for their contributions to ecosystem services, including carbon (C accumulation and storage. The survival of salt marshes and their capacity to store C under rising sea levels, however, is partially reliant upon sedimentation rates and influenced by a combination of physical and biological factors. In this study, we use several complementary methods to assess short-term (days deposition and medium-term (months accretion dynamics within a single marsh that contains three salt marsh vegetation types common throughout southeastern (SE Australia.We found that surface accretion varies among vegetation assemblages, with medium-term (19 months bulk accretion rates in the upper marsh rush (Juncus assemblage (1.74 ± 0.13 mm yr−1 consistently in excess of estimated local sea-level rise (1.15 mm yr−1. Accretion rates were lower and less consistent in both the succulent (Sarcocornia, 0.78 ± 0.18 mm yr−1 and grass (Sporobolus, 0.88 ± 0.22 mm yr−1 assemblages located lower in the tidal frame. Short-term (6 days experiments showed deposition within Juncus plots to be dominated by autochthonous organic inputs with C deposition rates ranging from 1.14 ± 0.41 mg C cm−2 d−1 (neap tidal period to 2.37 ± 0.44 mg C cm−2 d−1 (spring tidal period, while minerogenic inputs and lower C deposition dominated Sarcocornia (0.10 ± 0.02 to 0.62 ± 0.08 mg C cm−2 d−1 and Sporobolus (0.17 ± 0.04 to 0.40 ± 0.07 mg C cm−2 d−1 assemblages.Elemental (C : N, isotopic (δ13C, mid-infrared (MIR and 13C nuclear magnetic resonance (NMR analyses revealed little difference in either the source or character of materials being deposited among neap versus spring tidal periods. Instead, these analyses point to substantial redistribution of materials within the Sarcocornia and

  20. Coral reef fish assemblages along a disturbance gradient in the northern Persian Gulf: A seasonal perspective.

    Science.gov (United States)

    Ghazilou, Amir; Shokri, Mohammad Reza; Gladstone, William

    2016-04-30

    Seasonal dynamics of coral reef fish assemblages were assessed along a gradient of potential anthropogenic disturbance in the Northern Persian Gulf. Overall, the attributes of coral reef fish assemblages showed seasonality at two different levels: seasonal changes irrespective of the magnitude of disturbance level (e.g. species richness), and seasonal changes in response to disturbance level (e.g. total abundance and assemblage composition). The examined parameters mostly belonged to the second group, but the interpretation of the relationship between patterns of seasonal changes and the disturbance level was not straightforward. The abundance of carnivorous fishes did not vary among seasons. SIMPER identified the family Nemipteridae as the major contributor to the observed spatiotemporal variations in the composition of coral reef fish assemblages in the study area. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Presence of riparian vegetation increases biotic condition of fish assemblages in two Brazilian reservoirs

    Directory of Open Access Journals (Sweden)

    Fabio Cop Ferreira

    2015-09-01

    Full Text Available Abstract The riparian vegetation in lakes and reservoirs is source of course wood structures such as trunks and branches and is used as sheltering, spawning and foraging habitats for fishes. The reduction of these submerged structures can thus, affect the composition and structure of fish assemblages in reservoirs. Aim To evaluate the influence of riparian vegetation on the biotic condition of fish assemblage by adapting the Reservoir Fish Assemblage Index (RFAI to two reservoirs in the Upper Paranapanema river basin, São Paulo State, Brazil. Methods The RFAI was adapted from metrics related to the functional characteristics and composition of fish assemblages through a protocol of metric selection and validation, and to its response to the presence of riparian vegetation. Results The final RFAI was composed by nine metrics, been lower in sites without riparian vegetation as consequence of the predominance of larger individuals and the percent of piscivorous and detritivorous fishes. Conclusions These results suggest that increasing shore habitat complexity in reservoirs by maintaining riparian vegetation increases fish biotic integrity.

  2. Detection of zoonotic and livestock-specific assemblages of Giardia duodenalis in free-living wild lizards

    Directory of Open Access Journals (Sweden)

    Aurora Reboredo-Fernández

    Full Text Available Abstract Giardia duodenalis is a zoonotic parasite that infects the gut of a wide range of vertebrates, including numerous wildlife species. However, little is known about this protozoan parasite in reptiles. Fecal samples from 31 wild lizards were collected in Galicia (northwest Spain and screened for the presence of Giardia by PCR amplification and sequencing of the ITS1-5.8S-ITS2 region in the ribosomal unit. This allowed detection of the parasite in 5 samples (16.1%, and enabled identification of G. duodenalis assemblage A2 in two samples of Iberian rock lizard (Iberolacerta monticola, G. duodenalis assemblage B in other two samples of I. monticola, and G. duodenalis assemblage E in one sample of Bocage’s wall lizard (Podarcis bocagei. The results obtained after PCR amplification and sequencing of the SSU-rDNA gene confirmed the presence of G. duodenalis assemblage A in two samples of I. monticola. This is the first report of G. duodenalis in free-living lizards, although further studies are needed to distinguish between actual infection and mechanical dissemination of cysts. The detection of zoonotic and livestock-specific assemblages of G. duodenalis demonstrates the wide environmental contamination by this parasite, possibly due to human activities.

  3. Unusual Deep Water sponge assemblage in South China—Witness of the end-Ordovician mass extinction

    Science.gov (United States)

    Li, Lixia; Feng, Hongzhen; Janussen, Dorte; Reitner, Joachim

    2015-11-01

    There are few sponges known from the end-Ordovician to early-Silurian strata all over the world, and no records of sponge fossils have been found yet in China during this interval. Here we report a unique sponge assemblage spanning the interval of the end-Ordovician mass extinction from the Kaochiapien Formation (Upper Ordovician-Lower Silurian) in South China. This assemblage contains a variety of well-preserved siliceous sponges, including both Burgess Shale-type and modern type taxa. It is clear that this assemblage developed in deep water, low energy ecosystem with less competitors and more vacant niches. Its explosion may be related to the euxinic and anoxic condition as well as the noticeable transgression during the end-Ordovician mass extinction. The excellent preservation of this assemblage is probably due to the rapid burial by mud turbidites. This unusual sponge assemblage provides a link between the Burgess Shale-type deep water sponges and the modern forms. It gives an excellent insight into the deep sea palaeoecology and the macroevolution of Phanerozoic sponges, and opens a new window to investigate the marine ecosystem before and after the end-Ordovician mass extinction. It also offers potential to search for exceptional fossil biota across the Ordovician-Silurian boundary interval in China.

  4. Unusual Deep Water sponge assemblage in South China-Witness of the end-Ordovician mass extinction.

    Science.gov (United States)

    Li, Lixia; Feng, Hongzhen; Janussen, Dorte; Reitner, Joachim

    2015-11-05

    There are few sponges known from the end-Ordovician to early-Silurian strata all over the world, and no records of sponge fossils have been found yet in China during this interval. Here we report a unique sponge assemblage spanning the interval of the end-Ordovician mass extinction from the Kaochiapien Formation (Upper Ordovician-Lower Silurian) in South China. This assemblage contains a variety of well-preserved siliceous sponges, including both Burgess Shale-type and modern type taxa. It is clear that this assemblage developed in deep water, low energy ecosystem with less competitors and more vacant niches. Its explosion may be related to the euxinic and anoxic condition as well as the noticeable transgression during the end-Ordovician mass extinction. The excellent preservation of this assemblage is probably due to the rapid burial by mud turbidites. This unusual sponge assemblage provides a link between the Burgess Shale-type deep water sponges and the modern forms. It gives an excellent insight into the deep sea palaeoecology and the macroevolution of Phanerozoic sponges, and opens a new window to investigate the marine ecosystem before and after the end-Ordovician mass extinction. It also offers potential to search for exceptional fossil biota across the Ordovician-Silurian boundary interval in China.

  5. Temporal variation in fish assemblage composition on a tidal flat

    Directory of Open Access Journals (Sweden)

    Henry L. Spach

    2004-03-01

    Full Text Available Annual variation in the fish assemblage characteristics on a tidal flat was studied in coastal Paraná, in southern Brazil. Fish were collected between August 1998 and July 1999, during the diurnal high tide and diurnal and nocturnal low tide of the syzygial (full moon and quadrature (waning moon tides, to characterize temporal change in assemblage composition. A total of 64,265 fish in 133 species were collected. The average number of species and individuals, biomass, species richness, diversity (mass and equitability varied significantly over time . The dissimilarity of the assemblage was greatest in August, September and October in contrast with the period from November to January, with the lowest dissimilarity. The combined action of water temperature, salinity and wind intensity had a great influence over the structure of the fish assemblage.Os peixes de uma planície de maré da praia Balneário de Pontal do Sul, Paraná, foram coletados, na preamar diurna e na baixa-mar diurna e noturna das marés de sizígia e de quadratura, visando caracterizar as mudanças temporais entre agosto de 1998 e julho de 1999. As coletas totalizaram 64.265 peixes de 133 espécies. Foram observadas diferenças significativas na captura média em número de espécies e de peixes, peso total e nos índices de riqueza, diversidade (H' peso e eqüitatividade entre os meses de coleta. A dissimilaridade da ictiofauna foi maior entre os meses de agosto, setembro e outubro em comparação com o período de novembro a janeiro. A ação combinada da temperatura da água, salinidade e intensidade do vento, influenciaram mais sobre a estrutura da assembléia de peixes.

  6. The distribution patterns of Red Sea Chaetodontid assemblages

    NARCIS (Netherlands)

    Zekeria, ZA; Afeworki, Y; Videler, JJ; Zekeria, A.

    2005-01-01

    1. The occurrence and abundance of butterflyfishes were investigated in northern, central and southern areas of the Eritrean Red Sea coast. Visual census was used to estimate the presence and abundance of the species along 100-metre long transects. 2. The assemblages of buttertlyfishes from the

  7. Microfloral assemblage, age and paleoenvironment of the Upper ...

    African Journals Online (AJOL)

    Microfloral assemblage, age and paleoenvironment of the Upper Cretaceous Patti Formation, southeastern Bida Basin, Nigeria. OJ Ojo, SO Akande. Abstract. No Abstract. Journal of Mining and Geology Vol. 44 (1) 2008: pp. 71-82. Full Text: EMAIL FULL TEXT EMAIL FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD ...

  8. Response of phytoplankton assemblages isolated for short periods ...

    African Journals Online (AJOL)

    The response of phytoplankton assemblages isolated in enclosures for short periods of time was examined in hyper-eutrophic Lake Chivero (Harare, Zimbabwe), to determine the factors that influenced the structure of the phytoplankton community, after noticing a marked decline in the dominance of Microcystis aeruginosa ...

  9. A new Lower Triassic ichthyopterygian assemblage from Fossil Hill, Nevada

    Directory of Open Access Journals (Sweden)

    Neil P. Kelley

    2016-01-01

    Full Text Available We report a new ichthyopterygian assemblage from Lower Triassic horizons of the Prida Formation at Fossil Hill in central Nevada. Although fragmentary, the specimens collected so far document a diverse fauna. One partial jaw exhibits isodont dentition with blunt tipped, mesiodistally compressed crowns and striated enamel. These features are shared with the Early Triassic genus Utatsusaurus known from coeval deposits in Japan and British Columbia. An additional specimen exhibits a different dentition characterized by relatively small, rounded posterior teeth resembling other Early Triassic ichthyopterygians, particularly Grippia. This Nevada assemblage marks a southward latitudinal extension for Early Triassic ichthyopterygians along the eastern margin of Panthalassa and indicates repeated trans-hemispheric dispersal events in Early Triassic ichthyopterygians.

  10. Movers and stayers: Novel assemblages in changing environments

    Science.gov (United States)

    Hobbs, Richard L.; Valentine, Leonie E.; Standish, Rachel J.; Jackson, Stephen T.

    2018-01-01

    How species will respond to ongoing climate and other change is of increasing concern.Most attention is given to how species move or are moved, but many species stay.Understanding the dynamics of new species combinations is essential for successful conservation in a changing climate.Increased attention to species movement in response to environmental change highlights the need to consider changes in species distributions and altered biological assemblages. Such changes are well known from paleoecological studies, but have accelerated with ongoing pervasive human influence. In addition to species that move, some species will stay put, leading to an array of novel interactions. Species show a variety of responses that can allow movement or persistence. Conservation and restoration actions have traditionally focused on maintaining or returning species in particular places, but increasingly also include interventions that facilitate movement. Approaches are required that incorporate the fluidity of biotic assemblages into the goals set and interventions deployed.

  11. Nematode assemblages in the rhizosphere of spring barley (Hordeum vulgare L.) depended on fertilisation and plant growth phase

    DEFF Research Database (Denmark)

    Madsen, Mette Vestergård

    2004-01-01

    rhizosphere; nitrogen and phosphorus fertilisation; nematode assemblages; plant parasites; barley......rhizosphere; nitrogen and phosphorus fertilisation; nematode assemblages; plant parasites; barley...

  12. Fish composition and assemblage in the anthropogenic-modified tidally-restricted Doñana (Spain) marshlands

    Science.gov (United States)

    Moreno-Valcárcel, Raquel; Oliva-Paterna, Francisco J.; Arribas, Carmen; Fernández-Delgado, Carlos

    2013-03-01

    The Guadalquivir estuary is the largest estuarine area on the southern Atlantic coast of Europe; its anthropogenic tidally-restricted marshes are partly within the boundary of the Doñana National Park, southern Spain. Our two-year study describes the spatial and temporal patterns of the fish assemblages in the Doñana marshlands in terms of species richness, abundance and biomass. The main families were Mugilidae and Cyprinidae, which accounted for 40.9% of the total species richness. Unlike the fish assemblages found in other European estuaries, Doñana was dominated in both biomass and abundance by freshwater species, mainly invasive exotic species. The spatial analysis of the assemblage showed four significant fish groups corresponding to different habitats established a priori and related to the salinity gradient. Assemblages did not show a seasonal pattern and the temporal fish groups observed were mainly related to the hydrological cycle and the extreme drought that occurred during the study period.

  13. Fish assemblages on fringing reefs in the southern Caribbean: biodiversity, biomass and feeding types

    Directory of Open Access Journals (Sweden)

    Jahson B. Alemu I.

    2014-09-01

    Full Text Available Reef fish assemblages in the Caribbean are under increasing pressure from human activities. Inadequate enforcement of legislation coupled with unreliable and data-poor landings in Tobago have led to the unregulated exploitation of reef fish for decades. This study addresses the lack of data on major reefs. Visual observations of fish fauna were conducted from November 2011-May 2013 at open access reef sites (Speyside, Charlotteville, Culloden, Arnos Vale, Mt. Irvine, La Guira, Kilgwyn, Plymouth and Black Rock and one protected area (Buccoo Reef Marine Park. Belt transects surveys were used to determine fish density, species diversity and abundance at the 10-15m depth contour. Fish sizes were converted to biomass using the length-weight relationship of fish W=aLb. Most fish assemblages were dominated by small herbivores (40cm e.g. Serranidae, were noted, which is indicative of fishing pressure. MDS ordination identified three fish assemblages: i northeastern, ii southwestern and iii intermediate. The northwestern cluster (Speyside and Charlotteville were most representative of reef fish assemblages across the entire island, and exhibited the highest species richness, diversity and biomass. However, the southwestern cluster the highest numerical abundance. The marine protected area contained higher fish biomass, abundance, diversity and richness, but it was only representative of reef fish assemblages on the southwest of the island and not the entire Tobago. Research on the reef fishery, particularly spear fishing, is recommended to determine impact.

  14. Spatial and seasonal variations of fish assemblages in mangrove creek systems in Zanzibar (Tanzania)

    Science.gov (United States)

    Mwandya, Augustine W.; Gullström, Martin; Andersson, Mathias H.; Öhman, Marcus C.; Mgaya, Yunus D.; Bryceson, Ian

    2010-11-01

    Spatial and seasonal variations of fish assemblage composition were studied in three non-estuarine mangrove creeks of Zanzibar (Tanzania). Fish were collected monthly for one year at three sites (lower, intermediate and upper reaches) in each creek using a seine net (each haul covering 170 m 2). Density, species number and diversity of fish were all higher at sites with dense cover of macrophytes (seagrass and macroalgae) than over unvegetated sandy sites. In general, fish assemblages mainly comprised juveniles of a few abundant taxa, e.g. Mugil cephalus, Mugilidae spp. and Leiognathus equulus at sites with mud substratum and Gerres oyena, Lethrinus harak and Sillago sihama at sites dominated by macrophytes. Multivariate analyses revealed significant separations in fish assemblage composition within the two creeks where the bottom substratum differed among sites. Overall, season seemed to have little effect on density, species number, diversity index ( H') and assemblage structure of fish. Water condition variables were also relatively stable across the season, although a short-term fluctuation primarily induced by decreased salinity, occurred during the heavy rains in April and May. Fish assemblage structure was not significantly affected by any of the abiotic factors tested. However, significant regressions were found between the other fish variables and environmental variables, but since these associations were mostly species-specific and generally inconsistent, we suggest that the overall distribution patterns of fish were mainly an effect of particular substrate preferences of fish species rather than contemporary water conditions.

  15. Effects of environmental and water quality parameters on the functioning of copepod assemblages in tropical estuaries

    Science.gov (United States)

    Araujo, Adriana V.; Dias, Cristina O.; Bonecker, Sérgio L. C.

    2017-07-01

    We examined changes in the functioning of copepod assemblages with increasing pollution in estuaries, using sampling standardization of the salinity range to enable comparisons. Copepod assemblages were analyzed in four southeast Brazilian estuaries with different water quality levels and hydrodynamic characteristics over two years. We obtained mesozooplankton samples together with environmental and water quality parameters in the estuaries, every two months under predetermined salinities ranging from 15 to 25. The values of parameters, except species size, associated with the functioning of the copepod assemblages (biomass, productivity, and turnover rate) did not differ among estuaries. However, in the more polluted estuaries, the biomass and productivity of copepod assemblages of mesozooplankton were negatively correlated with concentration of pollution indicator parameters. Conversely, in the less polluted estuaries some degree of enrichment still seems to increase the system biomass and productivity, as these parameters were inversely related to indicators of improved water quality. The pollution level of estuaries distorted the relationship between temperature and the efficiency of converting energy to organic matter. In the less polluted estuaries, the relationship between turnover rate and temperature was over 70%, while in the most polluted estuaries, this relationship was only approximately 50%. Our results demonstrated that the functioning of assemblages in the estuaries was affected differently by increasing pollution depending on the water quality level of the system. Thus, investigating the functioning of assemblages can be a useful tool for the analysis of estuarine conditions.

  16. Long-term monitoring of coral reef fish assemblages in the Western central pacific.

    Science.gov (United States)

    Heenan, Adel; Williams, Ivor D; Acoba, Tomoko; DesRochers, Annette; Kosaki, Randall K; Kanemura, Troy; Nadon, Marc O; Brainard, Russell E

    2017-12-05

    Throughout the tropics, coral reef ecosystems, which are critically important to people, have been greatly altered by humans. Differentiating human impacts from natural drivers of ecosystem state is essential to effective management. Here we present a dataset from a large-scale monitoring program that surveys coral reef fish assemblages and habitats encompassing the bulk of the US-affiliated tropical Pacific, and spanning wide gradients in both natural drivers and human impact. Currently, this includes >5,500 surveys from 39 islands and atolls in Hawaii (including the main and Northwestern Hawaiian Islands) and affiliated geo-political regions of American Samoa, the Commonwealth of the Northern Mariana Islands, Guam, and the Pacific Remote Islands Areas. The dataset spans 2010-2017, during which time, each region was visited at least every three years, and ~500-1,000 surveys performed annually. This standardised dataset is a powerful resource that can be used to understand how human, environmental and oceanographic conditions influence coral reef fish community structure and function, providing a basis for research to support effective management outcomes.

  17. Emerging trends in the discovery of natural product antibacterials

    DEFF Research Database (Denmark)

    Bologa, Cristian G; Ursu, Oleg; Oprea, Tudor

    2013-01-01

    This article highlights current trends and advances in exploiting natural sources for the deployment of novel and potent anti-infective countermeasures. The key challenge is to therapeutically target bacterial pathogens that exhibit a variety of puzzling and evolutionarily complex resistance...... mechanisms. Special emphasis is given to the strengths, weaknesses, and opportunities in the natural product antibacterial drug discovery arena, and to emerging applications driven by advances in bioinformatics, chemical biology, and synthetic biology in concert with exploiting bacterial phenotypes....... These efforts have identified a critical mass of natural product antibacterial lead compounds and discovery technologies with high probability of successful implementation against emerging bacterial pathogens....

  18. Electrical conductivity measurements of bacterial nanowires from Pseudomonas aeruginosa

    International Nuclear Information System (INIS)

    Maruthupandy, Muthusamy; Anand, Muthusamy; Beevi, Akbar Sait Hameedha; Priya, Radhakrishnan Jeeva; Maduraiveeran, Govindhan

    2015-01-01

    The extracellular appendages of bacteria (flagella) that transfer electrons to electrodes are called bacterial nanowires. This study focuses on the isolation and separation of nanowires that are attached via Pseudomonas aeruginosa bacterial culture. The size and roughness of separated nanowires were measured using transmission electron microscopy (TEM) and atomic force microscopy (AFM), respectively. The obtained bacterial nanowires indicated a clear image of bacterial nanowires measuring 16 nm in diameter. The formation of bacterial nanowires was confirmed by microscopic studies (AFM and TEM) and the conductivity nature of bacterial nanowire was investigated by electrochemical techniques. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS), which are nondestructive voltammetry techniques, suggest that bacterial nanowires could be the source of electrons—which may be used in various applications, for example, microbial fuel cells, biosensors, organic solar cells, and bioelectronic devices. Routine analysis of electron transfer between bacterial nanowires and the electrode was performed, providing insight into the extracellular electron transfer (EET) to the electrode. CV revealed the catalytic electron transferability of bacterial nanowires and electrodes and showed excellent redox activities. CV and EIS studies showed that bacterial nanowires can charge the surface by producing and storing sufficient electrons, behave as a capacitor, and have features consistent with EET. Finally, electrochemical studies confirmed the development of bacterial nanowires with EET. This study suggests that bacterial nanowires can be used to fabricate biomolecular sensors and nanoelectronic devices. (paper)

  19. Molecular characterization of soil bacterial community in a perhumid, low mountain forest.

    Science.gov (United States)

    Lin, Yu-Te; Whitman, William B; Coleman, David C; Chih-Yu, Chiu

    2011-01-01

    Forest disturbance often results in changes in soil properties and microbial communities. In the present study, we characterized a soil bacterial community subjected to disturbance using 16S rRNA gene clone libraries. The community was from a disturbed broad-leaved, low mountain forest ecosystem at Huoshaoliao (HSL) located in northern Taiwan. This locality receives more than 4,000 mm annual precipitation, one of the highest precipitations in Taiwan. Based on the Shannon diversity index, Chao1 estimator, richness and rarefaction curve analysis, the bacterial community in HSL forest soils was more diverse than those previously investigated in natural and disturbed forest soils with colder or less humid weather conditions. Analysis of molecular variance also revealed that the bacterial community in disturbed soils significantly differed from natural forest soils. Most of the abundant operational taxonomic units (OTUs) in the disturbed soil community at HSL were less abundant or absent in other soils. The disturbances influenced the composition of bacterial communities in natural and disturbed forests and increased the diversity of the disturbed forest soil community. Furthermore, the warmer and humid weather conditions could also increase community diversity in HSL soils.

  20. Diatom Surface Sediment Assemblages from the Bering Sea Shelf: a Tossed Salad or Faithful Recorder of 50 Years of Environmental Change?

    Science.gov (United States)

    Caissie, B.; Brigham-Grette, J.; Kanamaru-Shinn, K.

    2010-12-01

    Recent environmental change in the Bering Sea includes a shift from the negative to positive phase of the Pacific Decadal Oscillation in 1976/77, a secondary shift in sea level pressure and sea surface temperatures in 1998, increasing sea surface temperatures, an earlier spring, an increase in the number of days that sea ice is present along the shelf-slope break, and a decrease in the number of days that sea ice is present in the Chukchi Sea and Arctic Ocean. These physical changes have manifest biological changes such as a northward migration of invertebrates and fish from the southern Bering Sea and shifts in the timing and duration of sea-ice related primary productivity and the spring bloom. We aim to see if diatom sediment assemblages are faithful recorders of these ecological changes in the Bering Sea or if bioturbation has essentially mixed today’s rapid change down core such that the signal is either muted or no longer apparent. Six continental shelf areas were examined in the Bering Sea ranging from northeast of St. Lawrence Island to the shelf-slope break in the south-central Bering Sea. Diatom assemblages from core tops collected as part of the PROBES program in the 1960s were compared to core tops taken nearby (7 m) multi-year ice so their decline may be related to the decrease in multi-year ice over the past 30 years. Additionally, in most cases, species diversity has declined over the past 50 years with Fragilariopsis oceanica and Fragilariopsis cylindrus accounting for a greater percentage of the sediment assemblages today. These two species are collectively considered indicators of seasonal sea ice; their relative abundance peaks when ice is present for 5 months per year. Ongoing down core analyses in these six areas will further reveal the nature of these assemblage changes.

  1. Recovery of prairie fish assemblages at the transition from channelized to nonchannelized: Implications for conservation of natural channels

    Science.gov (United States)

    Vokoun, Jason C.; Rabeni, Charles F.

    2003-01-01

    Fish assemblages were systematically sampled along the transition from channelized to unchannelized reaches in seven streams in nort