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Sample records for bacterioplankton

  1. Annual patterns in bacterioplankton community variability in a humic lake.

    Science.gov (United States)

    Kent, A D; Jones, S E; Yannarell, A C; Graham, J M; Lauster, G H; Kratz, T K; Triplett, E W

    2004-11-01

    Bacterioplankton community composition (BCC) was monitored in a shallow humic lake in northern Wisconsin, USA, over 3 years using automated ribosomal intergenic spacer analysis (ARISA). Comparison of ARISA profiles of bacterial communities over time indicated that BCC was highly variable on a seasonal and annual scale. Nonmetric multidimensional scaling (MDS) analysis indicated little similarity in BCC from year to year. Nevertheless, annual patterns in bacterioplankton community diversity were observed. Trends in bacterioplankton community diversity were correlated to annual patterns in community succession observed for phytoplankton and zooplankton populations, consistent with the notion that food web interactions affect bacterioplankton community structure in this humic lake. Bacterioplankton communities experience a dramatic drop in richness and abundance each year in early summer, concurrent with an increase in the abundance of both mixotrophic and heterotrophic flagellates. A second drop in richness, but not abundance, is observed each year in late summer, coinciding with an intense bloom of the nonphagotrophic dinoflagellate Peridinium limbatum. A relationship between bacterial community composition, size, and abundance and the population dynamics of Daphnia was also observed. The noted synchrony between these major population and species shifts suggests that linkages across trophic levels play a role in determining the annual time course of events for the microbial and metazoan components of the plankton.

  2. Systems Biology and Ecology of Streamlined Bacterioplankton

    Science.gov (United States)

    Giovannoni, S. J.

    2014-12-01

    The salient feature of streamlined cells is their small genome size, but "streamlining" refers more generally to selection that favors minimization of cell size and complexity. The essence of streamlining theory is that selection is most efficient in organisms that have large effective population sizes, and, in nutrient-limited systems, favors cell architecture that minimizes resources required for replication. Regardless of the cause of genome reduction, lost coding potential eventually dictates loss of function, raising the questions, what genome features are expendable, and how do cells become highly successful with a minimal genomic repertoire? One consequence of reductive evolution in streamlined organisms is atypical patterns of prototrophy, for example the recent discovery of a requirement for the thiamin precursor 4-amino-5-hydroxymethyl-2-methylpyrimidine in some plankton taxa. Examples such as this fit within the framework of the Black Queen Hypothesis, which describes genome reduction that results in reliance on community goods and increased community connectivity. Other examples of genome reduction include losses of regulatory functions, or replacement with simpler regulatory systems, and increased metabolic integration. In one such case, in the order Pelagibacterales, the PII system for regulating responses to N limitation has been replaced with a simpler system composed of fewer genes. Both the absence of common regulatory systems and atypical patterns of prototrophy have been linked to difficulty in culturing Pelagibacterales, lending credibility to the idea that streamlining might broadly explain the phenomenon of the uncultured microbial majority. The success of streamlined osmotrophic bacterioplankton suggests that they successfully compete for labile organic matter and capture a large share of this resource, but an alternative theory postulates they are not good resource competitors and instead prosper by avoiding predation. The answers to these

  3. Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling.

    Science.gov (United States)

    Lindh, Markus V; Sjöstedt, Johanna; Andersson, Anders F; Baltar, Federico; Hugerth, Luisa W; Lundin, Daniel; Muthusamy, Saraladevi; Legrand, Catherine; Pinhassi, Jarone

    2015-07-01

    Multiyear comparisons of bacterioplankton succession reveal that environmental conditions drive community shifts with repeatable patterns between years. However, corresponding insight into bacterioplankton dynamics at a temporal resolution relevant for detailed examination of variation and characteristics of specific populations within years is essentially lacking. During 1 year, we collected 46 samples in the Baltic Sea for assessing bacterial community composition by 16S rRNA gene pyrosequencing (nearly twice weekly during productive season). Beta-diversity analysis showed distinct clustering of samples, attributable to seemingly synchronous temporal transitions among populations (populations defined by 97% 16S rRNA gene sequence identity). A wide spectrum of bacterioplankton dynamics was evident, where divergent temporal patterns resulted both from pronounced differences in relative abundance and presence/absence of populations. Rates of change in relative abundance calculated for individual populations ranged from 0.23 to 1.79 day(-1) . Populations that were persistently dominant, transiently abundant or generally rare were found in several major bacterial groups, implying evolution has favoured a similar variety of life strategies within these groups. These findings suggest that high temporal resolution sampling allows constraining the timescales and frequencies at which distinct populations transition between being abundant or rare, thus potentially providing clues about physical, chemical or biological forcing on bacterioplankton community structure.

  4. Unusual bacterioplankton community structure in ultra-oligotrophic Crater Lake

    Science.gov (United States)

    Urbach, Ena; Vergin, Kevin L.; Morse, Ariel

    2001-01-01

    The bacterioplankton assemblage in Crater Lake, Oregon (U.S.A.), is different from communities found in other oxygenated lakes, as demonstrated by four small subunit ribosomal ribonucleic acid (SSU rRNA) gene clone libraries and oligonucleotide probe hybridization to RNA from lake water. Populations in the euphotic zone of this deep (589 m), oligotrophic caldera lake are dominated by two phylogenetic clusters of currently uncultivated bacteria: CL120-10, a newly identified cluster in the verrucomicrobiales, and ACK4 actinomycetes, known as a minor constituent of bacterioplankton in other lakes. Deep-water populations at 300 and 500 m are dominated by a different pair of uncultivated taxa: CL500-11, a novel cluster in the green nonsulfur bacteria, and group I marine crenarchaeota. b-Proteobacteria, dominant in most other freshwater environments, are relatively rare in Crater Lake (chemistry of infiltrating hydrothermal waters, and irradiation by high levels of ultraviolet light.

  5. Effects of UV-B Radiation on the Structural and Physiological Diversity of Bacterioneuston and Bacterioplankton

    Science.gov (United States)

    Santos, Ana L.; Oliveira, Vanessa; Baptista, Inês; Henriques, Isabel; Gomes, Newton C. M.; Almeida, Adelaide; Correia, António

    2012-01-01

    The effects of UV radiation (UVR) on estuarine bacterioneuston and bacterioplankton were assessed in microcosm experiments. Bacterial abundance and DNA synthesis were more affected in bacterioplankton. Protein synthesis was more inhibited in bacterioneuston. Community analysis indicated that UVR has the potential to select resistant bacteria (e.g., Gammaproteobacteria), particularly abundant in bacterioneuston. PMID:22247171

  6. Bacterioplankton carbon cycling along the Subtropical Frontal Zone off New Zealand

    Science.gov (United States)

    Baltar, Federico; Stuck, Esther; Morales, Sergio; Currie, Kim

    2015-06-01

    Marine heterotrophic bacterioplankton (Bacteria and Archaea) play a central role in ocean carbon cycling. As such, identifying the factors controlling these microbial populations is crucial to fully understanding carbon fluxes. We studied bacterioplankton activities along a transect crossing three water masses (i.e., Subtropical waters [STW], Sub-Antarctic waters [SAW] and neritic waters [NW]) with contrasting nutrient regimes across the Subtropical Frontal Zone. In contrast to bacterioplankton production and community respiration, bacterioplankton respiration increased in the offshore SAW, causing a seaward increase in the contribution of bacteria to community respiration (from 7% to 100%). Cell-specific bacterioplankton respiration also increased in SAW, but cell-specific production did not, suggesting that prokaryotic cells in SAW were investing more energy towards respiration than growth. This was reflected in a 5-fold decline in bacterioplankton growth efficiency (BGE) towards SAW. One way to explain this decrease in BGE could be due to the observed reduction in phytoplankton biomass (and presumably organic matter concentration) towards SAW. However, this would not explain why bacterioplankton respiration was highest in SAW, where phytoplankton biomass was lowest. Another factor affecting BGE could be the iron limitation characteristic of high-nutrient low-chlorophyll (HNLC) regions like SAW. Our field-study based evidences would agree with previous laboratory experiments in which iron stress provoked a decrease in BGE of marine bacterial isolates. Our results suggest that there is a strong gradient in bacterioplankton carbon cycling rates along the Subtropical Frontal Zone, mainly due to the HNLC conditions of SAW. We suggest that Fe-induced reduction of BGE in HNLC regions like SAW could be relevant in marine carbon cycling, inducing bacterioplankton to act as a link or a sink of organic carbon by impacting on the quantity of organic carbon they incorporate

  7. Coupling bacterioplankton populations and environment to community function in coastal temperate waters

    DEFF Research Database (Denmark)

    Traving, S. J.; Bentzon-Tilia, Mikkel; Knudsen-Leerbeck, H.;

    2016-01-01

    Bacterioplankton play a key role in marine waters facilitating processes important for carbon cycling. However, the influence of specific bacterial populations and environmental conditions on bacterioplankton community performance remains unclear. The aim of the present study was to identify...... surface waters over a full year indicated that specific bacterial populations were linked to measured functions. Namely, Synechococcus (Cyanobacteria) was strongly correlated with protease activity. Both function and community composition showed seasonal variation. However, the pattern of substrate...... of common drivers of bacterioplankton community functions in two different systems indicates that the drivers may be of broader relevance in coastal temperate waters....

  8. Distribution of biomass of heterotrophic bacterioplankton in the Bohai Sea

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Distribution, variation and impact factors of biomass of bacterioplankton from April to May 1999in Bohai Sea were studied in DAPI method with epifluorescence microscopy. The biomass in surface waters showed a small day-night variation, varying from 0.13 to 2.51 μg/dm3 with an average of 0.84 μg/dm3. The biomass in bottom waters showed, however, a large variation, changing from 0.15 to 4.18 μg/dm3 with an average of 1.36 μg/dm3. The peak values occurred at 5 and 11 a.m. The bottom water biomass showed a significant correlation with particulate organic carbon (r=0.639, P<0.05). Heterotrophic bacterioplankton biomass was high in nearshore waters and low in offshore areas with a high biomass zone around Huanghe (Yellow) River mouth,showing the same distribution of nutrients. In vertical distribution, heterotrophic bacteria biomass in bottom waters was higher than that in surface water.

  9. Marine bacterioplankton biomass, activity and community structure in the vicinity of Antarctic icebergs

    Science.gov (United States)

    Murray, Alison E.; Peng, Vivian; Tyler, Charlotte; Wagh, Protima

    2011-06-01

    We studied marine bacterioplankton in the Scotia Sea in June 2008 and in the northwest Weddell Sea in March to mid April 2009 in waters proximal to three free-drifting icebergs (SS-1, A-43k, and C-18a), in a region with a high density of smaller icebergs (iceberg alley), and at stations that were upstream of the iceberg trajectories designated as far-field reference sites that were between 16-75 km away. Hydrographic parameters were used to define water masses in which comparisons between bacterioplankton-associated characteristics (abundance, leucine incorporation into protein, aminopeptidase activities and community structure) within and between water masses could be made. Early winter Scotia Sea bacterioplankton had low levels of cells and low heterotrophic production rates in the upper 50 m. Influences of the icebergs on bacterioplankton at this time of year were minimal, if not deleterious, as we found lower levels of heterotrophic production near A-43k in comparison to stations >16 km away. Additionally, the results point to small but significant differences in cell abundance, heterotrophic production, and community structure between the two icebergs studied. These icebergs differed greatly in size and the findings suggest that the larger iceberg had a greater effect. In the NW Weddell Sea in March-mid April bacterioplankton were twice as abundant and had heterotrophic productions rates that were 8-fold higher than what we determined in the Scotia Sea, though levels were still quite low, which is typical for autumn. We did not detect direct iceberg-related influences on the bacterioplankton characteristics studied here. Clues to understanding bacterioplankton responses may lie in the details of community structure, as there were some significant differences in community structure in the winter water and underlying upper circumpolar deep-water masses between stations occupied close to C-18a and at stations 18 km away (i.e. Polaribacter and Pelagibacter

  10. Coupling bacterioplankton populations and environment to community function in coastal temperate waters

    DEFF Research Database (Denmark)

    Traving, S. J.; Bentzon-Tilia, Mikkel; Knudsen-Leerbeck, H.

    2016-01-01

    utilization capacity could not be directly linked to the community dynamics. The overall importance of dissolved organic matter (DOM) parameters in the LASSO models indicate that bacterioplankton respond to the present substrate landscape, with a particular importance of nitrogenous DOM. The identification......Bacterioplankton play a key role in marine waters facilitating processes important for carbon cycling. However, the influence of specific bacterial populations and environmental conditions on bacterioplankton community performance remains unclear. The aim of the present study was to identify...... surface waters over a full year indicated that specific bacterial populations were linked to measured functions. Namely, Synechococcus (Cyanobacteria) was strongly correlated with protease activity. Both function and community composition showed seasonal variation. However, the pattern of substrate...

  11. Energetic differences between bacterioplankton trophic groups and coral reef resistance.

    Science.gov (United States)

    McDole Somera, Tracey; Bailey, Barbara; Barott, Katie; Grasis, Juris; Hatay, Mark; Hilton, Brett J; Hisakawa, Nao; Nosrat, Bahador; Nulton, James; Silveira, Cynthia B; Sullivan, Chris; Brainard, Russell E; Rohwer, Forest

    2016-04-27

    Coral reefs are among the most productive and diverse marine ecosystems on the Earth. They are also particularly sensitive to changing energetic requirements by different trophic levels. Microbialization specifically refers to the increase in the energetic metabolic demands of microbes relative to macrobes and is significantly correlated with increasing human influence on coral reefs. In this study, metabolic theory of ecology is used to quantify the relative contributions of two broad bacterioplankton groups, autotrophs and heterotrophs, to energy flux on 27 Pacific coral reef ecosystems experiencing human impact to varying degrees. The effective activation energy required for photosynthesis is lower than the average energy of activation for the biochemical reactions of the Krebs cycle, and changes in the proportional abundance of these two groups can greatly affect rates of energy and materials cycling. We show that reef-water communities with a higher proportional abundance of microbial autotrophs expend more metabolic energy per gram of microbial biomass. Increased energy and materials flux through fast energy channels (i.e. water-column associated microbial autotrophs) may dampen the detrimental effects of increased heterotrophic loads (e.g. coral disease) on coral reef systems experiencing anthropogenic disturbance.

  12. Interactions between hydrology and water chemistry shape bacterioplankton biogeography across boreal freshwater networks.

    Science.gov (United States)

    Niño-García, Juan Pablo; Ruiz-González, Clara; Del Giorgio, Paul A

    2016-07-01

    Disentangling the mechanisms shaping bacterioplankton communities across freshwater ecosystems requires considering a hydrologic dimension that can influence both dispersal and local sorting, but how the environment and hydrology interact to shape the biogeography of freshwater bacterioplankton over large spatial scales remains unexplored. Using Illumina sequencing of the 16S ribosomal RNA gene, we investigate the large-scale spatial patterns of bacterioplankton across 386 freshwater systems from seven distinct regions in boreal Québec. We show that both hydrology and local water chemistry (mostly pH) interact to shape a sequential structuring of communities from highly diverse assemblages in headwater streams toward larger rivers and lakes dominated by fewer taxa. Increases in water residence time along the hydrologic continuum were accompanied by major losses of bacterial richness and by an increased differentiation of communities driven by local conditions (pH and other related variables). This suggests that hydrology and network position modulate the relative role of environmental sorting and mass effects on community assembly by determining both the time frame for bacterial growth and the composition of the immigrant pool. The apparent low dispersal limitation (that is, the lack of influence of geographic distance on the spatial patterns observed at the taxonomic resolution used) suggests that these boreal bacterioplankton communities derive from a shared bacterial pool that enters the networks through the smallest streams, largely dominated by mass effects, and that is increasingly subjected to local sorting of species during transit along the hydrologic continuum.

  13. Bacterioplankton responses to iron enrichment during the SAGE experiment

    Science.gov (United States)

    Kuparinen, J.; Hall, J.; Ellwood, M.; Safi, K.; Peloquin, J.; Katz, D.

    2011-03-01

    We studied the microbial food web in the upper 100 m of the water column in iron-limited sub-Antarctic HNLC waters south-east of New Zealand in the SAGE experiment in 2004, with focus on bacterioplankton. Samples were collected daily from inside and outside the iron enriched patch. Short term enrichment experiments were conducted on board in 4 L polycarbonate bottles with water outside the iron enriched patch to study single and combined effects of micronutrient additions on microbial food web. Low bacterial growth was recorded in the study area with community turnover times of 50 h or more during the study period. Measurements of bacterial standing stocks and production rates in the study show minor responses to the large scale iron enrichment, with increase in rates and stocks after the first enrichment and at the end of the study period after the third iron enrichment when solar radiation increased and wind mixing decreased. The average daily bacterial production rates were 31.5 and 33.7 mgCm -2 d -1 for the OUT and IN stations, respectively; thus overall there was not a significant difference between the control and the iron-enriched patch. In the bottle experiments bacterial thymidine incorporation showed responses to single iron and silicic acid enrichments and a major growth response to the combined iron and sucrose enrichments. Phytoplankton chlorophyll- a showed clear stimulation by single additions of iron and silicic acid and silicic acid enhanced the iron impact. Cobalt additions had no effect on bacteria growth and a negative effect on phytoplankton growth. Low bacterial in situ growth rates and the enrichment experiments suggest that bacteria are co-limited by iron and carbon, and that bacterial iron uptake is dependent on carbon supply by the food web. With the high iron quota (μmol Fe mol C -1) bacteria may scavenge considerable amounts of the excess iron, and thus influence the relative importance of the microbial food web as a carbon sink.

  14. Changes of bacterioplankton apparent species richness in two ornamental fish aquaria

    OpenAIRE

    2013-01-01

    We analysed the 16S rRNA gene diversity within the bacterioplankton community in the water column of the ornamental fish Pterophyllum scalare and Archocentrus nigrofasciatus aquaria during a 60-day growth experiment in order to detect any dominant bacterial species and their possible association with the rearing organisms. The basic physical and chemical parameters remained stable but the bacterial community at 0, 30 and 60 days showed marked differences in bacterial cell abundance and divers...

  15. Characterization of lysogens in bacterioplankton assemblages of the southern California borderland.

    Science.gov (United States)

    Hewson, Ian; Fuhrman, Jed A

    2007-05-01

    Viruses cause significant mortality of marine microorganisms; however, their role in shaping the composition of microbial assemblages has not been fully elucidated. Because viruses may form lysogenic relationships with their hosts, temperate viruses may influence bacterial assemblage structures through direct lysis of hosts when induced by environmental stimuli or by homoimmunity (i.e., immunity to closely related viruses). We investigated the components of bacterioplankton assemblages that bore prophage using the lysogenic induction agent mitomycin C. Seawater was collected at two locations (the San Pedro Ocean Time Series Station and in the Santa Barbara Channel) in the Southern California Borderland and amended with mitomycin C. After 24-h incubation, the community structure of bacterioplankton was compared with unamended controls using automated rRNA intergenic spacer analysis. The addition of mitomycin C to seawater had effects on the community structure of bacterioplankton, stimulating detectable overall diversity and richness of fingerprints and causing the assemblages within incubations to become different to control assemblages. Most negatively impacted operational taxonomic units (OTU) in mitomycin C-amended incubations individually comprised a large fraction of total amplified DNA in initial seawater (5.3-23.3% of amplified DNA fluorescence) fingerprints, and data suggest that these include organisms putatively classified as members of the gamma-Proteobacteria, SAR11 cluster, and Synechococcus groups. The stimulation of assemblage richness by induction of lysogens, and the reduction in the contribution to total DNA of common OTU (and concomitant increase in rare OTU), suggests that temperate phage have the potential to strongly influence the diversity of bacterioplankton assemblages. Because lysogenic OTU may also be resistant to closely related lytic (i.e., free-living) viruses, the impact of lytic virioplankton on assemblages may only be pronounced

  16. Combined Carbohydrates Support Rich Communities of Particle-Associated Marine Bacterioplankton

    Science.gov (United States)

    Sperling, Martin; Piontek, Judith; Engel, Anja; Wiltshire, Karen H.; Niggemann, Jutta; Gerdts, Gunnar; Wichels, Antje

    2017-01-01

    Carbohydrates represent an important fraction of labile and semi-labile marine organic matter that is mainly comprised of exopolymeric substances derived from phytoplankton exudation and decay. This study investigates the composition of total combined carbohydrates (tCCHO; >1 kDa) and the community development of free-living (0.2–3 μm) and particle-associated (PA) (3–10 μm) bacterioplankton during a spring phytoplankton bloom in the southern North Sea. Furthermore, rates were determined for the extracellular enzymatic hydrolysis that catalyzes the initial step in bacterial organic matter remineralization. Concentrations of tCCHO greatly increased during bloom development, while the composition showed only minor changes over time. The combined concentration of glucose, galactose, fucose, rhamnose, galactosamine, glucosamine, and glucuronic acid in tCCHO was a significant factor shaping the community composition of the PA bacteria. The richness of PA bacteria greatly increased in the post-bloom phase. At the same time, the increase in extracellular β-glucosidase activity was sufficient to explain the observed decrease in tCCHO, indicating the efficient utilization of carbohydrates by the bacterioplankton community during the post-bloom phase. Our results suggest that carbohydrate concentration and composition are important factors in the multifactorial environmental control of bacterioplankton succession and the enzymatic hydrolysis of organic matter during phytoplankton blooms. PMID:28197132

  17. Spatial and temporal dynamics of phytoplankton and bacterioplankton biomass in Sanya Bay, northern South China Sea

    Institute of Scientific and Technical Information of China (English)

    ZHOU Weihua; LI Tao; XU Jirong; WANG Hankui; CAI Chuanghua; DONG Junde; ZHANG Si

    2009-01-01

    The composition of phytoplankton and the dynamics of phytoplankton and bacterioplankton biomass (PB and BB, respectively) of Sanya Bay, South China Sea, were determined. A total of 168 species (67 genera) phytoplankton were identified, including Bacillariophyta (diatom, 128 species), Pyrrophyta (35 species), Cyanophyta (3 species), and Chrysophyta (2 species). Annual average abundance of phytoplankton was 1.2 × 107 cells/m3, with the highest abundance in autumn, and the lowest in summer. Annual average diversity index (H′) and evenness (J) values were 3.86 and 0.70, respectively. Average chlorophyll a was 2.5 mg/m3, and the average PB was 124 mg C/m3, with the highest value in autumn. Surface PB was higher than the bottom, except for summer. Annual mean bacterioplankton abundance and BB were 6.9 × 1011 cells/m3 and 13.8 mg C/m3, respectively. The highest BB was found in summer, followed by winter, spring, and autumn. Surface BB was higher than bottom all year round. The spatial distribution patterns of PB and BB were very similar with the highest biomass in the estuary and decreasing seaward, primarily due to terrestrial input from the Sanya River and influx of oceanic water. The main factor influencing on PB and BB was DIN, with other factors such as temperature, which was above 22℃ throughout the year, having a negligible impact. The correlation between BB and PB was significant (P < 0.01). The annual average ratio of BB/PB was 0.12 (0.06--0.15). Phytoplankton primary production was one of the most important factors in controlling the distribution of bacterioplankton.

  18. Diazotrophic bacterioplankton in a coral reef lagoon: phylogeny, diel nitrogenase expression and response to phosphate enrichment.

    Science.gov (United States)

    Hewson, Ian; Moisander, Pia H; Morrison, Amanda E; Zehr, Jonathan P

    2007-05-01

    We investigated diazotrophic bacterioplankton assemblage composition in the Heron Reef lagoon (Great Barrier Reef, Australia) using culture-independent techniques targeting the nifH fragment of the nitrogenase gene. Seawater was collected at 3 h intervals over a period of 72 h (i.e. over diel as well as tidal cycles). An incubation experiment was also conducted to assess the impact of phosphate (PO(4)3*) availability on nifH expression patterns. DNA-based nifH libraries contained primarily sequences that were most similar to nifH from sediment, microbial mat and surface-associated microorganisms, with a few sequences that clustered with typical open ocean phylotypes. In contrast to genomic DNA sequences, libraries prepared from gene transcripts (mRNA amplified by reverse transcription-polymerase chain reaction) were entirely cyanobacterial and contained phylotypes similar to those observed in open ocean plankton. The abundance of Trichodesmium and two uncultured cyanobacterial phylotypes from previous studies (group A and group B) were studied by quantitative-polymerase chain reaction in the lagoon samples. These were detected as transcripts, but were not detected in genomic DNA. The gene transcript abundance of these phylotypes demonstrated variability over several diel cycles. The PO(4)3* enrichment experiment had a clearer pattern of gene expression over diel cycles than the lagoon sampling, however PO(4)3* additions did not result in enhanced transcript abundance relative to control incubations. The results suggest that a number of diazotrophs in bacterioplankton of the reef lagoon may originate from sediment, coral or beachrock surfaces, sloughing into plankton with the flooding tide. The presence of typical open ocean phylotype transcripts in lagoon bacterioplankton may indicate that they are an important component of the N cycle of the coral reef.

  19. Stimulated bacterioplankton growth and selection for certain bacterial taxa in the vicinity of the ctenophore Mnemiopsis leidyi

    Directory of Open Access Journals (Sweden)

    Julie eDinasquet

    2012-08-01

    Full Text Available Episodic blooms of voracious gelatinous zooplankton, such as the ctenophore Mnemiopsis leidyi, affect pools of inorganic nutrients and dissolved organic carbon by intensive grazing activities and mucus release. This will potentially influence bacterioplankton activity and community composition, at least at local scales; however, available studies on this are scarce. In the present study we examined effects of M. leidyi on bacterioplankton growth and composition in incubation experiments. Moreover, we examined community composition of bacteria associated with the surface and gut of M. leidyi. High release of ammonium and high bacterial growth was observed in the treatments with M. leidyi relative to controls. Deep 454 pyrosequencing of 16S rRNA genes showed specific bacterial communities in treatments with M. leidyi as well as specific communities associated with M. leidyi tissue and gut. In particular, members of Flavobacteriaceae were associated with M. leidyi. Our study shows that M. leidyi influences bacterioplankton activity and community composition in the vicinity of the jellyfish. In particular during temporary aggregations of jellyfish, these local zones of high bacterial growth may contribute significantly to the spatial heterogeneity of bacterioplankton activity and community composition in the sea.

  20. Phytoplankton, bacterioplankton and virioplankton structure and function across the southern Great Barrier Reef shelf

    Science.gov (United States)

    Alongi, Daniel M.; Patten, Nicole L.; McKinnon, David; Köstner, Nicole; Bourne, David G.; Brinkman, Richard

    2015-02-01

    Bacterioplankton and phytoplankton dynamics, pelagic respiration, virioplankton abundance, and the diversity of pelagic diazotrophs and other bacteria were examined in relation to water-column nutrients and vertical mixing across the southern Great Barrier Reef (GBR) shelf where sharp inshore to offshore gradients in water chemistry and hydrology prevail. A principal component analysis (PCA) revealed station groups clustered geographically, suggesting across-shelf differences in plankton function and structure driven by changes in mixing intensity, sediment resuspension, and the relative contributions of terrestrial, reef and oceanic nutrients. At most stations and sampling periods, microbial abundance and activities peaked both inshore and at channels between outer shelf reefs of the Pompey Reef complex. PCA also revealed that virioplankton numbers and biomass correlated with bacterioplankton numbers and production, and that bacterial growth and respiration correlated with net primary production, suggesting close virus-bacteria-phytoplankton interactions; all plankton groups correlated with particulate C, N, and P. Strong vertical mixing facilitates tight coupling of pelagic and benthic shelf processes as, on average, 37% and 56% of N and P demands of phytoplankton are derived from benthic nutrient regeneration and resuspension. These across-shelf planktonic trends mirror those of the benthic microbial community.

  1. Phylogenetic diversity and phenotypic characterization of cultivable bacterioplankton isolated from polar oceans

    Institute of Scientific and Technical Information of China (English)

    ZENG Yinxin; LI Huirong; YU Yong; CHEN Bo; ZHENG Tianling

    2007-01-01

    A set of 27 marine planktonic bacteria isolated from the polar regions was characterized by 16S rDNA sequencing and physiological and biochemical testing. More than half of these bacteria were positive for caseinase, gelatinase and β-glucosidase, and could utilize glucose, maltose or malic acid as carbon source for cell growth. Twelve isolates expressed nitrate reduction activities. Except for one antarctic isolate BSw10175 belonging to Actinobacteria phylum, these isolates were classified as γ-Proteobacteria, suggesting that γ-Proteobacteria dominated in cultivable marine bacterioplankton at both poles. Genus Pseudoalteromonas was the predominant group in the Chukchi Sea and the Bering Sea, and genus Shewanella dominated in cultivable bacterioplankton in the Prydz Bay. With sequence similarities above 97%, genus Psychrobacter was found at both poles. These 27 isolates were psychrotolerant, and significant 16S rDNA sequence similarities were found not only between arctic and antarctic marine bacteria ( > 99% ),but also between polar marine bacteria and bacteria from other aquatic environments ( ≥98.8% ) , including temperate ocean,deep sea, pond and lake, suggesting that in the polar oceans less temperature-sensitive bacteria may be cosmopolitan and have a bipolar, even global, distribution at the species level.

  2. Response of marine bacterioplankton pH homeostasis gene expression to elevated CO2

    Science.gov (United States)

    Bunse, Carina; Lundin, Daniel; Karlsson, Christofer M. G.; Akram, Neelam; Vila-Costa, Maria; Palovaara, Joakim; Svensson, Lovisa; Holmfeldt, Karin; González, José M.; Calvo, Eva; Pelejero, Carles; Marrasé, Cèlia; Dopson, Mark; Gasol, Josep M.; Pinhassi, Jarone

    2016-05-01

    Human-induced ocean acidification impacts marine life. Marine bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes; hence, understanding their performance under projected climate change scenarios is crucial for assessing ecosystem functioning. Whereas genetic and physiological responses of phytoplankton to ocean acidification are being disentangled, corresponding functional responses of bacterioplankton to pH reduction from elevated CO2 are essentially unknown. Here we show, from metatranscriptome analyses of a phytoplankton bloom mesocosm experiment, that marine bacteria responded to lowered pH by enhancing the expression of genes encoding proton pumps, such as respiration complexes, proteorhodopsin and membrane transporters. Moreover, taxonomic transcript analysis showed that distinct bacterial groups expressed different pH homeostasis genes in response to elevated CO2. These responses were substantial for numerous pH homeostasis genes under low-chlorophyll conditions (chlorophyll a 20 μg l-1) were low. Given that proton expulsion through pH homeostasis mechanisms is energetically costly, these findings suggest that bacterioplankton adaptation to ocean acidification could have long-term effects on the economy of ocean ecosystems.

  3. Spatio.temporal variations of the bacterioplankton community composition in Chaohu Lake,China

    Institute of Scientific and Technical Information of China (English)

    Chaoling Wei; Sumin Bao; Xinyan Zhu; Xiangming Huang

    2008-01-01

    Despite considerable attention paid to Chaohu Lake in China,the dynamics of bacterioplankton community composition(BCC) on spatial and seasonal scales are poorly understood.In this study.water samples were collected from autumn 2006 to summer 2007 at five positions in Chaohu Lake with different trophic status.BCC of these samples was determined by both the PCR amplifieation of the 16S rDNA gene and the denaturing gradient gel electrophoresis (DGGE).The abundance and diversity of bacterioplankton communities at different sampling positions showed similar seasonal pattems.The BCCs in the samples varied substantially,and the pattern of changes indicated that the seasonal difiefence might have a significant impact on the BCC'S structure iU the lake.Canonical correspondence anal-ysis(CCA)on the DGGE patterns and physicochemical parameters indicated that the temperature and the levels of 5-d biochemical O2 demand(BODs),NH3-N,CODMn,total nitrogen,total phosphorous,and dissolved oxygen significantly influenced the BCC,and four of the seven variables were related to the level of eutrophication.Our results indicate that eutrophic status and season are the most inttu-ential factors in determining BCC in Chaohu Lake.

  4. Metagenomic identification of bacterioplankton taxa and pathways involved in microcystin degradation in lake erie.

    Science.gov (United States)

    Mou, Xiaozhen; Lu, Xinxin; Jacob, Jisha; Sun, Shulei; Heath, Robert

    2013-01-01

    Cyanobacterial harmful blooms (CyanoHABs) that produce microcystins are appearing in an increasing number of freshwater ecosystems worldwide, damaging quality of water for use by human and aquatic life. Heterotrophic bacteria assemblages are thought to be important in transforming and detoxifying microcystins in natural environments. However, little is known about their taxonomic composition or pathways involved in the process. To address this knowledge gap, we compared the metagenomes of Lake Erie free-living bacterioplankton assemblages in laboratory microcosms amended with microcystins relative to unamended controls. A diverse array of bacterial phyla were responsive to elevated supply of microcystins, including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria of the alpha, beta, gamma, delta and epsilon subdivisions and Verrucomicrobia. At more detailed taxonomic levels, Methylophilales (mainly in genus Methylotenera) and Burkholderiales (mainly in genera Bordetella, Burkholderia, Cupriavidus, Polaromonas, Ralstonia, Polynucleobacter and Variovorax) of Betaproteobacteria were suggested to be more important in microcystin degradation than Sphingomonadales of Alphaproteobacteria. The latter taxa were previously thought to be major microcystin degraders. Homologs to known microcystin-degrading genes (mlr) were not overrepresented in microcystin-amended metagenomes, indicating that Lake Erie bacterioplankton might employ alternative genes and/or pathways in microcystin degradation. Genes for xenobiotic metabolism were overrepresented in microcystin-amended microcosms, suggesting they are important in bacterial degradation of microcystin, a phenomenon that has been identified previously only in eukaryotic systems.

  5. Metagenomic identification of bacterioplankton taxa and pathways involved in microcystin degradation in lake erie.

    Directory of Open Access Journals (Sweden)

    Xiaozhen Mou

    Full Text Available Cyanobacterial harmful blooms (CyanoHABs that produce microcystins are appearing in an increasing number of freshwater ecosystems worldwide, damaging quality of water for use by human and aquatic life. Heterotrophic bacteria assemblages are thought to be important in transforming and detoxifying microcystins in natural environments. However, little is known about their taxonomic composition or pathways involved in the process. To address this knowledge gap, we compared the metagenomes of Lake Erie free-living bacterioplankton assemblages in laboratory microcosms amended with microcystins relative to unamended controls. A diverse array of bacterial phyla were responsive to elevated supply of microcystins, including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria of the alpha, beta, gamma, delta and epsilon subdivisions and Verrucomicrobia. At more detailed taxonomic levels, Methylophilales (mainly in genus Methylotenera and Burkholderiales (mainly in genera Bordetella, Burkholderia, Cupriavidus, Polaromonas, Ralstonia, Polynucleobacter and Variovorax of Betaproteobacteria were suggested to be more important in microcystin degradation than Sphingomonadales of Alphaproteobacteria. The latter taxa were previously thought to be major microcystin degraders. Homologs to known microcystin-degrading genes (mlr were not overrepresented in microcystin-amended metagenomes, indicating that Lake Erie bacterioplankton might employ alternative genes and/or pathways in microcystin degradation. Genes for xenobiotic metabolism were overrepresented in microcystin-amended microcosms, suggesting they are important in bacterial degradation of microcystin, a phenomenon that has been identified previously only in eukaryotic systems.

  6. Short-term dynamics of North Sea bacterioplankton-dissolved organic matter coherence on molecular level

    Directory of Open Access Journals (Sweden)

    Judith eLucas

    2016-03-01

    Full Text Available Remineralisation and transformation of dissolved organic matter (DOM by marine microbes shape the DOM composition and thus, have large impact on global carbon and nutrient cycling. However, information on bacterioplankton-DOM interactions on a molecular level is limited. We examined the variation of bacterial community composition at Helgoland Roads (North Sea in relation to variation of molecular DOM composition and various environmental parameters on short-time scales. Surface water samples were taken daily over a period of twenty days. Bacterial community and molecular DOM composition were assessed via 16S rRNA gene tag sequencing and ultrahigh resolution Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS, respectively. Environmental conditions were driven by a coastal water influx during the first half of the sampling period and the onset of a summer phytoplankton bloom towards the end of the sampling period. These phenomena led to a distinct grouping of bacterial communities and DOM composition which was particularly influenced by total dissolved nitrogen concentration, temperature and salinity, as revealed by distance-based linear regression analyses. Bacterioplankton-DOM interaction was demonstrated in strong correlations between specific bacterial taxa and particular DOM molecules, thus, suggesting potential specialization on particular substrates. We propose that a combination of high resolution techniques, as used in this study, may provide substantial information on substrate generalists and specialists and thus, contribute to prediction of bacterial community composition variation.

  7. Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient

    Science.gov (United States)

    Fortunato, Caroline S; Herfort, Lydie; Zuber, Peter; Baptista, Antonio M; Crump, Byron C

    2012-01-01

    Few studies of microbial biogeography address variability across both multiple habitats and multiple seasons. Here we examine the spatial and temporal variability of bacterioplankton community composition of the Columbia River coastal margin using 16S amplicon pyrosequencing of 300 water samples collected in 2007 and 2008. Communities separated into seven groups (ANOSIM, P850 m). The ordination of these samples was correlated with salinity (ρ=−0.83) and depth (ρ=−0.62). Temporal patterns were obscured by spatial variability among the coastal environments, and could only be detected within individual groups. Thus, structuring environmental factors (for example, salinity, depth) dominate over seasonal changes in determining community composition. Seasonal variability was detected across an annual cycle in the river, estuary and plume where communities separated into two groups, early year (April–July) and late year (August–Nov), demonstrating annual reassembly of communities over time. Determining both the spatial and temporal variability of bacterioplankton communities provides a framework for modeling these communities across environmental gradients from river to deep ocean. PMID:22011718

  8. Impact of warming on phyto-bacterioplankton coupling and bacterial community composition in experimental mesocosms.

    Science.gov (United States)

    von Scheibner, Markus; Dörge, Petra; Biermann, Antje; Sommer, Ulrich; Hoppe, Hans-Georg; Jürgens, Klaus

    2014-03-01

    Global warming is assumed to alter the trophic interactions and carbon flow patterns of aquatic food webs. The impact of temperature on phyto-bacterioplankton coupling and bacterial community composition (BCC) was the focus of the present study, in which an indoor mesocosm experiment with natural plankton communities from the western Baltic Sea was conducted. A 6 °C increase in water temperature resulted, as predicted, in tighter coupling between the diatom-dominated phytoplankton and heterotrophic bacteria, accompanied by a strong increase in carbon flow into bacterioplankton during the phytoplankton bloom phase. Suppressed bacterial development at cold in situ temperatures probably reflected lowered bacterial production and grazing by protists, as the latter were less affected by low temperatures. BCC was strongly influenced by the phytoplankton bloom stage and to a lesser extent by temperature. Under both temperature regimes, Gammaproteobacteria clearly dominated during the phytoplankton peak, with Glaciecola sp. as the single most abundant taxon. However, warming induced the appearance of additional bacterial taxa belonging to Betaproteobacteria and Bacteroidetes. Our results show that warming during an early phytoplankton bloom causes a shift towards a more heterotrophic system, with the appearance of new bacterial taxa suggesting a potential for utilization of a broader substrate spectrum.

  9. Impact of photochemical processing of DOC on the bacterioplankton respiratory quotient in aquatic ecosystems

    Science.gov (United States)

    Allesson, Lina; Ström, Lena; Berggren, Martin

    2016-07-01

    Many studies assume a respiratory quotient (RQ = molar ratio of CO2 produced to O2 consumed) close to 1 when calculating bacterioplankton respiration. However, evidence suggests that RQ depends on the chemical composition of the respired substrate pool that may be altered by photochemical production of oxygen-rich substrates, resulting in elevated RQs. Here we conducted a novel study of the impact of photochemical processing of dissolved organic carbon (DOC) on RQ. We monitored the bacterial RQ in bioassays of both ultraviolet light irradiated and nonirradiated humic lake water, using optic gas-pressure sensors. In the experimentally irradiated samples the average RQ value was significantly higher (3.4-3.5 [±0.4 standard error (SE)]) than that in the dark controls (1.3 [±0.1 SE]). Our results show that the RQ is systematically higher than 1 when the bacterial metabolism in large part is based on photoproducts. By assuming an RQ of 1, bacterioplankton respiration in freshwater ecosystems may be greatly underestimated.

  10. Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton.

    Science.gov (United States)

    Bryson, Samuel; Li, Zhou; Pett-Ridge, Jennifer; Hettich, Robert L; Mayali, Xavier; Pan, Chongle; Mueller, Ryan S

    2016-01-01

    Heterotrophic marine bacterioplankton are a critical component of the carbon cycle, processing nearly a quarter of annual primary production, yet defining how substrate utilization preferences and resource partitioning structure microbial communities remains a challenge. In this study, proteomic stable isotope probing (proteomic SIP) was used to characterize population-specific assimilation of dissolved free amino acids (DFAAs), a major source of dissolved organic carbon for bacterial secondary production in aquatic environments. Microcosms of seawater collected from Newport, Oregon, and Monterey Bay, California, were incubated with 1 µM (13)C-labeled amino acids for 15 and 32 h. The taxonomic compositions of microcosm metaproteomes were highly similar to those of the sampled natural communities, with Rhodobacteriales, SAR11, and Flavobacteriales representing the dominant taxa. Analysis of (13)C incorporation into protein biomass allowed for quantification of the isotopic enrichment of identified proteins and subsequent determination of differential amino acid assimilation patterns between specific bacterioplankton populations. Proteins associated with Rhodobacterales tended to have a significantly high frequency of (13)C-enriched peptides, opposite the trend for Flavobacteriales and SAR11 proteins. Rhodobacterales proteins associated with amino acid transport and metabolism had an increased frequency of (13)C-enriched spectra at time point 2. Alteromonadales proteins also had a significantly high frequency of (13)C-enriched peptides, particularly within ribosomal proteins, demonstrating their rapid growth during incubations. Overall, proteomic SIP facilitated quantitative comparisons of DFAA assimilation by specific taxa, both between sympatric populations and between protein functional groups within discrete populations, allowing an unprecedented examination of population level metabolic responses to resource acquisition in complex microbial communities

  11. Marine bacterioplankton community turnover within seasonally hypoxic waters of a subtropical sound

    DEFF Research Database (Denmark)

    Parsons, Rachel J.; Nelson, Craig E.; Carlson, Craig A.

    2015-01-01

    changes, including both direct counts and rRNA gene sequencing. During stratification, the surface waters were dominated by the SAR11 clade of Alphaproteobacteria and the cyanobacterium Synechococcus. In the suboxic bottom waters, cells from the order Chlorobiales prevailed, with gene sequences indicating......, Bermuda during the 6-week annual transition from a strongly stratified water column with suboxic and high-pCO2 bottom waters to a fully mixed and ventilated state during 2008. A suite of culture-independent methods provided a quantitative spatiotemporal characterization of bacterioplankton community...... members of the genera Chlorobium and Prosthecochloris – anoxygenic photoautotrophs that utilize sulfide as a source of electrons for photosynthesis. Transitional zones of hypoxia also exhibited elevated levels of methane- and sulfur-oxidizing bacteria relative to the overlying waters. The abundance...

  12. Temporal Patterns in Bacterioplankton Community Composition in Three Reservoirs of Similar Trophic Status in Shenzhen, China

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    Jiancheng Li

    2016-06-01

    Full Text Available The bacterioplankton community composition’s (BCC spatial and temporal variation patterns in three reservoirs (Shiyan, Xikeng, and LuoTian Reservoir of similar trophic status in Bao’an District, Shenzhen (China, were investigated using PCR amplification of the 16S rDNA gene and the denaturing gradient gel electrophoresis (DGGE techniques. Water samples were collected monthly in each reservoir during 12 consecutive months. Distinct differences were detected in band number, pattern, and density of DGGE at different sampling sites and time points. Analysis of the DGGE fingerprints showed that changes in the bacterial community structure mainly varied with seasons, and the patterns of change indicated that seasonal forces might have a more significant impact on the BCC than eutrophic status in the reservoirs, despite the similar Shannon-Weiner index among the three reservoirs. The sequences obtained from excised bands were affiliated with Cyanobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Actinobacteria, Planctomycetes, and Proteobacteria.

  13. Transient changes in bacterioplankton communities induced by the submarine volcanic eruption of El Hierro (Canary Islands.

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    Isabel Ferrera

    Full Text Available The submarine volcanic eruption occurring near El Hierro (Canary Islands in October 2011 provided a unique opportunity to determine the effects of such events on the microbial populations of the surrounding waters. The birth of a new underwater volcano produced a large plume of vent material detectable from space that led to abrupt changes in the physical-chemical properties of the water column. We combined flow cytometry and 454-pyrosequencing of 16S rRNA gene amplicons (V1-V3 regions for Bacteria and V3-V5 for Archaea to monitor the area around the volcano through the eruptive and post-eruptive phases (November 2011 to April 2012. Flow cytometric analyses revealed higher abundance and relative activity (expressed as a percentage of high-nucleic acid content cells of heterotrophic prokaryotes during the eruptive process as compared to post-eruptive stages. Changes observed in populations detectable by flow cytometry were more evident at depths closer to the volcano (~70-200 m, coinciding also with oxygen depletion. Alpha-diversity analyses revealed that species richness (Chao1 index decreased during the eruptive phase; however, no dramatic changes in community composition were observed. The most abundant taxa during the eruptive phase were similar to those in the post-eruptive stages and to those typically prevalent in oceanic bacterioplankton communities (i.e. the alphaproteobacterial SAR11 group, the Flavobacteriia class of the Bacteroidetes and certain groups of Gammaproteobacteria. Yet, although at low abundance, we also detected the presence of taxa not typically found in bacterioplankton communities such as the Epsilonproteobacteria and members of the candidate division ZB3, particularly during the eruptive stage. These groups are often associated with deep-sea hydrothermal vents or sulfur-rich springs. Both cytometric and sequence analyses showed that once the eruption ceased, evidences of the volcano-induced changes were no longer

  14. Transient Changes in Bacterioplankton Communities Induced by the Submarine Volcanic Eruption of El Hierro (Canary Islands)

    Science.gov (United States)

    Ferrera, Isabel; Arístegui, Javier; González, José M.; Montero, María F.; Fraile-Nuez, Eugenio; Gasol, Josep M.

    2015-01-01

    The submarine volcanic eruption occurring near El Hierro (Canary Islands) in October 2011 provided a unique opportunity to determine the effects of such events on the microbial populations of the surrounding waters. The birth of a new underwater volcano produced a large plume of vent material detectable from space that led to abrupt changes in the physical-chemical properties of the water column. We combined flow cytometry and 454-pyrosequencing of 16S rRNA gene amplicons (V1–V3 regions for Bacteria and V3–V5 for Archaea) to monitor the area around the volcano through the eruptive and post-eruptive phases (November 2011 to April 2012). Flow cytometric analyses revealed higher abundance and relative activity (expressed as a percentage of high-nucleic acid content cells) of heterotrophic prokaryotes during the eruptive process as compared to post-eruptive stages. Changes observed in populations detectable by flow cytometry were more evident at depths closer to the volcano (~70–200 m), coinciding also with oxygen depletion. Alpha-diversity analyses revealed that species richness (Chao1 index) decreased during the eruptive phase; however, no dramatic changes in community composition were observed. The most abundant taxa during the eruptive phase were similar to those in the post-eruptive stages and to those typically prevalent in oceanic bacterioplankton communities (i.e. the alphaproteobacterial SAR11 group, the Flavobacteriia class of the Bacteroidetes and certain groups of Gammaproteobacteria). Yet, although at low abundance, we also detected the presence of taxa not typically found in bacterioplankton communities such as the Epsilonproteobacteria and members of the candidate division ZB3, particularly during the eruptive stage. These groups are often associated with deep-sea hydrothermal vents or sulfur-rich springs. Both cytometric and sequence analyses showed that once the eruption ceased, evidences of the volcano-induced changes were no longer observed

  15. Quantification of carbon and phosphorus co-limitation in bacterioplankton: new insights on an old topic.

    Directory of Open Access Journals (Sweden)

    Irene Dorado-García

    Full Text Available Because the nature of the main resource that limits bacterioplankton (e.g. organic carbon [C] or phosphorus [P] has biogeochemical implications concerning organic C accumulation in freshwater ecosystems, empirical knowledge is needed concerning how bacteria respond to these two resources, available alone or together. We performed field experiments of resource manipulation (2×2 factorial design, with the addition of C, P, or both combined in two Mediterranean freshwater ecosystems with contrasting trophic states (oligotrophy vs. eutrophy and trophic natures (autotrophy vs. heterotrophy, measured as gross primary production:respiration ratio. Overall, the two resources synergistically co-limited bacterioplankton, i.e. the magnitude of the response of bacterial production and abundance to the two resources combined was higher than the additive response in both ecosystems. However, bacteria also responded positively to single P and C additions in the eutrophic ecosystem, but not to single C in the oligotrophic one, consistent with the value of the ratio between bacterial C demand and algal C supply. Accordingly, the trophic nature rather than the trophic state of the ecosystems proves to be a key feature determining the expected types of resource co-limitation of bacteria, as summarized in a proposed theoretical framework. The actual types of co-limitation shifted over time and partially deviated (a lesser degree of synergism from the theoretical expectations, particularly in the eutrophic ecosystem. These deviations may be explained by extrinsic ecological forces to physiological limitations of bacteria, such as predation, whose role in our experiments is supported by the relationship between the dynamics of bacteria and bacterivores tested by SEMs (structural equation models. Our study, in line with the increasingly recognized role of freshwater ecosystems in the global C cycle, suggests that further attention should be focussed on the biotic

  16. The UV responses of bacterioneuston and bacterioplankton isolates depend on the physiological condition and involve a metabolic shift.

    Science.gov (United States)

    Santos, Ana L; Baptista, Inês; Lopes, Sílvia; Henriques, Isabel; Gomes, Newton C M; Almeida, Adelaide; Correia, António; Cunha, Angela

    2012-06-01

    Bacteria from the surface microlayer (bacterioneuston) and underlying waters (bacterioplankton) were isolated upon exposure to UV-B radiation, and their individual UV sensitivity in terms of CFU numbers, activity (leucine and thymidine incorporation), sole-carbon source use profiles, repair potential (light-dependent and independent), and photoadaptation potential, under different physiological conditions, was compared. Colony counts were 11.5-16.2% more reduced by UV-B exposure in bacterioplankton isolates (P < 0.05). Inhibition of leucine incorporation in bacterioneuston isolates was 10.9-11.5% higher than in bacterioplankton (P < 0.05). These effects were accompanied by a shift in sole-carbon source use profiles, assessed with Biolog(®) EcoPlates, with a reduction in consumption of amines and amino acids and increased use of polymers, particularly in bacterioneuston isolates. Recovery under starvation was generally enhanced compared with nourished conditions, especially in bacterioneuston isolates. Overall, only insignificant increases in the induction of antibiotic resistant mutant phenotypes (Rif(R) and Nal(R) ) were observed. In general, a potential for photoadaptation could not be detected among the tested isolates. These results indicate that UV effects on bacteria are influenced by their physiological condition and are accompanied by a shift in metabolic profiles, more significant in bacterioneuston isolates, suggesting the presence of bacterial strains adapted to high UV levels in the SML.

  17. Modeling the impact of riverine DON removal by marine bacterioplankton on primary production in the Arctic Ocean

    Directory of Open Access Journals (Sweden)

    V. Le Fouest

    2014-12-01

    Full Text Available The planktonic and biogeochemical dynamics of the Arctic shelves exhibit a strong variability in response to Arctic warming. In this study, in order to elucidate on the processes regulating the production of phytoplankton (PP and bacterioplankton (BP and their interactions, we employ a biogeochemical model coupled to a pan-Arctic ocean-sea ice model (MITgcm to explicitly simulate and quantify the contribution of usable dissolved organic nitrogen (DON drained by the major circum-Arctic rivers on PP and BP in a scenario of melting sea ice (1998–2011. Model simulations suggest that on average between 1998 and 2011, the removal of usable RDON by bacterioplankton is responsible of a ~26% increase of the annual BP for the whole Arctic Ocean. With respect to total PP, the model simulates an increase of ~8% on an annual basis and of ~18% in summer. Recycled ammonium is responsible for the PP increase. The recycling of RDON by bacterioplankton promotes higher BP and PP but there is no significant temporal trend in the BP : PP ratio within the ice-free shelves over the 1998–2011 period. This suggests no significant evolution in the balance between autotrophy and heterotrophy in the last decade with a constant annual flux of RDON into the coastal ocean although changes in RDON supply and further reduction in sea ice cover could potentially alter this delicate balance.

  18. Changes of bacterioplankton apparent species richness in two ornamental fish aquaria.

    Science.gov (United States)

    Vlahos, Nikolaos; Kormas, Konstantinos Ar; Pachiadaki, Maria G; Meziti, Alexandra; Hotos, George N; Mente, Eleni

    2013-12-01

    We analysed the 16S rRNA gene diversity within the bacterioplankton community in the water column of the ornamental fish Pterophyllum scalare and Archocentrus nigrofasciatus aquaria during a 60-day growth experiment in order to detect any dominant bacterial species and their possible association with the rearing organisms. The basic physical and chemical parameters remained stable but the bacterial community at 0, 30 and 60 days showed marked differences in bacterial cell abundance and diversity. We found high species richness but no dominant phylotypes were detected. Only few of the phylotypes were found in more than one time point per treatment and always with low relative abundance. The majority of the common phylotypes belonged to the Proteobacteria phylum and were closely related to Acinetobacter junii, Pseudomonas sp., Nevskia ramosa, Vogesella perlucida, Chitinomonas taiwanensis, Acidovorax sp., Pelomonas saccharophila and the rest belonged to the α-Proteobacteria, Bacteroidetes, Actinobacteria, candidate division OP11 and one unaffiliated group. Several of these phylotypes were closely related to known taxa including Sphingopyxis chilensis, Flexibacter aurantiacus subsp. excathedrus and Mycobacterium sp. Despite the high phylogenetic diversity most of the inferred ecophysiological roles of the found phylotypes are related to nitrogen metabolism, a key process for fish aquaria.

  19. The hidden seasonality of the rare biosphere in coastal marine bacterioplankton

    KAUST Repository

    Alonso-Sáez, Laura

    2015-04-08

    Summary: Rare microbial taxa are increasingly recognized to play key ecological roles, but knowledge of their spatio-temporal dynamics is lacking. In a time-series study in coastal waters, we detected 83 bacterial lineages with significant seasonality, including environmentally relevant taxa where little ecological information was available. For example, Verrucomicrobia had recurrent maxima in summer, while the Flavobacteria NS4, NS5 and NS2b clades had contrasting seasonal niches. Among the seasonal taxa, only 4 were abundant and persistent, 20 cycled between rare and abundant and, remarkably, most of them (59) were always rare (contributing <1% of total reads). We thus demonstrate that seasonal patterns in marine bacterioplankton are largely driven by lineages that never sustain abundant populations. A fewer number of rare taxa (20) also produced episodic \\'blooms\\', and these events were highly synchronized, mostly occurring on a single month. The recurrent seasonal growth and loss of rare bacteria opens new perspectives on the temporal dynamics of the rare biosphere, hitherto mainly characterized by dormancy and episodes of \\'boom and bust\\', as envisioned by the seed-bank hypothesis. The predictable patterns of seasonal reoccurrence are relevant for understanding the ecology of rare bacteria, which may include key players for the functioning of marine ecosystems. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  20. Functional diversity of bacterioplankton in three North Florida freshwater lakes over an annual cycle.

    Science.gov (United States)

    Dickerson, Tamar L; Williams, Henry N

    2014-01-01

    The phylogenetic diversity of freshwater bacterioplankton is widely known; however, there is minimal information on the functional diversity of the bacterial communities in these systems. Understanding the functional diversity of freshwater bacterial communities is important because heterotrophic bacteria can be impacted by anthropogenic perturbation, which in turn can alter biogeochemical cycling. The objective of this study was to use Biolog EcoPlates to acquire spatial and temporal community-level physiological profiles (CLPPs) for three freshwater lakes of different trophic levels and to assess the phylogenetic affiliation of the bacteria responsible for utilizing the various carbon guilds within them by denaturing gradient gel electrophoresis (DGGE). CLPP results showed that bacterial communities utilized the carbon guilds similarly between sites within the three lakes. However, when the metabolic profile of each lake was compared, Lake Bradford and Moore Lake were more similar to one another than to Lake Munson, the eutrophic lake. Additionally, although the bacteria that utilized the five carbon guilds included representatives from the classes α-, β-, γ-Proteobacteria, Flavobacteria and Sphingobacteria, Lake Munson had the largest number of Flavobacteria and γ-Proteobacteria in comparison to Moore Lake and Lake Bradford. Overall, Biolog analysis was useful in identifying differences in the functional diversity of bacterial communities between lakes of different trophic statuses and can be used as a tool to assess ecosystem health.

  1. Bacterioplankton community analysis in tilapia ponds by Illumina high-throughput sequencing.

    Science.gov (United States)

    Fan, Li Min; Barry, Kamira; Hu, Geng Dong; Meng, Shun long; Song, Chao; Wu, Wei; Chen, Jia Zhang; Xu, Pao

    2016-01-01

    The changes of microbial community in aquaculture systems under the effects of stocking densities and seasonality were investigated in tilapia ponds. Total DNAs were extracted from the water samples, 16S rRNA gene was amplified and the bacterial community analyzed by Illumina high-throughput sequencing obtaining 3486 OTUs, from a total read of 715,842 sequences. Basing on the analysis of bacterial compositions, richness, diversity, bacterial 16S rRNA gene abundance, water sample comparisons and existence of specific bacterial taxa within three fish ponds in a 4 months period, the study conclusively observed that the dominant phylum in all water samples were similar, and they included; Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Planctomycetes and Chlorobi, distributed in different proportions in the different months and ponds. The seasonal changes had a more pronounced effect on the bacterioplankton community than the stocking densities; however some differences between the ponds were more likely caused by feed coefficient than by stocking densities. At the same time, most bacterial communities were affected by the nutrient input except phylum Cyanobacteria that was also affected by the feed control of tilapia.

  2. Bacterioplankton abundance, biomass and production in a Brazilian coastal lagoon and in two German lakes

    Directory of Open Access Journals (Sweden)

    ANDRÉ L. S. FURTADO

    2001-03-01

    Full Text Available The bacterioplanktonic abundance, biomass, and production within a tropical lagoon (Cabiúnas, Brazil and two temperate lakes (Stechlin and Dagow, Germany were compared. Bacterial abundance and production were significantly different among the three water bodies. The lowest bacterial production ( 0.8mug C l-1 d-1 was observed in the tropical Cabiúnas Lagoon despite its higher mean temperature and dissolved organic carbon concentration. Highest bacterioplankton abundance ( 2.6 x 10(9 cells l-1 and production ( 68.5mug C l-1 d-1 were measured in eutrophic Lake Dagow. In oligotrophic Lake Stechlin, the lowest bacterial biomass ( 48.05mug C l-1 was observed because of lower bacterial biovolume ( 0.248mum³ and lower bacterial abundance. Bacterial populations in the temperate lakes show higher activity (production/biomass ratio than in the tropical lagoon. The meaning of isotopic dilution and leucine incorporation by non-bacterial micro-organisms were evaluated in the oligotrophic temperate system. Leucine uptake by non-bacterial micro-organisms did not have significant influence on bacterial production.A abundância, biomassa e produção bacterioplanctônica em uma lagoa tropical (lagoa Cabiúnas, Brasil e em dois lagos temperados (lago Stechlin e lago Dagow, Alemanha foram comparadas. A abundância e a produção bacteriana foram significativamente diferente entre os três ecossistemas aquáticos. A menor produção bacteriana ( 0.8mig C l-1 d-1 foi observada na lagoa Cabiúnas, apesar da alta temperatura da água e concentração de carbono orgânico dissolvido. A maior abundância ( 2.6 x 10(9 células l-1 e produção bacterioplanctônica ( 68.5mig C l-1 d-1 foram medidas no eutrófico lago Dagow. No oligotrófico lago Stechlin, foi observada a menor biomassa bacteriana ( 48.05mig C l-1, refletindo o menor volume ( 0.248mim³ e abundância bacteriana. Populações bacterianas nos lagos temperados mostraram maior atividade (razão produ

  3. Alkane Hydroxylase Gene (alkB Phylotype Composition and Diversity in Northern Gulf of Mexico Bacterioplankton

    Directory of Open Access Journals (Sweden)

    Conor Blake Smith

    2013-12-01

    Full Text Available Natural and anthropogenic activities introduce alkanes into marine systems where they are degraded by alkane hydroxylases expressed by phylogenetically diverse bacteria. Partial sequences for alkB, one of the structural genes of alkane hydroxylase, have been used to assess the composition of alkane-degrading communities, and to determine their responses to hydrocarbon inputs. We present here the first spatially extensive analysis of alkB in bacterioplankton of the northern Gulf of Mexico (nGoM, a region that experiences numerous hydrocarbon inputs. We have analyzed 401 partial alkB gene sequences amplified from genomic extracts collected during March 2010 from 17 water column samples that included surface waters and bathypelagic depths. Previous analyses of 16S rRNA gene sequences for these and related samples have shown that nGoM bacterial community composition and structure stratify strongly with depth, with distinctly different communities above and below 100 m. Although we hypothesized that alkB gene sequences would exhibit a similar pattern, PCA analyses of operational protein units (OPU indicated that community composition did not vary consistently with depth or other major physical-chemical variables. We observed 22 distinct OPUs, one of which was ubiquitous and accounted for 57% of all sequences. This OPU clustered with alkB sequences from known hydrocarbon oxidizers (e.g., Alcanivorax and Marinobacter. Some OPUs could not be associated with known alkane degraders, however, and perhaps represent novel hydrocarbon-oxidizing populations or genes. These results indicate that the capacity for alkane hydrolysis occurs widely in the nGoM, but that alkane degrader diversity varies substantially among sites and responds differently than bulk communities to physical-chemical variables.

  4. Influence of salinity on bacterioplankton communities from the Brazilian rain forest to the coastal Atlantic Ocean.

    Directory of Open Access Journals (Sweden)

    Cynthia B Silveira

    parameters. Furthermore, this paper reveals for the first time the pristine bacterioplankton communities in a tropical island at the South Atlantic Ocean.

  5. Bacterioplankton features and its relations with doc characteristics and other limnological variables in Paraná river floodplain environments (PR/MS-Brazil

    Directory of Open Access Journals (Sweden)

    Mariana Carolina Teixeira

    2011-09-01

    Full Text Available Since the introduction of the Microbial Loop concept, many studies aimed to explain the role of bacterioplankton and dissolved organic carbon (DOC in aquatic ecosystems. Paraná River floodplain system is a very complex environment where these subjects were little explored. The aim of this work was to characterize bacterial community in terms of density, biomass and biovolume in some water bodies of this floodplain and to verify its temporal variation and its relation with some limnological variables, including some indicators of DOC quality, obtained through Ultraviolet-visible (UV-VIS and fluorescence spectroscopic analysis. Bacterial density, biomass and biovolume are similar to those from other freshwater environments and both density and biomass were higher in the period with less rain. The limnological and spectroscopic features that showed any relation with bacterioplankton were the concentrations of N-NH4 and P-PO4, water transparency, and some indicators of DOC quality and origin. The analysis of these relations showed a possible competition between bacterioplankton and phytoplankton for inorganic nutrients and that the DOC used by bacterioplankton is labile and probably from aquatic macrophytes.

  6. Seasonality in molecular and cytometric diversity of marine bacterioplankton: the reshuffling of bacterial taxa by vertical mixing

    KAUST Repository

    García, Francisca C.

    2015-07-17

    The ’cytometric diversity’ of phytoplankton communities has been studied based on single-cell properties, but the applicability of this method to characterize bacterioplankton has been unexplored. Here, we analysed seasonal changes in cytometric diversity of marine bacterioplankton along a decadal time-series at three coastal stations in the Southern Bay of Biscay. Shannon-Weaver diversity estimates and Bray-Curtis similarities obtained by cytometric and molecular (16S rRNA tag sequencing) methods were significantly correlated in samples from a 3.5-year monthly time-series. Both methods showed a consistent cyclical pattern in the diversity of surface bacterial communities with maximal values in winter. The analysis of the highly resolved flow cytometry time-series across the vertical profile showed that water column mixing was a key factor explaining the seasonal changes in bacterial composition and the winter increase in bacterial diversity in coastal surface waters. Due to its low cost and short processing time as compared to genetic methods, the cytometric diversity approach represents a useful complementary tool in the macroecology of aquatic microbes.

  7. Bacterioplankton communities of Crater Lake, OR: Dynamic changes with euphotic zone food web structure and stable deep water populations

    Science.gov (United States)

    Urbach, E.; Vergin, K.L.; Larson, G.L.; Giovannoni, S.J.

    2007-01-01

    The distribution of bacterial and archaeal species in Crater Lake plankton varies dramatically over depth and with time, as assessed by hybridization of group-specific oligonucleotides to RNA extracted from lakewater. Nonmetric, multidimensional scaling (MDS) analysis of relative bacterial phylotype densities revealed complex relationships among assemblages sampled from depth profiles in July, August and September of 1997 through 1999. CL500-11 green nonsulfur bacteria (Phylum Chloroflexi) and marine Group I crenarchaeota are consistently dominant groups in the oxygenated deep waters at 300 and 500 m. Other phylotypes found in the deep waters are similar to surface and mid-depth populations and vary with time. Euphotic zone assemblages are dominated either by ??-proteobacteria or CL120-10 verrucomicrobia, and ACK4 actinomycetes. MDS analyses of euphotic zone populations in relation to environmental variables and phytoplankton and zooplankton population structures reveal apparent links between Daphnia pulicaria zooplankton population densities and microbial community structure. These patterns may reflect food web interactions that link kokanee salmon population densities to community structure of the bacterioplankton, via fish predation on Daphnia with cascading consequences to Daphnia bacterivory and predation on bacterivorous protists. These results demonstrate a stable bottom-water microbial community. They also extend previous observations of food web-driven changes in euphotic zone bacterioplankton community structure to an oligotrophic setting. ?? 2007 Springer Science+Business Media B.V.

  8. Consequences of contaminant mixture on the dynamics and functional diversity of bacterioplankton in a southwestern Mediterranean coastal ecosystem.

    Science.gov (United States)

    Pringault, Olivier; Lafabrie, Céline; Avezac, Murielle; Bancon-Montigny, Chrystelle; Carre, Claire; Chalghaf, Mohamed; Delpoux, Sophie; Duvivier, Adrien; Elbaz-Poulichet, Françoise; Gonzalez, Catherine; Got, Patrice; Leboulanger, Christophe; Spinelli, Sylvie; Hlaili, Asma Sakka; Bouvy, Marc

    2016-02-01

    Contamination of coastal environments is often due to a complex mixture of pollutants, sometimes in trace levels, that may have significant effects on diversity and function of organisms. The aim of this study was to evaluate the short-term dynamics of bacterioplankton exposed to natural and artificial mixtures of contaminants. Bacterial communities from a southwestern Mediterranean ecosystem, lagoon and the bay (offshore) of Bizerte were exposed to i) elutriate from resuspension of contaminated sediment, and ii) an artificial mixture of metals and herbicides mimicking the contamination observed during sediment resuspension. Elutriate incubation as well as artificial spiking induced strong enrichments in nutrients (up to 18 times), metals (up to six times) and herbicides (up to 20 times) relative to the in situ concentrations in the offshore station, whereas the increases in contaminants were less marked in the lagoon station. In the offshore waters, the artificial mixture of pollutants provoked a strong inhibition of bacterial abundance, production and respiration and significant modifications of the potential functional diversity of bacterioplankton with a strong decrease of the carbohydrate utilization. In contrast, incubation with elutriate resulted in a stimulation of bacterial activities and abundances, suggesting that the toxic effects of pollutants were modified by the increase in nutrient and DOM concentrations due to the sediment resuspension. The effects of elutriate and the artificial mixture of pollutants on bacterial dynamics and the functional diversity were less marked in the lagoon waters, than in offshore waters, suggesting a relative tolerance of lagoon bacteria against contaminants.

  9. Effect of Natural Sunlight on Bacterial Activity and Differential Sensitivity of Natural Bacterioplankton Groups in Northwestern Mediterranean Coastal Waters

    Science.gov (United States)

    Alonso-Sáez, Laura; Gasol, Josep M.; Lefort, Thomas; Hofer, Julia; Sommaruga, Ruben

    2006-01-01

    We studied the effects of natural sunlight on heterotrophic marine bacterioplankton in short-term experiments. We used a single-cell level approach involving flow cytometry combined with physiological probes and microautoradiography to determine sunlight effects on the activity and integrity of the cells. After 4 h of sunlight exposure, most bacterial cells maintained membrane integrity and viability as assessed by the simultaneous staining with propidium iodide and SYBR green I. In contrast, a significant inhibition of heterotrophic bacterial activity was detected, measured by 5-cyano-2,3 ditolyl tetrazolium chloride reduction and leucine incorporation. We applied microautoradiography combined with catalyzed reporter deposition-fluorescence in situ hybridization to test the sensitivity of the different bacterial groups naturally occurring in the Northwestern Mediterranean to sunlight. Members of the Gammaproteobacteria and Bacteroidetes groups appeared to be highly resistant to solar radiation, with small changes in activity after exposure. On the contrary, Alphaproteobacteria bacteria were more sensitive to radiation as measured by the cell-specific incorporation of labeled amino acids, leucine, and ATP. Within Alphaproteobacteria, bacteria belonging to the Roseobacter group showed higher resistance than members of the SAR11 cluster. The activity of Roseobacter was stimulated by exposure to photosynthetic available radiation compared to the dark treatment. Our results suggest that UV radiation can significantly affect the in situ single-cell activity of bacterioplankton and that naturally dominating phylogenetic bacterial groups have different sensitivity to natural levels of incident solar radiation. PMID:16957198

  10. Molecular analyses of the diversity in marine bacterioplankton assemblages along the coastline of the northeastern Gulf of Mexico.

    Science.gov (United States)

    Olapade, Ola A

    2010-10-01

    Bacterial community diversity in marine bacterioplankton assemblages were examined in 3 coastal locations along the northeastern Gulf of Mexico (GOM) using 16S rRNA gene libraries and fluorescence in situ hybridization approaches. The majority of the sequences (30%-60%) were similar to the 16S rRNA gene sequences of unknown bacteria; however, the operational taxonomic units from members of the Cyanobacteria, Proteobacteria, and Bacteroidetes were also present at the 3 GOM sites. Overall, sequence diversity was more similar between the Gulf sites of Carrabelle and Ochlockonee than between either of the Gulf sites and Apalachicola Bay. Fluorescence in situ hybridization analyses revealed the quantitative predominance of members of the Alphaproteobacteria subclass and the Cytophaga-Flavobacterium cluster within the bacterioplankton assemblages. In general, the study further reveals the presence of many bacterial taxa that have been previously found to be dominant in coastal marine environments. Differences observed in the representation of the various bacterial phylogenetic groups among the GOM coastal sites could be partly attributed to dynamic variations in several site-specific conditions, including intermittent tidal events, nutrient availability, and anthropogenic influences.

  11. [Bacterioplankton index of biotic integrity (BP-IBI): an approach for assessing river ecosystem health in Dianchi watershed].

    Science.gov (United States)

    Huang, Yi; Shu, Zhong-Ya

    2013-08-01

    The index of biotic integrity (IBI) has been widely applied to the health assessment of river ecosystems. However, the currently available IBI methods are lack of decomposer-based assessment. Based on the T-RFLP result of bacterioplankton, we developed the bacterioplankton index of biotic integrity (BP-IBI) after the screening of major environmental factors and candidate metrics to assess the health of the inflow rivers in Dianchi Watershed. The evaluation result indicated that the eco-health conditions of 11 reference sites were either level I (8 sites) or level II (3 sites), while the 27 damaged sites were level I (4 sites), level II (14 sites), level III (7 sites), and level IV (2 sites), and there was no level V site. Compared with the other IBI methods and the integrated pollution index, BP-IBI showed better effect in reflecting the influence of the key environmental factors, the land use types and the upstream water types in river ecosystems. Therefore, BP-IBI is a good method to characterize the health status of river ecosystems.

  12. Contribution of chemical water properties to the differential responses of bacterioneuston and bacterioplankton to ultraviolet-B radiation.

    Science.gov (United States)

    Santos, Ana L; Baptista, Inês; Gomes, Newton C M; Henriques, Isabel; Almeida, Adelaide; Correia, António; Cunha, Angela

    2014-02-01

    The surface microlayer (SML) is characterized by different physicochemical properties from underlying waters (UW). However, whether these differences in abiotic factors underlie the distinct sensitivity of bacterioneuston (i.e. SML bacteria) and bacterioplankton to environmental stressors remains to be addressed. We investigated the contribution of abiotic factors to the UV-B sensitivity of bacterioneuston and bacterioplankton. Nutrients (especially nitrogen and phosphate) emerged as important determinants of bacterial UV-B sensitivity. The role of particles, nutrients, and dissolved organic components on bacterial UV-B sensitivity was further evaluated using dilution cultures. Filtered samples were twofold more UV sensitive than unfiltered samples, suggesting a UV-protective effect of particles. High nutrient concentrations attenuated bacterial UV-B sensitivity (up to 40%), compared with unamended conditions, by influencing bacterial physiology and/or community composition. Suspending cells in natural water, particularly from the SML, also attenuated UV-B sensitivity (up to 23%), compared with suspension in an artificial mineral solution. Bioassays using Pseudomonas sp. strain NT5I1.2B revealed that chemical water properties influence UV-induced oxidative damage. UV-B sensitivity was associated with high cell-specific activities. The chemical environment of the SML and UW influences UV-B effects on the corresponding bacterial communities. Maintaining low cell activities might be advantageous in stressful environments, like the SML.

  13. The study of bacterioplankton dynamics in the Berlengas Archipelago (West coast of Portugal by applying the HJ-biplot method

    Directory of Open Access Journals (Sweden)

    Susana Mendes

    2009-01-01

    Full Text Available The relationship between bacterioplankton and environmental forcing in the Berlengas Archipelago (Western Coast of Portugal were studied between February 2006 and February 2007 in two sampling stations: Berlenga and Canal, using an HJ-biplot. The HJ-biplot showed a simultaneous display of the three main metabolic groups of bacteria involved in carbon cycling (aerobic heterotrophic bacteria, sulphate-reducing bacteria and nitrate-reducing bacteria and environmental parameters, in low dimensions. Our results indicated thatbacterial dynamics are mainly affected by temporal gradients (seasonal gradients with a clear winter versus summer opposition, and less by the spatial structure (Berlenga and Canal. The yearly variation in the abundance of aerobic heterotrophic bacteria were positively correlated with those in chlorophyll a concentration, whereas ammonium concentration and temperature decreased with increasing phosphates and nitrites concentration. The relationship between aerobic heterotrophic bacteria, chlorophyll a and ammonium reveals that phytoplankton is an important source of organic substrates for bacteria.

  14. Comparison of Different Denaturing Gradient Gel Electrophoresis Primer Sets for the Study of Marine Bacterioplankton Communities▿ †

    Science.gov (United States)

    Sánchez, Olga; Gasol, Josep M.; Massana, Ramon; Mas, Jordi; Pedrós-Alió, Carlos

    2007-01-01

    An annual seasonal cycle of composition of a bacterioplankton community in an oligotrophic coastal system was studied by denaturing gradient gel electrophoresis (DGGE) using five different primer sets. Analysis of DGGE fingerprints showed that primer set 357fGC-907rM grouped samples according to seasons. Additionally, we used the set of 16S rRNA genes archived in the RDPII database to check the percentage of perfect matches of each primer for the most abundant bacterial groups inhabiting coastal plankton communities. Overall, primer set 357fGC-907rM was the most suitable for the routine use of PCR-DGGE analyses in this environment. PMID:17660308

  15. Contrasting patterns of free-living bacterioplankton diversity in macrophyte-dominated versus phytoplankton blooming regimes in Dianchi Lake, a shallow lake in China

    Science.gov (United States)

    Wang, Yujing; Li, Huabing; Xing, Peng; Wu, Qinglong

    2016-04-01

    Freshwater shallow lakes typically exhibit two alternative stable states under certain nutrient loadings: macrophyte-dominated and phytoplankton-dominated water regimes. An ecosystem regime shift from macrophytes to phytoplankton blooming typically reduces the number of species of invertebrates and fishes and results in the homogenization of communities in freshwater lakes. We investigated how microbial biodiversity has responded to a shift of the ecosystem regime in Dianchi Lake, which was previously fully covered with submerged macrophytes but currently harbors both ecological states. We observed marked divergence in the diversity and community composition of bacterioplankton between the two regimes. Although species richness, estimated as the number of operational taxonomic units and phylogenetic diversity (PD), was higher in the phytoplankton dominated ecosystem after this shift, the dissimilarity of bacterioplankton community across space decreased. This decrease in beta diversity was accompanied by loss of planktonic bacteria unique to the macrophyte-dominated ecosystem. Mantel tests between bacterioplankton community distances and Euclidian distance of environmental parameters indicated that this reduced bacterial community diff erentiation primarily reflected the loss of environmental niches, particularly in the macrophyte regime. The loss of this small-scale heterogeneity in bacterial communities should be considered when assessing long-term biodiversity changes in response to ecosystem regime conversions in freshwater lakes.

  16. Combining culture-dependent and -independent methodologies for estimation of richness of estuarine bacterioplankton consuming riverine dissolved organic matter.

    Science.gov (United States)

    Kisand, Veljo; Wikner, Johan

    2003-06-01

    Three different methods for analyzing natural microbial community diversity were combined to maximize an estimate of the richness of bacterioplankton catabolizing riverine dissolved organic matter (RDOM). We also evaluated the ability of culture-dependent quantitative DNA-DNA hybridization, a 16S rRNA gene clone library, and denaturing gradient gel electrophoresis (DGGE) to detect bacterial taxa in the same sample. Forty-two different cultivatable strains were isolated from rich and poor solid media. In addition, 50 unique clones were obtained by cloning of the bacterial 16S rDNA gene amplified by PCR from the community DNA into an Escherichia coli vector. Twenty-three unique bands were sequenced from 12 DGGE profiles, excluding a composite fuzzy band of the Cytophaga-Flavobacterium group. The different methods gave similar distributions of taxa at the genus level and higher. However, the match at the species level among the methods was poor, and only one species was identified by all three methods. Consequently, all three methods identified unique subsets of bacterial species, amounting to a total richness of 97 operational taxonomic units in the experimental system. The confidence in the results was, however, dependent on the current precision of the phylogenetic determination and definition of the species. Bacterial consumers of RDOM in the studied estuary were primarily both cultivatable and uncultivable taxa of the Cytophaga-Flavobacterium group, a concordant result among the methods applied. Culture-independent methods also suggested several not-yet-cultivated beta-proteobacteria to be RDOM consumers.

  17. Comparison of growth rates of aerobic anoxygenic phototrophic bacteria and other bacterioplankton groups in coastal Mediterranean waters.

    Science.gov (United States)

    Ferrera, Isabel; Gasol, Josep M; Sebastián, Marta; Hojerová, Eva; Koblízek, Michal

    2011-11-01

    Growth is one of the basic attributes of any living organism. Surprisingly, the growth rates of marine bacterioplankton are only poorly known. Current data suggest that marine bacteria grow relatively slowly, having generation times of several days. However, some bacterial groups, such as the aerobic anoxygenic phototrophic (AAP) bacteria, have been shown to grow much faster. Two manipulation experiments, in which grazing, viruses, and resource competition were reduced, were conducted in the coastal Mediterranean Sea (Blanes Bay Microbial Observatory). The growth rates of AAP bacteria and of several important phylogenetic groups (the Bacteroidetes, the alphaproteobacterial groups Roseobacter and SAR11, and the Gammaproteobacteria group and its subgroups the Alteromonadaceae and the NOR5/OM60 clade) were calculated from changes in cell numbers in the manipulation treatments. In addition, we examined the role that top-down (mortality due to grazers and viruses) and bottom-up (resource availability) factors play in determining the growth rates of these groups. Manipulations resulted in an increase of the growth rates of all groups studied, but its extent differed largely among the individual treatments and among the different groups. Interestingly, higher growth rates were found for the AAP bacteria (up to 3.71 day⁻¹) and for the Alteromonadaceae (up to 5.44 day⁻¹), in spite of the fact that these bacterial groups represented only a very low percentage of the total prokaryotic community. In contrast, the SAR11 clade, which was the most abundant group, was the slower grower in all treatments. Our results show that, in general, the least abundant groups exhibited the highest rates, whereas the most abundant groups were those growing more slowly, indicating that some minor groups, such the AAP bacteria, very likely contribute much more to the recycling of organic matter in the ocean than what their abundances alone would predict.

  18. Phylogenetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit genes of bacterioplankton in the East China Sea

    Institute of Scientific and Technical Information of China (English)

    ZENG Yonghui; JIAO Nianzhi; CAI Haiyuan; CHEN Xihan; WEI Chaoling

    2004-01-01

    Phylogenetic diversity of Form I and Form Ⅱ ribulose-1, 5-bisphosphate carboxylase/oxygenase (RubisCO) large subunit (rbcL) genes in the inshore and offshore areas of the East China Sea were investigated. Two new primer sets were designed for amplifying partial sequences of rbcL genes from Proteobacteria. Four rbcL gene clone libraries were constructed by amplification and cloning of approximately 640~800 bp sequences of bacterioplankton populations.The method of screening library by denaturing gradient gel electrophoresis (DGGE) was introduced. The results show that the diversity of Form I is higher in offshore waters with higher salinity and lower productivity, while that of Form Ⅱ is higher at the inshore station where salinity is lower and productivity is higher. Several clusters of sequences obtained are deeply rooted and show low similarity (60%~78%) to the known rbcL in existing databases.The degree of diversity of rbcL genes is directly related to environmental variables, including temperature, salinity,pH, dissolved oxygen, etc. These results indicate that rbcL gene can be used as an effective indicator for genetic diversity and population variability of bacterioplankton with the ability of carbon dioxide fixation in the sea.

  19. Response of bacterioplankton activity in an Arctic fjord system to elevated pCO2: results from a mesocosm perturbation study

    Directory of Open Access Journals (Sweden)

    U. Riebesell

    2013-01-01

    Full Text Available The effect of elevated seawater carbon dioxide (CO2 on the activity of a natural bacterioplankton community in an Arctic fjord system was investigated by a mesocosm perturbation study in the frame of the European Project on Ocean Acidification (EPOCA. A pCO2 range of 175–1085 μatm was set up in nine mesocosms deployed in the Kongsfjorden (Svalbard. The activity of natural extracellular enzyme assemblages increased in response to acidification. Rates of β-glucosidase and leucine-aminopeptidase increased along the gradient of mesocosm pCO2. A decrease in seawater pH of 0.5 units almost doubled rates of both enzymes. Heterotrophic bacterial activity was closely coupled to phytoplankton productivity in this experiment. The bacterioplankton community responded to rising chlorophyll a concentrations after a lag phase of only a few days with increasing protein production and extracellular enzyme activity. Time-integrated primary production and bacterial protein production were positively correlated, strongly suggesting that higher amounts of phytoplankton-derived organic matter were assimilated by heterotrophic bacteria at increased primary production. Primary production increased under high pCO2 in this study, and it can be suggested that the efficient heterotrophic carbon utilisation had the potential to counteract the enhanced autotrophic CO2 fixation. However, our results also show that beneficial pCO2-related effects on bacterial activity can be mitigated by the top-down control of bacterial abundances in natural microbial communities.

  20. The Impact of Nutrient Enrichment on Bacterioplankton Richness In Nan’ao, Daya Bay%大亚湾南澳海域浮游细菌丰度对营养盐添加的响应

    Institute of Scientific and Technical Information of China (English)

    严瑶仙; 梁柱源; 朱泉剑; 徐智焕; 王海丽; 杨季芳

    2014-01-01

    2011年9月于大亚湾南澳东山码头附近海域设置生态围隔,通过人为对围隔水体中N、P营养元素的加富试验,进一步分析营养盐添加对浮游细菌的丰度影响。结果表明:营养盐添加能促进生态围隔中浮游细菌丰度的增加;并且N、P同时添加于围隔中的效果要比单独添加的效果好,即能更快促进浮游细菌对营养盐的吸收和利用;浮游细菌对氨氮的吸收利用效率最高,其次是硝酸盐;N、P营养盐的添加影响生态围隔中叶绿素a以及溶解氧浓度的变化,从而间接影响浮游细菌的丰度。%A ten-day mesocosm experiment was carried out in Nan’ao of Daya Bay in September of 2011. In total, seven mesocosms (M0~M6) were operated in the study by adding different combinations of N and P on the first day only or daily enrichment, in order to assess the biomass and richness of bacterioplankton with nutrient enrichment. The results showed that nutrient enrichment benefited the growth of bacterioplankton. N and P enriched together increased the biomass of bacterioplankton more efficiently than N and P enriched separately. Bacterioplankton was more eager to uptake ammonium than nitrate as N source. Concentration of chlorophyll a has changed due to nutrient enrichment , which resulted in the changes of bacterioplankton growth.

  1. Effect of elevated CO2 on the dynamics of particle attached and free living bacterioplankton communities in an Arctic fjord

    Directory of Open Access Journals (Sweden)

    S. Romac

    2012-08-01

    Full Text Available The increase in atmospheric carbon dioxide (CO2 results in acidification of the oceans, expected to lead to the fastest drop in ocean pH in the last 300 million years, if anthropogenic emissions are continued at present rate. Due to higher solubility of gases in cold waters and increased exposure to the atmosphere by decreasing ice cover, the Arctic Ocean will be among the areas most strongly affected by ocean acidification. Yet, the response of the plankton community of high latitudes to ocean acidification has not been studied so far. This work is part of the Arctic campaign of the European Project on Ocean Acidification (EPOCA in 2010, employing 9 in situ mesocosms of about 45 000 l each to simulate ocean acidification in Kongsfjorden, Svalbard (78°56.2' N 11°53.6' E. In the present study, we investigated effects of elevated CO2 on the composition and richness of particle attached (PA; >3 μm and free living (FL; 0.2 μm bacterial communities by Automated Ribosomal Intergenic Spacer Analysis (ARISA in 6 of the mesocosms and the surrounding fjord, ranging from 185 to 1050 initial μatm pCO2. ARISA was able to resolve about 20–30 bacterial band-classes per sample and allowed for a detailed investigation of the explicit richness. Both, the PA and the FL bacterioplankton community exhibited a strong temporal development, which was driven mainly by temperature and phytoplankton development. In response to the breakdown of a picophytoplankton bloom (phase 3 of the experiment, number of ARISA-band classes in the PA-community were reduced at low and medium CO2 (∼180–600 μatm by about 25%, while it was more or less stable at high CO2 (∼ 650–800 μatm. We hypothesise that enhanced viral lysis and enhanced availability of organic substrates at high CO2 resulted in a more diverse PA-bacterial community in the post-bloom phase. Despite lower cell numbers and extracellular enzyme activities in the post-bloom phase, bacterial protein production

  2. Response of bacterioplankton activity in an Arctic fjord system to elevated pCO2: results from a mesocosm perturbation study

    Directory of Open Access Journals (Sweden)

    U. Riebesell

    2012-08-01

    Full Text Available The effect of elevated seawater carbon dioxide (CO2 on the activity of a natural bacterioplankton community in an Arctic fjord system was investigated by a mesocosm perturbation study in the frame of the European Project on Ocean Acidification (EPOCA. A pCO2 range of 175–1085 μatm was set up in nine mesocosms deployed in the Kongsfjorden (Svalbard. The bacterioplankton communities responded to rising chlorophyll a concentrations after a lag phase of only a few days with increasing protein production and extracellular enzyme activity and revealed a close coupling of heterotrophic bacterial activity to phytoplankton productivity in this experiment. The natural extracellular enzyme assemblages showed increased activity in response to moderate acidification. A decrease in seawater pH of 0.5 units roughly doubled rates of β-glucosidase and leucine-aminopeptidase. Activities of extracellular enzymes in the mesocosms were directly related to both seawater pH and primary production. Also primary production and bacterial protein production in the mesocosms at different pCO2 were positively correlated. Therefore, it can be suggested that the efficient heterotrophic carbon utilization in this Arctic microbial food web had the potential to counteract increased phytoplankton production that was achieved under elevated pCO2 in this study. However, our results also show that the transfer of beneficial pCO2-related effects on the cellular bacterial metabolism to the scale of community activity and organic matter degradation can be mitigated by the top-down control of bacterial abundances in natural microbial communities.

  3. Seasonal and spatial distribution of Bacterioplankton in a fluvial-lagunar system of a tropical region: density, biomass, cellular volume and morphologic variation

    Directory of Open Access Journals (Sweden)

    Magnólia Fernandes Florêncio de Araújo

    2008-02-01

    Full Text Available The temporal and spatial fluctuations of Bacterioplankton in a fluvial-lagunar system of a tropical region (Pitimbu River and Jiqui Lake, RN were studied during the dry and the rainy periods. The bacterial abundance varied from 2.67 to 5.1 Cells10(7mL-1 and did not show a typical temporal variation, presenting only small oscillations between the rainy and the dry periods. The bacterial biomass varied from 123 µgC L-1 to 269 µgC L-1 in the sampling sites and the average cellular volume varied from 0.12 to 0.54µm³, showing a predominance of the rods. The temperature showed a positive correlation with the cellular volume of the rods (R=0.55; p=0.02 and vibrio (R=0.53; p=0.03. Significant spatial differences of biomass (Mann Whitney: p=0.01 and cellular volume of the morphotypes (Mann Whitney: p=0.003 were found between the sampling sites. The strong positive correlations of the water temperature and oxygen with bacterioplankton showed a probable high bacterial activity in this system.A variação temporal e espacial do bacterioplâncton em um sistema fluvial-lagunar de região tropical foi estudada em períodos seco e chuvoso. As médias da abundância bacteriana variaram de 2,67 a 5,1 x 10(7 e não exibiram uma variação temporal marcante, tendo apresentado apenas pequenas oscilações entre os períodos chuvoso e seco. A biomassa bacteriana variou de 123 µg C L-1 a 269 µg C L-1 entre os locais de coleta e o volume celular médio de 0,12µm³ a 0,54µm³, ocorrendo predominância de bacilos. A temperatura mostrou correlação positiva com o volume celular de bacilos (R=0,55; p=0,02 e de vibriões (R=0,53; p=0,03. Foram encontradas diferenças espaciais significativas de biomassa (Mann Whitney: p=0,01 e volume celular dos morfotipos (Mann Whitney: p= 0,003, entre os locais de coleta. As fortes correlações positivas da temperatura da água e do oxigênio, com o bacterioplâncton, são sugestivas de uma provavelmente elevada atividade

  4. Enhanced viral production and virus-mediated mortality of bacterioplankton in a natural iron-fertilized bloom event above the Kerguelen Plateau

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    A. Malits

    2014-07-01

    Full Text Available Above the Kerguelen Plateau in the Southern Ocean natural iron fertilization sustains a large phytoplankton bloom over three months during austral summer. During the KEOPS1 project (KErguelen Ocean and Plateau compared Study1 we sampled this phytoplankton bloom during its declining phase along with the surrounding HNLC waters to study the effect of natural iron fertilization on the role of viruses in the microbial food web. Bacterial and viral abundances were 1.7 and 2.1 times, respectively, higher within the bloom than in HNLC waters. Viral production and virus-mediated mortality of bacterioplankton was 4.1 and 4.9 times, respectively, higher in the bloom, while the fraction of infected cells (FIC and the fraction of lysogenic cells (FLC showed no significant differences between environments. The present study suggests viruses to be more important for bacterial mortality within the bloom and dominate over protozoan grazing during the late bloom phase. As a consequence, at least at a late bloom stage, viral lysis shunts part of the photosynthetically fixed carbon in iron-fertilized regions into the dissolved organic matter (DOM pool with potentially less particulate organic carbon transfered to larger members of the food web or exported.

  5. Enhanced viral production and virus-mediated mortality of bacterioplankton in a natural iron-fertilized bloom event above the Kerguelen Plateau

    Science.gov (United States)

    Malits, A.; Christaki, U.; Obernosterer, I.; Weinbauer, M. G.

    2014-12-01

    Above the Kerguelen Plateau in the Southern Ocean natural iron fertilization sustains a large phytoplankton bloom over 3 months during austral summer. During the KEOPS1 project (KErguelen Ocean and Plateau compared Study1) we sampled this phytoplankton bloom during its declining phase along with the surrounding high-nutrient-low-chlorophyll (HNLC) waters to study the effect of natural iron fertilization on the role of viruses in the microbial food web. Bacterial and viral abundances were 1.7 and 2.1 times, respectively, higher within the bloom than in HNLC waters. Viral production and virus-mediated mortality of bacterioplankton were 4.1 and 4.9 times, respectively, higher in the bloom, while the fraction of infected cells (FIC) and the fraction of lysogenic cells (FLC) showed no significant differences between environments. The present study suggests viruses to be more important for bacterial mortality within the bloom and dominate over grazing of heterotrophic nanoflagellates (HNFs) during the late bloom phase. As a consequence, at least at a late bloom stage, viral lysis shunts part of the photosynthetically fixed carbon in iron-fertilized regions into the dissolved organic matter (DOM) pool with potentially less particulate organic carbon transferred to larger members of the food web or exported.

  6. A new molecular approach to help conclude drowning as a cause of death: simultaneous detection of eight bacterioplankton species using real-time PCR assays with TaqMan probes.

    Science.gov (United States)

    Uchiyama, Taketo; Kakizaki, Eiji; Kozawa, Shuji; Nishida, Sho; Imamura, Nahoko; Yukawa, Nobuhiro

    2012-10-10

    We developed a novel tool for concluding drowning as a cause of death. We designed nine primer pairs to detect representative freshwater or marine bacterioplankton (aquatic bacteria) and then used real-time PCR with TaqMan probes to rapidly and specifically detect them. We previously cultured the genus Aeromonas, which is a representative freshwater bacterial species, in blood samples from 94% of victims who drowned in freshwater and the genera Vibrio and/or Photobacterium that are representative marine bacteria in 88% of victims who drowned in seawater. Based on these results, we simultaneously detected eight species of bacterioplankton (Aeromonas hydrophila, A. salmonicida; Vibrio fischeri, V. harveyi, V. parahaemolyticus; Photobacterium damselae, P. leiognathi, P. phosphoreum) using three sets of triplex real-time PCR assays and TaqMan probes labelled with fluorophores (FAM, NED, Cy5). We assayed 266 specimens (109 blood, 157 tissues) from 43 victims, including 32 who had drowned in rivers, ditches, wells, sea or around estuaries. All lung samples of these 32 victims were TaqMan PCR-positive including the lung periphery into which water does not readily enter postmortem. On the other hand, findings in blood and/or closed organs (kidney or liver) were PCR-positive in 84% of the drowned victims (except for those who drowned in baths) although the conventional test detected diatoms in closed organs in only 44% of the victims. Thus, the results of the PCR assay reinforced those of diatom tests when only a few diatoms were detectable in organs due to the low density of diatoms in the water where they were found. Multiplex TaqMan PCR assays for bacterioplankton were rapid, less laborious and high-throughput as well as sensitive and specific. Therefore, these assays would be useful for routine forensic screening tests to estimate the amount and type of aspirated water.

  7. Direct and indirect effects of vertical mixing, nutrients and ultraviolet radiation on the bacterioplankton metabolism in high-mountain lakes from southern Europe

    Directory of Open Access Journals (Sweden)

    C. Durán

    2014-05-01

    availability even led to higher HBP. Consequently, EOC satisfied BCD in the clear lakes, particularly in the clearest one [LC]. Our results suggest that the higher vulnerability of bacteria to the damaging effects of UVR may be particularly accentuated in the opaque lakes and further recognizes the relevance of light exposure history and biotic interactions on bacterioplankton metabolism when coping with fluctuating radiation and nutrient inputs.

  8. DIVERSITY AND COMMUNITY COMPOSITION OF BACTERIOPLANKTON IN THE BERING SEA DURING SUMMER 2010%2010年夏季白令海浮游细菌的多样性和群落组成分析

    Institute of Scientific and Technical Information of China (English)

    刘莹; 张芳; 凌云; 林凌; 陶妍; 何培民; 何剑锋

    2013-01-01

    海洋浮游细菌在海洋生态系统的运行中起着关键性的生物地球化学作用.利用2010年夏季第4次北极考察获得的白令海不同深度水样,运用变性梯度凝胶电泳技术以及克隆建库等方法,来了解白令海中浮游细菌的多样性和群落组成等信息.结果表明:在白令海海盆区B07站位的50 m处,其浮游细菌的香农多样性指数是最高的,为2.61;香农多样性指数最低的是B07站位的3 m处,为1.99.白令海海盆区的细菌多样性变化比陆架区要大,有可能与海洋环境的复杂变化有关.通过克隆测序,鉴定出的浮游细菌类群分为4大类:α-变形杆菌、β-变形杆菌、γ-变形杆菌和拟杆菌.其中γ-变形杆菌所占的比例最大,为53%,是白令海中的优势种群;拟杆菌其次,为37%.这些浮游细菌在白令海中的分布情况为:γ-变形杆菌和拟杆菌存在于3个位点的所有水层中,α-变形杆菌只存在于B07站位的50 m和100m水层中,β-变形杆菌除B13站位的0m处外,存在于其他站位的所有水层中.白令海B断面3个站位的温度随着深度的增加而降低,盐度随着深度的增加而升高.大体上白令海海盆区(B07站位)的硝酸盐、磷酸盐和硅酸盐浓度比陆架区(B15和B13站位)高,陆架区的铵盐浓度较海盆区高.%Marine bacterioplankton play a key biogeochemical role in the marine ecosystem.To investigate the diversity and community composition of bacterioplankton in the Bering Sea (Arctic Ocean),we collected samples from different depths during the Fourth Chinese National Arctic Research Expedition (2010 summer).Samples were analyzed using DGGE and clone libraries were constructed.In the basin area of the Bering Sea,the Shannon diversity index of bacterioplankton was highest (2.61) from B07-50 m,and lowest (1.99) from B07-3 m.There was greater variability in bacterial diversity within the basin than on the shelf of the Bering Sea,possibly related to complex changes

  9. The potential impacts of temperature and nutrient levels on freshwater bacterioplankton community structure%温度和营养盐水平对淡水浮游细菌群落结构的潜在影响

    Institute of Scientific and Technical Information of China (English)

    陈祯; 何聃; 任丽娟

    2016-01-01

    To investigate bacterioplankton community composition (BCC)under different temperature and nutrient conditions,18 microcosms combining three temperature scenarios(15 ℃,25 ℃ and 35 ℃,respectively)and two nutrient levels(control and enriched)were established.After three months experiment,water environmental factors, plant biomass(mainly Filamentous green aglea,FGA),bacterioplankton community abundance and composition were studied.Extremely differences of DO,pH,NO-3-N,NO-2-N,FGA biomass were detected under different temperature and nutrient treatments.Both increased temperature (25 ℃ and 35 ℃)and nutrient enrichment stimulated the extensive growth of FGA.The proliferation of FGA had pronounced removal of water nutrients,so that the concentrations of N and P together with the bacterioplankton abundance were similar in nutrient enriched groups.In 1 5 ℃ treatments without nutrient enrichment,the influence of FGA was least and the nutrient concentrations were evidently higher than others,thus BCC there was pronouncedly different from the other treatments.Between 1 5 ℃ treatments without nutrient enrichment and the other treatments,the BCC divergence increased with the increasing differences of temperatures.In summary,we found that temperature and nutrient,as important abiotic factors for freshwater ecosystems,had complex interactions with plants and bacterioplankton community composition in freshwater ecosystem.The elevated temperature and nutrient conditions not only directly shifted BCC,but also indirectly impacted BCC through the growth of FGA.%为研究温度与水体营养条件对淡水浮游细菌群落的影响,进行室内模拟实验,设立了15℃、25℃和35℃三种温度处理和添加营养盐、未添加营养盐两种营养处理,总计6个处理组,每个处理组设计3个重复。实验结束后测定了环境因子、植物生物量、浮游细菌群落丰度和结构。结果发现,不同温度和营养盐条件下,环境中的 DO

  10. Bacterioplankton Diversity in Xiamen Houxi River Watershed Along an Urban-rural Gradient and Its Relation to Environmental Factors%厦门后溪流域沿城乡梯度浮游细菌多样性及其与环境因子的关系

    Institute of Scientific and Technical Information of China (English)

    刘乐冕; 杨军; 余小青; 余正; 张永雨; 田野; 张冬红

    2012-01-01

    为研究城市化对河流浮游细菌的影响,选取厦门后溪流域沿城乡梯度采集样品,并利用变性梯度凝胶电泳(Denaturing gradient gel electrophoresis,DGGE)和多元统计方法对浮游细菌群落空间分布格局进行分析.结果表明,Shannon-Weiner多样性指数和DGGE条带数随着采样站点和城市中心距离的减小呈现先升高后下降的趋势.聚类分析(Cluster)和多维尺度分析(Multidimensional scaling,MDS)将12个站点的浮游细菌群落分为4组,测序结果显示β-变形菌( Betaproteobacteria)是优势类群,占40.0%.统计分析表明,pH和总氮(Total nitrogen,TN)是影响后溪浮游细菌群落组成最主要的环境因子,他们共同解释了47.6%的群落组成变化.总之,沿城乡梯度随着水体理化指标的变化,浮游细菌群落也发生明显转变,表明后溪浮游细菌受到城市化的强烈影响此外,结果也提示DGGE可以作为监测与评价河流生态系统健康的重要工具.%To investigate the urbanization effect on riverine bacterioplankton, surface water samples were collected along an urban - rural gradient in the Houxi River Watershed, Xiamen, southeast China. Denaturing gradient gel electrophoresis (DGGE) and nvultivariable statistical approaches were used to characterize the spatial patterns of change in the bacterioplankton communities. The overall trend of Shannon-Weiner index and DGGE bands increased from site 1 to site 5 and then decreased from site 6 to site 12 with the decreasing distance between the sampling sites and downtown Xiamen. The cluster and multidimensional scaling analysis (MDS) resulted in four identical groups from the 12 sites, and Betaproteobacteria (40,0%) was the most dominant taxon derived from DGGE bands. Redundancy analysis (RDA) revealed that pH and total nitrogen (TN) were the main factors influencing bacterioplankton community composition in the Houxi River Watershed. Further, both pH and TN explained 47.6% of the variation

  11. Biogeochemical cycling and phyto- and bacterioplankton communities in a large and shallow tropical lagoon (Términos Lagoon, Mexico) under 2009-2010 El Niño Modoki drought conditions

    Science.gov (United States)

    Conan, Pascal; Pujo-Pay, Mireille; Agab, Marina; Calva-Benítez, Laura; Chifflet, Sandrine; Douillet, Pascal; Dussud, Claire; Fichez, Renaud; Grenz, Christian; Gutierrez Mendieta, Francisco; Origel-Moreno, Montserrat; Rodríguez-Blanco, Arturo; Sauret, Caroline; Severin, Tatiana; Tedetti, Marc; Torres Alvarado, Rocío; Ghiglione, Jean-François

    2017-03-01

    The 2009-2010 period was marked by an episode of intense drought known as the El Niño Modoki event. Sampling of the Términos Lagoon (Mexico) was carried out in November 2009 in order to understand the influence of these particular environmental conditions on organic matter fluxes within the lagoon's pelagic ecosystem and, more specifically, on the relationship between phyto- and bacterioplankton communities. The measurements presented here concern biogeochemical parameters (nutrients, dissolved and particulate organic matter [POM], and dissolved polycyclic aromatic hydrocarbons [PAHs]), phytoplankton (biomass and photosynthesis), and bacteria (diversity and abundance, including PAH degradation bacteria and ectoenzymatic activities). During the studied period, the water column of the Términos Lagoon functioned globally as a sink and, more precisely, as a nitrogen assimilator. This was due to the high production of particulate and dissolved organic matter (DOM), even though exportation of autochthonous matter to the Gulf of Mexico was weak. We found that bottom-up control accounted for a large portion of the variability of phytoplankton productivity. Nitrogen and phosphorus stoichiometry mostly accounted for the heterogeneity in phytoplankton and free-living prokaryote distribution in the lagoon. In the eastern part, we found a clear decoupling between areas enriched in dissolved inorganic nitrogen near the Puerto Real coastal inlet and areas enriched in phosphate (PO4) near the Candelaria estuary. Such a decoupling limited the potential for primary production, resulting in an accumulation of dissolved organic carbon and nitrogen (DOC and DON, respectively) near the river mouths. In the western part of the lagoon, maximal phytoplankton development resulted from bacterial activity transforming particulate organic phosphorus (PP) and dissolved organic phosphorus (DOP) to available PO4 and the coupling between Palizada River inputs of nitrate (NO3) and PP. The

  12. Impacts of combined overfishing and oil spills on the plankton trophodynamics of the West Florida shelf over the last half century of 1965-2011: A two-dimensional simulation analysis of biotic state transitions, from a zooplankton- to a bacterioplankton-modulated ecosystem.

    Science.gov (United States)

    Walsh, J. J.; Lenes, J. M.; Darrow, B.; Parks, A.; Weisberg, R. H.

    2016-03-01

    Over 50 years of multiple anthropogenic perturbations, Florida zooplankton stocks of the northeastern Gulf of Mexico declined ten-fold, with increments of mainly dominant toxic dinoflagellate harmful algal blooms (HABs), rather than diatoms, and a shift in loci of nutrient remineralization and oxygen depletion by bacterioplankton, from the sea floor to near surface waters. Yet, lytic bacterial biomass and associated ammonification only increased at most five-fold over the same time period, with consequently little indication of new, expanded "dead zones" of diatom-induced hypoxia. After bacterial lysis of intact cells of these increased HABs, the remaining residues of zooplankton biomass decrements evidently instead exited the water column as malign aerosolized HAB asthma triggers, correlated by co-traveling mercury aerosols, within wind-borne sea sprays. To unravel the causal mechanisms of these inferred decadal food web transitions, a 36-state variable plankton model of algal, bacterial, protozoan, and copepod component communities replicated daily time series of each plankton group's representatives on the West Florida shelf (WFS) during 1965-2011. At the lower phytoplankton trophic levels, 52% of the ungrazed HAB increments, between 1965-1967 and 2001-2002 before recent oil spills, remained in the water column to kill fishes and fuel bacterioplankton. But, another 48% of the WFS primary production then left the ocean's surface as a harbinger of increased public health hazards during continuing sea spray exports of salts, HAB toxins, and Hg poisons. Following the Deepwater Horizon petroleum releases in 2010, little additional change of element partition among the altered importance of WFS food web components of the trophic pyramid then pertained between 2001-2002 and 2010-2011, despite when anomalous upwelled nutrient supplies instead favored retrograde benign, oil-tolerant diatoms over the HABs during 2010. Indeed, by 2011 HABs were back, with biomass

  13. Heterotrophic activities of bacterioplankton and bacteriobenthos.

    Science.gov (United States)

    Chocair, J A; Albright, L J

    1981-03-01

    Several marine waters and surface sediments of coastal British Columbia were analyzed and compared for bacterial colony forming units (CFU) and numbers of active bacteria (NAB) as indicated by microautoradiography, glucose and alanine heterotrophic activities, and dissolved (DOC) and particulate organic carbon (POC). Bacteria numbers (CFU, NAB) were usually much greater (by several orders of magnitude) in surface sediments than in overlying waters. DOC and POC were also generally greater in surface sediments than in overlying waters, often by as much as one order of magnitude. Both glucose and alanine heterotrophic potentials were greater in surface sediments; however, on a per active cell (NAB) basis, no significant differences were noted between the glucose-specific activities of the bacteria of the surface sediments and overlying waters. The data suggest that these surface sediments carry greater standing crops of bacteria than overlying waters without significant decreases in glucose-specific activities.

  14. Culture-independent characterization of the bacterioplankton community composition of a mesotrophic reservoir (Embalse Río III, Argentina Caracterización independiente de la composición de la comunidad del bacterioplancton en un embalse mesotrófico (embalse Río III, Argentina

    Directory of Open Access Journals (Sweden)

    Daniela Polverino

    2012-06-01

    Full Text Available This study represents the first analysis of the bacterioplankton community structure from a freshwater reservoir of Argentina using amplification of the entire 16S rDNA gene. It includes the description and the phylogenetic relationships of the bacterioplankton community from the photic and aphotic layers of the Río III Reservoir in Córdoba, Argentina. The classical ecological approach indicated that the photic layer had greater diversity whereas the aphotic layer had a better distribution of species and higher abundance. Nevertheless, when the microbial communities in both layers were compared using phylogenetic information, this analysis indicated that both environments were similar and that neither was enriched for any particular lineage. The phyla present in the Río III reservoir were Acidobacteria, Actinobacteria, and Proteobacteria and the 2 dominant species in both layers were "Candidatus Planktophila sp." (class Actinobacteria and Polynucleobacter sp. (class Betaproteobacteria.Este estudio constituye el primer análisis de la estructura de la comunidad del bacterioplancton en un reservorio de agua dulce de Argentina utilizando amplificación completa del gen ADNr 16S. Incluye las relaciones filogenéticas y una descripción del bacterioplacton de las zonas fótica y afótica del Embalse Río III, Córdoba, Argentina. El análisis ecológico clásico indicó que la zona fótica tenía mayor diversidad, mientras que la afótica tenía mayor abundancia y una distribución más uniforme de especies. Sin embargo, cuando se utilizó la información filogenética para comparar las comunidades microbianas de ambas zonas, este análisis indicó que ambos ambientes eran similares y que en ninguno predominaba algún linaje en particular. Los phyla identificados en el Embalse del Río III fueron Acidobacteria, Actinobacteria y Proteobacteria. Las especies dominantes en ambas zonas fueron "Candidatus Planktophila sp." (clase Actinobacteria y

  15. 基于浮游细菌生物完整性指数的河流生态系统健康评价——以滇池流域为例%Bacterioplankton Index of Biotic Integrity (BP-IBI): An Approach for Assessing River Ecosystem Health in Dianchi Watershed

    Institute of Scientific and Technical Information of China (English)

    黄艺; 舒中亚

    2013-01-01

    生物完整性指数(IBI)已被广泛运用于河流生态系统的健康评价中.然而,现存的IBI缺少基于分解者的评价方法.因此,基于浮游细菌的T-RFLP结果,通过对关键环境因子与候选生物参数的筛选和确定,建立浮游细菌生物完整性指数(BPIBI)评价体系,对滇池流域入湖河流生态系统健康状况进行评价.评价结果表明,作为参照点的11个滇池流域入湖河流水源地或上游出水口样点健康状况为Ⅰ级健康(8个)或Ⅱ级亚健康(3个),27个下游入湖口样点健康状况分别为Ⅰ级健康(4个)、Ⅱ级亚健康(14个)、Ⅲ级一般(7个)和Ⅳ级较差(2个),无Ⅴ级极差点.对BP-IBI的可行性验证结果表明,与底栖IBI、着生藻IBI和综合污染指数相比,BP-IBI结果能够更好地反映各主要环境因子、不同土地利用方式以及上游的来水方式对生态系统的影响,对退化生态系统的健康状况具有良好的表征作用.因此,BP-IBI是评价受损河流生态系统健康的一种良好方法.%The index of biotic integrity (IBI) has been widely applied to the health assessment of river ecosystems.However,the currently available IBI methods are lack of decomposer-based assessment.Based on the T-RFLP result of bacterioplankton,we developed the bacterioplankton index of biotic integrity (BP-IBI) after the screening of major environmental factors and candidate metrics to assess the health of the inflow rivers in Dianchi Watershed.The evaluation result indicated that the eco-health conditions of 11 reference sites were either level Ⅰ (8 sites) or level Ⅱ (3 sites),while the 27 damaged sites were level Ⅰ (4 sites),level Ⅱ (14 sites),level Ⅲ (7 sites),and level Ⅳ (2 sites),and there was no level Ⅴ site.Compared with the other IBI methods and the integrated pollution index,BP-IBI showed better effect in reflecting the influence of the key environmental factors,the land use types and the upstream water types in river

  16. Bacterioplankton abundance and production in Indian Ocean Regions

    Digital Repository Service at National Institute of Oceanography (India)

    Ramaiah, N.; Fernandes, V.; Rodrigues, V.V.; Paul, J.T.; Gauns, M.

    of Earth Sciences, New Delhi under JGOFS (India), BOBPS, and surveys for cobalt crust programs. We also thank the late M. Madhupratap for his leadership and guidance. We gratefully thank Raleigh Hood and the anonymous reviewers for their numerous...

  17. Latitudinal patterns in the abundance of major marine bacterioplankton groups

    DEFF Research Database (Denmark)

    Wietz, Matthias; Gram, Lone; Jørgensen, Bo

    2010-01-01

    ) and Gammaproteobacteria (polar stations) varied between major oceanic regions (biomes), as did absolute abundances of Roseobacter (peaking at temperate and polar stations). For almost all groups absolute abundances were positively correlated with nutrient concentrations in warmer oceans, and negatively with oxygen...

  18. Zonation of bacterioplankton communities along aging upwelled water in the northern Benguela upwelling

    Directory of Open Access Journals (Sweden)

    Benjamin eBergen

    2015-06-01

    Full Text Available Upwelling areas are shaped by enhanced primary production in surface waters, accompanied by a well-investigated planktonic succession. Although bacteria play an important role in biogeochemical cycles of upwelling systems, little is known about bacterial community composition and its development during upwelling events. The aim of this study was to investigate the succession of bacterial assemblages in aging upwelled water of the Benguela upwelling from coastal to offshore sites. Water from the upper mixed layer at 12 stations was sampled along two transects from the origin of the upwelling to a distance of 220 km. 16S rRNA gene amplicon sequencing was then used in a bacterial diversity analysis and major bacterial taxa were quantified by catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH. Additionally, bacterial cell numbers and bacterial production were assessed . Community statistical analysis revealed a reproducible zonation along the two transects, with four clusters of significantly different microbial assemblages. Clustering was mainly driven by phytoplankton composition and abundance. Similar to the temporal succession that occurs during phytoplankton blooms in temperate coastal waters, operational taxonomic units (OTUs affiliated with Bacteroidetes and Gammaproteobacteria were dominant during algal blooming whereas Pelagibacterales were highly abundant in regions with low algal abundance. The most dominant heterotrophic OTU (9% of all reads was affiliated with Pelagibacterales and showed a strong negative correlation with phytoplankton. By contrast, the second most abundant heterotrophic OTU (6% of all reads was affiliated with the phylum Verrucomicrobia and correlated positively with phytoplankton. Together with the close relation of bacterial production and phytoplankton abundance, our results showed that bacterial community dynamics is strongly driven by the development and composition of the phytoplankton community.

  19. Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations.

    Science.gov (United States)

    Cordero, Otto X; Ventouras, Laure-Anne; DeLong, Edward F; Polz, Martin F

    2012-12-01

    A common strategy among microbes living in iron-limited environments is the secretion of siderophores, which can bind poorly soluble iron and make it available to cells via active transport mechanisms. Such siderophore-iron complexes can be thought of as public goods that can be exploited by local communities and drive diversification, for example by the evolution of "cheating." However, it is unclear whether bacterial populations in the environment form stable enough communities such that social interactions significantly impact evolutionary dynamics. Here we show that public good games drive the evolution of iron acquisition strategies in wild populations of marine bacteria. We found that within nonclonal but ecologically cohesive genotypic clusters of closely related Vibrionaceae, only an intermediate percentage of genotypes are able to produce siderophores. Nonproducers within these clusters exhibited selective loss of siderophore biosynthetic pathways, whereas siderophore transport mechanisms were retained, suggesting that these nonproducers can act as cheaters that benefit from siderophore producers in their local environment. In support of this hypothesis, these nonproducers in iron-limited media suffer a significant decrease in growth, which can be alleviated by siderophores, presumably owing to the retention of transport mechanisms. Moreover, using ecological data of resource partitioning, we found that cheating coevolves with the ecological specialization toward association with larger particles in the water column, suggesting that these can harbor stable enough communities for dependencies among organisms to evolve.

  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.

    for the present study, as it receives 35% of the total freshwater discharge through the River Periyar (Srinivas et al., 2003). Moreover, a fertilizer factory situated in the upstream north forms a major source of ammonia in the study region (Joy et al., 1990... mouth of the estuary. On the other hand, PCA indicates that amino/carboxylic acids are support- ing community metabolism at high salinity (Table 2). This shift can be due to the availability of substrates which induce bacterial cells to synthesize ecto...

  1. Bacterioplankton abundance and production and nanozooplankton abundance in Kenyan coastal waters (Western Indian Ocean)

    NARCIS (Netherlands)

    Goosen, N.K.; Van Rijswijk, P.; De Bie, M.J.M.; Peene, J.; Kromkamp, J.C.

    1997-01-01

    Bacterial abundance, [H-3]thymidine incorporation rate and heterotrophic nanoflagellate abundance were measured in the water column along transects perpendicular to the Kenyan coast (western Indian Ocean) during June-July (SE monsoon) and November-December (intermonsoon) 1992. Bacterial abundance wa

  2. The Temporal Dynamics of Coastal Phytoplankton and Bacterioplankton in the Eastern Mediterranean Sea.

    Directory of Open Access Journals (Sweden)

    Ofrat Raveh

    Full Text Available This study considers variability in phytoplankton and heterotrophic bacterial abundances and production rates, in one of the most oligotrophic marine regions in the world-the Levantine Basin. The temporal dynamics of these planktonic groups were studied in the coastal waters of the southeastern Mediterranean Sea approximately every two weeks for a total of two years. Heterotrophic bacteria were abundant mostly during late summer and midwinter, and were positively correlated with bacterial production and with N2 fixation. Based on size fractionating, picophytoplankton was abundant during the summer, whereas nano-microphytoplankton predominated during the winter and early spring, which were also evident in the size-fractionated primary production rates. Autotrophic abundance and production correlated negatively with temperature, but did not correlate with inorganic nutrients. Furthermore, a comparison of our results with results from the open Levantine Basin demonstrates that autotrophic and heterotrophic production, as well as N2 fixation rates, are considerably higher in the coastal habitat than in the open sea, while nutrient levels or cell abundance are not different. These findings have important ecological implications for food web dynamics and for biological carbon sequestration in this understudied region.

  3. Allochthonous Carbon--a Major Driver of Bacterioplankton Production in the Subarctic Northern Baltic Sea.

    Science.gov (United States)

    Figueroa, D; Rowe, O F; Paczkowska, J; Legrand, C; Andersson, A

    2016-05-01

    Heterotrophic bacteria are, in many aquatic systems, reliant on autochthonous organic carbon as their energy source. One exception is low-productive humic lakes, where allochthonous dissolved organic matter (ADOM) is the major driver. We hypothesized that bacterial production (BP) is similarly regulated in subarctic estuaries that receive large amounts of riverine material. BP and potential explanatory factors were measured during May-August 2011 in the subarctic Råne Estuary, northern Sweden. The highest BP was observed in spring, concomitant with the spring river-flush and the lowest rates occurred during summer when primary production (PP) peaked. PLS correlations showed that ∼60% of the BP variation was explained by different ADOM components, measured as humic substances, dissolved organic carbon (DOC) and coloured dissolved organic matter (CDOM). On average, BP was threefold higher than PP. The bioavailability of allochthonous dissolved organic carbon (ADOC) exhibited large spatial and temporal variation; however, the average value was low, ∼2%. Bioassay analysis showed that BP in the near-shore area was potentially carbon limited early in the season, while BP at seaward stations was more commonly limited by nitrogen-phosphorus. Nevertheless, the bioassay indicated that ADOC could contribute significantly to the in situ BP, ∼60%. We conclude that ADOM is a regulator of BP in the studied estuary. Thus, projected climate-induced increases in river discharge suggest that BP will increase in subarctic coastal areas during the coming century.

  4. Strong variability in bacterioplankton abundance and production in central and western Bay of Bengal

    Digital Repository Service at National Institute of Oceanography (India)

    Fernandes, V.; Ramaiah, N.; Paul, J.T.; Sardessai, S.; Jyothibabu, R.; Gauns, M.

    -98 Garrison D L, Gowing MM., Hughes M P, Campbell L, Caron DA., Dennett MR, Shalapyonok A, Olson RJ, Landry MR, Brown SL, Liu HB, Azam F, Steward GF, Ducklow HW, Smith DC (2000) Microbial food web structure in the Arabian Sea: a US JGOFS study. Deep-Sea Res...-36 Biddanda BA, Benner R (1997) Major contribution of mesopelagic plankton to heterotrophic metabolism in the upper ocean. Deep-Sea Res 14: 2069-2085 Biddanda BA, Pomeroy LR (1988) Microbial aggregation and degradation of phytoplankton derived detritus...

  5. Relevance of bacterioplankton abundance and production in the oligotrophic equatorial Indian Ocean

    Digital Repository Service at National Institute of Oceanography (India)

    Fernandes, V.; Rodrigues, V.; Ramaiah, N.; Paul, J.T.

    degrees N to 5 degrees S along 83 degrees E. The average bacterial abundance was 0.52 plus or minus 0.29, 0.62 plus or minus 0.33 and 0.46 plus or minus 0.19 (x 10 sup(8) cells l sup(–1)), respectively during NEM, SWM and SpIM in the top 100 m. In the deep...

  6. Response of bacterioplankton to iron fertilization of the Southern Ocean, Antarctica

    Digital Repository Service at National Institute of Oceanography (India)

    Singh, S.K.; Kotakonda, A.; Kapardar, R.K.; Kankipati, H.K.; Rao, P.S.; Sankaranarayanan, P.M.; Vetaikorumagan, S.R.; Gundlapally, S.R.; Ramaiah, N.; Shivaji, S.

    structure following iron fertilization-induced phytoplankton bloom of the seawater from different depths. 16S rRNA gene libraries were constructed using metagenomic DNA from seawater prior to and after iron fertilization and the clones were sequenced...

  7. Pollution impacts on bacterioplankton diversity in a tropical urban coastal lagoon system.

    Directory of Open Access Journals (Sweden)

    Gigliola R B Salloto

    Full Text Available Despite a great number of published studies addressing estuarine, freshwater and marine bacterial diversity, few have examined urban coastal lagoons in tropical habitats. There is an increasing interest in monitoring opportunistic pathogens as well as indigenous microbial community members in these water bodies by current molecular and microbiological approaches. In this work, bacterial isolates were obtained through selective plate dilution methods to evaluate antibiotic resistances. In addition, 16S rRNA gene libraries were prepared from environmental waters and mixed cultures grown in BHI medium inoculated with Jacarepaguá lagoon waters. Denaturing gradient gel electrophoresis (DGGE analyses showed distinct community profiles between environmental communities from each studied site and their cultured counterparts. A total of 497 bacterial sequences were analyzed by MOTHUR, yielding 245 operational taxonomic units (OTUs grouped at 97% similarity. CCA diagrams showcased how several environmental variables affect the distribution of 18 bacterial orders throughout the three distinct habitats. UniFrac metrics and Venn diagrams revealed that bacterial communities retrieved through each experimental approach were significantly different and that only one OTU, closely related to Vibrio cholerae, was shared between them. Potentially pathogenic bacteria were isolated from most sampled environments, fifty percent of which showed antibiotic resistance.

  8. Major effect of hydrogen peroxide on bacterioplankton metabolism in the Northeast Atlantic.

    Directory of Open Access Journals (Sweden)

    Federico Baltar

    Full Text Available Reactive oxygen species such as hydrogen peroxide have the potential to alter metabolic rates of marine prokaryotes, ultimately impacting the cycling and bioavailability of nutrients and carbon. We studied the influence of H2O2 on prokaryotic heterotrophic production (PHP and extracellular enzymatic activities (i.e., β-glucosidase [BGase], leucine aminopeptidase [LAPase] and alkaline phosphatase [APase] in the subtropical Atlantic. With increasing concentrations of H2O2 in the range of 100-1000 nM, LAPase, APase and BGase were reduced by up to 11, 23 and 62%, respectively, in the different water layers. Incubation experiments with subsurface waters revealed a strong inhibition of all measured enzymatic activities upon H2O2 amendments in the range of 10-500 nM after 24 h. H2O2 additions also reduced prokaryotic heterotrophic production by 36-100% compared to the rapid increases in production rates occurring in the unamended controls. Our results indicate that oxidative stress caused by H2O2 affects prokaryotic growth and hydrolysis of specific components of the organic matter pool. Thus, we suggest that oxidative stress may have important consequences on marine carbon and energy fluxes.

  9. Major Effect of Hydrogen Peroxide on Bacterioplankton Metabolism in the Northeast Atlantic

    NARCIS (Netherlands)

    Baltar, F.; Reinthaler, T.; Herndl, G.J.; Pinhassi, J.

    2013-01-01

    Reactive oxygen species such as hydrogen peroxide have the potential to alter metabolic rates of marine prokaryotes, ultimately impacting the cycling and bioavailability of nutrients and carbon. We studied the influence of H2O2 on prokaryotic heterotrophic production (PHP) and extracellular enzymati

  10. Global patterns of marine bacterioplankton diversity and characterisation of bioactive Vibrionaceae isolates

    DEFF Research Database (Denmark)

    Wietz, Matthias

    the abundance of major bacterial groups, potential biogeographical patterns, and their relation to environmental parameters. The original aim was to determine whether the composition of the total microbiota correlates with the occurrence of culturable bioactive bacteria. No such correlation was found...... distribution. Studies of antagonistic isolates focused on six bioactive Vibrionaceae isolated during Galathea 3. The six strains were identified as Vibrio coralliilyticus (two strains), V. neptunius (two strains), V. nigripulchritudo (one strain), and Photobacterium halotolerans (one strain) by sequencing...... from P. halotolerans and a novel siderophore-like compound from V. nigripulchritudo were isolated. All three compounds interfere with quorum sensing in S. aureus. During LOMROG-II further seventeen strains with antagonistic activity were isolated, affiliating with the Actinobacteria (8 strains...

  11. Biogeography of pelagic bacterioplankton across an antagonistic temperature-salinity gradient in the Red Sea

    KAUST Repository

    Ngugi, David

    2011-12-01

    The Red Sea is a unique marine ecosystem with contrasting gradients of temperature and salinity along its north-to-south axis. It is an extremely oligotrophic environment that is characterized by perpetual year-round water column stratification, high annual solar irradiation, and negligible riverine and precipitation inputs. In this study, we investigated whether the contemporary environmental conditions shape community assemblages by pyrosequencing 16S rRNA genes of bacteria in surface water samples collected from the northeastern half of this water body. A combined total of 1855 operational taxonomic units (OTUs) were recovered from the \\'small-cell\\' and \\'large-cell\\' fractions. Here, a few major OTUs affiliated with Cyanobacteria and Proteobacteria accounted for â93% of all sequences, whereas a tail of \\'rare\\' OTUs represented most of the diversity. OTUs allied to Surface 1a/b SAR11 clades and Prochlorococcus related to the high-light-adapted (HL2) ecotype were the most widespread and predominant sequence types. Interestingly, the frequency of taxa that are typically found in the upper mesopelagic zone was significantly elevated in the northern transects compared with those in the central, presumably as a direct effect of deep convective mixing in the Gulf of Aqaba and water exchange with the northern Red Sea. Although temperature was the best predictor of species richness across all major lineages, both spatial and environmental distances correlated strongly with phylogenetic distances. Our results suggest that the bacterial diversity of the Red Sea is as high as in other tropical seas and provide evidence for fundamental differences in the biogeography of pelagic communities between the northern and central regions. © 2011 Blackwell Publishing Ltd.

  12. Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data

    Directory of Open Access Journals (Sweden)

    Wilhelm Larry J

    2007-11-01

    Full Text Available Abstract Background One objective of metagenomics is to reconstruct information about specific uncultured organisms from fragmentary environmental DNA sequences. We used the genome of an isolate of the marine alphaproteobacterium SAR11 ('Candidatus Pelagibacter ubique'; strain HTCC1062, obtained from the cold, productive Oregon coast, as a query sequence to study variation in SAR11 metagenome sequence data from the Sargasso Sea, a warm, oligotrophic ocean gyre. Results The average amino acid identity of SAR11 genes encoded by the metagenomic data to the query genome was only 71%, indicating significant evolutionary divergence between the coastal isolates and Sargasso Sea populations. However, an analysis of gene neighbors indicated that SAR11 genes in the Sargasso Sea metagenomic data match the gene order of the HTCC1062 genome in 96% of cases (> 85,000 observations, and that rearrangements are most frequent at predicted operon boundaries. There were no conserved examples of genes with known functions being found in the coastal isolates, but not the Sargasso Sea metagenomic data, or vice versa, suggesting that core regions of these diverse SAR11 genomes are relatively conserved in gene content. However, four hypervariable regions were observed, which may encode properties associated with variation in SAR11 ecotypes. The largest of these, HVR2, is a 48 kb region flanked by the sole 5S and 23S genes in the HTCC1062 genome, and mainly encodes genes that determine cell surface properties. A comparison of two closely related 'Candidatus Pelagibacter' genomes (HTCC1062 and HTCC1002 revealed a number of "gene indels" in core regions. Most of these were found to be polymorphic in the metagenomic data and showed evidence of purifying selection, suggesting that the same "polymorphic gene indels" are maintained in physically isolated SAR11 populations. Conclusion These findings suggest that natural selection has conserved many core features of SAR11 genomes across broad oceanic scales, but significant variation was found associated with four hypervariable genome regions. The data also led to the hypothesis that some gene insertions and deletions might be polymorphisms, similar to allelic polymorphisms.

  13. The hidden seasonality of the rare biosphere in coastal marine bacterioplankton.

    Science.gov (United States)

    Alonso-Sáez, Laura; Díaz-Pérez, Laura; Morán, Xosé Anxelu G

    2015-10-01

    Rare microbial taxa are increasingly recognized to play key ecological roles, but knowledge of their spatio-temporal dynamics is lacking. In a time-series study in coastal waters, we detected 83 bacterial lineages with significant seasonality, including environmentally relevant taxa where little ecological information was available. For example, Verrucomicrobia had recurrent maxima in summer, while the Flavobacteria NS4, NS5 and NS2b clades had contrasting seasonal niches. Among the seasonal taxa, only 4 were abundant and persistent, 20 cycled between rare and abundant and, remarkably, most of them (59) were always rare (contributing biosphere, hitherto mainly characterized by dormancy and episodes of 'boom and bust', as envisioned by the seed-bank hypothesis. The predictable patterns of seasonal reoccurrence are relevant for understanding the ecology of rare bacteria, which may include key players for the functioning of marine ecosystems.

  14. Salinity as a structuring factor for the composition and performance of bacterioplankton degrading riverine DOC.

    Science.gov (United States)

    Langenheder, Silke; Kisand, Veljo; Wikner, Johan; Tranvik, Lars J

    2003-07-01

    Abstract The impact of salinity on the composition and functional performance (biomass production, growth efficiency and growth rates) of bacterial communities was investigated using batch cultures growing on dissolved organic carbon from a river draining into the Northern Baltic Sea. The cultures were adjusted to riverine or estuarine salinity levels and inoculated with bacteria from these two environments. Bacterial growth efficiencies differed in response to salinity and the origin of the inoculum. When salinity was adjusted to correspond to the salinity at the site where the inoculum was retrieved, growth efficiency was relatively high (11.5+/-2.6%). However, when bacteria were confronted with a shift in salinity, growth efficiency was lower (7.5+/-2.0%) and more of the utilized carbon was respired. In contrast, growth rates were higher when bacteria were exposed to a change in salinity. The composition of the bacterial communities developing in the batch cultures differed, as shown by 16S rDNA DGGE, depending on the origin of the inoculum and salinity. Reverse and direct DNA-DNA hybridization revealed salinity optima in the growth of specific bacterial strains as well as broader phylogenetic groups. Strains belonging to the alpha- and beta-Proteobacteria, Actinobacteria and gamma-Proteobacteria other than the genus Pseudomonas showed higher relative abundance under freshwater conditions, whereas strains of the genus Pseudomonas and the Cytophaga-Flavobacterium-Bacteroides group were favored by estuarine conditions. Generally, our results demonstrate functional changes associated with changes in community composition. We suggest that even moderate changes in salinity affect bacterial community composition, which subsequently leads to altered growth characteristics.

  15. Jellyfish-associated bacterial communities and bacterioplankton in Indonesian Marine lakes

    NARCIS (Netherlands)

    Cleary, D.F.R.; Becking, L.E.; Polonia, A.; Freitas, B.M.; Gomes, N.

    2016-01-01

    In the present study, we compared communities of bacteria in two jellyfish species (the ‘golden’ jellyfish Mastigias cf. papua and the box jellyfish Tripedalia cf. cystophora) and water in three marine lakes located in the Berau region of northeastern Borneo, Indonesia. Jellyfish-associated bacteria

  16. Nitrogenase expression in estuarine bacterioplankton influenced by organic carbon and availability of oxygen

    DEFF Research Database (Denmark)

    Severin, Ina; Bentzon-Tilia, Mikkel; Moisander, Pia H.;

    2015-01-01

    of carbon and inhibition by oxygen constrain N fixation by diazotrophs in coastal seawater. The goal was to test whether by alleviating these constraints an increased overlap between nitrogenase (nifH)-gene- carrying and -expressing organisms could be achieved. We incubated water from a eutrophic but N......-limited fjord in Denmark under high carbon/low oxygen conditions and determined bacterial growth and production, diazotrophic community composition (Illumina nifH amplicon sequencing), and nifH gene abundance and expression (quantitative PCR (qPCR) and quantitative Reverse Transcriptase PCR (q...

  17. pH Tolerance in Freshwater Bacterioplankton: Trait Variation of the Community as Measured by Leucine Incorporation

    OpenAIRE

    Bååth, Erland; Kritzberg, Emma

    2015-01-01

    pH is an important factor determining bacterial community composition in soil and water. We have directly determined the community tolerance (trait variation) to pH in communities from 22 lakes and streams ranging in pH from 4 to 9 using a growth-based method not relying on distinguishing between individual populations. The pH in the water samples was altered to up to 16 pH values, covering in situ pH ± 2.5 U, and the tolerance was assessed by measuring bacterial growth (Leu incorporation) in...

  18. QUANTIFICATION OF RECA GENE EXPRESSION AS AN INDICATOR OF REPAIR POTENTIAL IN MARINE BACTERIOPLANKTON COMMUNITIES OF ANTARCTICA.

    Science.gov (United States)

    Marine bacteria in surface waters must cope daily with the damaging effects of exposure to solar radiation (containing both UV-A and UV-B wavelengths), which produces lesions in their DNA. As the stratospheric ozone layer is depleted, these coping mechanisms are likely to play an...

  19. Offshore distribution patterns of the cyanobacterium Trichodesmium erythraeum ehrenberg and associated phyto- and bacterioplankton in the southern Atlantic coast (Paraná, Brazil

    Directory of Open Access Journals (Sweden)

    Adriana Siqueira

    2006-03-01

    Full Text Available Studies were carried out on Thrichodesmium erythraeum occurring on the inner shelf in the state of Paraná, Brazil. Temperature, salinity, rainfall, wind velocity, total bacteria, bacterial biomass, chlorophyll-a, phytoplankton, Anabaena sp., Merismopedia sp. and T. erythraeum densities were measured in surface water. Centric and pennate diatoms, Anabaena sp. and Merismopedia sp. were most abundant at 15 m isobath, while dinoflagellate abundance was relatively constant among stations. Similarly, total bacterial densities were relatively homogeneous throughout the sampling area, suggesting that blooms of T. erythraeum were not yet in the senescent phase. Results showed that T. erythraeum was capable of surviving in relatively inhospitable environmental conditions, due to its ability to fix nitrogen and to photosynthesis at high light intensities.O propósito principal da presente pesquisa foi investigar as florações de Trichodesmium erythraeum na plataforma continental interna do Estado do Paraná, Brasil. Foram medidas, em águas de superfície a temperatura, salinidade, bactérias totais, biomassa bacteriana, clorofila-a, densidade fitoplanctônica, densidade das cianobactérias Anabaena sp., Merismopedia sp. e T. erythraeum. Ao contrário dos dinoflagelados, cuja abundância foi relativamente constante em todas as estações, as diatomáceas cêntricas e penadas, Anabaena sp. e Merismopedia sp. foram mais abundantes até a isóbata dos 15 m. A densidade de bactérias totais também foi relativamente homogênea na área amostrada, o que sugere que as florações de T. erythraeum não se encontravam em fase senescente. Os resultados confirmam que T. erythraeum é capaz de sobreviver em condições ambientais relativamente inóspitas devido à sua capacidade de fixar nitrogênio e efetuar a fotossíntese em altas intensidades de luz.

  20. Offshore distribution patterns of the cyanobacterium Trichodesmium erythraeum ehrenberg and associated phyto- and bacterioplankton in the southern Atlantic coast (Paraná, Brazil)

    OpenAIRE

    Adriana Siqueira; Hedda Elisabeth Kolm; Frederico Pereira Brandini

    2006-01-01

    Studies were carried out on Thrichodesmium erythraeum occurring on the inner shelf in the state of Paraná, Brazil. Temperature, salinity, rainfall, wind velocity, total bacteria, bacterial biomass, chlorophyll-a, phytoplankton, Anabaena sp., Merismopedia sp. and T. erythraeum densities were measured in surface water. Centric and pennate diatoms, Anabaena sp. and Merismopedia sp. were most abundant at 15 m isobath, while dinoflagellate abundance was relatively constant among stations. Similarl...

  1. ACTIVITIES OF AMMONIA ASSIMILATION ENZYMES AS INDICATORS OF THE RELATIVE SUPPLY OF NITROGEN SUBSTRATES FOR MARINE BACTERIOPLANKTON IN SUB-TROPICAL COASTAL WATER

    Science.gov (United States)

    The supply of nitrogen substrates available for bacterial production in seawater was determined using the activities of ammonia assimilation enzymes, glutamine synthetase (GS) and glutamate dehydrogenase (GDH). Expression of GS and GDH by bacteria in pure culture is generally ind...

  2. Nitrogen and carbon limitation of planktonic primary production and phytoplankton-bacterioplankton coupling in ponds on the McMurdo Ice Shelf, Antarctica

    DEFF Research Database (Denmark)

    Sorrell, B.K.; Hawes, I.; Safi, K.

    2013-01-01

    The nature of nutrient limitation and coupling of planktonic primary and secondary production were investigated in meltwater ponds of the Ross Ice Shelf, Antarctica, using regression tree analysis and multiple regression. Phytoplankton were primaril N-limited but inorganic carbon apparently co...

  3. Local environmental conditions shape generalist but not specialist components of microbial metacommunities in the Baltic Sea

    DEFF Research Database (Denmark)

    Lindh, Markus V.; Sjöstedt, Johanna; Casini, Michele

    2016-01-01

    Marine microbes exhibit biogeographical patterns linked with fluxes of matter and energy. Yet, knowledge of the mechanisms shaping bacterioplankton community assembly across temporal scales remains poor. We examined bacterioplankton 16S rRNA gene fragments obtained from Baltic Sea transects to de...

  4. Proceedings of the Plankton Ecology Group (PEG) Workshop in Mexico City (12–18 February 2012)

    NARCIS (Netherlands)

    Sarma, S.S.S.; Gulati, R.D.; Nandini, S.

    2014-01-01

    Plankton is an important constituent of aquatic ecosystems, dominated in freshwater ecosystems by diverse groups of bacterioplankton, phytoplankton, and zooplankton. The Plankton Ecology Group (PEG) has made noteworthy headway in understanding ecosystem dynamics through a series of formal PEG meetin

  5. Bacteria and viruses of the ice-free aquatic area of the Barents Sea at the beginning of polar night.

    Science.gov (United States)

    Shirokolobova, T I; Zhichkin, A P; Venger, M P; Vodopyanova, V V; Moiseev, D V

    2016-07-01

    The most massive components of the microplankton were studied in the open sea waters for the first time at the end of the autumn season. It has been found that abundance of the virio- and bacterioplankton exceeded that observed in winter in the coastal zone. Against the background of a relatively uniform distribution of bacteria, the viral abundance and the lysis-mediated bacterioplankton death rate reached the maximum values in the most cold and salty waters of the northern sea areas.

  6. Comparable light stimulation of organic nutrient uptake by SAR11 and Prochlorococcus in the North Atlantic subtropical gyre.

    Science.gov (United States)

    Gómez-Pereira, Paola R; Hartmann, Manuela; Grob, Carolina; Tarran, Glen A; Martin, Adrian P; Fuchs, Bernhard M; Scanlan, David J; Zubkov, Mikhail V

    2013-03-01

    Subtropical oceanic gyres are the most extensive biomes on Earth where SAR11 and Prochlorococcus bacterioplankton numerically dominate the surface waters depleted in inorganic macronutrients as well as in dissolved organic matter. In such nutrient poor conditions bacterioplankton could become photoheterotrophic, that is, potentially enhance uptake of scarce organic molecules using the available solar radiation to energise appropriate transport systems. Here, we assessed the photoheterotrophy of the key microbial taxa in the North Atlantic oligotrophic gyre and adjacent regions using (33)P-ATP, (3)H-ATP and (35)S-methionine tracers. Light-stimulated uptake of these substrates was assessed in two dominant bacterioplankton groups discriminated by flow cytometric sorting of tracer-labelled cells and identified using catalysed reporter deposition fluorescence in situ hybridisation. One group of cells, encompassing 48% of all bacterioplankton, were identified as members of the SAR11 clade, whereas the other group (24% of all bacterioplankton) was Prochlorococcus. When exposed to light, SAR11 cells took 31% more ATP and 32% more methionine, whereas the Prochlorococcus cells took 33% more ATP and 34% more methionine. Other bacterioplankton did not demonstrate light stimulation. Thus, the SAR11 and Prochlorococcus groups, with distinctly different light-harvesting mechanisms, used light equally to enhance, by approximately one-third, the uptake of different types of organic molecules. Our findings indicate the significance of light-driven uptake of essential organic nutrients by the dominant bacterioplankton groups in the surface waters of one of the less productive, vast regions of the world's oceans-the oligotrophic North Atlantic subtropical gyre.

  7. Final Technical Report: DOE-Biological Ocean Margins Program. Microbial Ecology of Denitrifying Bacteria in the Coastal Ocean.

    Energy Technology Data Exchange (ETDEWEB)

    Lee Kerkhof

    2013-01-01

    The focus of our research was to provide a comprehensive study of the bacterioplankton populations off the coast of New Jersey near the Rutgers University marine field station using terminal restriction fragment polymorphism analysis (TRFLP) coupled to 16S rRNA genes for large data set studies. Our three revised objectives to this study became: (1) to describe bacterioplankton population dynamics in the Mid Atlantic Bight using TRFLP analysis of 16S rRNA genes. (2) to determine whether spatial and temporal factors are driving bacterioplankton community dynamics in the MAB using monthly samping along our transect line over a 2-year period. (3) to identify dominant members of a coastal bacterioplankton population by clonal library analysis of 16S rDNA genes and sequencing of PCR product corresponding to specific TRFLP peaks in the data set. Although open ocean time-series sites have been areas of microbial research for years, relatively little was known about the population dynamics of bacterioplankton communities in the coastal ocean on kilometer spatial and seasonal temporal scales. To gain a better understanding of microbial community variability, monthly samples of bacterial biomass were collected in 1995-1996 along a 34-km transect near the Long-Term Ecosystem Observatory (LEO-15) off the New Jersey coast. Surface and bottom sampling was performed at seven stations along a transect line with depths ranging from 1 to 35m (n=178). The data revealed distinct temporal patterns among the bacterioplankton communities in the Mid-Atlantic Bight rather than grouping by sample location or depth (figure 2-next page). Principal components analysis models supported the temporal patterns. In addition, partial least squares regression modeling could not discern a significant correlation from traditional oceanographic physical and phytoplankton nutrient parameters on overall bacterial community variability patterns at LEO-15. These results suggest factors not traditionally

  8. Comparison between MICRO-CARD-FISH and 16S rRNA gene clone libraries to assess the active versus total bacterial community in the coastal Arctic

    NARCIS (Netherlands)

    De Corte, Daniele; Sintes, Eva; Yokokawa, Taichi; Herndl, Gerhard J.

    2013-01-01

    We collected surface- and deep-water samples (maximum depth 300m) during the springsummer transition in the coastal Arctic along a transect in the Kongsfjorden (Ny-angstrom lesund, Spitsbergen, Norway) to determine the structure of the active versus total marine bacterioplankton community using diff

  9. Comparison between MICRO-CARD-FISH and 16S rRNA gene clone libraries toassess the active versus total bacterial community in the coastal Arctic

    NARCIS (Netherlands)

    De Corte, D.; Sintes, E.; Yokokawa, T.; Herndl, G.; De Corte, D.

    2013-01-01

    We collected surface- and deep-water samples (maximum depth 300m) during the springsummer transition in the coastal Arctic along a transect in the Kongsfjorden (Ny-angstrom lesund, Spitsbergen, Norway) to determine the structure of the active versus total marine bacterioplankton community using diff

  10. Effects of oxygen loss on carbon processing and heterotrophic prokaryotes from an estuarine ecosystem: results from stable isotope probing and cytometry analyses

    NARCIS (Netherlands)

    Tadonléké, R.D.; Pollet, T.; van Rijswijk, P.; Leberre, B.; Middelburg, J.J.

    2016-01-01

    Many aquatic ecosystems are experiencing a decline in their oxygen (O2) content and this is predicted to continue. Implications of this change on several properties of bacterioplankton (heterotrophic prokaryotes) remain however are poorly known. In this study, oxic samples (~170 µM O

  11. Effects of oxygen loss on carbon processing and heterotrophic prokaryotes from an estuarine ecosystem: Results from stable isotope probing and cytometry analyses

    NARCIS (Netherlands)

    Tadonléké, Rémy D.; Pollet, Thomas; van Rijswijk, Pieter; Leberre, Brigitte; Middelburg, Jack J.

    2016-01-01

    Many aquatic ecosystems are experiencing a decline in their oxygen (O2) content and this is predicted to continue. Implications of this change on several properties of bacterioplankton (heterotrophic prokaryotes) remain however are poorly known. In this study, oxic samples (∼170 μM O2 = controls) fr

  12. Carbon dynamics modelization and biological community sensitivity to temperature in an oligotrophic freshwater Antarctic lake

    DEFF Research Database (Denmark)

    Antonio Villaescusa, Juan; Jorgensen, Sven Erik; Rochera, Carlos

    2016-01-01

    food web. This preliminary model aims to describe part of the carbon dynamics, especially for bacterioplankton and associated factors, in this maritime Antarctic lake highly affected by temperature increase linked to regional warming. To describe the system, the effects of the variation of different...

  13. Microbial Biogeography along an Estuarine Salinity Gradient: Combined Influences of Bacterial Growth and Residence Time

    OpenAIRE

    Crump, Byron C.; Hopkinson, Charles S.; Sogin, Mitchell L.; Hobbie, John E

    2004-01-01

    Shifts in bacterioplankton community composition along the salinity gradient of the Parker River estuary and Plum Island Sound, in northeastern Massachusetts, were related to residence time and bacterial community doubling time in spring, summer, and fall seasons. Bacterial community composition was characterized with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA. Average community doubling time was calculated from bacterial production ([14C]leucine incorpo...

  14. Mixotrophy in the marine plankton

    DEFF Research Database (Denmark)

    Stoecker, Diane K.; Hansen, Per Juel; Caron, David;

    2017-01-01

    Mixotrophs are important components of the bacterioplankton, phytoplankton, microzooplankton, and (sometimes) zooplankton in coastal and oceanic waters. Bacterivory among the phytoplankton may be important for alleviating inorganic nutrient stress and may increase primary production in oligotrophic...... waters. Mixotrophic phytoflagellates and dinoflagellates are often dominant components of the plankton during seasonal stratification. Many of the microzooplankton grazers, including ciliates and Rhizaria, are mixotrophic owing to their retention of functional algal organelles or maintenance of algal...

  15. Active bacteria (CTC+) in temperate lakes: temporal and cross-system variations

    DEFF Research Database (Denmark)

    Søndergaard, Morten; Danielsen, M.

    2001-01-01

    -phenylindole (DAPI) staining. The proportion of CTC+ cells in Lake Esrum and Frederiksborg Slotssø was normally ... consequence of the low abundance of active bacteria is that in situ growth rates scaled to CTC+ cells are 3- to 7-fold higher than those scaled to DAPI counts. It is suggested that studies on factors controlling bacterioplankton activity at the single-cell level should be investigated scaled to active cells....

  16. Ecological Studies and Molecular Characterization of Thraustochytrids and Aplanochytrids from Oceanic Water Column

    Digital Repository Service at National Institute of Oceanography (India)

    Damare, V.

    versus polyclonal antibodies: distinguishing characteristics, applications, and information resources. ILAR Journal., 46 (3), 258-268. Loganathan B., Venugopalan V. K. & Raghukumar S. 1985. Schizochytrium sp. associated with external lesions of some...-induction’ of turtlegrass phenolics near wasting disease lesions. Mar. Ecol. Prog. Ser., 303, 123-131. Stoderegger K. E. & Herndl G. J. 1999. Production of exopolymer particles by marine bacterioplankton under contrasting turbulence conditions. Mar. Ecol. Prog. Ser. 189...

  17. Genomics and ecophysiology of heterotrophic nitrogen-fixing bacteria isolated from estuarine surface water

    DEFF Research Database (Denmark)

    Bentzon-Tilia, Mikkel; Severin, Ina; Hansen, Lars H.;

    2015-01-01

    ABSTRACT The ability to reduce atmospheric nitrogen (N 2) to ammonia, known as N 2 fixation, is a widely distributed trait among prokaryotes that accounts for an essential input of new N to a multitude of environments. Nitrogenase reductase gene (nifH) composition suggests that putative N 2-fixing...... heterotrophic organisms are widespread in marine bacterioplankton, but their autecology and ecological significance are unknown. Here, we report genomic and ecophysiology data in relation to N 2 fixation by three environmentally ...

  18. Expression patterns reveal niche diversification in a marine microbial assemblage.

    Science.gov (United States)

    Gifford, Scott M; Sharma, Shalabh; Booth, Melissa; Moran, Mary Ann

    2013-02-01

    Resolving the ecological niches of coexisting marine microbial taxa is challenging due to the high species richness of microbial communities and the apparent functional redundancy in bacterial genomes and metagenomes. Here, we generated over 11 million Illumina reads of protein-encoding transcripts collected from well-mixed southeastern US coastal waters to characterize gene expression patterns distinguishing the ecological roles of hundreds of microbial taxa sharing the same environment. The taxa with highest in situ growth rates (based on relative abundance of ribosomal protein transcripts) were typically not the greatest contributors to community transcription, suggesting strong top-down ecological control, and their diverse transcriptomes indicated roles as metabolic generalists. The taxa with low in situ growth rates typically had low diversity transcriptomes dominated by specialized metabolisms. By identifying protein-encoding genes with atypically high expression for their level of conservation, unique functional roles of community members emerged related to substrate use (such as complex carbohydrates, fatty acids, methanesulfonate, taurine, tartrate, ectoine), alternative energy-conservation strategies (proteorhodopsin, AAnP, V-type pyrophosphatases, sulfur oxidation, hydrogen oxidation) and mechanisms for negotiating a heterogeneous environment (flagellar motility, gliding motility, adhesion strategies). On average, the heterotrophic bacterioplankton dedicated 7% of their transcriptomes to obtaining energy by non-heterotrophic means. This deep sequencing of a coastal bacterioplankton transcriptome provides the most highly resolved view of bacterioplankton niche dimensions yet available, uncovering a spectrum of unrecognized ecological strategies.

  19. Pole-to-pole biogeography of surface and deep marine bacterial communities.

    Science.gov (United States)

    Ghiglione, Jean-François; Galand, Pierre E; Pommier, Thomas; Pedrós-Alió, Carlos; Maas, Elizabeth W; Bakker, Kevin; Bertilson, Stefan; Kirchmanj, David L; Lovejoy, Connie; Yager, Patricia L; Murray, Alison E

    2012-10-23

    The Antarctic and Arctic regions offer a unique opportunity to test factors shaping biogeography of marine microbial communities because these regions are geographically far apart, yet share similar selection pressures. Here, we report a comprehensive comparison of bacterioplankton diversity between polar oceans, using standardized methods for pyrosequencing the V6 region of the small subunit ribosomal (SSU) rRNA gene. Bacterial communities from lower latitude oceans were included, providing a global perspective. A clear difference between Southern and Arctic Ocean surface communities was evident, with 78% of operational taxonomic units (OTUs) unique to the Southern Ocean and 70% unique to the Arctic Ocean. Although polar ocean bacterial communities were more similar to each other than to lower latitude pelagic communities, analyses of depths, seasons, and coastal vs. open waters, the Southern and Arctic Ocean bacterioplankton communities consistently clustered separately from each other. Coastal surface Southern and Arctic Ocean communities were more dissimilar from their respective open ocean communities. In contrast, deep ocean communities differed less between poles and lower latitude deep waters and displayed different diversity patterns compared with the surface. In addition, estimated diversity (Chao1) for surface and deep communities did not correlate significantly with latitude or temperature. Our results suggest differences in environmental conditions at the poles and different selection mechanisms controlling surface and deep ocean community structure and diversity. Surface bacterioplankton may be subjected to more short-term, variable conditions, whereas deep communities appear to be structured by longer water-mass residence time and connectivity through ocean circulation.

  20. Abundance and biomass responses of microbial food web components to hydrology and environmental gradients within a floodplain of the River Danube.

    Science.gov (United States)

    Palijan, Goran

    2012-07-01

    This study investigated the relationships of time-dependent hydrological variability and selected microbial food web components. Samples were collected monthly from the Kopački Rit floodplain in Croatia, over a period of 19 months, for analysis of bacterioplankton abundance, cell size and biomass; abundance of heterotrophic nanoflagellates and nanophytoplankton; and concentration of chlorophyll a. Similar hydrological variability at different times of the year enabled partition of seasonal effects from hydrological changes on microbial community properties. The results suggested that, unlike some other studies investigating sites with different connectivity, bacterioplankton abundance, and phytoplankton abundance and biomass increased during lentic conditions. At increasing water level, nanophytoplankton showed lower sensitivity to disturbance in comparison with total phytoplankton biomass: this could prolong autotrophic conditions within the floodplain. Bacterioplankton biomass, unlike phytoplankton, was not impacted by hydrology. The bacterial biomass less affected by hydrological changes can be an important additional food component for the floodplain food web. The results also suggested a mechanism controlling bacterial cell size independent of hydrology, as bacterial cell size was significantly decreased as nanoflagellate abundance increased. Hydrology, regardless of seasonal sucession, has the potential to structure microbial food webs, supporting microbial development during lentic conditions. Conversely, other components appear unaffected by hydrology or may be more strongly controlled by biotic interactions. This research, therefore, adds to understanding on microbial food web interactions in the context of flood and flow pulses in river-floodplain ecosystems.

  1. Resilience of SAR11 bacteria to rapid acidification in the high-latitude open ocean.

    Science.gov (United States)

    Hartmann, Manuela; Hill, Polly G; Tynan, Eithne; Achterberg, Eric P; Leakey, Raymond J G; Zubkov, Mikhail V

    2016-02-01

    Ubiquitous SAR11 Alphaproteobacteria numerically dominate marine planktonic communities. Because they are excruciatingly difficult to cultivate, there is comparatively little known about their physiology and metabolic responses to long- and short-term environmental changes. As surface oceans take up anthropogenic, atmospheric CO2, the consequential process of ocean acidification could affect the global biogeochemical significance of SAR11. Shipping accidents or inadvertent release of chemicals from industrial plants can have strong short-term local effects on oceanic SAR11. This study investigated the effect of 2.5-fold acidification of seawater on the metabolism of SAR11 and other heterotrophic bacterioplankton along a natural temperature gradient crossing the North Atlantic Ocean, Norwegian and Greenland Seas. Uptake rates of the amino acid leucine by SAR11 cells as well as other bacterioplankton remained similar to controls despite an instant ∼50% increase in leucine bioavailability upon acidification. This high physiological resilience to acidification even without acclimation, suggests that open ocean dominant bacterioplankton are able to cope even with sudden and therefore more likely with long-term acidification effects.

  2. Relationships between physico-chemical and microbiological parameters in the monimolimnion of a forest meromictic lake

    Directory of Open Access Journals (Sweden)

    Dorota Górniak

    2014-05-01

    Full Text Available The small meromictic Lake Zapadłe in North-Eastern Poland was the subject of our research in the vegetation period between April and November. Our study were to aim a better recognition of meromixis phenomenon and find connections between hydrochemical and microbiological parameters. Here, the monimolimnion layer was below 10 m depth with the chemocline between 13-14 m. Highly significant Spearman’s ranks correlations of P<0.05 were found between conductivity and biochemical oxygen demand (0.91, ammonium nitrogen (0.96, phosphate (0.91, iron (0.77 and manganese (0.82. Favourable conditions for bacterioplankton growth and function here included; the absence of water circulation, the presence of anaerobic conditions and hydrogen sulphide, a constant water temperature and highly significant correlations between total bacterial counts (TBC, bacterial biomass (BB and biochemical oxygen demand (BOD, conductivity, total organic carbon (TOC and dissolved organic carbon (DOC. The pool of bacteria-forming biomass increased significantly in the lower part of the monimolimnion. A highly significant correlation (P<0.05 existed between bacterial biomass (BB and their anaerobic metabolic products: ammonium (r=0.75, hydrogen sulphide (r=0.45 and phosphate (r=0.68 anaerobic metabolic products. This correlation indicated the significant proportion of anaerobic sulfate-reducing bacteria. The impact of physico-chemical parameters on bacterioplankton biomass during the June-November growth season was clearly illustrated in the correspondence canonical analysis (CCA. This recorded its greatest mass at 15 to 17 metres above the lake bed. Although no clear seasonal variations were noted in bacterioplankton composition described by Denaturing Gradient Gel Electrophoresis (DGGE. The monimolimnion lake layer contained 46 Operational Taxonomic Units (OTUs. Subsequent comparison of the upper and lower minimolimnion layers showed 37 of these OTUs were common, while 5 were

  3. Effects of coral reef benthic primary producers on dissolved organic carbon and microbial activity.

    Directory of Open Access Journals (Sweden)

    Andreas F Haas

    Full Text Available Benthic primary producers in marine ecosystems may significantly alter biogeochemical cycling and microbial processes in their surrounding environment. To examine these interactions, we studied dissolved organic matter release by dominant benthic taxa and subsequent microbial remineralization in the lagoonal reefs of Moorea, French Polynesia. Rates of photosynthesis, respiration, and dissolved organic carbon (DOC release were assessed for several common benthic reef organisms from the backreef habitat. We assessed microbial community response to dissolved exudates of each benthic producer by measuring bacterioplankton growth, respiration, and DOC drawdown in two-day dark dilution culture incubations. Experiments were conducted for six benthic producers: three species of macroalgae (each representing a different algal phylum: Turbinaria ornata--Ochrophyta; Amansia rhodantha--Rhodophyta; Halimeda opuntia--Chlorophyta, a mixed assemblage of turf algae, a species of crustose coralline algae (Hydrolithon reinboldii and a dominant hermatypic coral (Porites lobata. Our results show that all five types of algae, but not the coral, exuded significant amounts of labile DOC into their surrounding environment. In general, primary producers with the highest rates of photosynthesis released the most DOC and yielded the greatest bacterioplankton growth; turf algae produced nearly twice as much DOC per unit surface area than the other benthic producers (14.0±2.8 µmol h⁻¹ dm⁻², stimulating rapid bacterioplankton growth (0.044±0.002 log10 cells h⁻¹ and concomitant oxygen drawdown (0.16±0.05 µmol L⁻¹ h⁻¹ dm⁻². Our results demonstrate that benthic reef algae can release a significant fraction of their photosynthetically-fixed carbon as DOC, these release rates vary by species, and this DOC is available to and consumed by reef associated microbes. These data provide compelling evidence that benthic primary producers differentially influence

  4. Autotrophic and heterotrophic metabolism of microbial planktonic communities in an oligotrophic coastal marine ecosystem: seasonal dynamics and episodic events

    Directory of Open Access Journals (Sweden)

    O. Bonilla-Findji

    2010-11-01

    Full Text Available A 18 month study was performed in the Bay of Villefranche to assess the episodic and seasonal variation of autotrophic and heterotrophic ecosystem processes. A typical spring bloom was encountered, where maximum of gross primary production (GPP was followed by maxima of bacterial respiration (BR and production (BP. The trophic balance (heterotrophy vs. autotrophy of the system did not exhibit any seasonal trend although a strong intra-annual variability was observed. On average, the community tended to be net heterotrophic with a GPP threshold for a balanced metabolism of 1.1 μmol O2 l−1 d−1. Extended forest fires in summer 2003 and a local episodic upwelling in July 2003 likely supplied orthophosphate and nitrate into the system. These events were associated with an enhanced bacterioplankton production (up to 2.4-fold, respiration (up to 4.5-fold and growth efficiency (up to 2.9-fold but had no effect on GPP. A Sahara dust wet deposition event in February 2004 stimulated bacterial abundance, production and growth efficiency but not GPP. Our study suggests that short-term disturbances such as wind-driven upwelling, forest fires and Sahara dust depositions can have a significant but previously not sufficiently considered influence on phytoplankton- and bacterioplankton-mediated ecosystem functions and can modify or even mask the seasonal dynamics. The study also indicates that atmospheric deposition of nutrients and particles not only impacts phytoplankton but also bacterioplankton and could, at times, also shift systems stronger towards net heterotrophy.

  5. Seasonal dynamics of phytoplankton and planktonic protozoan communities in a northern temperate humic lake: diversity in a dinoflagellate dominated system.

    Science.gov (United States)

    Graham, J M; Kent, A D; Lauster, G H; Yannarell, A C; Graham, L E; Triplett, E W

    2004-11-01

    Species diversity and richness, and seasonal population dynamics of phytoplankton, planktonic protozoa, and bacterioplankton sampled from the epilimnion of Crystal Bog in 2000, were examined in order to test the hypothesis that these groups' diversity and abundance patterns might be linked. Crystal Bog, a humic lake in Vilas County, Wisconsin, is part of the North Temperate Lakes Long-Term Ecological Research Site. Phytoplankton and planktonic protozoa were identified and enumerated in a settling chamber with an inverted microscope. Bacterial cells were enumerated with the use of fluorescence 4', 6'-diamidino-2-phenylindole (DAPI)-staining procedures, and automated ribosomal intergenic spacer analysis (ARISA) was used to assess bacterioplankton diversity. Bacterial cell counts showed little seasonal variation and averaged 2.6 x 10(6) cells/mL over the ice-free season. Phytoplankton and planktonic protozoan numbers varied by up to two orders of magnitude and were most numerous in late spring and summer. Dinoflagellates largely dominated Crystal Bog throughout the ice-free period, specifically Peridiniopsis quadridens in the spring, Peridinium limbatum in summer, and Gymnodinium fuscum and P. quadridens in fall. Brief blooms of Cryptomonas, Dinobryon, and Synura occurred between periods of dinoflagellate domination. The dominant dinoflagellate, Peridinium limbatum, was calculated to have a growth rate of 0.065 day(-1) and a doubling time of 10.7 days. Heterotrophic nanoflagellates (HNFs) were a consistent component of the planktonic protozoa; seasonal patterns were determined for three genera of HNFs (Monosiga, Bicosoeca, and Desmarella moniliformis). Three genera of ciliates (Coleps, Strobilidium, and Strombidium) comprised the greater part of the planktonic protozoa in Crystal Bog. The number of species of planktonic protozoa was too low to calculate a diversity index. Shannon-Weaver diversity indices for phytoplankton and bacterioplankton in the epilimnion

  6. Short-term changes in the composition of active marine bacterial assemblages in response to diesel oil pollution.

    Science.gov (United States)

    Lanfranconi, Mariana P; Bosch, Rafael; Nogales, Balbina

    2010-09-01

    The changes caused by diesel oil pollution in the metabolically active bacterioplankton from an oligotrophic coastal location were analysed in laboratory microcosms (44 l) using 16S ribosomal RNA (16S rRNA) as molecular marker. The aim was to simulate typical hydrocarbon pollution events in a coastal area exploited for seasonal touristic activities. The experiment consisted in addition of low amounts of diesel oil without nutrients to seawater collected at different times (winter and summer). Bacterial diversity was analysed by terminal-restriction fragment length polymorphism (T-RFLP) profiling of 16S rRNAs after reverse transcription polymerase chain reaction (RT-PCR), and by generation of 16S rRNA clone libraries in control and diesel-polluted microcosms. Diesel addition caused a twofold increase in prokaryotic numbers in comparison with controls at the end of the experiment, both in winter and summer microcosms. Bacterioplankton composition, determined by 16S rRNA T-RFLP data, changed rapidly (within 17 h) in response to treatment. The resulting communities were different in microcosms with water collected in summer and winter. A reduction in diversity (Shannon index, calculated on the basis of T-RFLP data) was observed only in summer microcosms. This was due to the rapid increase of phylotypes affiliated to the Oceanospirillaceae, not observed in winter microcosms. After diesel treatment there was a reduction in the number of phylotypes related to SAR11, SAR86 and picocyanobacteria, while phylotypes of the Roseobacter clade, and the OMG group seemed to be favoured. Our results show that diesel pollution alone caused profound effects on the bacterioplankton of oligotrophic seawater, and explained many of the differences in diversity reported previously in pristine and polluted sites in this coastal area.

  7. Metabolism of DMSP, DMS and DMSO by the cultivable bacterial community associated with the DMSP-producing dinoflagellate Scrippsiella trochoidea

    Digital Repository Service at National Institute of Oceanography (India)

    Hatton, A.D.; Shenoy, D.M.; Hart, M.C.; Mogg, A.; Green, D.H.

    of carbon, reduced sulphur and energy for bacterioplankton (Kiene and Linn 2000a). The precursor of DMS, dimethylsulfoniopropionate (DMSP), is produced by marine micro- and macro-algae. Studies examining the distribution of chlorophyll a as a measure... by Green et al. (2004). To gain a fuller understanding of the total bacterial diversity of this culture, a culture independent approach was also used. Total bacterial 16S ribosomal RNA genes (16S rRNA) were amplified by PCR and cloned into pGEM-T Easy...

  8. Influence of filtration and glucose amendment on bacterial growth rate at different tidal conditions in the Minho Estuary River (NW Portugal)

    DEFF Research Database (Denmark)

    Anne, I.; Fidalgo, M. L.; Thosthrup, L.;

    2006-01-01

    Bacterioplankton abundance, biomass and growth rates were studied in the Minho Estuary River (NW Portugal). The influence of tidal conditions, glucose amendment, and the filtration process on total bacterial abundance, total and faecal coliforms, as well as faecal streptococci, were evaluated....... In contrast, a significant decrease of bacterial indicators of faecal pollution at high tide was probably the result of various causes, such as the decrease of continental and agriculturalland mn-off effect by dilution, aml/or increase in the abundance of potential specific predators. Thus, drastic changes...

  9. Role of nutrient recycling in upwelling ecosystems

    Energy Technology Data Exchange (ETDEWEB)

    Whitledge, T E

    1979-01-01

    The regeneration of nitrogen is an important process that increases the efficiency of the upwelling ecosystem by enlarging their spatial scales. Ammonium regeneration was considered to contribute 42 to 72 percent of phytoplankton nitrogen requirements in the northwest Africa, Peru, and Baja California upwelling systems. Zooplankton are responsible for the largest portion of regenerated nitrogen; however, fish and benthic sediments may be nearly as large. Comparisons of the importance of ammonium regeneration in upwelling areas with coastal and open ocean regions indicate that the percentage contributions are similar. Future nutrient regeneration studies are needed to assess the recycling of benthic sediments, microzooplankton, gelatinous zooplankton, demersal fish, bacterioplankton, and mollusks.

  10. Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea

    DEFF Research Database (Denmark)

    Carlson, Craig A; Morris, Robert; Parsons, Rachel

    2009-01-01

    Bacterioplankton belonging to the SAR11 clade of a-proteobacteria were counted by fluorescence in situ hybridization (FISH) over eight depths in the surface 300 m at the Bermuda Atlantic Time-series Study (BATS) site from 2003 to 2005. SAR11 are dominant heterotrophs in oligotrophic systems; thus...... correlated with seasonal mixing and stratification of the water column. Terminal restriction fragment length polymorphism (T-RFLP) data generated from a decade of samples collected at BATS were combined with the FISH data to model the annual dynamics of SAR11 subclade populations. 16S rRNA gene clone...

  11. Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton.

    Science.gov (United States)

    Stewart, Frank J

    2013-01-01

    High-throughput sequencing and analysis of microbial community cDNA (metatranscriptomics) are providing valuable insight into in situ microbial activity and metabolism in the oceans. A critical first step in metatranscriptomic studies is the preparation of high-quality cDNA. At the minimum, preparing cDNA for sequencing involves steps of biomass collection, RNA preservation, total RNA extraction, and cDNA synthesis. Each of these steps may present unique challenges for marine microbial samples, particularly for deep-sea samples whose transcriptional profiles may change between water collection and RNA preservation. Because bacterioplankton community RNA yields may be relatively low (microbiology research.

  12. Limited resolution of 16S rDNA DGGE caused by melting properties and closely related DNA sequences.

    Science.gov (United States)

    Kisand, Veljo; Wikner, Johan

    2003-08-01

    The phylogenetic affiliation of 91 operational taxonomic units, randomly sampled from three aquatic microcosm experiments, was investigated by two PCR based and one culture dependent method. The occurrence of multiple melting domains and poor coupling between Tm and DGGE retardation was demonstrated to cause poor resolution at the species level in PCR-DGGE analysis of microbial communities. We also showed that the problem of multiple melting domains was particularly prone for brackish water bacterioplankton in the Flavobacterium genus, providing characteristic band morphology for this genus. Banding patterns from DGGE analysis may therefore be misinterpreted in terms of the species richness in natural bacterial communities, when using commonly applied universal primers.

  13. Abundance of broad bacterial Taxa in the Sargasso Sea explained by environmental conditions but not water mass

    DEFF Research Database (Denmark)

    Sjöstedt, Johanna; Martiny, Jennifer Bellanca Hughes; Munk, Peter;

    2014-01-01

    of Synechococcus, Prochlorococcus, and picoalgae were determined by flow cytometry. Linear multiple-regression models determining the relative effects of eight environmental variables and of water mass explained 35 to 86% of the variation in abundance of the quantified taxa, even though only one to three variables......To explore the potential linkage between distribution of marine bacterioplankton groups, environmental conditions, and water mass, we investigated the factors determining the abundance of bacterial taxa across the hydrographically complex Subtropical Convergence Zone in the Sargasso Sea. Based...

  14. Overview of the US JGOFS Bermuda Atlantic Time-series Study (BATS): a decade-scale look at ocean biology and biogeochemistry

    Science.gov (United States)

    Steinberg, Deborah K.; Carlson, Craig A.; Bates, Nicholas R.; Johnson, Rodney J.; Michaels, Anthony F.; Knap, Anthony H.

    The Bermuda Atlantic Time-series Study (BATS) commenced monthly sampling in October 1988 as part of the US Joint Global Ocean Flux Study (JGOFS) program. The goals of the US JGOFS time-series research are to better understand the basic processes that control ocean biogeochemistry on seasonal to decadal time-scales, determine the role of the oceans in the global carbon budget, and ultimately improve our ability to predict the effects of climate change on ecosystems. The BATS program samples the ocean on a biweekly to monthly basis, a strategy that resolves major seasonal patterns and interannual variability. The core cruises last 4-5 d during which hydrography, nutrients, particle flux, pigments and primary production, bacterioplankton abundance and production, and often complementary ancillary measurements are made. This overview focuses on patterns in ocean biology and biogeochemistry over a decade at the BATS site, concentrating on seasonal and interannual changes in community structure, and the physical forcing and other factors controlling the temporal dynamics. Significant seasonal and interannual variability in phytoplankton and bacterioplankton production, biomass, and community structure exists at BATS. No strong relationship exists between primary production and particle flux during the 10 yr record, with the relationship slightly improved by applying an artificial lag of 1 week between production and flux. The prokaryotic picoplankton regularly dominate the phytoplankton community; diatom blooms are rare but occur periodically in the BATS time series. The increase in Chl a concentrations during bloom periods is due to increases by most of the taxa present, rather than by any single group, and there is seasonal succession of phytoplankton. The bacterioplankton often dominate the living biomass, indicating the potential to consume large amounts of carbon and play a major ecological role within the microbial food web. Bacterial biomass, production, and

  15. Metatranscriptomic and functional metagenomic analysis of methylphosphonate utilization by marine bacteria

    Directory of Open Access Journals (Sweden)

    Asuncion eMartinez

    2013-11-01

    Full Text Available Aerobic degradation of methylphosphonate (MPn by marine bacterioplankton has been hypothesized to contribute significantly to the ocean’s methane supersaturation, yet little is known about MPn utilization by marine microbes. To identify the microbial taxa and metabolic functions associated with MPn-driven methane production we performed parallel metagenomic, metatranscriptomic, and functional screening of microcosm perturbation experiments using surface water collected in North Pacific Subtropical Gyre. In nutrient amended microcosms containing MPn, a substrate-driven microbial succession occurred. Initially, the addition of glucose and nitrate resulted in a bloom of Vibrionales and a transcriptional profile dominated by glucose-specific PTS transport and polyhydroxyalkanoate biosynthesis. Transcripts associated with phosphorus (P acquisition were also overrepresented and suggested that the addition of glucose and nitrate had driven the community to P depletion. At this point, a second community shift occurred characterized by the increase in C-P lyase containing microbes of the Vibrionales and Rhodobacterales orders. Transcripts associated with C-P lyase components were among the most highly expressed at the community level, and only C-P lyase clusters were recovered in a functional screen for MPn utilization, consistent with this pathway being responsible for the majority, if not all the methane accumulation we observed. Our results identify specific bacterioplankton taxa that can utilize MPn aerobically under conditions of P limitation using the C-P lyase pathway, and thereby elicit a significant increase in the dissolved methane concentration.

  16. Nitrogen fixation in the Southern Ocean: a case of study of the Fe-fertilized Kerguelen region (KEOPS II cruise

    Directory of Open Access Journals (Sweden)

    M. L. González

    2014-12-01

    Full Text Available N2 fixation rates were measured during the KEOPS2 cruise in the HNLC area of Southern Ocean and in naturally iron-fertilized waters (Kerguelen Island 49.25° S, 69.58° E using the 15N isotopic technique. We detected N2 fixation within the mixed layer at all stations, from the surface to 140 m depth. The data shows high variability with rates ranging between 0.42 and 20.11 nmol N L−1 d−1. The highest rates were concentrated in the euphotic layer and maximum values were obtained north of polar front (station F-L, which coincide with a positive N* ([NO3]–16[PO4], high chlorophyll concentration and dissolved iron. N2 fixation rates were also obtained in stations with moderate (A3-2; E-4W and also low (R-2 iron levels as well as Chl a, suggesting that beside the microbial biomass, its composition/structure is a driving factor controlling N2 fixation activities. Molecular analysis showed a diazotrophic community dominated by heterotrophic bacterioplankton. Size fractioned experiments indicated that most of N2 fixating activities came from 2 fixation is occurring in the Southern Ocean, at rates exceeding previous reports for high latitudes. Our findings suggest an indirect role of dFe in the regulation of N2 fixation through the enhancement of regenerated primary production and the availability of phytoplankton-derived dissolved organic matter, which in turn may stimulate heterotrophic bacterioplankton.

  17. Heterotrophic bacteria of the Dapeng Bay in the South China Sea: community structure, abundance, and the relationships of culturablity with environmental factors

    Institute of Scientific and Technical Information of China (English)

    JIANG Fajun; HU Zhangli; HU Chaoqun

    2010-01-01

    The community composition,abundance and culturablity of heterotrophic bacterioplankton in the Dapeng Bay of the South China Sea were investigated by morphological method,bacterial cultivation and biochemical methods over an annual cycle.Aeromonas and Pseudomonas were the predominant genera among the Gram-negative bacteria.The bacterioplankton abundance fluctuated from 2.07×10s to 2.44×109 cells/dm3,and culturable bacteria abundance ranged between0.1×106 and 16.07×106 CFU/dm3.The Culturablity of heterotrophic bacteria ranged between0.01% and 1.31%.The relationship between bacterial culturablity and the environmental factors was also studied in different sites of the Dapeng Bay.Throughout the bay,a significantly positive relationship was evidenced between bacterial culturability and temperature,meanswhile bacterial culturability was significantly inversely related with salinity.The positive relationship was shown at the central bay while a negative relationship was observed at the bay mouth and there was no significant correlation at top bay between bacterial culturablity and chlorophyll a of sea water.A positive relationship was found between culturability and DIN all the bay,but DIP showed a significantly negative relationship with bacterial culturability only at the mouth of the bay.

  18. Drastic changes in aquatic bacterial populations from the Cuatro Cienegas Basin (Mexico) in response to long-term environmental stress.

    Science.gov (United States)

    Pajares, Silvia; Eguiarte, Luis E; Bonilla-Rosso, German; Souza, Valeria

    2013-12-01

    Understanding the changes of aquatic microbial community composition in response to changes in temperature and ultraviolet irradiation is relevant for predicting biogeochemical modifications in the functioning of natural microbial communities under global climate change scenarios. Herein we investigate shifts in the bacterioplankton composition in response to long-term changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with composite aquatic microbial communities from natural pools within the Cuatro Cienegas Basin (Mexican Chihuahuan desert) and were subject to different temperatures and UV conditions. 16S rRNA gene clone libraries were obtained from water samples at the mid-point (4 months) and the end of the experiment (8 months). An increase in bacterial diversity over time was found in the treatment of constant temperature and UV protection, which suggests that stable environments promote the establishment of complex and diverse bacterial community. Drastic changes in the phylogenetic bacterioplankton composition and structure were observed in response to fluctuating temperature and increasing UV radiation and temperature. Fluctuating temperature induced the largest decrease of bacterial richness during the experiment, indicating that frequent temperature changes drive the reduction in abundance of several species, most notably autotrophs. The long-term impact of these environmental stresses reduced diversity and selected for generalist aquatic bacterial populations, such as Porphyrobacter. These changes at the community level occur at an ecological time scale, suggesting that under global warming scenarios cascade effects on the food web are possible if the microbial diversity is modified.

  19. [Monitoring of the Moskva River Water Using Microbiological Parameters and Chlorophyll a Fluorescence].

    Science.gov (United States)

    Mosharova, I V; Il'inskii, V V; Matorin, D N; Mosharov, S A; Akulova, A Yu; Protopopov, F F

    2015-01-01

    The results of investigations of three Moskva River sites with different degree of pollution using a complex of microbiological characteristics and the parameters of chlorophyll a fluorescence are presented. We determined that the bacterioplankton seasonal dynamics at less polluted waters (Tushino and Vorobyovy Gory) were similar and differed significantly from one in more polluted waters (Dzerzhinskii). The number of bacteria with active electron transport chain, as well as their share in the bacterioplankton structure, was higher in the water of Dzerzhinskii (average annual values of 0.23 x 10(6) cells/mL and 14%), that in the less polluted water of Tushino and Vorobyovy Gory (0.14 x 10(6) cells/mL; 6% and 0.15 x 10(6) cells/mL; 7%, respectively). From April to October, the content of chlorophyll a and its photosynthetic activity were the highest in Tushino. In Dzerzhinskii, during spring the increase in photosynthetic activity commenced earlier and was more intensive that the increase in chlorophyll a content, i.e., the increase in phytoplankton biomass was temporarily suppressed. We suggest association of this phenomenon with suppression of organic matter synthesis by phytoplankton due to the high water pollution in Dzerzhinskii. The second autumn peak of chlorophyll a content, that was typical of clear water and was observed in Tushino, did not occur in Dzerzhinskii. We recommend combined application of these microbiological parameters and characteristics of chlorophyll a fluorescence for a monitoring.

  20. Bacterial survival governed by organic carbon release from senescent oceanic phytoplankton

    Directory of Open Access Journals (Sweden)

    S. Lasternas

    2013-10-01

    Full Text Available Bacteria recycle vast amounts of organic carbon, playing key biogeochemical and ecological roles in the ocean. Bacterioplankton dynamics are expected to be dependent on phytoplankton primary production, but there is a high diversity of processes (e.g. sloppy feeding, cell exudation, viral lysis involved in the transference of primary production to dissolved organic carbon available to bacteria. Here we show cell survival of heterotrophic bacterioplankton in the subtropical Atlantic Ocean to be determined by phytoplankton extracellular carbon release (PER. PER represents the fraction of primary production released as dissolved organic carbon, and changes in the PER variability was explained by phytoplankton cell death, with the communities experiencing the highest phytoplankton cell mortality showing a larger proportion of extracellular carbon release. Both PER and the percent of dead phytoplankton cells increased from eutrophic to oligotrophic waters, while heterotrophic bacteria communities, including 60 to 95% of living cells (%LC, increased from the productive to the most oligotrophic waters. The percentage of living heterotrophic bacterial cells increased with increasing phytoplankton extracellular carbon release, across oligotrophic to productive waters in the NE Atlantic, where lower PER have resulted in a decrease in the flux of phytoplankton DOC per bacterial cell. The results highlight phytoplankton cell death as a process influencing the flow of dissolved photosynthetic carbon in the NE Atlantic Ocean, and demonstrated a close coupling between the fraction of primary production released and heterotrophic bacteria survival.

  1. Virioplankton in the Kara Sea: The impact of viruses on mortality of heterotrophic bacteria

    Science.gov (United States)

    Kopylov, A. I.; Sazhin, A. F.; Zabotkina, E. A.; Romanova, N. D.

    2015-07-01

    Studies were conducted in shallow and deepwater areas of the Kara Sea. The abundance of bacteria ( N B ) and the abundance of viruses ( N V ) ranged within (19.4-2215.1) × 103 cells/ml and (97.6-5796.8) × 103 particles/ml, respectively. The virus to bacteria ratio varied from 1.4 to 29.1. A positive correlation was found between N B and N V ( R = 0.87, n = 45, p = 0.05. Using electron transmission microscopy it was detected that the frequency of visibly infected cells of bacteria (FVIC) varied from 0.2 to 1.9% of N B . The maximum values of FVIC were recorded in the estuary of the Yenisei River. The infected cells of bacteria contained from 4 to 127 (an average of 12) phages/cell of mature viruses. Virus-mediated mortality of bacteria was 0.5% and varied from 1.4 to 16.1% of the total mortality of bacterioplankton. This indicates a minor role of viruses in the control of overabundance and production of bacterioplankton in the Kara Sea during the surveyed period.

  2. Viruses, bacteria, and heterotrophic nanoflagellates in Laptev Sea plankton

    Science.gov (United States)

    Kopylov, A. I.; Sazhin, A. F.; Zabotkina, E. A.; Romanenko, A. V.; Romanova, N. D.; Makarevich, P. R.; Wenger, M. P.

    2016-11-01

    The paper considers the concentrations and functional characteristics of viruses, bacteria, and heterotrophic nanoflagellates determined for the first time in the Laptev Sea in August-September, 2014. The abundance of bacteria, viruses, and heterotrophic nanoflagellates varied from 110.1 × 103 to 828.4 × 103 cells/mL, from 384.2 × 103 to 2932.8 × 103 particles/mL, and from 108 to 651 cells/mL, respectively. The daily bacterioplankton production varied from 4.2 × 103 to 381.7 × 103 cells/mL, with an average of 117.6 × 103 cells/mL. Electron transmission microscopy has for the first time shown that the frequency of visibly infected bacterial cells varied from 0.2 to 2.0% (0.8% on average) of NB. The average virus-induced mortality of bacteria was 6.3% of bacterioplankton production, with variations ranging from 1.4 to 16.9%. Grazing on bacteria by heterotrophic nanoflagellates contributed more to bacteria mortality than virus-induced bacterial lysis. By grazing on bacteria, heterotrophic nanoflagellates consumed large quantities of viruses located on the surface and inside bacterial cells.

  3. Direct and indirect evidence of size-selective grazing on pelagic bacteria by freshwater nanoflagellates.

    Science.gov (United States)

    Simek, K; Chrzanowski, T H

    1992-11-01

    Size-selective grazing of three heterotrophic nanoflagellates (with cell sizes of 21, 44, and 66 mum) isolated from Lake Arlington, Texas was examined by using a natural mixture of fluorescence labelled lake bacteria. Sizes of ingested bacteria in food vacuoles were directly measured. Larger bacterial cells were ingested at a frequency much higher than that at which they occurred in the assemblage, indicating preferential flagellate grazing on the larger size classes within the lake bacterioplankton. Water samples were collected biweekly from June through September, 1989, fractionated by filtration, and incubated for 40 h at in situ temperatures. The average bacterial size was always larger in water which was passed through 1-mum-pore-size filters (1-mum-filtered water) (which was predator free) than in 5-mum-filtered water (which contained flagellates only) or in unfiltered water (in which all bacterivores were present). The increase of bacterial-cell size in 1-mum-filtered water was caused by a shift in the size structure of the bacterioplankton population. Larger cells became more abundant in the absence of flagellate grazing.

  4. Experimental manipulations of microbial food web interactions in a humic lake: shifting biological drivers of bacterial community structure.

    Science.gov (United States)

    Kent, Angela D; Jones, Stuart E; Lauster, George H; Graham, James M; Newton, Ryan J; McMahon, Katherine D

    2006-08-01

    A previous multiyear study observed correlations between bacterioplankton community composition (BCC) and abundance and the dynamics of phytoplankton populations and bacterivorous grazers in a humic lake. These observations generated hypotheses about the importance of trophic interactions (both top-down and bottom-up) for structuring bacterial communities in this lake, which were tested using two multifactorial food web manipulation experiments that separately manipulated the intensity of grazing and the composition of the phytoplankton community. Our results, combined with field observations, suggest that a hierarchy of drivers structures bacterial communities in this lake. While other studies have noted links between aggregate measures of phytoplankton and bacterioplankton communities, we demonstrate here correlations between succession of phytoplankton assemblages and BCC as assessed by automated ribosomal intergenic spacer analysis (ARISA). We used a novel approach linking community ARISA data to phylogenetic assignments from sequence analysis of 16S rRNA gene clone libraries to examine the responses of specific bacterial phylotypes to the experimental manipulations. The synchronous dynamics of these populations suggests that primary producers may mediate BCC and diversity through labile organic matter production, which evolves in quality and quantity during phytoplankton succession. Superimposed on this resource-mediated control of BCC are brief periods of intense bacterivory that impact bacterial abundance and composition.

  5. Distribution and relation of total bacteria, active bacteria, bacterivory, and volume of organic detritus in Atlantic continental shelf waters off Cape Hatteras NC, USA

    Science.gov (United States)

    Sherr, Evelyn B.; Sherr, Barry F.; Verity, Peter G.

    During the Ocean Margins Program, we obtained data on the abundances of bacterioplankton and heterotrophic flagellates, and on rates of bacterivory, across the mid-Atlantic continental shelf off Cape Hatteras, NC, during four spring and summer cruises from 1993 to 1996. Bacterial and grazing parameters were compared for inner, middle, and outer shelf regions. In 1996, we sampled during two seasons: early spring (March) and mid-summer (July), and in addition determined the fractions of in situ bacterioplankton that had visible nucleoids (NV cells), or that had highly active electron transport systems (ETS), i.e. that were positive for reduction of the fluorogenic formazan compound, 5 cyano-2,3 ditolyl tetrazolium chloride (CTC+ cells), as well as the volumetric concentration of organic detrital particles. Detrital volumes and abundances of bacterioplankton and of heterotrophic flagellates, varied by an order of magnitude, and decreased from inshore to offshore shelf regions. In 1996, bacterial abundances and percentages of CTC+ cells were higher across the shelf during the early spring bloom season (March) compared to the post-bloom season (July). In March 1996, percentages of bacterial cells with visible nucleoids varied between 20% and 70%, but showed little change across the shelf; while fractions of total bacteria with highly active ETS were lower and more variable (1-16% CTC+ cells), and on average were twice as high in the inner shelf region compared to the rest of the shelf. Percentages of CTC+ cells were also higher for particle-associated bacteria. There was a strong positive relationship between percent CTC+ cells and volume of organic detrital particles. However, % CTC+ cells and detrital volume were not consistently related to either bulk particulate organic carbon or chlorophyll. Bacterivory, assessed via rate of ingestion of fluorescently labeled bacteria, could remove 2-9% (4-18% accounting for motile cells) of total bacterial stocks per day. If

  6. Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation.

    Directory of Open Access Journals (Sweden)

    Laura Gómez-Consarnau

    Full Text Available Proteorhodopsins are globally abundant photoproteins found in bacteria in the photic zone of the ocean. Although their function as proton pumps with energy-yielding potential has been demonstrated, the ecological role of proteorhodopsins remains largely unexplored. Here, we report the presence and function of proteorhodopsin in a member of the widespread genus Vibrio, uncovered through whole-genome analysis. Phylogenetic analysis suggests that the Vibrio strain AND4 obtained proteorhodopsin through lateral gene transfer, which could have modified the ecology of this marine bacterium. We demonstrate an increased long-term survival of AND4 when starved in seawater exposed to light rather than held in darkness. Furthermore, mutational analysis provides the first direct evidence, to our knowledge, linking the proteorhodopsin gene and its biological function in marine bacteria. Thus, proteorhodopsin phototrophy confers a fitness advantage to marine bacteria, representing a novel mechanism for bacterioplankton to endure frequent periods of resource deprivation at the ocean's surface.

  7. COUPLED PHYSICAL-ECOLOGICAL MODELLING IN THE CENTRAL PART OF JIAOZHOU BAY Ⅱ. COUPLED WITH AN ECOLOGICAL MODEL

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Sharples' 1-D physical model employing tide-wind driven turbulence closure and surface heating-cooling physics, was coupled with an ecological model with 9-biochemical components: phytoplankton, zooplankton, shellfish, autotrophic and heterotrophic bacterioplankton, dissolved organic carbon (DOC), suspended detritus and sinking particles to simulate the annual evolution of ecosystem in the central part of Jiaozhou Bay. The coupled modeling results showed that the phytoplankton shading effect could reduce seawater temperature by 2℃, so that photosynthesis efficiency should be less than 8%; that the loss of phytoplankton by zooplankton grazing in winter tended to be compensated by phytoplankton advection and diffusion from the outside of the Bay; that the incident irradiance intensity could be the most important factor for phytoplankton growth rate; and that it was the bacterial secondary production that maintained the maximum zooplankton biomass in winter usually observed in the 1990s, indicating that the microbial food loop was extremely important for ecosystem study of Jiaozhou Bay.

  8. Mixotrophy in the Marine Plankton

    Science.gov (United States)

    Stoecker, Diane K.; Hansen, Per Juel; Caron, David A.; Mitra, Aditee

    2017-01-01

    Mixotrophs are important components of the bacterioplankton, phytoplankton, microzooplankton, and (sometimes) zooplankton in coastal and oceanic waters. Bacterivory among the phytoplankton may be important for alleviating inorganic nutrient stress and may increase primary production in oligotrophic waters. Mixotrophic phytoflagellates and dinoflagellates are often dominant components of the plankton during seasonal stratification. Many of the microzooplankton grazers, including ciliates and Rhizaria, are mixotrophic owing to their retention of functional algal organelles or maintenance of algal endosymbionts. Phototrophy among the microzooplankton may increase gross growth efficiency and carbon transfer through the microzooplankton to higher trophic levels. Characteristic assemblages of mixotrophs are associated with warm, temperate, and cold seas and with stratification, fronts, and upwelling zones. Modeling has indicated that mixotrophy has a profound impact on marine planktonic ecosystems and may enhance primary production, biomass transfer to higher trophic levels, and the functioning of the biological carbon pump.

  9. Quick stimulation of Alcanivorax sp. by bioemulsificant EPS₂₀₀₃ on microcosm oil spill simulation.

    Science.gov (United States)

    Cappello, Simone; Genovese, Maria; Denaro, Renata; Santisi, Santina; Volta, Anna; Bonsignore, Martina; Mancini, Giuseppe; Giuliano, Laura; Genovese, Lucrezia; Yakimov, Michail M

    2014-01-01

    Oil spill microcosms experiments were carried out to evaluate the effect of bioemulsificant exopolysaccharide (EPS₂₀₀₃) on quick stimulation of hydrocarbonoclastic bacteria. Early hours of oil spill, were stimulated using an experimental seawater microcosm, supplemented with crude oil and EPS₂₀₀₃ (SW+OIL+EPS₂₀₀₃); this system was monitored for 2 days and compared to control microcosm (only oil-polluted seawater, SW+OIL). Determination of bacterial abundance, heterotrophic cultivable and hydrocarbon-degrading bacteria were carried out. Community composition of marine bacterioplankton was determined by 16S rRNA gene clone libraries. Data obtained indicated that bioemulsificant addition stimulated an increase of total bacterial abundance and, in particular, selection of bacteria related to Alcanivorax genus; confirming that EPS₂₀₀₃ could be used for the dispersion of oil slicks and could stimulate the selection of marine hydrocarbon degraders thus increasing bioremediation process.

  10. The vertical distribution of the fluorescence of the photosynthetic pigments in Kaliningrad Bay of the Baltic Sea

    Science.gov (United States)

    Solov'yev, A. N.

    2010-12-01

    The annual (2004-2006) series of probing using a multichannel filter-fluorimeter from the water's surface to the bottom at fixed sites in Kaliningrad Bay and the adjacent areas were carried out. The following parameters were recorded: the water turbidity and temperature, the intensity of the fluorescence of the photosynthetic pigment (excitation at 450 nm, detection band 675-820 nm), and the intensity of the background fluorescence of the dissolved organic matter. The high levels of "red fluorescence" presumably related to the presence of photosynthetic bacterioplankton, live phytoplankton, or their mixture (which demands further biological identification) annually registered in the aphotic zone of the water column represent specific feature of the obtained data.

  11. Quick stimulation of Alcanivorax sp. by bioemulsificant EPS2003 on microcosm oil spill simulation

    Directory of Open Access Journals (Sweden)

    Simone Cappello

    2014-12-01

    Full Text Available Oil spill microcosms experiments were carried out to evaluate the effect of bioemulsificant exopolysaccharide (EPS2003 on quick stimulation of hydrocarbonoclastic bacteria. Early hours of oil spill, were stimulated using an experimental seawater microcosm, supplemented with crude oil and EPS2003 (SW+OIL+EPS2003; this system was monitored for 2 days and compared to control microcosm (only oil-polluted seawater, SW+OIL. Determination of bacterial abundance, heterotrophic cultivable and hydrocarbon-degrading bacteria were carried out. Community composition of marine bacterioplankton was determined by 16S rRNA gene clone libraries. Data obtained indicated that bioemulsificant addition stimulated an increase of total bacterial abundance and, in particular, selection of bacteria related to Alcanivorax genus; confirming that EPS2003 could be used for the dispersion of oil slicks and could stimulate the selection of marine hydrocarbon degraders thus increasing bioremediation process.

  12. Phylogenetic relationship and phenotypic comparison of Psychrobacter species isolated from polar oceans

    Institute of Scientific and Technical Information of China (English)

    ZENG Yinxin; LI Huirong; YU Yong; CHEN Bo

    2007-01-01

    To investigate the phylogenetic relationship and biogeography of bacterioplankton in polar oceans, four Psychrobacter strains, BSw10170, BSw20352, BSw20370, and BSw20461, isolated from seawater of the Bering Sea, the Chukchi Sea, and the Prydz Bay, were characterized by 16S rDNA sequencing and physiological and biochemical testing. Results demonstrated that close relationships existed between the Arctic and Antarctic strains with sequence similarities higher than 97%. These four Psychrobacter strains not only showed almost identical phenotypic characteristics among them, but also shared a lot of similarities with those related Psychrobacter species, indicating that psychrotolerance and halotolerance of Psychrobacter strains may be among the reasons for their bipolar, even global distribution in marine environments at the genus level.

  13. Heterotrophic bacterial responses to the winter–spring phytoplankton bloom in open waters of the NW Mediterranean

    KAUST Repository

    Gomes, Ana

    2014-12-03

    The response of planktonic heterotrophic prokaryotes to the NW Mediterranean winter–spring offshore phytoplankton bloom was assessed in 3 cruises conducted in March, April–May and September 2009. Bulk measurements of phytoplankton and bacterioplankton biomass and production were complemented with an insight into bacterial physiological structure by single-cell analysis of nucleic acid content [low (LNA) vs. high (HNA)] and membrane integrity (“Live” vs. “Dead” cells). Bacterial production empirical conversion factors (0.82±0.25 SE kg C mol leucine−1) were almost always well below the theoretical value. Major differences in most microbial variables were found among the 3 periods, which varied from extremely high phytoplankton biomass and production during the bloom in March (>1 g C m−2 d−1 primary production) to typically oligotrophic conditions during September stratification (<200 mg C m−2 d−1). In both these periods bacterial production was ~30 mg C m−2 d−1 while very large bacterial production (mean 228, with some stations exceeding 500 mg C m−2 d−1) but low biomass was observed during the April–May post-bloom phase. The contribution of HNA (30–67%) and “Live” cells (47–97%) were temporally opposite in the study periods, with maxima in March and September, respectively. Different relationships were found between physiological structure and bottom-up variables, with HNA bacteria apparently more responsive to phytoplankton only during the bloom, coinciding with larger average cell sizes of LNA bacteria. Moderate phytoplankton–bacterioplankton coupling of biomass and activity was only observed in the bloom and post-bloom phases, while relationships between both compartments were not significant under stratification. With all data pooled, bacteria were only weakly bottom-up controlled. Our analyses show that the biomass and production of planktonic algae and bacteria followed opposite paths in the transition from bloom to

  14. Impact of multiple anthropogenic stressors on freshwater: how do glyphosate and the invasive mussel Limnoperna fortunei affect microbial communities and water quality?

    Science.gov (United States)

    Pizarro, Haydée; Di Fiori, Eugenia; Sinistro, Rodrigo; Ramírez, Marina; Rodríguez, Patricia; Vinocur, Alicia; Cataldo, Daniel

    2016-01-01

    The study of the joint effect of multiple anthropogenic stressors is important because the emerging consequences are often unpredictable on the basis of knowledge of single effects. We explored the joint impact of glyphosate and the invasive golden mussel Limnoperna fortunei on freshwater phytoplankton, bacterioplankton and periphyton, and on the physical and chemical properties of the water. We manipulated both stressors simultaneously in a 25-day experiment using outdoor mesocosms; we assayed technical-grade glyphosate acid at four concentrations: 0, 1, 3 and 6 mg gly L(−1) under scenarios with and without mussels. The addition of the glyphosate significantly increased total phosphorus according to the concentration used; the high clearance rate of L. fortunei significantly decreased phytoplanktonic abundance leading to low values of turbidity. The mussel significantly stimulated the development of filamentous green algae (metaphyton). Interestingly, the combined effect revealed that L. fortunei accelerated the dissipation of glyphosate, which showed a 4-fold decrease in its half-life; this promoted the rapid bioavailability of glyphosate-derived phosphorus in the water. The interaction had a synergistic effect on soluble reactive phosphorus concentrations and was directly dependent on the concentration of glyphosate. A synergistic effect was also observed on bacterioplankton, water turbidity and metaphyton, thus inducing enhanced and rapid eutrophication. The ability of mussels to reduce glyphosate in water may be valued as positive, but our results allow us to predict that the invasion of Limnoperna fortunei in natural freshwater systems contaminated by glyphosate will accelerate the negative impact of the herbicide associated with eutrophication.

  15. Direct and indirect effects of the glyphosate formulation Glifosato Atanor® on freshwater microbial communities.

    Science.gov (United States)

    Vera, María Solange; Di Fiori, Eugenia; Lagomarsino, Leonardo; Sinistro, Rodrigo; Escaray, Roberto; Iummato, María Mercedes; Juárez, Angela; Ríos de Molina, María del Carmen; Tell, Guillermo; Pizarro, Haydée

    2012-10-01

    Glyphosate-based formulations are among the most widely used herbicides in the world. The effect of the formulation Glifosato Atanor(®) on freshwater microbial communities (phytoplankton, bacterioplankton, periphyton and zooplankton) was assessed through a manipulative experiment using six small outdoor microcosms of small volume. Three of the microcosms were added with 3.5 mg l(-1) of glyphosate whereas the other three were left as controls without the herbicide. The treated microcosms showed a significant increase in total phosphorus, not fully explained by the glyphosate present in the Glifosato Atanor(®). Therefore, part of the phosphorus should have come from the surfactants of the formulation. The results showed significant direct and indirect effects of Glifosato Atanor(®) on the microbial communities. A single application of the herbicide caused a fast increase both in the abundance of bacterioplankton and planktonic picocyanobacteria and in chlorophyll a concentration in the water column. Although metabolic alterations related to oxidative stress were induced in the periphyton community, the herbicide favored its development, with a large contribution of filamentous algae typical of nutrient-rich systems, with shallow and calm waters. An indirect effect of the herbicide on the zooplankton was observed due to the increase in the abundance of the rotifer Lecane spp. as a consequence of the improved food availability given by picocyanobacteria and bacteria. The formulation affected directly a fraction of copepods as a target. It was concluded that the Glifosato Atanor(®) accelerates the deterioration of the water quality, especially when considering small-volume water systems.

  16. Carbon dynamics in highly heterotrophic subarctic thaw ponds

    Directory of Open Access Journals (Sweden)

    T. Roiha

    2015-07-01

    Full Text Available Global warming has accelerated the formation of permafrost thaw ponds in several subarctic and arctic regions. These ponds are net heterotrophic as evidenced by their greenhouse gas (GHG supersaturation levels (CO2 and CH4, and generally receive large terrestrial carbon inputs from the thawing and eroding permafrost. We measured seasonal and vertical variations in the concentration and type of dissolved organic matter (DOM in five subarctic thaw (thermokarst ponds in northern Quebec, and explored how environmental gradients influenced heterotrophic and phototrophic biomass and productivity. Late winter DOM had low aromaticity indicating reduced inputs of terrestrial carbon, while the high concentration of dissolved organic carbon (DOC suggests that some production of non-chromophoric dissolved compounds by the microbial food web took place under the ice cover. Summer DOM had a strong terrestrial signature, but was also characterized with significant inputs of algal-derived carbon, especially at the pond surface. During late winter, bacterial production was low (maximum of 0.8 mg C m−3 d−1 and was largely based on free-living bacterioplankton (58 %. Bacterial production in summer was high (up to 58 mg C m−3 d−1, dominated by particle-attached bacteria (67 %, and strongly correlated to the amount of terrestrial carbon. Primary production was restricted to summer surface waters due to strong light limitation deeper in the water column or in winter. The phototrophic biomass was equal to the heterotrophic biomass, but as the algae were mostly composed of mixotrophic species, most probably they used bacteria rather than solar energy in such shaded ponds. According to the δ13C analyses, non-algal carbon supported 51 % of winter and 37 % of summer biomass of the phantom midge larvae, Chaoborus sp., that are at the top of the trophic chain. Our results point to a strong heterotrophic energy pathway in these thaw pond ecosystems, where

  17. Carbon dynamics in highly heterotrophic subarctic thaw ponds

    Science.gov (United States)

    Roiha, T.; Laurion, I.; Rautio, M.

    2015-12-01

    Global warming has accelerated the formation of permafrost thaw ponds in several subarctic and arctic regions. These ponds are net heterotrophic as evidenced by their greenhouse gas (GHG) supersaturation levels (CO2 and CH4), and generally receive large terrestrial carbon inputs from the thawing and eroding permafrost. We measured seasonal and vertical variations in the concentration and type of dissolved organic matter (DOM) in five subarctic thaw (thermokarst) ponds in northern Quebec, and explored how environmental gradients influenced heterotrophic and phototrophic biomass and productivity. Late winter DOM had low aromaticity indicating reduced inputs of terrestrial carbon, while the high concentration of dissolved organic carbon (DOC) suggests that some production of non-chromophoric dissolved compounds by the microbial food web took place under the ice cover. Summer DOM had a strong terrestrial signature, but was also characterized with significant inputs of algal-derived carbon, especially at the pond surface. During late winter, bacterial production was low (maximum of 0.8 mg C m-3 d-1) and was largely based on free-living bacterioplankton (58 %). Bacterial production in summer was high (up to 58 mg C m-3 d-1), dominated by particle-attached bacteria (67 %), and strongly correlated with the amount of terrestrial carbon. Primary production was restricted to summer surface waters due to strong light limitation deeper in the water column or in winter. The phototrophic biomass was equal to the heterotrophic biomass, but as the algae were mostly composed of mixotrophic species, most probably they used bacteria rather than solar energy in such shaded ponds. Our results point to a strong heterotrophic energy pathway in these thaw pond ecosystems, where bacterioplankton dominates the production of new carbon biomass in both summer and winter.

  18. Limno-chemical and microbiology aspects in Uranium Pit Mine Lake (Osamu Utsumi), in Antas and Bortolan reservoirs under the influence of effluent Ore Treatment Unit, Caldas - Minas Gerais State, Brazil

    Energy Technology Data Exchange (ETDEWEB)

    Ronqui, Leilane B.; Nasciment, Marcos R.L. do; Roque, Claudio V.; Bruschi, Armando; Borba Junior, Palvo J.; Nascimento, Heliana A. F. do, E-mail: leilanebio@yahoo.com.br, E-mail: pmarcos@cnen.gov.br, E-mail: cvroque@cnen.gov.br, E-mail: abruschi@cnen.gov.br, E-mail: jouber_borba@hotmail.com, E-mail: hazevedo@cnen.gov.br [Comissao Nacional de Energia Nuclear (LAPOC/CNEN), Pocos de Caldas, MG (Brazil). Laboratorio de Pocos de Caldas; Almeida, Tito C.M. de, E-mail: titoalmeida2008@gmail.com [Universidade do Vale do Itajai (CTT-Mar/UNIVALI), SC (Brazil). Centro de Ciencias Tecnologicas da Terra e do Mar

    2013-07-01

    Due to high natural radioactivity there in Pocos de Caldas Plateau (Minas Gerais State, Brazil) and the existence of the first uranium mine in Brazil (Pit Mine Osamu Utsumi - Mineral Treatment Unit/Brazilian Nuclear Industries, MTU/BNI), which is characterized by an open-pit mine presents as increased environmental liability the formation of acid mine drainage, this study was conducted to evaluate the limno-chemicals and microbiology aspects (protozooplankton and bacterioplankton) belonging to uranium pit mine lake (PM) and evaluate the possible effects of acid effluents treated and discharged by MTU/BNI in Antas reservoir-AR and downstream of this, the Bortolan reservoir-BR. Besides the realization of abiotic and microbiology analysis of protozooplankton and bacterioplankton; was held standardization and deployment of the Fluorescence 'In Situ' Hybridization (FISH) technical using oligonucleotide probes for extremophile Archaea and Bacteria. According to the results, the PM showed the highest values for the chemical variables, lower pH values, lower protozooplankton density, however, protozooplanktonic high biomass showing the presence of tolerant species in this extreme environment. Antas and Bortolan reservoirs showed differences in the abiotic and biotic variables, AR showed suffer greater interference of acid effluents released at P41point and downstream of this at P14 point, lower protozooplankton biomass, lower bacterial density and pollution characteristics of inorganic sources. Using the FISH technique standard in this study to water bodies evaluated, it was possible to detect the presence of the extremophile bacteria of the Archaea domain in the three water bodies. The results of this study contribute to the knowledge of the pit mine lakes limnology which have become a major concern due to increased mining in the open. (author)

  19. More, smaller bacteria in response to ocean's warming?

    KAUST Repository

    Moran, Xose Anxelu G.

    2015-06-10

    Heterotrophic bacteria play a major role in organic matter cycling in the ocean. Although the high abundances and relatively fast growth rates of coastal surface bacterioplankton make them suitable sentinels of global change, past analyses have largely overlooked this functional group. Here, time series analysis of a decade of monthly observations in temperate Atlantic coastal waters revealed strong seasonal patterns in the abundance, size and biomass of the ubiquitous flow-cytometric groups of low (LNA) and high nucleic acid (HNA) content bacteria. Over this relatively short period, we also found that bacterioplankton cells were significantly smaller, a trend that is consistent with the hypothesized temperature-driven decrease in body size. Although decadal cell shrinking was observed for both groups, it was only LNA cells that were strongly coherent, with ecological theories linking temperature, abundance and individual size on both the seasonal and interannual scale. We explain this finding because, relative to their HNA counterparts, marine LNA bacteria are less diverse, dominated by members of the SAR11 clade. Temperature manipulation experiments in 2012 confirmed a direct effect of warming on bacterial size. Concurrent with rising temperatures in spring, significant decadal trends of increasing standing stocks (3% per year) accompanied by decreasing mean cell size (-1% per year) suggest a major shift in community structure, with a larger contribution of LNA bacteria to total biomass. The increasing prevalence of these typically oligotrophic taxa may severely impact marine foodwebs and carbon fluxes by an overall decrease in the efficiency of the biological pump. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  20. Potential changes in bacterial metabolism associated with increased water temperature and nutrient inputs in tropical humic lagoons.

    Science.gov (United States)

    Scofield, Vinicius; Jacques, Saulo M S; Guimarães, Jean R D; Farjalla, Vinicius F

    2015-01-01

    Temperature and nutrient concentrations regulate aquatic bacterial metabolism. However, few studies have focused on the effect of the interaction between these factors on bacterial processes, and none have been performed in tropical aquatic ecosystems. We analyzed the main and interactive effects of changes in water temperature and N and P concentrations on bacterioplankton production (BP), bacterioplankton respiration (BR) and bacterial growth efficiency (BGE) in tropical coastal lagoons. We used a factorial design with three levels of water temperature (25, 30, and 35°C) and four levels of N and/or P additions (Control, N, P, and NP additions) in five tropical humic lagoons. When data for all lagoons were pooled together, a weak interaction was observed between the increase in water temperature and the addition of nutrients. Water temperature alone had the greatest impact on bacterial metabolism by increasing BR, decreasing BP, and decreasing BGE. An increase of 1°C lead to an increase of ~4% in BR, a decrease of ~0.9% in BP, and a decrease of ~4% in BGE. When data were analyzed separately, lagoons responded differently to nutrient additions depending on Dissolved Organic Carbon (DOC) concentration. Lagoons with lowest DOC concentrations showed the strongest responses to nutrient additions: BP increased in response to N, P, and their interaction, BR increased in response to N and the interaction between N and P, and BGE was negatively affected, mainly by the interaction between N and P additions. Lagoons with the highest DOC concentrations showed almost no significant relationship with nutrient additions. Taken together, these results show that different environmental drivers impact bacterial processes at different scales. Changes of bacterial metabolism related to the increase of water temperature are consistent between lagoons, therefore their consequences can be predicted at a regional scale, while the effect of nutrient inputs is specific to different

  1. Strong seasonal effect of moderate experimental warming on plankton respiration in a temperate estuarine plankton community

    Science.gov (United States)

    Panigrahi, Satya; Nydahl, Anna; Anton, Peter; Wikner, Johan

    2013-12-01

    Climate change projections forecast a 1.1-6.4 °C global increase in surface water temperature and a 3 °C increase for the Baltic Sea. This study examined the short-term interactive effects of a realistic future temperature increase (3 °C) on pelagic respiration and bacterioplankton growth and phytoplankton photosynthesis in situ. This study was undertaken throughout a full seasonal cycle in the northern Baltic Sea. We found marked positive short-term effects of temperature on plankton respiration but no significant effect on bacterioplankton growth or phytoplankton photosynthesis. Absolute respiration rates remained similar to other comparable environments at the in situ temperature. With the 3 °C temperature increase, respiration rates in situ increased up to 5-fold during the winter and 2-fold during the summer. A maximum seasonal Q10 value of 332 was observed for respiration during the cold winter months (twater ≈ 0 °C), and summer Q10 values were comparatively high (9.1). Q10 values exhibited a significant inverse relationship to water temperature during winter. Our results thereby suggest that plankton respiration in this coastal zone is more temperature sensitive than previously reported. In addition, field data indicated that plankton respiration switched from being temperature limited to being limited by dissolved organic carbon (DOC) after the simulated temperature increase. Assuming that our observations are relevant over longer time scales, climate change may worsen hypoxia, increase CO2 emissions and create a more heterotrophic food web in coastal zones with a high load of riverine DOC.

  2. Jellyfish blooms result in a major microbial respiratory sink of carbon in marine systems.

    Science.gov (United States)

    Condon, Robert H; Steinberg, Deborah K; del Giorgio, Paul A; Bouvier, Thierry C; Bronk, Deborah A; Graham, William M; Ducklow, Hugh W

    2011-06-21

    Jellyfish blooms occur in many estuarine and coastal regions and may be increasing in their magnitude and extent worldwide. Voracious jellyfish predation impacts food webs by converting large quantities of carbon (C), fixed by primary producers and consumed by secondary producers, into gelatinous biomass, which restricts C transfer to higher trophic levels because jellyfish are not readily consumed by other predators. In addition, jellyfish release colloidal and dissolved organic matter (jelly-DOM), and could further influence the functioning of coastal systems by altering microbial nutrient and DOM pathways, yet the links between jellyfish and bacterioplankton metabolism and community structure are unknown. Here we report that jellyfish released substantial quantities of extremely labile C-rich DOM, relative to nitrogen (25.6 ± 31.6 C:1N), which was quickly metabolized by bacterioplankton at uptake rates two to six times that of bulk DOM pools. When jelly-DOM was consumed it was shunted toward bacterial respiration rather than production, significantly reducing bacterial growth efficiencies by 10% to 15%. Jelly-DOM also favored the rapid growth and dominance of specific bacterial phylogenetic groups (primarily γ-proteobacteria) that were rare in ambient waters, implying that jelly-DOM was channeled through a small component of the in situ microbial assemblage and thus induced large changes in community composition. Our findings suggest major shifts in microbial structure and function associated with jellyfish blooms, and a large detour of C toward bacterial CO(2) production and away from higher trophic levels. These results further suggest fundamental transformations in the biogeochemical functioning and biological structure of food webs associated with jellyfish blooms.

  3. The passive yet successful way of planktonic life: genomic and experimental analysis of the ecology of a free-living polynucleobacter population.

    Directory of Open Access Journals (Sweden)

    Martin W Hahn

    Full Text Available The bacterial taxon Polynucleobacter necessarius subspecies asymbioticus represents a group of planktonic freshwater bacteria with cosmopolitan and ubiquitous distribution in standing freshwater habitats. These bacteria comprise <1% to 70% (on average about 20% of total bacterioplankton cells in various freshwater habitats. The ubiquity of this taxon was recently explained by intra-taxon ecological diversification, i.e. specialization of lineages to specific environmental conditions; however, details on specific adaptations are not known. Here we investigated by means of genomic and experimental analyses the ecological adaptation of a persistent population dwelling in a small acidic pond.The investigated population (F10 lineage contributed on average 11% to total bacterioplankton in the pond during the vegetation periods (ice-free period, usually May to November. Only a low degree of genetic diversification of the population could be revealed. These bacteria are characterized by a small genome size (2.1 Mb, a relatively small number of genes involved in transduction of environmental signals, and the lack of motility and quorum sensing. Experiments indicated that these bacteria live as chemoorganotrophs by mainly utilizing low-molecular-weight substrates derived from photooxidation of humic substances.Evolutionary genome streamlining resulted in a highly passive lifestyle so far only known among free-living bacteria from pelagic marine taxa dwelling in environmentally stable nutrient-poor off-shore systems. Surprisingly, such a lifestyle is also successful in a highly dynamic and nutrient-richer environment such as the water column of the investigated pond, which was undergoing complete mixis and pronounced stratification in diurnal cycles. Obviously, metabolic and ecological versatility is not a prerequisite for long-lasting establishment of abundant bacterial populations under highly dynamic environmental conditions. Caution should be exercised

  4. ASSESSMENT OF THE DEVELOPMЕNT OF POND FORAGE BASE WHEN REARING CARP (CYPRINUS CARPIO CARPIO FISH SEEDS AT FISH FARM «MERKURIY»

    Directory of Open Access Journals (Sweden)

    B. Grishin

    2015-09-01

    Full Text Available Purpose. To assess the development of main components of natural forage base in nursery ponds during the period of rearing the carp fish seeds in monoculture. Methodology. Hydrobiological (bacterioplankton, phytoplankton, zooplankton, zoobenthos and hydrochemical samples have been collected and processes according to generally accepted methods. Findings. Qualitative and quantitative parameters of the development of bacterio-, phyto-, zooplankton and zoobenthos in nursery ponds have been studied when rearing young-of-the-year Lubin few scale carp, Antoninsko-Zozulenets carp and their reciprocal crosses in monoculture (50 thousand fish/ha. General water mineralization in ponds was 292.7–315.7 mg/dm3 and according to O.A. Alekin’s classification, pond water belonged to hydrocarbonate class of calcium group. Water pH was 7.4–7.5. Permanganate values were 12.5–14.9 mgO/dm3. On average, average ammonium nitrogen content, nitrite nitrogen and nitrate nitrogen, mineral phosphorus, total iron did not exceed normative values. Qualitative and quantitative parameters of phyto-, bacterio-, zooplankton of nursery ponds have been studied. The seasonal development of phytoplankton was within 15.96–20.88 mg/dm3 with the predominance of Chlorococcales in the floristic spectrum. The development of bacterioplankton was within 5.08–5.81 mg/dm3. Zooplankton was dominated by cladoceran-copepod complex with average seasonal values of 5.27–17.20 g/m3. Zoobenthos was formed of Diptera larvae (Chironomidae and Chaoboridae with average seasonal biomasses of 0.51–1.8 g/m2. According to saprobic parameters, pond water belonged to β-mesosabrobic zone and corresponded to the water quality class II (“clean enough” category. Fish productivity of nursery ponds was within 617.2–815.2 kg/ha; output of carp young-of-the-year was within 39.82–43.56%, mean weight of young-of-the-year was 31.0–39.3 g. Originality. For the first time we carried out a

  5. SELF-PURIFICATION OF THE DNIPROVS’KE RESERVOIR AS A LEADING FORMING FACTOR FOR THE ECOLOGICALLY SAFE HABITAT OF FISHES

    Directory of Open Access Journals (Sweden)

    А. Dvoretsky

    2014-12-01

    Full Text Available Purpose. To study the development of the water quality of the Dniprovs’ke reservoir, which is a water of body of complex including fisheries importance and is characterized by an increased anthropogenic pressure as a result of the processes of the toxification and self-purification determined based on toxicity index (Іt. Methodology. We used the methods of bioindication (determination of the number and biomass of phytoplankton and heterotrophic bacterioplankton, biotesting (Іt determinaiton with the aid of Daphnia magna, hydrochemistry (determination of main trophic-saprobiological parameters of water quality as well as the correlation analysis of these parameters. Findings. According to the 2012 data, tropho-saprobiologic, algological, microbiological parameters and toxicity index as an integral parameter were analyzed concerning to water quality. Regularities of dynamics and relationship of the indexes were studied. The environmental assessment of water quality of the most polluted upper part of the Dniprovs’ke reservoirs was carried out for each of the parameters studied: in areas where agro-industrial wastes enter, water is classified as «moderately polluted» – «very dirty». The data testify to strong local water pollution of the reservoir and a good renewable ability of the ecosystem. It was shown that in conditions of human toxification the adequate response concerning water quality gives the toxicity index as an integral indicator of toxification and self-purification processes. The dual role of phytoplankton and heterotrophic bacterioplankton in formation of water quality of the anthropogenically loaded reservoir was revealed: these components are involved in the processes of self-purification or toxification in accordance with periods of microalgae development during the season. This is displayed in corresponding changes of TI and the correlation coefficient. It was found that the self-cleaning of the reservoir is a major

  6. Culture-based Identification Of Microcystin-Degrading Bacteria In the Sandusky Bay and Maumee Bay of Lake Erie

    Science.gov (United States)

    Ormiston, A.; Mou, X.

    2012-12-01

    Harmful cyanobacteria blooms (cyanoHABs) are a serious issue that affects wildlife, human health, recreation and local economics worldwide. CyanoHABs produce cyanotoxins, such as microcystins (MCs) that lead to skin irritation, illness and liver tumors. Bacterially mediated degradation of MCs plays a key role to transform these toxic substrates to less harmful metabolites in natural environments. However, only a few Sphingomonos species have been isolated for degradation of MCs and many of which are from other habitats such as water plants. This project aims to isolate and identify bacteria that can degrade MC-LR and MC-RR, two major forms of MCs found during cyanoHABs in Lake Erie. Water samples were collected from the surface of Sandusky Bay and Maumee Bay of Lake Erie and immediately filtered through 3.0 -μm-pore-size membrane filters to obtain bacterioplankton fraction. The filtrates were amended with excessive inorganic nitrogen and phosphorus compounds and incubated in the dark for a week to purposely establish a carbon-limited condition. Afterwards, enrichment microcosms were established in flasks filled with pre-incubated bacterioplankton and single MC compounds (final concentration 10 μM). Once cell growth was confirmed by flow cytometry-based cell counting, bacterial cells in enriched microcosms were transferred onto solid surfaces, i.e., GFF filter and noble agar for colony isolation. Obtained single colonies were inoculated in defined liquid media with MCs as single carbon source. DNA was extracted from each purified isolate and analyzed by restriction fragment length polymorphism analysis (RFLP). A total of 18 different RFLP banding patterns were found, indicating MC-degrading bacteria may be heterogeneous in studied water samples. 16S rRNA genes of selected bacterial isolates were PCR amplified and sequenced for taxonomic identification. Our results demonstrated that MCs can be degraded by multiple bacterial species in Lake Erie. Future directions

  7. Bacterial community structure and composition in Lake Poyang:a case study in the Songmenshan Region, China%鄱阳湖湖泊细菌群落组成及结构--以松门山为例

    Institute of Scientific and Technical Information of China (English)

    寇文伯; 黄正云; 张杰; 刘倩纯; 刘芳鹏; 刘以珍; 吴兰

    2015-01-01

    is important for the maintenance of the unique biota of the Yangtze floodplain ecosystem. However, in contrast to the contamination and the water quality of Lake Poyang, little is known about the bacteria and their ecosystem functions in Lake Poyang. In this study, genomic DNA of the microbial community was extracted from sediment and water collected in May 2011 from Songmenshan Region, Lake Poyang, China. The benthic and planktonic bacterial community structures were examined by 454 pyrosequencing of the v4-v6 16S rRNA gene region. We used OTU-based analyses to identify changes in bacterial diversity and community structure. Chao1 estimator, inverse Simpson index, Shannon index, coverage, and the rarefaction curve were used to describe the richness and diversity of separate samples collected from different environments. The libshuff test was used to describe whether benthic and planktonic bacterial communities have the same structure. In addition, correlation analysis between the abundance of bacterial phyla and their diversity in each environment was performed to reveal whether they were related to each other. Overall, the dataset comprised 5751 sequences that were affiliated to Bacteria; of these, 1454 and 269 OTUs were obtained from the sediment and water column, respectively, indicating that benthic bacterial communities have higher bacterial diversity and richness. The results also revealed different bacterial community structures between the sediment and water column. In benthic bacterial communities, 228 bacterial genera belonging to 20 phyla, dominated by Deltaproteobacteria, Betaproteobacteria, and Verrucomicrobia, were found. A further 116 genera were obtained for bacterioplankton, which belonged to 13 phyla, with Betaproteobacteria, Bacteroidetes, and Actinobacteria being dominant. Significant variations in the relative abundance of bacterial phyla and proteobacterial classes were observed between environments. At the genus level, significant differences

  8. Complete ecological isolation and cryptic diversity in Polynucleobacter bacteria not resolved by 16S rRNA gene sequences.

    Science.gov (United States)

    Hahn, Martin W; Jezberová, Jitka; Koll, Ulrike; Saueressig-Beck, Tanja; Schmidt, Johanna

    2016-07-01

    Transplantation experiments and genome comparisons were used to determine if lineages of planktonic Polynucleobacter almost indistinguishable by their 16S ribosomal RNA (rRNA) sequences differ distinctively in their ecophysiological and genomic traits. The results of three transplantation experiments differing in complexity of biotic interactions revealed complete ecological isolation between some of the lineages. This pattern fits well to the previously detected environmental distribution of lineages along chemical gradients, as well as to differences in gene content putatively providing adaptation to chemically distinct habitats. Patterns of distribution of iron transporter genes across 209 Polynucleobacter strains obtained from freshwater systems and representing a broad pH spectrum further emphasize differences in habitat-specific adaptations. Genome comparisons of six strains sharing ⩾99% 16S rRNA similarities suggested that each strain represents a distinct species. Comparison of sequence diversity among genomes with sequence diversity among 240 cultivated Polynucleobacter strains indicated a large cryptic species complex not resolvable by 16S rRNA sequences. The revealed ecological isolation and cryptic diversity in Polynucleobacter bacteria is crucial in the interpretation of diversity studies on freshwater bacterioplankton based on ribosomal sequences.

  9. Low diversity of planktonic bacteria in the tropical ocean

    Science.gov (United States)

    Milici, Mathias; Tomasch, Jürgen; Wos-Oxley, Melissa L.; Wang, Hui; Jáuregui, Ruy; Camarinha-Silva, Amelia; Deng, Zhi-Luo; Plumeier, Iris; Giebel, Helge-Ansgar; Wurst, Mascha; Pieper, Dietmar H.; Simon, Meinhard; Wagner-Döbler, Irene

    2016-01-01

    The diversity of macro-organisms increases towards the equator, with almost no exceptions. It is the most conserved biogeographical pattern on earth and is thought to be related to the increase of temperature and productivity in the tropics. The extent and orientation of a latitudinal gradient of marine bacterioplankton diversity is controversial. Here we studied the euphotic zone of the Atlantic Ocean based on a transect covering ~12.000 km from 51°S to 47 °N. Water samples were collected at 26 stations at five depths between 20 and 200 m and sequentially filtered through 8 μm, 3 μm and 0,22 μm filters, resulting in a total of 359 samples. Illumina sequencing of the V5–V6 region of the 16S rRNA gene revealed a clear biogeographic pattern with a double inverted latitudinal gradient. Diversity was higher in mid-latitudinal regions of the Atlantic Ocean and decreased towards the equator. This pattern was conserved for bacteria from all three planktonic size fractions. Diversity showed a non-linear relationship with temperature and was negatively correlated with bacterial cell numbers in the upper depth layers (<100 m). The latitudinal gradients of marine bacterial diversity and the mechanisms that govern them are distinct from those found in macro-organisms.

  10. Heterologous expression of proteorhodopsin enhances H2 production in Escherichia coli when endogenous Hyd-4 is overexpressed.

    Science.gov (United States)

    Kuniyoshi, Taís M; Balan, Andrea; Schenberg, Ana Clara G; Severino, Divinomar; Hallenbeck, Patrick C

    2015-07-20

    Proteorhodopsin (PR) is a light harvesting protein widely distributed among bacterioplankton that plays an integral energetic role in a new pathway of marine light capture. The conversion of light into chemical energy in non-chlorophyll-based bacterial systems could contribute to overcoming thermodynamic and metabolic constraints in biofuels production. In an attempt to improve biohydrogen production yields, H2 evolution catalyzed by endogenous hydrogenases, Hyd-3 and/or Hyd-4, was measured when recombinant proteorhodopsin (PR) was concomitantly expressed in Escherichia coli cells. Higher amounts of H2 were obtained with recombinant cells in a light and chromophore dependent manner. This effect was only observed when HyfR, the specific transcriptional activator of the hyf operon encoding Hyd-4 was overexpressed in E. coli, suggesting that an excess of protons generated by PR activity could increase hydrogen production by Hyd-4 but not by Hyd-3. Although many of the subunits of Hyd-3 and Hyd-4 are very similar, Hyd-4 possesses three additional proton-translocating NADH-ubiquinone oxidoreductase subunits, suggesting that it is dependent upon ΔμH(+). Altogether, these results suggest that protons generated by proteorhodopsin in the periplasm can only enhance hydrogen production by hydrogenases with associated proton translocating subunits.

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

    Directory of Open Access Journals (Sweden)

    J. Comte

    2015-07-01

    Full Text Available 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, and then analyzed these results relative to environmental variables to identify factors 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.

  12. Picoplankton Community Composition by CARD-FISH and Flow Cytometric Techniques: A Preliminary Study in Central Adriatic Sea Water

    Directory of Open Access Journals (Sweden)

    Anita Manti

    2012-01-01

    Full Text Available Data concerning picoplanktonic community composition and abundance in the Central Adriatic Sea are presented in an effort to improve the knowledge of bacterioplankton and autotrophic picoplankton and their seasonal changes. Flow cytometry analyses revealed the presence of two distinct bacteria populations: HNA and LNA cells. HNA cells showed an explicit correlation with viable and actively respiring cells. The study of viability and activity may increase our knowledge of the part that contributes really to the remineralization and bacterial biomass production. Authotrophic picoplankton abundance, especially picocyanobacteria, was strongly influenced by seasonality, indicating that light availability and water temperature are very important regulating factors. In terms of total carbon biomass, the main contribution came from heterotrophic bacteria with a lower contribution from autotrophic picoplankton. CARD-FISH evidenced, within the Eubacteria domain, the dominance of members of the phyla Alphaproteobacteria, with a strong contribution from SAR11clade, followed by Cytophaga-Flavobacterium and Gammaproteobacteria. The bacterial groups detected contributed differently depending when the sample was taken, suggesting possible seasonal patterns. This study documents for the first time picoplankton community composition in the Central Adriatic Sea using two different approaches, FCM and CARD-FISH, and could provide preliminary data for future studies.

  13. Differential response of planktonic primary, bacterial, and dimethylsulfide production rates to vertically-moving and static incubations in upper mixed-layer summer sea waters

    Science.gov (United States)

    Galí, M.; Simó, R.; Pérez, G. L.; Ruiz-González, C.; Sarmento, H.; Royer, S.-J.; Fuentes-Lema, A.; Gasol, J. M.

    2013-05-01

    Microbial plankton experience fluctuations in total solar irradiance and in its spectral composition as they are vertically moved by turbulence in the oceanic upper mixed layer (UML). The fact that the light exposure is not static but dynamic may have important consequences for biogeochemical processes and ocean-atmosphere fluxes. However, most biogeochemical processes other than primary production, like bacterial production or dimethylsulfide (DMS) production, are seldom measured in sunlight and even less often in dynamic light fields. We conducted four experiments in oligotrophic summer stratified Mediterranean waters, where a sample from the UML was incubated in ultraviolet (UV)-transparent bottles at three fixed depths within the UML and on a vertically-moving basket across the same depth range. We assessed the response of the phyto- and bacterioplankton community with physiological indicators based on flow cytometry singe-cell measurements, Fast Repetition Rate fluorometry (FRRf), phytoplankton pigment concentrations and particulate light absorption. Dynamic light exposure caused a disruption of the photoinhibition and photoacclimation processes associated to ultraviolet radiation (UVR), which slightly alleviated bacterial photoinhibition but did not favor primary production. Gross DMS production (GPDMS) decreased sharply with depth in parallel to shortwave UVR, and displayed a dose-dependent response that mixing did not significantly disrupt. To our knowledge, we provide the first measurements of GPDMS under in situ UV-inclusive optical conditions.

  14. Differential response of planktonic primary, bacterial, and dimethylsulfide production rates to static vs. dynamic light exposure in upper mixed-layer summer sea waters

    Science.gov (United States)

    Galí, M.; Simó, R.; Pérez, G. L.; Ruiz-González, C.; Sarmento, H.; Royer, S.-J.; Fuentes-Lema, A.; Gasol, J. M.

    2013-12-01

    Microbial plankton experience short-term fluctuations in total solar irradiance and in its spectral composition as they are vertically moved by turbulence in the oceanic upper mixed layer (UML). The fact that the light exposure is not static but dynamic may have important consequences for biogeochemical processes and ocean-atmosphere fluxes. However, most biogeochemical processes other than primary production, like bacterial production or dimethylsulfide (DMS) production, are seldom measured in sunlight and even less often in dynamic light fields. We conducted four experiments in oligotrophic summer stratified Mediterranean waters, where a sample from the UML was incubated in ultraviolet (UV)-transparent bottles at three fixed depths within the UML and on a vertically moving basket across the same depth range. We assessed the response of the phyto- and bacterioplankton community with physiological indicators based on flow cytometry singe-cell measurements, fast repetition rate fluorometry (FRRf), phytoplankton pigment concentrations and particulate light absorption. Dynamic light exposure caused a subtle disruption of the photoinhibition and photoacclimation processes associated with ultraviolet radiation (UVR), which slightly alleviated bacterial photoinhibition but did not favor primary production. Gross DMS production (GPDMS) decreased sharply with depth in parallel to shortwave UVR, and displayed a dose-dependent response that mixing did not significantly disrupt. To our knowledge, we provide the first measurements of GPDMS under in situ UV-inclusive optical conditions.

  15. Dilution-to-extinction culturing of SAR11 members and other marine bacteria from the Red Sea

    KAUST Repository

    Mohamed, Roslinda B.

    2013-12-01

    Life in oceans originated about 3.5 billion years ago where microbes were the only life form for two thirds of the planet’s existence. Apart from being abundant and diverse, marine microbes are involved in nearly all biogeochemical processes and are vital to sustain all life forms. With the overgrowing number of data arising from culture-independent studies, it became necessary to improve culturing techniques in order to obtain pure cultures of the environmentally significant bacteria to back up the findings and test hypotheses. Particularly in the ultra-oligotrophic Red Sea, the ubiquitous SAR11 bacteria has been reported to account for more than half of the surface bacterioplankton community. It is therefore highly likely that SAR11, and other microbial life that exists have developed special adaptations that enabled them to thrive successfully. Advances in conventional culturing have made it possible for abundant, unculturable marine bacteria to be grown in the lab. In this study, we analyzed the effectiveness of the media LNHM and AMS1 in isolating marine bacteria from the Red Sea, particularly members of the SAR11 clade. SAR11 strains obtained from this study AMS1, and belonged to subgroup 1a and phylotype 1a.3. We also obtained other interesting strains which should be followed up with in the future. In the long run, results from this study will enhance our knowledge of the pelagic ecosystem and allow the impacts of rising temperatures on marine life to be understood.

  16. Distribution and diversity of Prochlorococcus ecotypes in the Red Sea

    KAUST Repository

    Shibl, Ahmed A.

    2014-06-19

    Photosynthetic prokaryotes of the genus Prochlorococcus play a major role in global primary production in the world\\'s oligotrophic oceans. A recent study on pelagic bacterioplankton communities in the northern and central Red Sea indicated that the predominant cyanobacterial 16S rRNA gene sequence types were from Prochlorococcus cells belonging to a high-light-adapted ecotype (HL II). In this study, we analyzed microdiversity of Prochlorococcus sp. at multiple depths within and below the euphotic zone in the northern, central, and southern regions of the Red Sea, as well as in surface waters in the same locations, but in a different season. Prochlorococcus dominated the communities in clone libraries of the amplified 16S-23S rRNA internal transcribed spacer (ITS) region. Almost no differences were found between samples from coastal or open-water sites, but a high diversity of Prochlorococcus ecotypes was detected at 100-meter depth in the water column. In addition, an unusual dominance of HL II-related sequences was observed in deeper waters. Our results indicate that the Red Sea harbors diverse Prochlorococcus lineages, but no novel ecotypes, despite its unusual physicochemical properties. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  17. Controls on marine carbon fluxes via phytoplankton-microzooplankton interactions in continental shelf waters. Progress report

    Energy Technology Data Exchange (ETDEWEB)

    1994-05-01

    The project is an in-depth evaluation of the phytoplankton-microzooplankton trophic link. The principal goals of the project remain as originally proposed: (1) Impact of grazing by phagotrophic microzooplankton on phytoplankton, particularly on phototrophic cells <5 {mu}m in size, which are not effectively grazed by macrozooplankton. (2) Impact of grazing by phagotrophic microzooplankton on bacterioplankton. (3) Taxon-specific growth rates of phytoplankton in situ, particularly of <5 {mu}m sized cells, as they are affected by phagotrophy rates. The authors are developing protocols for making quantitative estimates of grazing by phagotrophic protists on ultraphytoplankton, and for determining the intrinsic reproductive rates of phytoplankton species. They have also begun a series of experiments, testing and utilizing these methods, evaluating the grazing impact of flagellates and ciliates on phytoplankton species of different sizes and taxonomic affinities. A series of preliminary experiments in coastal waters adjacent to the Oregon Institute of Marine Biology have provided a coastal benchmark. They participated in a preliminary cruise in May, 1993 to the OMP field site off Cape Hatteras. Their purpose was to obtain background information on heterotrophic microbial distributional patterns in this region and to measure rates of protist bacterivory.

  18. The influence of light and water mass on bacterial population dynamics in the Amundsen Sea Polynya

    Directory of Open Access Journals (Sweden)

    Inga Richert

    2015-04-01

    Full Text Available Abstract Despite being perpetually cold, seasonally ice-covered and dark, the coastal Southern Ocean is highly productive and harbors a diverse microbiota. During the austral summer, ice-free coastal patches (or polynyas form, exposing pelagic organisms to sunlight, triggering intense phytoplankton blooms. This strong seasonality is likely to influence bacterioplankton community composition (BCC. For the most part, we do not fully understand the environmental drivers controlling high-latitude BCC and the biogeochemical cycles they mediate. In this study, the Amundsen Sea Polynya was used as a model system to investigate important environmental factors that shape the coastal Southern Ocean microbiota. Population dynamics in terms of occurrence and activity of abundant taxa was studied in both environmental samples and microcosm experiments by using 454 pyrosequencing of 16S rRNA genes. We found that the BCC in the photic epipelagic zone had low richness, with dominant bacterial populations being related to taxa known to benefit from high organic carbon and nutrient loads (copiotrophs. In contrast, the BCC in deeper mesopelagic water masses had higher richness, featuring taxa known to benefit from low organic carbon and nutrient loads (oligotrophs. Incubation experiments indicated that direct impacts of light and competition for organic nutrients are two important factors shaping BCC in the Amundsen Sea Polynya.

  19. Stable symbionts across the HMA-LMA dichotomy: low seasonal and interannual variation in sponge-associated bacteria from taxonomically diverse hosts.

    Science.gov (United States)

    Erwin, Patrick M; Coma, Rafel; López-Sendino, Paula; Serrano, Eduard; Ribes, Marta

    2015-10-01

    Marine sponges host bacterial communities with important ecological and economic roles in nature and society, yet these benefits depend largely on the stability of host-symbiont interactions and their susceptibility to changing environmental conditions. Here, we investigated the temporal stability of complex host-microbe symbioses in a temperate, seasonal environment over three years, targeting sponges across a range of symbiont density (high and low microbial abundance, HMA and LMA) and host taxonomy (six orders). Symbiont profiling by terminal restriction fragment length polymorphism analysis of 16S rRNA gene sequences revealed that bacterial communities in all sponges exhibited a high degree of host specificity, low seasonal dynamics and low interannual variability: results that represent an emerging trend in the field of sponge microbiology and contrast sharply with the seasonal dynamics of free-living bacterioplankton. Further, HMA sponges hosted more diverse, even and similar symbiont communities than LMA sponges and these differences in community structure extended to core members of the microbiome. Together, these findings show clear distinctions in symbiont structure between HMA and LMA sponges while resolving notable similarities in their stability over seasonal and inter-annual scales, thus providing insight into the ecological consequences of the HMA-LMA dichotomy and the temporal stability of complex host-microbe symbioses.

  20. Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions

    Science.gov (United States)

    Versluis, Dennis; D'Andrea, Marco Maria; Ramiro Garcia, Javier; Leimena, Milkha M.; Hugenholtz, Floor; Zhang, Jing; Öztürk, Başak; Nylund, Lotta; Sipkema, Detmer; Schaik, Willem Van; de Vos, Willem M.; Kleerebezem, Michiel; Smidt, Hauke; Passel, Mark W. J. Van

    2015-07-01

    Antibiotic resistance genes are found in a broad range of ecological niches associated with complex microbiota. Here we investigated if resistance genes are not only present, but also transcribed under natural conditions. Furthermore, we examined the potential for antibiotic production by assessing the expression of associated secondary metabolite biosynthesis gene clusters. Metatranscriptome datasets from intestinal microbiota of four human adults, one human infant, 15 mice and six pigs, of which only the latter have received antibiotics prior to the study, as well as from sea bacterioplankton, a marine sponge, forest soil and sub-seafloor sediment, were investigated. We found that resistance genes are expressed in all studied ecological niches, albeit with niche-specific differences in relative expression levels and diversity of transcripts. For example, in mice and human infant microbiota predominantly tetracycline resistance genes were expressed while in human adult microbiota the spectrum of expressed genes was more diverse, and also included β-lactam, aminoglycoside and macrolide resistance genes. Resistance gene expression could result from the presence of natural antibiotics in the environment, although we could not link it to expression of corresponding secondary metabolites biosynthesis clusters. Alternatively, resistance gene expression could be constitutive, or these genes serve alternative roles besides antibiotic resistance.

  1. INT (2-(4-Iodophenyl)-3-(4-Nitrophenyl)-5-(Phenyl) Tetrazolium Chloride) Is Toxic to Prokaryote Cells Precluding Its Use with Whole Cells as a Proxy for In Vivo Respiration.

    Science.gov (United States)

    Villegas-Mendoza, Josué; Cajal-Medrano, Ramón; Maske, Helmut

    2015-11-01

    Prokaryote respiration is expected to be responsible for more than half of the community respiration in the ocean, but the lack of a practical method to measure the rate of prokaryote respiration in the open ocean resulted in very few published data leaving the role of organotrophic prokaryotes open to debate. Oxygen consumption rates of oceanic prokaryotes measured with current methods may be biased due to pre-incubation size filtration and long incubation times both of which can change the physiological and taxonomic profile of the sample during the incubation period. In vivo INT reduction has been used in terrestrial samples to estimate respiration rates, and recently, the method was introduced and applied in aquatic ecology. We measured oxygen consumption rates and in vivo INT reduction to formazan in cultures of marine bacterioplankton communities, Vibrio harveyi and the eukaryote Isochrysis galbana. For prokaryotes, we observed a decrease in oxygen consumption rates with increasing INT concentrations between 0.05 and 1 mM. Time series after 0.5 mM INT addition to prokaryote samples showed a burst of in vivo INT reduction to formazan and a rapid decline of oxygen consumption rates to zero within less than an hour. Our data for non-axenic eukaryote cultures suggest poisoning of the eukaryote. Prokaryotes are clearly poisoned by INT on time scales of less than 1 h, invalidating the interpretation of in vivo INT reduction to formazan as a proxy for oxygen consumption rates.

  2. Microbial Experimental Evolution as a Novel Research Approach in the Vibrionaceae and Squid-Vibrio Symbiosis

    Directory of Open Access Journals (Sweden)

    William eSoto

    2014-12-01

    Full Text Available The Vibrionaceae are a genetically and metabolically diverse family living in aquatic habitats with a great propensity toward developing interactions with eukaryotic microbial and multicellular hosts (as either commensals, pathogens, and mutualists. The Vibrionaceae frequently possess a life history cycle where bacteria are attached to a host in one phase and then another where they are free from their host as either part of the bacterioplankton or adhered to a solid substrate such as marine sediment, riverbeds, lakebeds, or floating particulate debris. These two stages in their life history exert quite distinct and separate selection pressures. When bound to solid substrates or to host cells, the Vibrionaceae can also exist as complex biofilms. The association between bioluminescent Vibrio spp. and sepiolid squids (Cephalopoda: Sepiolidae is an experimentally tractable model to study bacteria and animal host interactions, since the symbionts and squid hosts can be maintained in the laboratory independently of one another. The bacteria can be grown in pure culture and the squid hosts raised gnotobiotically with sterile light organs. The partnership between free-living Vibrio symbionts and axenic squid hatchlings emerging from eggs must be renewed every generation of the cephalopod host. Thus, symbiotic bacteria and animal host can each be studied alone and together in union. Despite virtues provided by the Vibrionaceae and sepiolid squid-Vibrio symbiosis, these assets to evolutionary biology have yet to be fully utilized for microbial experimental evolution. Experimental evolution studies already completed are reviewed, along with exploratory topics for future study.

  3. Indicators of early successional trends in environmental condition and community function in constructed wetlands of the Athabasca Oilsands region

    Energy Technology Data Exchange (ETDEWEB)

    Ciborowski, J.; Kovalenko, K. [Windsor Univ., ON (Canada); Dixon, G.; Farwell, A. [Waterloo Univ., ON (Canada); Foote, L.; Mollard, F.; Roy, M. [Alberta Univ., Edmonton, AB (Canada); Smits, J.; Turcotte, D. [Saskatchewan Univ., Saskatoon, SK (Canada)

    2010-07-01

    This presentation reported on a study that compared interannual environmental variation in post-mining Athabasca oil sands landscapes. In particular, it compared biological, ecotoxicological and carbon dynamic aspects of sixteen 5 to 30 year old wetlands with different ages, reclamation materials and stockpiled surface materials such as peat. In addition to determining carbon fluxes, standing stocks of hydrocarbons were measured along with organic substrate, bacterioplankton, phytoplankton, biofilm, macrophytes, litter, zoobenthos, and aquatic insect emergence. Gas fluxes, microbial, plant, zoobenthic, amphibian, and tree swallow nestling production, and stable isotope signatures were used to determine carbon pathways, fluxes and budgets. Coarse taxon richness in reference wetlands reached an asymptote in 5 to 7 years. Richness, composition and emergent plant cover of oilsands-affected wetlands converged over a 15 to 20 year period with reference wetland patterns. The development of emergent but not submergent plant cover and associated biota accelerated with the addition of peat. Water chemistry was found to be more important than sediment in terms of regulating submergent biological properties. The study showed that the most important regulator of community composition may be residual salinity. Compared to more temperate biomes, the successional trends were slower.

  4. Sunlight-induced DNA damage in marine micro-organisms collected along a latitudinal gradient from 70 degrees N to 68 degrees S.

    Science.gov (United States)

    Meador, Jarah A; Baldwin, Amy J; Catala, Phillipe; Jeffrey, Wade H; Joux, Fabien; Moss, Joseph A; Dean Pakulski, J; Stevens, Richard; Mitchell, David L

    2009-01-01

    We examined ultraviolet radiation (UVR)-induced DNA damage in marine micro-organisms collected from surface seawater along a latitudinal transect in the Central Pacific Ocean from 70 degrees N to 68 degrees S. Samples were collected predawn and incubated under ambient UVR in transparent incubators at in situ temperatures until late afternoon at which time they were filtered into primarily bacterioplankton and eukaryotic fractions. Cyclobutane pyrimidine dimers (CPDs) and (6-4) photoproducts [(6-4)PDs] were quantified in DNA extracts using radioimmunoassays. UVB was lowest in the polar regions and highest near the equator and correlations between UVB and DNA damage were observed. The eukaryotic fraction showed significant CPDs across the entire transect; (6-4)PDs were detected only in the tropics. The bacterial fraction showed no accumulation of (6-4)PDs at any latitude, although residual (6-4)PDs were observed. Bacterial cell volumes were greatest in the sub-Arctic and northern temperate latitudes and lower in the tropics and southern hemisphere, a unique observation that parallels Bergmann's rule. A strong negative correlation was observed between cell volume and CPDs. The environmental impact of solar UVR on marine micro-organisms in the open ocean is complex and our results suggest that several factors such as DNA repair, cell size, temperature, salinity, nutrients and species composition are important in determining relative sensitivity.

  5. Phosphate limitation induces the intergeneric inhibition of Pseudomonas aeruginosa by Serratia marcescens isolated from paper machines.

    Science.gov (United States)

    Kuo, Pei-An; Kuo, Chih-Horng; Lai, Yiu-Kay; Graumann, Peter L; Tu, Jenn

    2013-06-01

    Phosphate is an essential nutrient for heterotrophic bacteria, affecting bacterioplankton in aquatic ecosystems and bacteria in biofilms. However, the influence of phosphate limitation on bacterial competition and biofilm development in multispecies populations has received limited attention in existing studies. To address this issue, we isolated 13 adhesive bacteria from paper machine aggregates. Intergeneric inhibition of Pseudomonas aeruginosa WW5 by Serratia marcescens WW4 was identified under phosphate-limited conditions, but not in Luria-Bertani medium or M9 minimal medium. The viable numbers of the pure S. marcescens WW4 culture decreased over 3 days in the phosphate-limited medium; however, the mortality of S. marcescens WW4 was significantly reduced when it was co-cultured with P. aeruginosa WW5, which appeared to sustain the S. marcescens WW4 biofilm. In contrast, viable P. aeruginosa WW5 cells immediately declined in the phosphate-limited co-culture. To identify the genetic/inhibitory element(s) involved in this process, we inserted a mini-Tn5 mutant of S. marcescens WW4 that lacked inhibitory effect. The results showed that an endonuclease bacteriocin was involved in this intergeneric inhibition by S. marcescens WW4 under phosphate limitation. In conclusion, this study highlights the importance of nutrient limitation in bacterial interactions and provides a strong candidate gene for future functional characterisation.

  6. Differential response of planktonic primary, bacterial, and dimethylsulfide production rates to vertically-moving and static incubations in upper mixed-layer summer sea waters

    Directory of Open Access Journals (Sweden)

    M. Galí

    2013-05-01

    Full Text Available Microbial plankton experience fluctuations in total solar irradiance and in its spectral composition as they are vertically moved by turbulence in the oceanic upper mixed layer (UML. The fact that the light exposure is not static but dynamic may have important consequences for biogeochemical processes and ocean-atmosphere fluxes. However, most biogeochemical processes other than primary production, like bacterial production or dimethylsulfide (DMS production, are seldom measured in sunlight and even less often in dynamic light fields. We conducted four experiments in oligotrophic summer stratified Mediterranean waters, where a sample from the UML was incubated in ultraviolet (UV-transparent bottles at three fixed depths within the UML and on a vertically-moving basket across the same depth range. We assessed the response of the phyto- and bacterioplankton community with physiological indicators based on flow cytometry singe-cell measurements, Fast Repetition Rate fluorometry (FRRf, phytoplankton pigment concentrations and particulate light absorption. Dynamic light exposure caused a disruption of the photoinhibition and photoacclimation processes associated to ultraviolet radiation (UVR, which slightly alleviated bacterial photoinhibition but did not favor primary production. Gross DMS production (GPDMS decreased sharply with depth in parallel to shortwave UVR, and displayed a dose-dependent response that mixing did not significantly disrupt. To our knowledge, we provide the first measurements of GPDMS under in situ UV-inclusive optical conditions.

  7. Microbial community structure of Arctic seawater as revealed by pyrosequencing

    Institute of Scientific and Technical Information of China (English)

    LI Yang; WANG Zhen; LIN Xuezheng

    2016-01-01

    This study aimed to determine the microbial community structure of seawater in (ICE-1) and out (FUBIAO) of the pack ice zone in the Arctic region. Approximate 10 L seawater was filtrated by 0.2 μm Whatman nuclepore filters and the environmental genomic DNA was extracted. We conducted a detailed census of microbial communities by pyrosequencing. Analysis of the microbial community structures indicated that these two samples had high bacterial, archaeal and eukaryotic diversity. Proteobacteria and Bacteroidetes were the two dominant members of the bacterioplankton community in both samples, and their relative abundance were 51.29% and 35.39%, 72.95%and 23.21%, respectively. Euryarchaeota was the most abundant archaeal phylum, and the relative abundance was nearly up to 100% in FUBIAO and 60% in ICE-1. As for the eukaryotes, no_rank_Eukaryota, Arthropoda and no_rank_Metazoa were the most abundant groups in Sample FUBIAO, accounting for 85.29% of the total reads. The relative abundance of the most abundant phylum in Sample ICE-1, no_rank_Eukaryota and no_rank_Metazoa, was up to 90.69% of the total reads. Alphaproteobacteria, Flavobacteria and Gammaproteobacteria were the top three abundant classes in the two samples at the bacterial class level. There were also differences in the top ten abundant bacterial, archaeal and eukaryotic OTUs at the level of 97% similarity between the two samples.

  8. Low-resolution characterization of the 3D structure of the Euglena gracilis photoreceptor.

    Science.gov (United States)

    Barsanti, Laura; Coltelli, Primo; Evangelista, Valtere; Passarelli, Vincenzo; Frassanito, Anna Maria; Vesentini, Nicoletta; Gualtieri, Paolo

    2008-10-24

    This paper deals with the first characterization of the structure of the photoreceptive organelle of the unicellular alga Euglena gracilis (Euglenophyta). This organelle has a three-dimensional organization consisting of up to 50 closely stacked membrane lamellae. Ionically induced unstacking of the photoreceptor lamellae revealed ordered arrays well suited to structural analysis by electron microscopy and image analysis, which ultimately yielded a low-resolution picture of the structure. Each lamella is formed by the photoreceptive membrane protein of the cell assembled within the membrane layer in a hexagonal lattice. The first order diffraction spots in the calculated Fourier transform reveals the presence of 6-fold symmetrized topography (better resolution about 90A). The 2D and 3D structural data are very similar with those recently published on proteorodopsin, a membrane protein used by marine bacterio-plankton as light-driven proton pump. In our opinion these similarity indicate that a photoreceptive protein belonging to the same superfamily of proteorodopsin could form the Euglena photoreceptor.

  9. Spatial patterns and light-driven variation of microbial population gene expression in surface waters of the oligotrophic open ocean.

    Science.gov (United States)

    Hewson, Ian; Poretsky, Rachel S; Tripp, H James; Montoya, Joseph P; Zehr, Jonathan P

    2010-07-01

    Because bacterioplankton production rates do not vary strongly across vast expanses of the ocean, it is unclear how variability in community structure corresponds with functional variability in the open ocean. We surveyed community transcript functional profiles at eight locations in the open ocean, in both the light and in the dark, using the genomic subsystems approach, to understand variability in gene expression patterns in surface waters. Metatranscriptomes from geographically distinct areas and collected during the day and night shared a large proportion of metabolic functional similarity (74%) at the finest metabolic resolution possible. The variability between metatranscriptomes could be explained by phylogenetic differences between libraries (Mantel test, P < 0.0001). Several key gene expression pathways, including Photosystem I, Photosystem II and ammonium uptake, demonstrated the most variability both geographically and between light and dark. Libraries were dominated by transcripts of the cyanobacterium Prochlorocococcus marinus, where most geographical and diel variability between metatranscriptomes reflected between-station differences in cyanobacterial phototrophic metabolism. Our results demonstrate that active genetic machinery in surface waters of the ocean is dominated by photosynthetic microorganisms and their site-to-site variability, while variability in the remainder of assemblages is dependent on local taxonomic composition.

  10. Metabolic and phylogenetic profile of bacterial community in Guishan coastal water (Pearl River Estuary), South China Sea

    Science.gov (United States)

    Hu, Xiaojuan; Liu, Qing; Li, Zhuojia; He, Zhili; Gong, Yingxue; Cao, Yucheng; Yang, Yufeng

    2014-10-01

    Characteristics of a microbial community are important as they indicate the status of aquatic ecosystems. In the present study, the metabolic and phylogenetic profile of the bacterioplankton community in Guishan coastal water (Pearl River Estuary), South China Sea, at 12 sites (S1-S12) were explored by community-level physiological profiling (CLPP) with BIOLOG Eco-plate and denaturing gradient gel electrophoresis (DGGE). Our results showed that the core mariculture area (S6, S7 and S8) and the sites associating with human activity and sewage discharge (S11 and S12) had higher microbial metabolic capability and bacterial community diversity than others (S1-5, S9-10). Especially, the diversity index of S11 and S12 calculated from both CLPP and DGGE data ( H>3.2) was higher than that of others as sewage discharge may increase water nitrogen and phosphorus nutrient. The bacterial community structure of S6, S8, S11 and S12 was greatly influenced by total phosphorous, salinity and total nitrogen. Based on DGGE fingerprinting, proteobacteria, especially γ- and α-proteobacteria, were found dominant at all sites. In conclusion, the aquaculture area and wharf had high microbial metabolic capability. The structure and composition of bacterial community were closely related to the level of phosphorus, salinity and nitrogen.

  11. Ecology of marine Bacteroidetes: a comparative genomics approach.

    Science.gov (United States)

    Fernández-Gómez, Beatriz; Richter, Michael; Schüler, Margarete; Pinhassi, Jarone; Acinas, Silvia G; González, José M; Pedrós-Alió, Carlos

    2013-05-01

    Bacteroidetes are commonly assumed to be specialized in degrading high molecular weight (HMW) compounds and to have a preference for growth attached to particles, surfaces or algal cells. The first sequenced genomes of marine Bacteroidetes seemed to confirm this assumption. Many more genomes have been sequenced recently. Here, a comparative analysis of marine Bacteroidetes genomes revealed a life strategy different from those of other important phyla of marine bacterioplankton such as Cyanobacteria and Proteobacteria. Bacteroidetes have many adaptations to grow attached to particles, have the capacity to degrade polymers, including a large number of peptidases, glycoside hydrolases (GHs), glycosyl transferases, adhesion proteins, as well as the genes for gliding motility. Several of the polymer degradation genes are located in close association with genes for TonB-dependent receptors and transducers, suggesting an integrated regulation of adhesion and degradation of polymers. This confirmed the role of this abundant group of marine bacteria as degraders of particulate matter. Marine Bacteroidetes had a significantly larger number of proteases than GHs, while non-marine Bacteroidetes had equal numbers of both. Proteorhodopsin containing Bacteroidetes shared two characteristics: small genome size and a higher number of genes involved in CO2 fixation per Mb. The latter may be important in order to survive when floating freely in the illuminated, but nutrient-poor, ocean surface.

  12. Dissolved Organic Nitrogen Inputs from Wastewater Treatment Plant Effluents Increase Responses of Planktonic Metabolic Rates to Warming.

    Science.gov (United States)

    Vaquer-Sunyer, Raquel; Conley, Daniel J; Muthusamy, Saraladevi; Lindh, Markus V; Pinhassi, Jarone; Kritzberg, Emma S

    2015-10-06

    Increased anthropogenic pressures on coastal marine ecosystems in the last century are threatening their biodiversity and functioning. Global warming and increases in nutrient loadings are two major stressors affecting these systems. Global warming is expected to increase both atmospheric and water temperatures and increase precipitation and terrestrial runoff, further increasing organic matter and nutrient inputs to coastal areas. Dissolved organic nitrogen (DON) concentrations frequently exceed those of dissolved inorganic nitrogen in aquatic systems. Many components of the DON pool have been shown to supply nitrogen nutrition to phytoplankton and bacteria. Predictions of how global warming and eutrophication will affect metabolic rates and dissolved oxygen dynamics in the future are needed to elucidate their impacts on biodiversity and ecosystem functioning. Here, we experimentally determine the effects of simultaneous DON additions and warming on planktonic community metabolism in the Baltic Sea, the largest coastal area suffering from eutrophication-driven hypoxia. Both bacterioplankton community composition and metabolic rates changed in relation to temperature. DON additions from wastewater treatment plant effluents significantly increased the activation energies for community respiration and gross primary production. Activation energies for community respiration were higher than those for gross primary production. Results support the prediction that warming of the Baltic Sea will enhance planktonic respiration rates faster than it will for planktonic primary production. Higher increases in respiration rates than in production may lead to the depletion of the oxygen pool, further aggravating hypoxia in the Baltic Sea.

  13. Seasonal variation of CO2 saturation in the Gulf of Bothnia: Indications of marine net heterotrophy

    Science.gov (United States)

    Algesten, Grete; Wikner, Johan; Sobek, Sebastian; Tranvik, Lars J.; Jansson, Mats

    2004-12-01

    Seasonal variation of pCO2 and primary and bacterioplankton production were measured in the Gulf of Bothnia during an annual cycle. Surface water was supersaturated with CO2 on an annual basis, indicating net heterotrophy and a source of CO2 to the atmosphere. However, the Gulf of Bothnia oscillated between being a sink and a source of CO2 over the studied period, largely decided by temporal variation in bacterial respiration (BR) and primary production (PP) in the water column above the pycnocline. The calculated annual respiration-production balance (BR-PP) was very similar to the estimated CO2 emission from the Gulf of Bothnia, which indicates that these processes were major determinants of the exchange of CO2 between water and atmosphere. The southern basin (the Bothnian Sea) had a lower net release of CO2 to the atmosphere than the northern Bothnian Bay (7.1 and 9.7 mmol C m-2 d-1, respectively), due to higher primary production, which to a larger extent balanced respiration in this basin.

  14. Southern Ocean biological iron cycling in the pre-whaling and present ecosystems

    Science.gov (United States)

    Maldonado, Maria T.; Surma, Szymon; Pakhomov, Evgeny A.

    2016-11-01

    This study aimed to create the first model of biological iron (Fe) cycling in the Southern Ocean food web. Two biomass mass-balanced Ecopath models were built to represent pre- and post-whaling ecosystem states (1900 and 2008). Functional group biomasses (tonnes wet weight km-2) were converted to biogenic Fe pools (kg Fe km-2) using published Fe content ranges. In both models, biogenic Fe pools and consumption in the pelagic Southern Ocean were highest for plankton and small nektonic groups. The production of plankton biomass, particularly unicellular groups, accounted for the highest annual Fe demand. Microzooplankton contributed most to biological Fe recycling, followed by carnivorous zooplankton and krill. Biological Fe recycling matched previous estimates, and, under most conditions, could entirely meet the Fe demand of bacterioplankton and phytoplankton. Iron recycling by large baleen whales was reduced 10-fold by whaling between 1900 and 2008. However, even under the 1900 scenario, the contribution of whales to biological Fe recycling was negligible compared with that of planktonic consumers. These models are a first step in examining oceanic-scale biological Fe cycling, highlighting gaps in our present knowledge and key questions for future research on the role of marine food webs in the cycling of trace elements in the sea. This article is part of the themed issue 'Biological and climatic impacts of ocean trace element chemistry'.

  15. Seasonal baseline of nutrients and stable isotopes in a saline lake of Argentina: biogeochemical processes and river runoff effects.

    Science.gov (United States)

    Kopprio, Germán A; Kattner, Gerhard; Freije, R Hugo; de Paggi, Susana José; Lara, Rubén J

    2014-05-01

    The seasonal variability of inorganic and organic nutrients and stable isotopes and their relations with plankton and environmental conditions were monitored in Lake Chasicó. Principal component analysis evidenced the strong influence of the river runoff on several biogeochemical variables. Silicate concentrations were controlled by diatom biomass and river discharge. Higher values of nitrate and soluble reactive phosphorus (SRP) indicated agricultural uses in the river basin. Elevated pH values (∼ 9) inhibiting nitrification in the lake explained partially the dominance of ammonium: ∼ 83 % of dissolved inorganic nitrogen (DIN). The low DIN/SRP ratio inferred nitrogen limitation, although the hypotheses of iron and CO2 limitation are relevant in alkaline lakes. Particulate organic matter (POM) and dissolved organic matter (DOM) were mainly of autochthonous origin. The main allochthonous input was imported by the river as POM owning to the arid conditions. Dissolved organic carbon was likely top-down regulated by the bacterioplankton grazer Brachionus plicatilis. The δ(13)C signature was a good indicator of primary production and its values were influenced probably by CO2 limitation. The δ(15)N did not evidence nitrogen fixation and suggested the effects of anthropogenic activities. The preservation of a good water quality in the lake is crucial for resource management.

  16. [Intestinal bacterial community is indicative for the healthy status of Litopenaeus vannamei].

    Science.gov (United States)

    Wu, Jin-feng; Xiong, Jin-bo; Wang, Xin; Qiu, Qian-ling-ling; Zheng, Jia-lai; Zhang, De-min

    2016-02-01

    High density and intensive Litopenaeus vannamei aquaculture has increased the frequency of shrimp disease, however, it remains uncertain whether change in intestinal bacteria could be indicative of shrimp health state (healthy or diseased). Therefore, we collected water and shrimp intestine samples from ponds with or without diseased shrimps. Using bacterial 16S rRNA gene as a biomarker, the bacterial community structure and diversity were evaluated with the Illumina MiSeq sequencing technique. The results showed that the variations of bacterioplankton community were primarily shaped by the levels of NO2(-)-N, chlorophyll a and PO4(3-)-P. Bacterial diversity was signif-7 icantly lower in diseased shrimps than in healthy ones. Using a response ratio analysis, we screened 28 operational taxonomic units (OTUs), and their abundances significantly changed in the intestines between healthy and diseased shrimps. In general, the abundances of OTUs belonged to Actinobacteria, Flavobacteria and Bacilli significantly decreased in diseased shrimps compared with those in healthy shrimps., while the OTUs affiliated to Clostridia showed an opposite pattern. In addition, we obtained 61 indicator species that primarily affiliated to Bacteroidetes, Proteobacteria, Firmicutes, Planctomycetes and Actinobacteria. Notably, the identified indicator taxa exhibited clearly discriminative patterns among habitats (water or intestine) and health status. Collectively, this study provided scientific information for development of new probiotics and disease prevention.

  17. Zooplankton community composition of high mountain lakes in the Tatra Mts., the Alps in North Tyrol, and Scotland: relationship to pH, depth, organic carbon, and chlorophyll-a concentration

    Directory of Open Access Journals (Sweden)

    Skála Ivan

    2015-10-01

    Full Text Available The European EMERGE (European Mountain lake Ecosystems: Regionalisation, diaGnostic & socio-economic Evaluation project was a survey of high mountain lakes (above treeline across Europe using unified methods of sampling and analysis. The sampling was carried out in summer or autumn 2000, and comprised biological samples, and samples for chemical analysis. Data from three lake districts are used in this paper: the Tatra Mts. in Slovakia and Poland (45 lakes, the Alps in Tyrol in Austria (22 lakes, and Scotland (30 lakes. As it is shown by multiple regression analysis, DTOC (dissolved or total organic carbon is the key variable for most groups of zooplankton. With increasing DTOC and mostly with chlorophyll-a decreasing, pH increasing and depth decreasing, macrofitrators with coarse filter meshes are replaced by microfiltrators with fine filter meshes. Higher DTOC may increase bacterioplankton production and advantage species able to consume bacteria (microfiltrators. Other zooplankton species also differ in their preference for DTOC, chlorophyll-a, pH and depth, but DTOC being positively correlated with chlorophyll-a and pH positively correlated with depth. It may be caused by their different preference for food quality in terms of C:P ratio.

  18. Temperature dependences of growth rates and carrying capacities of marine bacteria depart from metabolic theoretical predictions

    KAUST Repository

    Huete-Stauffer, Tamara Megan

    2015-09-11

    Using the metabolic theory of ecology (MTE) framework, we evaluated over a whole annual cycle the monthly responses to temperature of the growth rates (μ) and carrying capacities (K) of heterotrophic bacterioplankton at a temperate coastal site. We used experimental incubations spanning 6oC with bacterial physiological groups identified by flow cytometry according to membrane integrity (live), nucleic acid content (HNA and LNA) and respiratory activity (CTC+). The temperature dependence of μat the exponential phase of growth was summarized by the activation energy (E), which was variable (-0.52 to 0.72 eV) but followed a seasonal pattern, only reaching the hypothesized value for aerobic heterotrophs of 0.65 eV during the spring bloom for the most active bacterial groups (live, HNA, CTC+). K (i.e. maximum experimental abundance) peaked at 4 × 106 cells mL-1 and generally covaried with μbut, contrary to MTE predictions, it did not decrease consistently with temperature. In the case of live cells, the responses of μand K to temperature were positively correlated and related to seasonal changes in substrate availability, indicating that the responses of bacteria to warming are far from homogeneous and poorly explained by MTE at our site. © FEMS 2015.

  19. Potential contribution of planktonic components to ammonium cycling in the coastal area off central-southern Chile during non-upwelling conditions

    Science.gov (United States)

    Molina, Veronica; Morales, Carmen E.; Farías, Laura; Cornejo, Marcela; Graco, Michelle; Eissler, Yoanna; Cuevas, Luis A.

    2012-01-01

    The potential contributions of different microbial components (consumption and production, and carbon assimilation associated with photolithotrophic and chemolithoautotrophic (nitrification) metabolisms in the water column were performed. Despite low water column concentrations of ammonium in wintertime, intense ammonium transformations were registered. Prokaryotes (or bacterioplankton) contributed most to ammonium generation rates over the entire water column; these rates increased with depth (0.4-3.1 μM d -1). In surface waters (10 m depth), aerobic ammonium oxidation (potentially by Bacteria and Archaea) was the dominant consumption process (average 0.7 μM d -1) whereas in the subsurface layer (20 and 50 m depth), unexpectedly, eukaryotes accounted for most of its consumption (average 2.1 μM d -1). Nitrification oxidized an important proportion of the ammonium in both layers (from 25% to 100%) and provided regenerated nitrate. The integrated water column rates of chemosynthesis (0.005 g C m -2 d -1) represented a large proportion (51%) of the total dark carbon fixation during the non-upwelling season when integrated rates of photosynthesis are relatively low (0.42 g C m -2 d -1) and microbial food webs dominate the transfer of carbon within this coastal system.

  20. Phylogenomic analysis of marine Roseobacters.

    Directory of Open Access Journals (Sweden)

    Kai Tang

    Full Text Available BACKGROUND: Members of the Roseobacter clade which play a key role in the biogeochemical cycles of the ocean are diverse and abundant, comprising 10-25% of the bacterioplankton in most marine surface waters. The rapid accumulation of whole-genome sequence data for the Roseobacter clade allows us to obtain a clearer picture of its evolution. METHODOLOGY/PRINCIPAL FINDINGS: In this study about 1,200 likely orthologous protein families were identified from 17 Roseobacter bacteria genomes. Functional annotations for these genes are provided by iProClass. Phylogenetic trees were constructed for each gene using maximum likelihood (ML and neighbor joining (NJ. Putative organismal phylogenetic trees were built with phylogenomic methods. These trees were compared and analyzed using principal coordinates analysis (PCoA, approximately unbiased (AU and Shimodaira-Hasegawa (SH tests. A core set of 694 genes with vertical descent signal that are resistant to horizontal gene transfer (HGT is used to reconstruct a robust organismal phylogeny. In addition, we also discovered the most likely 109 HGT genes. The core set contains genes that encode ribosomal apparatus, ABC transporters and chaperones often found in the environmental metagenomic and metatranscriptomic data. These genes in the core set are spread out uniformly among the various functional classes and biological processes. CONCLUSIONS/SIGNIFICANCE: Here we report a new multigene-derived phylogenetic tree of the Roseobacter clade. Of particular interest is the HGT of eleven genes involved in vitamin B12 synthesis as well as key enzynmes for dimethylsulfoniopropionate (DMSP degradation. These aquired genes are essential for the growth of Roseobacters and their eukaryotic partners.

  1. Seasonal changes in the D / H ratio of fatty acids of pelagic microorganisms in the coastal North Sea

    Science.gov (United States)

    Mariam Heinzelmann, Sandra; Bale, Nicole Jane; Villanueva, Laura; Sinke-Schoen, Danielle; Philippart, Catharina Johanna Maria; Smede Sinninghe Damsté, Jaap; Schouten, Stefan; van der Meer, Marcel Teunis Jan

    2016-10-01

    Culture studies of microorganisms have shown that the hydrogen isotopic composition of fatty acids depends on their metabolism, but there are only few environmental studies available to confirm this observation. Here we studied the seasonal variability of the deuterium-to-hydrogen (D / H) ratio of fatty acids in the coastal Dutch North Sea and compared this with the diversity of the phyto- and bacterioplankton. Over the year, the stable hydrogen isotopic fractionation factor ɛ between fatty acids and water (ɛlipid/water) ranged between -172 and -237 ‰, the algal-derived polyunsaturated fatty acid nC20:5 generally being the most D-depleted (-177 to -235 ‰) and nC18:0 the least D-depleted fatty acid (-172 to -210 ‰). The in general highly D-depleted nC20:5 is in agreement with culture studies, which indicates that photoautotrophic microorganisms produce fatty acids which are significantly depleted in D relative to water. The ɛlipid/water of all fatty acids showed a transient shift towards increased fractionation during the spring phytoplankton bloom, indicated by increasing chlorophyll a concentrations and relative abundance of the nC20:5 polyunsaturated fatty acids, suggesting increased contributions of photoautotrophy. Time periods with decreased fractionation (less negative ɛlipid/water values) can potentially be explained by an increased contribution of heterotrophy to the fatty acid pool. Our results show that the hydrogen isotopic composition of fatty acids is a promising tool to assess the community metabolism of coastal plankton potentially in combination with the isotopic analysis of more specific biomarker lipids.<

  2. 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)

    M. Goutx

    2008-05-01

    Full Text Available Bacterioplankton play a central role in energy and matter fluxes at the sea, yet the factors that constrain their variation in the marine systems are still poorly understood. Here we show the explanatory power of multivariate statistical analysis of bacterial community structures coupled with fine measurements of numerous environmental parameters. 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 what makes it an ideal model to test hypothesis 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 behinds bacterial community structure shifts in the water column. Physico-chemical parameters such as phosphate, nitrate, salinity and to a lesser extend temperature, oxygen, dissolve organic carbon and photosynthetically active radiation acted in synergy to explain bacterial assemblages changes with depth. Analysis of lipid biomarkers of the organic matter sources and fates suggested that bacterial community structure at the surface layers was in part explained by lipids from 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. This study is probably the first example of an analysis employing a complex environmental

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

    Science.gov (United States)

    Ghiglione, J. F.; Palacios, C.; Marty, J. C.; Mével, G.; Labrune, C.; Conan, P.; Pujo-Pay, M.; Garcia, N.; Goutx, M.

    2008-12-01

    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.

  4. 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.

  5. Cultivation and biochemical characterization of heterotrophic bacteria associated with phytoplankton bloom in the Amundsen sea polynya, Antarctica

    Science.gov (United States)

    Choi, Seon-Bin; Kim, Jong-Geol; Jung, Man-Young; Kim, So-Jeong; Min, Ui-Gi; Si, Ok-Ja; Park, Soo-Je; Yeon Hwang, Chung; Park, Jisoo; Lee, SangHoon; Rhee, Sung-Keun

    2016-01-01

    Polynyas are a key ecosystem for carbon cycling in the Antarctic Ocean due to the intensive primary production. Most of the knowledge regarding the bacterioplankton community in the Antarctic Ocean that is responsible for re-mineralization of fixed carbon comes from metagenomic analyses. Here, the extinction-dilution method was used to obtain representative heterotrophs from a polynya in the Amundsen Sea, Antarctica, and their biochemical potential for carbon re-mineralization were assessed. All 23 strains have close relatives belonging to type strains within the following genera (number of strains; % 16S rRNA gene sequence similarity): Bizionia (4; >97.8%), Leeuwenhoekiella (1; 96.2%), Pseudoalteromonas (14; >98.5%), Pseudomonas (1; 99.4%) and Sulfitobacter (3; 100%), which were also observed in 454 pyrosequencing-based analysis of 16S rRNA gene sequences of the polynya. Although sequence reads related to Polaribacter were the most common, Polaribacter strains could only be obtained from colonies cultured on agar plates. The strain of Leeuwenhoekiella showed a prominent ability in hydrolyzing diverse esters, amides, and glycosides while the strains of Pseudoalteromonas, Polaribacter, and Bizionia showed extracellular enzyme activities only on a narrow range of amides. The strains of Leeuwenhoekiella, Pseudoalteromonas, and Sulfitobacter utilized various labile carbon sources: carbohydrates, organic acids, amino acids, and peptides. The most frequent isolates, strains of Pseudoaltermonas, showed marked differences in terms of their potential to utilize different types of labile carbon sources, which may reflect high genomic diversity. The strains of Bizionia and Pseudomonas did not utilize carbohydrates. Unique biochemical properties associated with extracellular hydrolase activities and labile carbon utilization were revealed for dominant culturable heterotrophs which gives insights into their roles in active re-mineralization of fixed carbons in polynya.

  6. 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.

  7. Heterotrophic bacterial production and metabolic balance during the VAHINE mesocosm experiment in the New Caledonia lagoon

    Science.gov (United States)

    Van Wambeke, F.; Pfreundt, U.; Barani, A.; Berthelot, H.; Moutin, T.; Rodier, M.; Hess, W. R.; Bonnet, S.

    2015-12-01

    N2 fixation fuels ~ 50 % of new primary production in the oligotrophic South Pacific Ocean. The VAHINE mesocosm experiment designed to track the fate of diazotroph derived nitrogen (DDN) in the New Caledonia lagoon. Here, we examined the temporal dynamics of heterotrophic bacterial production during this experiment. Three replicate large-volume (~ 50 m3) mesocosms were deployed and were intentionally fertilized with dissolved inorganic phosphorus (DIP) to stimulate N2 fixation. We specifically examined relationships between N2 fixation rates and primary production, determined bacterial growth efficiency and established carbon budgets of the system from the DIP fertilization to the end of the experiment (days 5-23). Heterotrophic bacterioplankton production (BP) and alkaline phosphatase activity (APA) were statistically higher during the second phase of the experiment (P2: days 15-23), when chlorophyll biomass started to increase compared to the first phase (P1: days 5-14). Among autotrophs, Synechococcus abundances increased during P2, possibly related to its capacity to assimilate leucine and to produce alkaline phosphatase. Bacterial growth efficiency based on the carbon budget was notably higher than generally cited for oligotrophic environments (27-43 %), possibly due to a high representation of proteorhodopsin-containing organisms within the picoplanctonic community. The carbon budget showed that the main fate of gross primary production (particulate + dissolved) was respiration (67 %), and export through sedimentation (17 %). BP was highly correlated with particulate primary production and chlorophyll biomass during both phases of the experiment but slightly correlated, and only during P2 phase, with N2 fixation rates. Our results suggest that most of the DDN reached the heterotrophic bacterial community through indirect processes, like mortality, lysis and grazing.

  8. Increased bacterial growth efficiency with environmental variability: results from DOC degradation by bacteria in pure culture experiments

    Directory of Open Access Journals (Sweden)

    M. Eichinger

    2010-06-01

    Full Text Available This paper assesses how considering variation in DOC availability and cell maintenance in bacterial models affects Bacterial Growth Efficiency (BGE estimations. For this purpose, we conducted two biodegradation experiments simultaneously. In experiment one, a given amount of substrate was added to the culture at the start of the experiment whilst in experiment two, the same amount of substrate was added, but using periodic pulses over the time course of the experiment. Three bacterial models, with different levels of complexity, (the Monod, Marr-Pirt and the dynamic energy budget – DEB – models, were used and calibrated using the above experiments. BGE has been estimated using the experimental values obtained from discrete samples and from model generated data. Cell maintenance was derived experimentally, from respiration rate measurements. The results showed that the Monod model did not reproduce the experimental data accurately, whereas the Marr-Pirt and DEB models demonstrated a good level of reproducibility, probably because cell maintenance was built into their formula. Whatever estimation method was used, the BGE value was always higher in experiment two (the periodically pulsed substrate as compared to the initially one-pulsed-substrate experiment. Moreover, BGE values estimated without considering cell maintenance (Monod model and empirical formula were always smaller than BGE values obtained from models taking cell maintenance into account. Since BGE is commonly estimated using constant experimental systems and ignore maintenance, we conclude that these typical methods underestimate BGE values. On a larger scale, and for biogeochemical cycles, this would lead to the conclusion that, for a given DOC supply rate and a given DOC consumption rate, these BGE estimation methods overestimate the role of bacterioplankton as CO2 producers.

  9. Increased bacterial growth efficiency with environmental variability: results from DOC degradation by bacteria in pure culture experiments

    Directory of Open Access Journals (Sweden)

    M. Eichinger

    2010-02-01

    Full Text Available This paper assesses how considering variation in DOC availability and cell maintenance in bacterial models affects Bacterial Growth Efficiency (BGE estimations. For this purpose, we conducted two biodegradation experiments simultaneously. In experiment one, a given amount of substrate was added to the culture at the start of the experiment whilst in experiment two, the same amount of substrate was added, but using periodic pulses over the time course of the experiment. Three bacterial models, with different levels of complexity, (the Monod, Marr-Pirt and the dynamic energy budget (DEB model, were used, and calibrated using the above experiments. BGE has been estimated using the experimental values obtained from discrete samples and from model generated data. Cell maintenance was derived experimentally, from respiration rate measurements. The results showed that the Monod model did not reproduce the experimental data accurately, whereas the Marr-Pirt and DEB models demonstrated a good level of reproducibility, probably because cell maintenance was built into their formula. Whatever estimation method was used, the BGE value was always higher in experiment two (the periodically pulsed substrate as compared to the initially one-pulsed-substrate experiment. Moreover, BGE values estimated without considering cell maintenance (Monod model and empirical formula were always smaller than BGE values obtained from models taking cell maintenance into account. Since BGE is commonly estimated using constant experimental systems and ignore maintenance, we conclude that these typical methods underestimate BGE values. On a larger scale, and for biogeochemical cycles, this would lead to the conclusion that, for a given DOC supply rate and a given DOC consumption rate, these BGE estimation methods overestimate the role of bacterioplankton as CO2 producers.

  10. Plankton assembly in an ultra-oligotrophic Antarctic lake over the summer transition from the ice-cover to ice-free period: A size spectra approach

    Science.gov (United States)

    Rochera, Carlos; Quesada, Antonio; Toro, Manuel; Rico, Eugenio; Camacho, Antonio

    2017-03-01

    Lakes from the Antarctic maritime region experience climate change as a main stressor capable of modifying their plankton community structure and function, essentially because summer temperatures are commonly over the freezing point and the lake's ice cap thaws. This study was conducted in such seasonally ice-covered lake (Lake Limnopolar, Byers Peninsula, Livingston Is., Antarctica), which exhibits a microbial dominated pelagic food web. An important feature is also the occurrence of benthic mosses (Drepanocladus longifolius) covering the lake bottom. Plankton dynamics were investigated during the ice-thawing transition to the summer maximum. Both bacterioplankton and viral-like particles were higher near the lake's bottom, suggesting a benthic support. When the lake was under dim conditions because of the snow-and-ice cover, autotrophic picoplankters dominated at deep layers. The taxa-specific photopigments indicated dominance of picocyanobacteria among them when the light availability was lower. By contrast, larger and less edible phytoplankton dominated at the onset of the ice melting. The plankton size spectra were fitted to the continuous model of Pareto distribution. Spectra evolved similarly at two sampled depths, in surface and near the bottom, with slopes increasing until mid-January. However, slopes were less steep (i.e., size classes more uniformly distributed) at the bottom, thus denoting a more efficient utilization of resources. These findings suggest that microbial loop pathways in the lake are efficiently channelized during some periods to the metazoan production (mainly the copepod Boeckella poppei). Our results point to that trophic interactions may still occur in these lakes despite environmental harshness. This results of interest in a framework of increasing temperatures that may reduce the climatic restrictions and therefore stimulate biotic interactions.

  11. Combined analyses of the ITS loci and the corresponding 16S rRNA genes reveal high micro- and macrodiversity of SAR11 populations in the Red Sea.

    KAUST Repository

    Ngugi, David

    2012-11-20

    Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24 °C throughout the year, and a remarkable uniform temperature (~22 °C) and salinity (~41 psu) from the mixed layer (~200 m) to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS) region of SAR11 in different depths of the Red Sea\\'s water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e.g., temperature, nutrient availability, and concentration of dissolved oxygen) on the population dynamics of this ubiquitous marine bacterium.

  12. High molecular weight dissolved organic matter enrichment selects for methylotrophs in dilution to extinction cultures.

    Science.gov (United States)

    Sosa, Oscar A; Gifford, Scott M; Repeta, Daniel J; DeLong, Edward F

    2015-12-01

    The role of bacterioplankton in the cycling of marine dissolved organic matter (DOM) is central to the carbon and energy balance in the ocean, yet there are few model organisms available to investigate the genes, metabolic pathways, and biochemical mechanisms involved in the degradation of this globally important carbon pool. To obtain microbial isolates capable of degrading semi-labile DOM for growth, we conducted dilution to extinction cultivation experiments using seawater enriched with high molecular weight (HMW) DOM. In total, 93 isolates were obtained. Amendments using HMW DOM to increase the dissolved organic carbon concentration 4x (280 μM) or 10x (700 μM) the ocean surface water concentrations yielded positive growth in 4-6% of replicate dilutions, whereas <1% scored positive for growth in non-DOM-amended controls. The majority (71%) of isolates displayed a distinct increase in cell yields when grown in increasing concentrations of HMW DOM. Whole-genome sequencing was used to screen the culture collection for purity and to determine the phylogenetic identity of the isolates. Eleven percent of the isolates belonged to the gammaproteobacteria including Alteromonadales (the SAR92 clade) and Vibrio. Surprisingly, 85% of isolates belonged to the methylotrophic OM43 clade of betaproteobacteria, bacteria thought to metabolically specialize in degrading C1 compounds. Growth of these isolates on methanol confirmed their methylotrophic phenotype. Our results indicate that dilution to extinction cultivation enriched with natural sources of organic substrates has a potential to reveal the previously unsuspected relationships between naturally occurring organic nutrients and the microorganisms that consume them.

  13. Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site.

    Science.gov (United States)

    Stingl, Ulrich; Tripp, Harry James; Giovannoni, Stephen J

    2007-08-01

    The introduction of high-throughput dilution-to-extinction culturing (HTC) of marine bacterioplankton using sterilized natural sea water as media yielded isolates of many abundant but previously uncultured marine bacterial clades. In early experiments, bacteria from the SAR11 cluster (class Alphaproteobacteria), which are presumed to be the most abundant prokaryotes on earth, were cultured. Although many additional attempts were made, no further strains of the SAR11 clade were obtained. Here, we describe improvements to the HTC technique, which led to the isolation of 17 new SAR11 strains from the Oregon coast and the Sargasso Sea, accounting for 28% and 31% of all isolates in these experiments. Phylogenetic analysis of the internal transcribed spacer (ITS) region showed that the isolates from the Oregon coast represent three different subclusters of SAR11, while isolates from the Sargasso Sea were more uniform and represented a single ITS cluster. A PCR assay proved the presence of proteorhodopsin (PR) in nearly all SAR11 isolates. Analysis of PR amino-acid sequences indicated that isolates from the Oregon coast were tuned to either green or blue light, while PRs from strains obtained from the Sargasso Sea were exclusively tuned to maximum absorbance in the blue. Interestingly, phylogenies based on PR and ITS did not correlate, suggesting lateral gene transfer. In addition to the new SAR11 strains, many novel strains belonging to clusters of previously uncultured or undescribed species of different bacterial phyla, including the first strain of the highly abundant alphaproteobacterial SAR116 clade, were isolated using the modified methods.

  14. Assembling the Marine Metagenome, One Cell at a Time

    Energy Technology Data Exchange (ETDEWEB)

    Woyke, Tanja; Xie, Gary; Copeland, Alex; Gonzalez, Jose M.; Han, Cliff; Kiss, Hajnalka; Saw, Jimmy H.; Senin, Pavel; Yang, Chi; Chatterji, Sourav; Cheng, Jan-Fang; Eisen, Jonathan A.; Sieracki, Michael E.; Stepanauskas, Ramunas

    2010-06-24

    taxa from a complex microbial community of marine bacterioplankton. A combination of single cell genomics and metagenomics enabled us to analyze the genome content, metabolic adaptations, and biogeography of these taxa.

  15. Ecosystem element transport model for Lake Eckarfjaerden

    Energy Technology Data Exchange (ETDEWEB)

    Konovalenko, L.; Bradshaw, C. [The Department of Ecology, Environment and Plant Sciences, Stockholm University (Sweden); Andersson, E.; Kautsky, U. [Swedish Nuclear Fuel and Waste Management Co. - SKB (Sweden)

    2014-07-01

    The ecosystem transport model of elements was developed for Lake Eckarfjaerden located in the Forsmark area in Sweden. Forsmark has currently a low level repository (SFR) and a repository for spent fuel is planned. A large number of data collected during site-investigation program 2002-2009 for planning the repository were available for the creation of the compartment model based on carbon circulation, physical and biological processes (e.g. primary production, consumption, respiration). The model is site-specific in the sense that the food web model is adapted to the actual food web at the site, and most estimates of biomass and metabolic rates for the organisms and meteorological data originate from site data. The functional organism groups of Lake Eckarfjaerden were considered as separate compartments: bacterio-plankton, benthic bacteria, macro-algae, phytoplankton, zooplankton, fish, benthic fauna. Two functional groups of bacteria were taken into account for the reason that they have the highest biomass of all functional groups during the winter, comprising 36% of the total biomass. Effects of ecological parameters, such as bacteria and algae biomass, on redistribution of a hypothetical radionuclide release in the lake were examined. The ecosystem model was used to estimate the environmental transfer of several elements (U, Th, Ra) and their isotopes (U-238, U-234,Th-232, Ra-226) to various aquatic organisms in the lake, using element-specific distribution coefficients for suspended particle and sediment. Results of chemical analyses of the water, sediment and biota were used for model validation. The model gives estimates of concentration factors for fish based on modelling rather on in situ measurement, which reduces the uncertainties for many radionuclides with scarce of data. Document available in abstract form only. (authors)

  16. Heterotrophic bacterial production and metabolic balance during the VAHINE mesocosm experiment in the New Caledonia lagoon

    Directory of Open Access Journals (Sweden)

    F. Van Wambeke

    2015-12-01

    Full Text Available N2 fixation fuels ~ 50 % of new primary production in the oligotrophic South Pacific Ocean. The VAHINE mesocosm experiment designed to track the fate of diazotroph derived nitrogen (DDN in the New Caledonia lagoon. Here, we examined the temporal dynamics of heterotrophic bacterial production during this experiment. Three replicate large-volume (~ 50 m3 mesocosms were deployed and were intentionally fertilized with dissolved inorganic phosphorus (DIP to stimulate N2 fixation. We specifically examined relationships between N2 fixation rates and primary production, determined bacterial growth efficiency and established carbon budgets of the system from the DIP fertilization to the end of the experiment (days 5–23. Heterotrophic bacterioplankton production (BP and alkaline phosphatase activity (APA were statistically higher during the second phase of the experiment (P2: days 15–23, when chlorophyll biomass started to increase compared to the first phase (P1: days 5–14. Among autotrophs, Synechococcus abundances increased during P2, possibly related to its capacity to assimilate leucine and to produce alkaline phosphatase. Bacterial growth efficiency based on the carbon budget was notably higher than generally cited for oligotrophic environments (27–43 %, possibly due to a high representation of proteorhodopsin-containing organisms within the picoplanctonic community. The carbon budget showed that the main fate of gross primary production (particulate + dissolved was respiration (67 %, and export through sedimentation (17 %. BP was highly correlated with particulate primary production and chlorophyll biomass during both phases of the experiment but slightly correlated, and only during P2 phase, with N2 fixation rates. Our results suggest that most of the DDN reached the heterotrophic bacterial community through indirect processes, like mortality, lysis and grazing.

  17. Spatio-temporal variability of dissolved organic nitrogen (DON), carbon (DOC), and nutrients in the Nile River, Egypt.

    Science.gov (United States)

    Badr, El-Sayed A

    2016-10-01

    Increases in human activity have resulted in enhanced anthropogenic inputs of nitrogen (N) and carbon (C) into the Nile River. The Damietta Branch of the Nile is subject to inputs from industrial, agricultural, and domestic wastewater. This study investigated the distribution and seasonality of dissolved organic nitrogen (DON), dissolved organic carbon (DOC), and nutrients in the Nile Damietta Branch. Water samples were collected from 24 sites between May 2009 and February 2010. Dissolved organic nitrogen concentrations averaged 251 ± 115 μg/l, with a range of 90.2-671 μg/l, and contributed 40.8 ± 17.7 % to the total dissolved nitrogen (TDN) pool. Relative to autumn and winter, DON was a larger fraction of the TDN pool during spring and summer indicating the influence of bacterioplankton on the nitrogen cycle. Concentrations of DOC ranged from 2.23 to 11.3 mg/l with an average of 5.15 ± 2.36 mg/l, reflecting a high organic matter load from anthropogenic sources within the study area, and were highest during autumn. Higher values of biochemical oxygen demand (BOD), chemical oxygen demand (COD), DON, nitrate, and phosphate occurred downstream of the Damietta Branch and were probably due to anthropogenic inputs to the Nile from the Damietta district. A bacterial incubation experiment indicated that 52.1-95.0 % of DON was utilized by bacteria within 21 days. The decrease in DON concentration was accompanied by an increase in nitrate concentration of 54.8-87.3 %, presumably through DON mineralization. Based on these results, we recommend that water quality assessments consider DON and DOC, as their omission may result in an underestimation of the total organic matter load and impact.

  18. Turbulence-driven shifts in holobionts and planktonic microbial assemblages in St Peter & St Paul Archipelago, Mid-Atlantic Ridge, Brazil

    Directory of Open Access Journals (Sweden)

    Ana Paula B. Moreira

    2015-10-01

    Full Text Available The aim of this study was to investigate the planktonic and the holobiont Madracis decactis (Scleractinia microbial diversity along a turbulence-driven upwelling event, in the world´s most isolated tropical island, St Peter and St Paul Archipelago (SPSPA, Brazil. Twenty one metagenomes were obtained for seawater (N=12, healthy and bleached holobionts (N=9 before, during and after the episode of high seawater turbulence and upwelling. Microbial assemblages differed between low turbulence-low nutrient (LLR and high-turbulence-high nutrient (HHR regimes in seawater. During LLR there was a balance between autotrophy and heterotrophy in the bacterioplankton and the ratio cyanobacteria:heterotrophs ~1 (C:H. Prochlorales, unclassified Alphaproteobacteria and Euryarchaeota were the dominant bacteria and archaea, respectively. Basic metabolisms and cyanobacterial phages characterized the LLR. During HHR C:H << 0.05 and Gammaproteobacteria approximated 50% of the most abundant organisms in seawater. Alteromonadales, Oceanospirillales and Thaumarchaeota were the dominant bacteria and archaea. Prevailing metabolisms were related to membrane transport, virulence, disease and defense. Phages targeting heterotrophs and virulence factor genes characterized HHR. Shifts were also observed in coral microbiomes, according to both annotation–indepent and -dependent methods. HHR bleached corals metagenomes were the most dissimilar and could be distinguished by their di- and tetranucleotides frequencies, Iron Acquision metabolism and virulence genes, such as V. cholerae-related virulence factors. The healthy coral holobiont was shown to be less sensitive to transient seawater-related perturbations than the diseased animals. A conceptual model for the turbulence-induced shifts is put forward.

  19. A nonpyrrolysine member of the widely distributed trimethylamine methyltransferase family is a glycine betaine methyltransferase.

    Science.gov (United States)

    Ticak, Tomislav; Kountz, Duncan J; Girosky, Kimberly E; Krzycki, Joseph A; Ferguson, Donald J

    2014-10-28

    COG5598 comprises a large number of proteins related to MttB, the trimethylamine:corrinoid methyltransferase. MttB has a genetically encoded pyrrolysine residue proposed essential for catalysis. MttB is the only known trimethylamine methyltransferase, yet the great majority of members of COG5598 lack pyrrolysine, leaving the activity of these proteins an open question. Here, we describe the function of one of the nonpyrrolysine members of this large protein family. Three nonpyrrolysine MttB homologs are encoded in Desulfitobacterium hafniense, a Gram-positive strict anaerobe present in both the environment and human intestine. D. hafniense was found capable of growth on glycine betaine with electron acceptors such as nitrate or fumarate, producing dimethylglycine and CO2 as products. Examination of the genome revealed genes for tetrahydrofolate-linked oxidation of a methyl group originating from a methylated corrinoid protein, but no obvious means to carry out corrinoid methylation with glycine betaine. DSY3156, encoding one of the nonpyrrolysine MttB homologs, was up-regulated during growth on glycine betaine. The recombinant DSY3156 protein converts glycine betaine and cob(I)alamin to dimethylglycine and methylcobalamin. To our knowledge, DSY3156 is the first glycine betaine:corrinoid methyltransferase described, and a designation of MtgB is proposed. In addition, DSY3157, an adjacently encoded protein, was shown to be a methylcobalamin:tetrahydrofolate methyltransferase and is designated MtgA. Homologs of MtgB are widely distributed, especially in marine bacterioplankton and nitrogen-fixing plant symbionts. They are also found in multiple members of the human microbiome, and may play a beneficial role in trimethylamine homeostasis, which in recent years has been directly tied to human cardiovascular health.

  20. Insight into the microbial community structure of a Norwegian deep-water coral reef environment

    Science.gov (United States)

    Jensen, Sigmund; Neufeld, Josh D.; Birkeland, Nils-Kåre; Hovland, Martin; Murrell, J. Colin

    2008-11-01

    Deep-water coral reefs support rich biological communities below the photic zone of fjords and continental shelves around the world. In this environment, life is enclosed within cold permanent darkness, in stark contrast to life in tropical coral reefs. We collected samples of water, sediment and a Desmacidon sp. sponge from a deep-water coral reef off the coast of Norway, and characterised bacterial communities with focus on primary producers in the dark. Following DNA extraction, PCR amplification and 16S rRNA gene library sequencing, bioinformatic analyses demonstrated significant differences between bacterial communities associated with the three samples. The finding that 50% of the clones showed cultured bacteria reflects the novel and uncharacterised diversity associated with these deep-water coral reefs. A total of 13 bacterial phyla were identified. Acidobacteria dominated the sponge library and Proteobacteria dominated the bacterioplankton and sediment libraries. Phylogenetic analysis revealed a possible new clade of sponge-associated Acidobacteria, which includes representatives from the Desmacidon sp. (Norway), Rhopaloeides odorabile (Australia) and Discodermia dissoluta (Curacao). Furthermore, the targeted recovery of a particulate methane monooxygenase ( pmoA) gene from the Desmacidon sp. DNA extract suggests that as yet uncultivated type I methanotrophs may mediate methane oxidation in this deep-water coral reef. Methanotrophs were not identified in the 16S rRNA gene libraries, but the presence of a high number (8%) of clones related to sulfide-, nitrite- and iodide-oxidising bacteria suggests chemosynthesis to be involved with maintenance of the deep-water coral reef ecosystem.

  1. Enhanced recycling of organic matter and Os-isotopic evidence for multiple magmatic or meteoritic inputs to the Late Permian Panthalassic Ocean, Opal Creek, Canada

    Science.gov (United States)

    Georgiev, Svetoslav V.; Stein, Holly J.; Hannah, Judith L.; Henderson, Charles M.; Algeo, Thomas J.

    2015-02-01

    The geochemical record for the Permian-Triassic boundary in northern latitudes is essential to evaluation of global changes associated with the most profound extinction of life on Earth. We present inorganic and organic geochemical data, and Re-Os isotope systematics in a critical stratigraphic interval of pre- and post-extinction Upper Permian-Lower Triassic sediments from Opal Creek, western Canada (paleolatitude of ∼30°N). We document significant and long-lived changes in Panthalassa seawater chemistry that were initiated during the first of four magmatic or meteoritic inputs to Late Permian seawater, evidenced by notable decreases of Os isotopic ratios upsection. Geochemical signals indicate establishment of anoxic bottom waters shortly after regional transgression reinitiated sedimentation in the Late Permian. Euxinic signals are most prominent in the Upper Permian sediments with low organic carbon and high sulfur contents, and gradually wane in the Lower Triassic. The observed features may have been generated in a strongly euxinic ocean in which high bacterioplankton productivity sustained prolific microbial sulfate reduction in the sediment and/or water column, providing hydrogen sulfide to form pyrite. This scenario requires nearly complete anaerobic decomposition of predominantly labile marine organic matter (OM) without the necessity for a complete collapse of primary marine productivity. Similar geochemical variations could have been achieved by widespread oxidation of methane by sulfate reducers after a methanogenic burst in the Late Permian. Both scenarios could have provided similar kill mechanisms for the latest Permian mass extinction. Despite the moderate thermal maturity of the section, OM in all studied samples is dominantly terrestrial and/or continentally derived, recycled and refractory ancient OM. We argue that, as such, the quantity of the OM in the section mainly reflects changes in terrestrial vegetation and/or weathering, and not in

  2. Trophic interactions between viruses, bacteria and nanoflagellates under various nutrient conditions and simulated climate change.

    Science.gov (United States)

    Bouvy, M; Bettarel, Y; Bouvier, C; Domaizon, I; Jacquet, S; Le Floc'h, E; Montanié, H; Mostajir, B; Sime-Ngando, T; Torréton, J P; Vidussi, F; Bouvier, T

    2011-07-01

    Population dynamics in the microbial food web are influenced by resource availability and predator/parasitism activities. Climatic changes, such as an increase in temperature and/or UV radiation, can also modify ecological systems in many ways. A series of enclosure experiments was conducted using natural microbial communities from a Mediterranean lagoon to assess the response of microbial communities to top-down control [grazing by heterotrophic nanoflagellates (HNF), viral lysis] and bottom-up control (nutrients) under various simulated climatic conditions (temperature and UV-B radiations). Different biological assemblages were obtained by separating bacteria and viruses from HNF by size fractionation which were then incubated in whirl-Pak bags exposed to an increase of 3°C and 20% UV-B above the control conditions for 96 h. The assemblages were also provided with an inorganic and organic nutrient supply. The data show (i) a clear nutrient limitation of bacterial growth under all simulated climatic conditions in the absence of HNF, (ii) a great impact of HNF grazing on bacteria irrespective of the nutrient conditions and the simulated climatic conditions, (iii) a significant decrease in burst size (BS) (number of intracellular lytic viruses per bacterium) and a significant increase of VBR (virus to bacterium ratio) in the presence of HNF, and (iv) a much larger temperature effect than UV-B radiation effect on the bacterial dynamics. These results show that top-down factors, essentially HNF grazing, control the dynamics of the lagoon bacterioplankton assemblage and that short-term simulated climate changes are only a secondary effect controlling microbial processes.

  3. Small Boreal Lake Ecosystem Evolution under the Influence of Natural and Anthropogenic Factors: Results of Multidisciplinary Long-Term Study

    Directory of Open Access Journals (Sweden)

    Liudmila Shirokova

    2016-07-01

    Full Text Available Small aquatic ecosystems of the boreal zone are known to be most sensitive indicators of on-going environmental change as well as local anthropogenic pressure, while being highly vulnerable to external impacts. Compared to rather detailed knowledge of the evolution of large and small lakes in Scandinavia and Canada, and large lakes in Eurasia, highly abundant small boreal lakes of northwest Russia have received very little attention, although they may become important centers of attraction of growing rural population in the near future. Here we present the results of a multidisciplinary, multi-annual study of a small boreal humic lake of NW Russia. A shallow (3 m and a deep (16 m site of this lake were regularly sampled for a range of chemical and biological parameters. Average multi-daily, summer-time values of the epilimnion (upper oxygenated layer of the lake provided indications of possible trends in temperature, nutrients, and bacterio-plankton concentration that revealed the local pollution impact in the shallow zone and overall environmental trend in the deep sampling point of the lake. Organic phosphorus, nitrate, and lead were found to be most efficient tracers of local anthropogenic pollution, especially visible in the surface layer of the shallow site of the lake. Cycling of trace elements between the epilimnion and hypolimnion is tightly linked to dissolved organic matter speciation and size fractionation due to the dominance of organic and organo-ferric colloids. The capacity of lake self-purification depends on the ratio of primary productivity to mineralization of organic matter. This ratio remained >1 both during winter and summer periods, which suggests a high potential of lake recovery from the input of allochthonous dissolved organic matter and local anthropogenic pollution.

  4. Contribution of picoplankton to the total particulate organic carbon (POC concentration in the eastern South Pacific

    Directory of Open Access Journals (Sweden)

    C. Grob

    2007-05-01

    Full Text Available Prochlorococcus, Synechococcus, picophytoeukaryotes and bacterioplankton abundances and contributions to the total particulate organic carbon concentration (POC, derived from the total particle beam attenuation coefficient (cp, were determined across the eastern South Pacific between the Marquesas Islands and the coast of Chile. All flow cytometrically derived abundances decreased towards the hyper-oligotrophic centre of the gyre and were highest at the coast, except for Prochlorococcus, which is not detected under eutrophic conditions. Temperature and nutrient availability appeared important in modulating picophytoplankton abundance, according to the prevailing trophic conditions. Although the non-vegetal particles tended to dominate the cp signal everywhere along the transect (50 to 83%, this dominance seemed to weaken from oligo- to eutrophic conditions, the contributions by vegetal and non-vegetal particles being about equal under mature upwelling conditions. Spatial variability in the vegetal compartment was more important than the non-vegetal one in shaping the water column particulate attenuation coefficient. Spatial variability in picophytoplankton biomass could be traced by changes in both Tchla and cp. Finally, picophytoeukaryotes contributed with ~38% on average to the total integrated phytoplankton carbon biomass or vegetal attenuation signal along the transect, as determined by direct size measurements on cells sorted by flow cytometry and optical theory. The role of picophytoeukaryotes in carbon and energy flow would therefore be very important, even under hyper-oligotrophic conditions.

  5. Alginate lyases from alginate-degrading Vibrio splendidus 12B01 are endolytic.

    Science.gov (United States)

    Badur, Ahmet H; Jagtap, Sujit Sadashiv; Yalamanchili, Geethika; Lee, Jung-Kul; Zhao, Huimin; Rao, Christopher V

    2015-03-01

    Alginate lyases are enzymes that degrade alginate through β-elimination of the glycosidic bond into smaller oligomers. We investigated the alginate lyases from Vibrio splendidus 12B01, a marine bacterioplankton species that can grow on alginate as its sole carbon source. We identified, purified, and characterized four polysaccharide lyase family 7 alginates lyases, AlyA, AlyB, AlyD, and AlyE, from V. splendidus 12B01. The four lyases were found to have optimal activity between pH 7.5 and 8.5 and at 20 to 25°C, consistent with their use in a marine environment. AlyA, AlyB, AlyD, and AlyE were found to exhibit a turnover number (kcat) for alginate of 0.60 ± 0.02 s(-1), 3.7 ± 0.3 s(-1), 4.5 ± 0.5 s(-1), and 7.1 ± 0.2 s(-1), respectively. The Km values of AlyA, AlyB, AlyD, and AlyE toward alginate were 36 ± 7 μM, 22 ± 5 μM, 60 ± 2 μM, and 123 ± 6 μM, respectively. AlyA and AlyB were found principally to cleave the β-1,4 bonds between β-d-mannuronate and α-l-guluronate and subunits; AlyD and AlyE were found to principally cleave the α-1,4 bonds involving α-l-guluronate subunits. The four alginate lyases degrade alginate into longer chains of oligomers.

  6. Assembling The Marine Metagenome, One Cell At A Time

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Gang [Los Alamos National Laboratory; Han, Shunsheng [Los Alamos National Laboratory; Kiss, Hajnalka [Los Alamos National Laboratory; Saw, Jimmy [Los Alamos National Laboratory; Senin, Pavel [Los Alamos National Laboratory; Woyke, Tanja [DOE JOINT GENOME INAT.; Copeland, Alex [DOE JOINT GENSOME INST.; Gonzalez, Jose [UNIV OF LAGUNA, SPAIN; Chatterji, Sourav [DOE JOINT GENSOME INST.; Cheng, Jan - Fang [DOE JOINT GENSOME INST.; Eisen, Jonathan A [DOE JOINT GENOME INST.; Sieracki, Michael E [UNIV OF CA-DAVIS; Stepanauskas, Ramunas [BIGELOW LAB

    2008-01-01

    microbial community of marine bacterioplankton. A combination of single cell genomics and metagenomics enabled us to analyze the genome content, metabolic adaptations, and biogeography of these taxa.

  7. Assembling the marine metagenome, one cell at a time.

    Directory of Open Access Journals (Sweden)

    Tanja Woyke

    taxa from a complex microbial community of marine bacterioplankton. A combination of single cell genomics and metagenomics enabled us to analyze the genome content, metabolic adaptations, and biogeography of these taxa.

  8. Taxonomic and Environmental Variability in the Elemental Composition and Stoichiometry of Individual Dinoflagellate and Diatom Cells from the NW Mediterranean Sea.

    Directory of Open Access Journals (Sweden)

    Mariona Segura-Noguera

    Full Text Available Here we present, for the first time, the elemental concentration, including C, N and O, of single phytoplankton cells collected from the sea. Plankton elemental concentration and stoichiometry are key variables in phytoplankton ecophysiology and ocean biogeochemistry, and are used to link cells and ecosystems. However, most field studies rely on bulk techniques that overestimate carbon and nitrogen because the samples include organic matter other than plankton organisms. Here we used X-ray microanalysis (XRMA, a technique that, unlike bulk analyses, gives simultaneous quotas of C, N, O, Mg, Si, P, and S, in single-cell organisms that can be collected directly from the sea. We analysed the elemental composition of dinoflagellates and diatoms (largely Chaetoceros spp. collected from different sites of the Catalan coast (NW Mediterranean Sea. As expected, a lower C content is found in our cells compared to historical values of cultured cells. Our results indicate that, except for Si and O in diatoms, the mass of all elements is not a constant fraction of cell volume but rather decreases with increasing cell volume. Also, diatoms are significantly less dense in all the measured elements, except Si, compared to dinoflagellates. The N:P ratio of both groups is higher than the Redfield ratio, as it is the N:P nutrient ratio in deep NW Mediterranean Sea waters (N:P = 20-23. The results suggest that the P requirement is highest for bacterioplankton, followed by dinoflagellates, and lowest for diatoms, giving them a clear ecological advantage in P-limited environments like the Mediterranean Sea. Finally, the P concentration of cells of the same genera but growing under different nutrient conditions was the same, suggesting that the P quota of these cells is at a critical level. Our results indicate that XRMA is an accurate technique to determine single cell elemental quotas and derived conversion factors used to understand and model ocean biogeochemical

  9. Prokaryotic diversity in one of the largest hypersaline coastal lagoons in the world.

    Science.gov (United States)

    Clementino, M M; Vieira, R P; Cardoso, A M; Nascimento, A P A; Silveira, C B; Riva, T C; Gonzalez, A S M; Paranhos, R; Albano, R M; Ventosa, A; Martins, O B

    2008-07-01

    Araruama Lagoon is an environment characterized by high salt concentrations. The low raining and high evaporation rates in this region favored the development of many salty ponds around the lagoon. In order to reveal the microbial composition of this system, we performed a 16S rRNA gene survey. Among archaea, most clones were related to uncultured environmental Euryarchaeota. In lagoon water, we found some clones related to Methanomicrobia and Methanothermococcus groups, while in the saline pond water members related to the genus Haloarcula were detected. Bacterial community was dominated by clones related to Gamma-proteobacteria, Actinobacteria, and Synechococcus in lagoon water, while Salinibacter ruber relatives dominated in saline pond. We also detected the presence of Alpha-proteobacteria, Pseudomonas-like bacteria and Verrucomicrobia. Only representatives of the genus Ralstonia were cosmopolitan, being observed in both systems. The detection of a substantial number of clones related to uncultured archaea and bacteria suggest that the hypersaline waters of Araruama harbor a pool of novel prokaryotic phylotypes, distinct from those observed in other similar systems. We also observed clones related to halophilic genera of cyanobacteria that are specific for each habitat studied. Additionally, two bacterioplankton molecular markers with ecological relevance were analyzed, one is linked to nitrogen fixation (nifH) and the other is linked to carbon fixation by bacterial photosynthesis, the protochlorophyllide genes, revealing a specific genetic distribution in this ecosystem. This is the first study of the biogeography and community structure of microbial assemblages in Brazilian tropical hypersaline environments. This work is directed towards a better understanding of the free-living prokaryotic diversity adapted to life in hypersaline waters.

  10. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea

    Directory of Open Access Journals (Sweden)

    C. Jeanthon

    2011-07-01

    Full Text Available Aerobic anoxygenic phototrophic (AAP bacteria play significant roles in the bacterioplankton productivity and biogeochemical cycles of the surface ocean. In this study, we applied both cultivation and mRNA-based molecular methods to explore the diversity of AAP bacteria along an oligotrophic gradient in the Mediterranean Sea in early summer 2008. Colony-forming units obtained on three different agar media were screened for the production of bacteriochlorophyll-a (BChl-a, the light-harvesting pigment of AAP bacteria. BChl-a-containing colonies represented a low part of the cultivable fraction. In total, 54 AAP strains were isolated and the phylogenetic analyses based on their 16S rRNA and pufM genes showed that they were all affiliated to the Alphaproteobacteria. The most frequently isolated strains belonged to Citromicrobium bathyomarinum, and Erythrobacter and Roseovarius species. Most other isolates were related to species not reported to produce BChl-a and/or may represent novel taxa. Direct extraction of RNA from seawater samples enabled the analysis of the expression of pufM, the gene coding for the M subunit of the reaction centre complex of aerobic anoxygenic photosynthesis. Clone libraries of pufM gene transcripts revealed that most phylotypes were highly similar to sequences previously recovered from the Mediterranean Sea and a large majority (~94 % was affiliated to the Gammaproteobacteria. The most abundantly detected phylotypes occurred in the western and eastern Mediterranean basins. However, some were exclusively detected in the eastern basin, reflecting the highest diversity of pufM transcripts observed in this ultra-oligotrophic region. To our knowledge, this is the first study to document extensively the diversity of AAP isolates and to unveil the active AAP community in an oligotrophic marine environment. By pointing out the discrepancies

  11. How do Bacteria Adapt to the Red Sea? Cultivation and Genomic and Physiological Characterization of Oligotrophic Bacteria of the PS1, OM43, and SAR11 Clades

    KAUST Repository

    Jimenez Infante, Francy M.

    2015-05-01

    isolates from the Ia (RS39) and Ib (RS40) subgroups, principally revealed unique putative systems for iron uptake and myo-inositol utilization in RS39, and a potential phosphonates biosynthetic pathway present in RS40. The findings presented here reflect how environments influence the genomic repertoire of microbial communities and shows novel metabolisms and putative pathways as unique adaptive qualities in diverse microbes encompassing from rare to predominant bacterioplankton groups from the Red Sea.

  12. Collection of Arctic Ocean Data from US Navy Submarines on the New SCICEX Program

    Science.gov (United States)

    Smethie, W. M.; Sambrotto, R.; Boyd, T.; Richter-Menge, J.; Corbett, J.

    2011-12-01

    The SCICEX submarine Arctic science program originated in the 1990s when six dedicated science cruises were conducted in the Arctic Ocean aboard US Navy Sturgeon class submarines. After the cold war era Sturgeon class submarines were retired, several Science Accommodation cruises, for which a few days for scientific measurements were added to planned submarine transits through the Arctic Ocean, were carried out when opportunities arose. Renewed interest in conducting further Science Accommodation cruises on a regular basis to better document and understand how the Arctic Ocean responds to climate change resulted in publication of a scientific plan in 2010 (http://www.arctic.gov/publications/scicex_plan.pdf). In the spring of 2011 testing of data collection and water sampling methods aboard newer Virginia and Seawolf class submarines on transit from a Navy ice camp in the Beaufort Sea, was conducted in order to develop protocols and evaluate techniques. Ice draft measurements were also taken in the vicinity of the ice camp and near the North Pole to evaluate new data collection systems. This evaluation will include a comparison of the ice draft data with a comprehensive set of in situ ice thickness measurements taken near the ice camp. Under-ice submarine-launched eXpendable Condutivity Temperature Depth (XCTD) probes were deployed from the USS Connecticut (SSN-22), a Seawolf class submarine, and the resulting profiles compared to CTD casts from the APLIS ice station and historical profiles. Water samples were collected through the hull for measurements of tritium, helium isotopes, oxygen isotopes, chlorofluorocarbons, sulfur hexafluoride, nutrients, dissolved organic carbon, bacterioplankton, phytoplankton and particulates levels. These samples were returned to Lamont-Doherty Earth Observatory and were in the process of being measured at the time this abstract was written. Measurements completed at this time indicate good samples can be collected for CFC-12

  13. [Causes of jellyfish blooms and their influence on marine environment].

    Science.gov (United States)

    Qu, Chang-feng; Song, Jin-ming; Li, Ning

    2014-12-01

    and finally made the ambient water become acidic and hypoxic. The pH decreased by 1.3, while the mean dissolved oxygen demand reached 32.8 micromol x kg(-1) x h(-1). Jellyfish blooms also influenced the marine organism community, which might reduce the biomass of some fish and zooplankton, increase the amount of bacterioplankton, indirectly .increase the quantity of phytoplankton and lead to abnormal primary production.

  14. Open source approaches to establishing Roseobacter clade bacteria as synthetic biology chassis for biogeoengineering.

    Science.gov (United States)

    Borg, Yanika; Grigonyte, Aurelija Marija; Boeing, Philipp; Wolfenden, Bethan; Smith, Patrick; Beaufoy, William; Rose, Simon; Ratisai, Tonderai; Zaikin, Alexey; Nesbeth, Darren N

    2016-01-01

    Aim. The nascent field of bio-geoengineering stands to benefit from synthetic biologists' efforts to standardise, and in so doing democratise, biomolecular research methods. Roseobacter clade bacteria comprise 15-20% of oceanic bacterio-plankton communities, making them a prime candidate for establishment of synthetic biology chassis for bio-geoengineering activities such as bioremediation of oceanic waste plastic. Developments such as the increasing affordability of DNA synthesis and laboratory automation continue to foster the establishment of a global 'do-it-yourself' research community alongside the more traditional arenas of academe and industry. As a collaborative group of citizen, student and professional scientists we sought to test the following hypotheses: (i) that an incubator capable of cultivating bacterial cells can be constructed entirely from non-laboratory items, (ii) that marine bacteria from the Roseobacter clade can be established as a genetically tractable synthetic biology chassis using plasmids conforming to the BioBrick(TM) standard and finally, (iii) that identifying and subcloning genes from a Roseobacter clade species can readily by achieved by citizen scientists using open source cloning and bioinformatic tools. Method. We cultivated three Roseobacter species, Roseobacter denitrificans, Oceanobulbus indolifexand Dinoroseobacter shibae. For each species we measured chloramphenicol sensitivity, viability over 11 weeks of glycerol-based cryopreservation and tested the effectiveness of a series of electroporation and heat shock protocols for transformation using a variety of plasmid types. We also attempted construction of an incubator-shaker device using only publicly available components. Finally, a subgroup comprising citizen scientists designed and attempted a procedure for isolating the cold resistance anf1 gene from Oceanobulbus indolifexcells and subcloning it into a BioBrick(TM) formatted plasmid. Results. All species were stable

  15. Open source approaches to establishing Roseobacter clade bacteria as synthetic biology chassis for biogeoengineering

    Directory of Open Access Journals (Sweden)

    Yanika Borg

    2016-07-01

    Full Text Available Aim. The nascent field of bio-geoengineering stands to benefit from synthetic biologists’ efforts to standardise, and in so doing democratise, biomolecular research methods. Roseobacter clade bacteria comprise 15–20% of oceanic bacterio-plankton communities, making them a prime candidate for establishment of synthetic biology chassis for bio-geoengineering activities such as bioremediation of oceanic waste plastic. Developments such as the increasing affordability of DNA synthesis and laboratory automation continue to foster the establishment of a global ‘do-it-yourself’ research community alongside the more traditional arenas of academe and industry. As a collaborative group of citizen, student and professional scientists we sought to test the following hypotheses: (i that an incubator capable of cultivating bacterial cells can be constructed entirely from non-laboratory items, (ii that marine bacteria from the Roseobacter clade can be established as a genetically tractable synthetic biology chassis using plasmids conforming to the BioBrickTM standard and finally, (iii that identifying and subcloning genes from a Roseobacter clade species can readily by achieved by citizen scientists using open source cloning and bioinformatic tools. Method. We cultivated three Roseobacter species, Roseobacter denitrificans, Oceanobulbus indolifexand Dinoroseobacter shibae. For each species we measured chloramphenicol sensitivity, viability over 11 weeks of glycerol-based cryopreservation and tested the effectiveness of a series of electroporation and heat shock protocols for transformation using a variety of plasmid types. We also attempted construction of an incubator-shaker device using only publicly available components. Finally, a subgroup comprising citizen scientists designed and attempted a procedure for isolating the cold resistance anf1 gene from Oceanobulbus indolifexcells and subcloning it into a BioBrickTM formatted plasmid. Results. All

  16. Phytoplankton diversity and productivity in a highly turbid, tropical coastal system (Bach Dang Estuary, Vietnam)

    Science.gov (United States)

    Rochelle-Newall, E. J.; Chu, V. T.; Pringault, O.; Amouroux, D.; Arfi, R.; Bettarel, Y.; Bouvier, T.; Bouvier, C.; Got, P.; Nguyen, T. M. H.; Mari, X.; Navarro, P.; Duong, T. N.; Cao, T. T. T.; Pham, T. T.; Ouillon, S.; Torréton, J.-P.

    2011-01-01

    The factors controlling estuarine phytoplankton diversity and production are relatively well known in temperate systems. Less however is known about the factors affecting phytoplankton community distribution in tropical estuaries. This is surprising given the economic and ecological importance of these large, deltaic ecosystems, such as are found in South East Asia. Here we present the results from an investigation into the factors controlling phytoplankton distribution and phytoplankton-bacterial coupling in the Bach Dang Estuary, a sub-estuary of the Red River system, in Northern Vietnam. Phytoplankton diversity and primary and bacterial production, nutrients and metallic contaminants (mercury and organotin) were measured during two seasons: wet (July 2008) and dry (March 2009). Phytoplankton community composition differed between the two seasons with only a 2% similarity between July and March. The large spatial extent and complexity of defining the freshwater sources meant that simple mixing diagrams could not be used in this system. We therefore employed multivariate analyses to determine the factors influencing phytoplankton community structure. Salinity and suspended particulate matter were important factors in determining phytoplankton distribution, particularly during the wet season. We also show that phytoplankton community structure is probably influenced by the concentrations of mercury species (inorganic mercury and methyl mercury in both the particulate and dissolved phases) and of tri-, di, and mono-butyl tin species found in this system. Freshwater phytoplankton community composition was associated with dissolved methyl mercury and particulate inorganic mercury concentrations during the wet season, whereas, during the dry season, dissolved methyl mercury and particulate butyl tin species were important factors for the discrimination of the phytoplankton community structure. Phytoplankton-bacterioplankton coupling was also investigated during both

  17. Response of the Eastern Mediterranean microbial ecosystem to dust and dust affected by acid processing in the atmosphere

    Directory of Open Access Journals (Sweden)

    Michael David Krom

    2016-08-01

    Full Text Available Acid processes in the atmosphere, particularly those caused by anthropogenic acid gases, increase the amount of bioavailable P in dust and hence are predicted to increase microbial biomass and primary productivity when supplied to oceanic surface waters. This is likely to be particularly important in the Eastern Mediterranean Sea (EMS, which is P limited during the winter bloom and N&P co-limited for phytoplankton in summer. However, it is not clear how the acid processes acting on Saharan dust will affect the microbial biomass and primary productivity in the EMS. Here, we carried out bioassay manipulations on EMS surface water on which Saharan dust was added as dust (Z, acid treated dust (ZA, dust plus excess N (ZN and acid treated dust with excess N (ZNA during springtime (May 2012 and measured bacterioplankton biomass, metabolic and other relevant chemical and biological parameters. We show that acid treatment of Saharan dust increased the amount of bioavailable P supplied by a factor of ~40 compared to non-acidified dust (18.4 nmoles P mg-1 dust vs. 0.45 nmoles P mg-1 dust, respectively. The increase in chlorophyll, primary and bacterial productivity for treatments Z and ZA were controlled by the amount of N added with the dust while those for treatments ZN and ZNA (in which excessive N was added were controlled by the amount of P added. These results confirm that the surface waters were N&P co-limited for phytoplankton during springtime. However, total chlorophyll and primary productivity in the acid treated dust additions (ZA and ZNA were less than predicted from that calculated from the amount of the potentially limiting nutrient added. This biological inhibition was interpreted as being due to labile trace metals being added with the acidified dust. A probable cause for this biological inhibition was the addition of dissolved Al, which forms potentially toxic Al nanoparticles when added to seawater. Thus, the effect of anthropogenic acid

  18. Microbial Diversity and Cyanobacterial Production in Dziani Dzaha Crater Lake, a Unique Tropical Thalassohaline Environment

    Science.gov (United States)

    Carré, Claire; Cellamare, Maria; Duval, Charlotte; Intertaglia, Laurent; Lavergne, Céline; Roques, Cécile

    2017-01-01

    This study describes, for the first time, the water chemistry and microbial diversity in Dziani Dzaha, a tropical crater lake located on Mayotte Island (Comoros archipelago, Western Indian Ocean). The lake water had a high level of dissolved matter and high alkalinity (10.6–14.5 g L-1 eq. CO32-, i.e. 160–220 mM compare to around 2–2.5 in seawater), with salinity up to 52 psu, 1.5 higher than seawater. Hierarchical clustering discriminated Dziani Dzaha water from other alkaline, saline lakes, highlighting its thalassohaline nature. The phytoplankton biomass was very high, with a total chlorophyll a concentration of 524 to 875 μg chl a L-1 depending on the survey, homogeneously distributed from surface to bottom (4 m). Throughout the whole water column the photosynthetic biomass was dominated (>97% of total biovolume) by the filamentous cyanobacteria Arthrospira sp. with a straight morphotype. In situ daily photosynthetic oxygen production ranged from 17.3 to 22.2 g O2 m-2 d-1, consistent with experimental production / irradiance measurements and modeling. Heterotrophic bacterioplankton was extremely abundant, with cell densities up to 1.5 108 cells mL-1 in the whole water column. Isolation and culture of 59 Eubacteria strains revealed the prevalence of alkaliphilic and halophilic organisms together with taxa unknown to date, based on 16S rRNA gene analysis. A single cloning-sequencing approach using archaeal 16S rDNA gene primers unveiled the presence of diverse extremophilic Euryarchaeota. The water chemistry of Dziani Dzaha Lake supports the hypothesis that it was derived from seawater and strongly modified by geological conditions and microbial activities that increased the alkalinity. Dziani Dzaha has a unique consortium of cyanobacteria, phytoplankton, heterotrophic Eubacteria and Archaea, with very few unicellular protozoa, that will deserve further deep analysis to unravel its uncommon diversity. A single taxon, belonging to the genus Arthrospira, was

  19. Phytoplankton diversity and productivity in a highly turbid, tropical coastal system (Bach Dang Estuary, Vietnam

    Directory of Open Access Journals (Sweden)

    E. J. Rochelle-Newall

    2011-01-01

    Full Text Available The factors controlling estuarine phytoplankton diversity and production are relatively well known in temperate systems. Less however is known about the factors affecting phytoplankton community distribution in tropical estuaries. This is surprising given the economic and ecological importance of these large, deltaic ecosystems, such as are found in South East Asia. Here we present the results from an investigation into the factors controlling phytoplankton distribution and phytoplankton-bacterial coupling in the Bach Dang Estuary, a sub-estuary of the Red River system, in Northern Vietnam. Phytoplankton diversity and primary and bacterial production, nutrients and metallic contaminants (mercury and organotin were measured during two seasons: wet (July 2008 and dry (March 2009. Phytoplankton community composition differed between the two seasons with only a 2% similarity between July and March. The large spatial extent and complexity of defining the freshwater sources meant that simple mixing diagrams could not be used in this system. We therefore employed multivariate analyses to determine the factors influencing phytoplankton community structure. Salinity and suspended particulate matter were important factors in determining phytoplankton distribution, particularly during the wet season. We also show that phytoplankton community structure is probably influenced by the concentrations of mercury species (inorganic mercury and methyl mercury in both the particulate and dissolved phases and of tri-, di, and mono-butyl tin species found in this system. Freshwater phytoplankton community composition was associated with dissolved methyl mercury and particulate inorganic mercury concentrations during the wet season, whereas, during the dry season, dissolved methyl mercury and particulate butyl tin species were important factors for the discrimination of the phytoplankton community structure. Phytoplankton-bacterioplankton coupling was also

  20. Effect of permafrost thawing on organic carbon and trace element colloidal speciation in the thermokarst lakes of western Siberia

    Directory of Open Access Journals (Sweden)

    O. S. Pokrovsky

    2011-03-01

    Full Text Available To examine the mechanisms of carbon mobilization and biodegradation during permafrost thawing and to establish a link between organic carbon (OC and other chemical and microbiological parameters in forming thermokarst (thaw lakes, we studied the biogeochemistry of OC and trace elements (TEs in a chronosequence of small lakes that are being formed due to permafrost thawing in the northern part of western Siberia. Twenty lakes and small ponds of various sizes and ages were sampled for dissolved and colloidal organic carbon, metals and culturable heterotrophic bacterial cell number. We observed a sequence of ecosystems from peat thawing and palsa degradation due to permafrost subsidence in small ponds to large, km-size lakes that are subject to drainage to, finally, the khasyrey (drained lake formation. There is a systematic evolution of both total dissolved and colloidal concentration of OC and TEs in the lake water along with the chronosequence of lake development that may be directly linked to the microbial mineralization of dissolved organic matter and the liberation of the inorganic components (Fe, Al, and TEs from the organo-mineral colloids.

    In this chronosequence of lake development, we observed an apparent decrease in the relative proportion of low molecular weight <1 kDa (1 kDa ~ 1 nm OC concentration along with a decrease in the concentration of total dissolved (<0.45 μm OC. This decrease was accompanied by an increase in the small size organic ligands (probably autochthonous exometabolites produced by the phytoplankton and a simultaneous decrease in the proportion of large-size organic (humic complexes of allochthonous (soil origin. This evolution may be due to the activity of heterotrophic bacterioplankton that use allochthonous organic matter and dissolved nutrients originating from peat lixiviation. Most insoluble TEs demonstrate a systematic decrease in concentration during filtration (5 μm, 0.45 μm exhibiting a similar

  1. Production of dissolved organic carbon by Arctic plankton communities: Responses to elevated carbon dioxide and the availability of light and nutrients

    Science.gov (United States)

    Poulton, Alex J.; Daniels, Chris J.; Esposito, Mario; Humphreys, Matthew P.; Mitchell, Elaine; Ribas-Ribas, Mariana; Russell, Benjamin C.; Stinchcombe, Mark C.; Tynan, Eithne; Richier, Sophie

    2016-05-01

    The extracellular release of dissolved organic carbon (DOC) by phytoplankton is a potentially important source of labile organic carbon for bacterioplankton in pelagic ecosystems. In the context of increasing seawater partial pressure of CO2 (pCO2), via the oceanic absorption of elevated atmospheric CO2 (ocean acidification), several previous studies have reported increases to the relative amount of carbon fixed into particulates, via primary production (PP), and dissolved phases (DOC). During the summer of 2012 we measured DOC production by phytoplankton communities in the Nordic seas of the Arctic Ocean (Greenland, Norwegian and Barents Sea) from both in situ sampling and during three bioassay experiments where pCO2 levels (targets ~550 μatm, ~750 μatm, ~1000 μatm) were elevated relative to ambient conditions. Measurements of DOC production and PP came from 24 h incubations and therefore represent net DOC production rates, where an unknown portion of the DOC released has potentially been utilised by heterotrophic organisms. Production of DOC (net pDOC) by in situ communities varied from 0.09 to 0.64 mmol C m-3 d-1 (average 0.25 mmol C m-3 d-1), with comparative rates in two of the experimental bioassays (0.04-1.23 mmol C m-3 d-1) and increasing dramatically in the third (up to 5.88 mmol C m-3 d-1). When expressed as a fraction of total carbon fixation (i.e., PP plus pDOC), percentage extracellular release (PER) was 14% on average (range 2-46%) for in situ measurements, with PER in the three bioassays having a very similar range (2-50%). A marked increase in pDOC (and PER) was only observed in one of the bioassays where nutrient levels (nitrate, silicic acid) dropped dramatically relative to starting (ambient) concentrations; no pCO2 treatment effect on pDOC (or PER) was evident across the three experiments. Examination of in situ net pDOC (and PER) found significant correlations with decreasing silicic acid and increasing euphotic zone depth, indicating that

  2. Viral and bacterial production in the North Water: in situ measurements, batch-culture experiments and characterization and distribution of a virus host system

    Science.gov (United States)

    Middelboe, Mathias; Nielsen, Torkel G.; Bjørnsen, Peter K.

    Growth and viral lysis of bacterioplankton at subzero temperatures were measured in the North Water polynya in July 1998. In situ measurements of bacterial carbon consumption in surface waters ranged from 15 to 63 μg C l -1 d -1 in the eastern and 6 to 7 μg C l -1 d -1 in the northern part of the polynya. Both bacterial abundance and activity appeared to increase in response to the decay of the phytoplankton bloom that developed in the North Water. Organic carbon was the limiting substrate for bacteria in the polynya since addition of glucose, but not inorganic nutrients, to batch cultures increased both the carrying capacity of the substrate and the growth rate of the bacteria. Bacterial growth rates ranged from 0.11 to 0.40 d -1, corresponding to bacterial generation times of 1.7-6.3 d. The in situ viral production rate was estimated both from the frequency of visibly infected cells and from the rate of viral production in batch cultures; it ranged from 0.04 to 0.52 d -1 and from 0.25 to 0.47 d -1, respectively. From 6% to 28% of bacterial production was found to be lost due to viral lysis. The average virus-bacteria ratio was 5.1±3.1, with the abundance of viruses being correlated positively with bacterial production. A Pseudoalteromonas sp. bacterial host and an infective virus were isolated from the polynya; characteristics and distribution of the virus-host system were examined. The Pseudoalteromonas sp. showed psychrotolerant growth and sustained significant production of viruses at 0°C. The virus-host system was found throughout the polynya. Overall the results suggested that a large amount of organic carbon released during the development and breakdown of the spring phytoplankton bloom was consumed by planktonic bacteria and that the microbial food web was an important and dynamic component of the planktonic food web in the North Water.

  3. Biogeography, Cultivation and Genomic Characterization of Prochlorococcus in the Red Sea

    KAUST Repository

    Shibl, Ahmed A.

    2015-12-16

    Aquatic primary productivity mainly depends on pelagic phytoplankton. The globally abundant marine picocyanobacteria Prochlorococcus comprises a significant fraction of the photosynthetic biomass in most tropical, oligotrophic oceans. The Red Sea is an enclosed narrow body of water characterized by continuous solar irradiance, and negligible annual rainfall, in addition to elevated temperatures and salinity levels, which mimics a global warming scenario. Analysis of 16S rRNA sequences of bacterioplankton communities indicated the predominance of a high-light adapted ecotype (HL II) of Prochlorococcus at the surface of the Northern and Central Red Sea. To this end, we analyzed the distribution of Prochlorococcus at multiple depths within and below the euphotic zone in different regions of the Red Sea, using clone libraries of the 16S–23S rRNA internal transcribed spacer (ITS) region. Results indicated a high diversity of Prochlorococcus ecotypes at the 100 m depth in the water column and an unusual dominance of HL II-related sequences in deeper waters of the Red Sea. To further investigate the microdiversity of Prochlorococcus over a wider biogeographical scope, we used a 454-pyrosequencing approach to analyze rpoC1 gene pyrotags. Samples were collected from the surface of the water column to up to 500 m at 45 stations that span the Red Sea’s main basin from 4 north to south. Phylogenetic analysis of abundant rpoC1 OTUs revealed genotypes of recently discovered strains that belong to the high-light and lowlight clades. In addition, we used a rapid community-profiling tool (GraftM) and quantitatively analyzed rpoC1 gene abundance from 45 metagenomes to assess the Prochlorococcus community structure across vertical and horizontal physicochemical gradients. Results revealed the clustering of samples according to their depth and a strong influence on ecotypic distribution by temperature and oxygen levels. In efforts to better understand how the cells survive the

  4. Characterization of biocenosis in the storage-reservoirs of liquid radioactive wastes of 'Mayak' PA

    Energy Technology Data Exchange (ETDEWEB)

    Pryakhin, E.; Tryapitsina, G.; Andreyev, S.; Akleyev, A. [Urals Research Center for Radiation Medicine - URCRM (Russian Federation); Mokrov, Y.; Ivanov, I. [Mayak PA (Russian Federation)

    2014-07-01

    A number of storage-reservoirs of liquid radioactive wastes of 'Mayak' Production Association ('Mayak' PA) with different levels of radioactive contamination: reservoir R-17 ('Staroye Boloto'), reservoir R-9 (Lake Karachay), reservoirs of the Techa Cascade R-3 (Koksharov pond), R-4 (Metlinsky pond), R-10 and R-11 is located in Chelyabinsk Oblast (Russia). The operation of these reservoirs began in 1949-1964. Full-scale hydro-biological studies of these reservoirs were started in 2007. The research into the status of biocenosis of these storage reservoirs of liquid radioactive wastes of 'Mayak' PA was performed in 2007 - 2011. The status of biocenosis was evaluated in accordance with the status of following communities: bacterio-plankton, phytoplankton, zooplankton, zoo-benthos, macrophytes and ichthyofauna. The status of ecosystems was determined by radioactive and chemical contamination of water bodies. The results of hydro-biological investigations showed that no changes in the status of biota in reservoir R-11 were revealed as compared to the biological parameters of the water bodies of this geographical zone. In terms of biological parameters the status of the ecosystem of the reservoir R-11 is characterized by a sufficient biological diversity, and can be considered acceptable. The ecosystem of the reservoir R-10 maintains its functional integrity, although there were registered negative effects in the zoo-benthos community associated with the decrease in the parameters of the development of pelophylic mollusks that live at the bottom of the water body throughout the entire life cycle. In reservoir R-4 the parameters of the development of phytoplankton did not differ from those in Reservoirs R-11 and R-10; however, a significant reduction in the quantity of Cladocera and Copepoda was registered in the zooplankton community, while in the zoo-benthos there were no small mollusks that live aground throughout the entire life

  5. Arctic sea-ice melting: Effects on hydroclimatic variability and on UV-induced carbon cycling

    Science.gov (United States)

    Sulzberger, Barbara

    2016-04-01

    Since 1980 both the perennial and the multiyear central Arctic sea ice areas have declined by approximately 13 and 15% per decade, respectively (IPCC, 2013). Arctic sea-ice melting has led to an increase in the amplitude of the Northern Hemisphere jet stream and, as a consequence, in more slowly moving Rossby waves which results in blocking of weather patterns such as heat waves, droughts, cold spells, and heavy precipitation events (Francis and Vavrus, 2012). Changing Rossby waves account for more than 30% of the precipitation variability over several regions of the northern middle and high latitudes, including the US northern Great Plains and parts of Canada, Europe, and Russia (Schubert et al., 2011). From 2007 to 2013, northern Europe experienced heavy summer precipitation events that were unprecedented in over a century, concomitant with Arctic sea ice loss (Screen, 2013). Heavy precipitation events tend to increase the runoff intensity of terrigenous dissolved organic matter (tDOM) (Haaland et al., 2010). In surface waters tDOM is subject to UV-induced oxidation to produce atmospheric CO2. Mineralization of DOM also occurs via microbial respiration. However, not all chemical forms of DOM are available to bacterioplankton. UV-induced transformations generally increase the bioavailability of tDOM (Sulzberger and Durisch-Kaiser, 2009). Mineralization of tDOM is an important source of atmospheric CO2 and this process is likely to contribute to positive feedbacks on global warming (Erickson et al., 2015). However, the magnitudes of these potential feedbacks remain unexplored. This paper will discuss the following items: 1.) Links between Arctic sea-ice melting, heavy precipitation events, and enhanced tDOM runoff. 2.) UV-induced increase in the bioavailability of tDOM. 3.) UV-mediated feedbacks on global warming. References Erickson, D. J. III, B. Sulzberger, R. G. Zepp, A. T. Austin (2015), Effects of stratospheric ozone depletion, solar UV radiation, and climate

  6. Distribution of HNA and LNA bacterial groups in the Southwest Atlantic Ocean Distribuição de bactérias HNA e LNA no Oceano Atlântico sudoeste

    Directory of Open Access Journals (Sweden)

    Luciana Andrade

    2007-06-01

    Full Text Available Bacterioplankton was studied in a large area of Southwest Atlantic Ocean between 13 and 25ºS and 28 and 42ºW. Samples were collected in 108 stations at 20 m depth. Bacteria were enumerated by flow cytometry after nucleic acid staining with syto13 and two subgroups were differentiated: low nucleic acid content (LNA and high nucleic acid content (HNA bacteria. Total bacterial numbers varied from 0.37 to 5.53 10(5 cells mL-1. HNA cells represented 15 to 70% of the total number while LNA cells represented 30 to 85%. Heterotrophic bacterial production was determined by incorporation of tritiated leucine and ranged from 2.7 to 171.07 ng C L-1 h-1. No significant correlation was found between abundance and production. Nevertheless with support of multivariate analysis between bacterial abundance, bacterial production, chlorophyll a and other oceanographic data the distribution of the groups in two different oceanic provinces could be explained by nutrient availability. HNA bacteria accounted for the high percentage of cells found in the area north of 19ºS, linked to higher temperature waters and riverine nutrients inputs. LNA bacteria were the dominant cells south of this latitude and were correlated to the higher values of nitrate found for the same area.Um estudo do bacterioplâncton foi realizado numa área extensa do Oceano Atlântico Sudoeste entre 13 e 25ºS e 28 e 42ºW. As amostras foram coletadas em 108 estações oceanográficas a 20 m de profundidade. A abundância bacteriana foi determinada por citometria de fluxo após coloração dos ácidos nucléicos com Syto13. Dois grupos de bactérias foram enumerados e distinguidos: bactérias com alto conteúdo de ácidos nucleicos (HNA e bactérias com baixo conteúdo de ácidos nucleicos (LNA. O número de bactérias variou de 0,37 a 5,53 10(5 células mL-1. As células HNA representaram de 15 a 70% da abundância total enquanto as células LNA representaram de 30 a 85%. A produ

  7. Decrease of concentration and colloidal fraction of organic carbon and trace elements in response to the anomalously hot summer 2010 in a humic boreal lake

    Energy Technology Data Exchange (ETDEWEB)

    Shirokova, L.S. [Institute of Ecological Problems of the North, Ural Branch of Russian Academy of Science, Naberezhnaya Severnoi Dviny, 23, Arkhangelsk, 163000 (Russian Federation); GET UMR 5563 CNRS, Université de Toulouse, 14 Avenue Edouard Belin, 31400 Toulouse (France); Pokrovsky, O.S., E-mail: oleg@get.obs-mip.fr [Institute of Ecological Problems of the North, Ural Branch of Russian Academy of Science, Naberezhnaya Severnoi Dviny, 23, Arkhangelsk, 163000 (Russian Federation); GET UMR 5563 CNRS, Université de Toulouse, 14 Avenue Edouard Belin, 31400 Toulouse (France); Moreva, O.Yu.; Chupakov, A.V.; Zabelina, S.A.; Klimov, S.I.; Shorina, N.V.; Vorobieva, T.Ya. [Institute of Ecological Problems of the North, Ural Branch of Russian Academy of Science, Naberezhnaya Severnoi Dviny, 23, Arkhangelsk, 163000 (Russian Federation)

    2013-10-01

    aerobic bacterioplankton and 3) photo-degradation of DOM and photo-chemical liberation of organic-bound TE. While the first process may have caused significant decreases in the total dissolved concentration of micronutrients (a factor of 2 to 5 for Cr, Mn, Fe, Ni, Cu, Zn and Cd and a factor of > 100 for Co), the second and third factors could have brought about the decrease of allochthonous DOC concentration as well as the concentration and proportion of organic and organo-mineral colloidal forms of non-essential low-soluble trace elements present in the form of organic colloids (Al, Y, Ti, Zr, Hf, Th, Pb, all REEs). It can be hypothesized that climate warming in high latitudes capable of significantly raising surface water temperatures will produce a decrease in the colloidal fraction of most trace elements and, as a result, an increase in the most labile low molecular weight LMW{sub <1} {sub kDa} fraction. - Graphical abstract: During anomalously hot summer (August 2010), significant decrease of the proportion of colloidal organic carbon occurred in a humic boreal lake. Highlights: • Anomalous hot summer 2010 changed boreal lake biogeochemistry • Carbon and trace element concentration in the epilimnion decreased by a factor of 1.3 to 6. • Colloidal fractions of carbon and metals decreased by a factor of 1.5 to 3. • Climate warming in boreal lakes may increase the metal and carbon bioavailability.

  8. MOLECULAR APPROACHES FOR IN SITU IDENTIFCIATION OF NITRATE UTILIZATION BY MARINE BACTERIA AND PHYTOPLANKTON

    Energy Technology Data Exchange (ETDEWEB)

    Frischer, Marc E. [Skidaway Institute of Oceanography; Verity, Peter G.; Gilligan, Mathew R.; Bronk, Deborah A.; Zehr, Jonathan P.; Booth, Melissa G.

    2013-09-12

    Traditionally, the importance of inorganic nitrogen (N) for the nutrition and growth of marine phytoplankton has been recognized, while inorganic N utilization by bacteria has received less attention. Likewise, organic N has been thought to be important for heterotrophic organisms but not for phytoplankton. However, accumulating evidence suggests that bacteria compete with phytoplankton for nitrate (NO3-) and other N species. The consequences of this competition may have a profound effect on the flux of N, and therefore carbon (C), in ocean margins. Because it has been difficult to differentiate between N uptake by heterotrophic bacterioplankton versus autotrophic phytoplankton, the processes that control N utilization, and the consequences of these competitive interactions, have traditionally been difficult to study. Significant bacterial utilization of DIN may have a profound effect on the flux of N and C in the water column because sinks for dissolved N that do not incorporate inorganic C represent mechanisms that reduce the atmospheric CO2 drawdown via the ?biological pump? and limit the flux of POC from the euphotic zone. This project was active over the period of 1998-2007 with support from the DOE Biotechnology Investigations ? Ocean Margins Program (BI-OMP). Over this period we developed a tool kit of molecular methods (PCR, RT-PCR, Q-PCR, QRT-PCR, and TRFLP) and combined isotope mass spectrometry and flow-cytometric approaches that allow selective isolation, characterization, and study of the diversity and genetic expression (mRNA) of the structural gene responsible for the assimilation of NO3- by heterotrophic bacteria (nasA). As a result of these studies we discovered that bacteria capable of assimilating NO3- are ubiquitous in marine waters, that the nasA gene is expressed in these environments, that heterotrophic bacteria can account for a significant fraction of total DIN uptake in different ocean margin systems, that the expression of nasA is

  9. Dissolved organic phosphorus and its bioavailable fraction in the Baltic Sea

    Science.gov (United States)

    Nausch, M.; Nausch, G.; Setzkorn, D.; Welz, Ä.

    2009-04-01

    In general, it is accepted that dissolved organic phosphorus (DOP) is besides dissolved inorganic phosphorus (DIP) a source for phosphorus nutrition of phyto- and bacterioplankton. If available, DIP is usually preferred to DOP. DOP becomes the most important source under DIP depleted conditions occurring in the Baltic Sea in summer. However, its contribution to nutrition and consequently its significance is very difficult to appraise because only the bioavailable fraction (BAP = bioavailable phosphorus) can be used by organisms. DOP comprises also inert compounds which persist over longer periods. Therefore, there is an urgent need to quantify the bioavailable DOP. In 2004 and 2005, DOP and BAP concentrations were detected in surface water at three stations in the central Baltic Sea from May until July. In June/July 2008 an intensive measuring campaign was performed throughout the whole Baltic Sea. DOP measurements were done from the entrance to the North Sea in the West until the innermost parts of the Gulf of Bothnia in the North and the Gulf of Finland in the East. BAP was determined at 14 stations in the central and northern parts. DOP was determined using the alkaline potassium peroxidisulphate oxidation method followed by the manual DIP determination. BAP has been detected in time course experiments using 0.8 µm filtered sea water containing free-living heterotrophic bacteria and amended with 7 µM ammonium chloride and 1mg l-1 D-(+) glucosemonohydrate to prevent nitrogen and carbon limitation and increase the phosphorus demand in bacteria. BAP is defined as that proportion of DOP which is used by bacteria and calculated as the difference of DOP concentrations at the beginning and the lowest concentrations during an incubation for 4-6 days. In 2004 and 2005, most DOP concentrations ranged between 0.18 and 0.32 µM, with a declining tendency from spring to summer probably due to elevated uptake compared to its release caused by higher temperatures and DIP

  10. Post-glacial, land rise-induced formation and development of lakes in the Forsmark area, central Sweden

    Energy Technology Data Exchange (ETDEWEB)

    Brunberg, Anna-Kristina; Blomqvist, Peter [Uppsala Univ. (Sweden). Dept. of Limnology, Evolutionary Biology Centre

    2000-03-15

    This report describes the lakes of Uppsala county, with special emphasis on the coastal lakes in the Forsmark area. The aim of the study is to characterise different main types of lakes within the Forsmark area and to create a basis for prediction of their ontogeny, that can be used also for new lakes which due to shoreline displacement will be formed during the next 10 000 years. Areas where future research is needed to fully understand the functioning of the lake ecosystems and their ontogeny have also been identified. Three main types of lake ecosystems could be identified: The oligotrophic hardwater lakes are to a large extent surrounded by mires. Inflow as well as outflow of water is often diffuse, via the surrounding mire. The lakes are small and shallow, with nutrient poor and highly alkaline water. Three key habitats have been identified within the lakes; i) the pelagic zone, characterised by low production of biota, ii) the presumably moderately productive emergent macrophyte zone, dominated by Sphagnum and Phragmites, and iii) the light-exposed soft-bottom zone with Chara meadows and an unusually rich and presumably highly productive microbial sediment community. In later stages of the lake ontogeny, Sphagnum becomes more and more dominant in the system, which successively turns acidic. The final stage is likely to be a raised bog ecosystem with an autonomous hydrological functioning. The brown water lakes are typically found within the main part of the River Forsmarksaan and are characterised by a high flow-through of water from the upper parts of the drainage area, which are dominated by mires. Their lake water is highly stained by allochtonous organic carbon imported from the catchment area. Also in this lake type a Sphagnum-littoral successively develops, and in a mature lake three key habitats can be identified; i) the pelagic zone, most likely the dominant habitat in terms of production of organisms and in which bacterioplankton dominates the