WorldWideScience

Sample records for survey microbial biodiversity

  1. A macroecological theory of microbial biodiversity.

    Science.gov (United States)

    Shoemaker, William R; Locey, Kenneth J; Lennon, Jay T

    2017-04-03

    Microorganisms are the most abundant, diverse and functionally important organisms on Earth. Over the past decade, microbial ecologists have produced the largest ever community datasets. However, these data are rarely used to uncover law-like patterns of commonness and rarity, test theories of biodiversity, or explore unifying explanations for the structure of microbial communities. Using a global scale compilation of >20,000 samples from environmental, engineered and host-related ecosystems, we test the power of competing theories to predict distributions of microbial abundance and diversity-abundance scaling laws. We show that these patterns are best explained by the synergistic interaction of stochastic processes that are captured by lognormal dynamics. We demonstrate that lognormal dynamics have predictive power across scales of abundance, a criterion that is essential to biodiversity theory. By understanding the multiplicative and stochastic nature of ecological processes, scientists can better understand the structure and dynamics of Earth's largest and most diverse ecological systems.

  2. Microbial biodiversity in glacier-fed streams.

    Science.gov (United States)

    Wilhelm, Linda; Singer, Gabriel A; Fasching, Christina; Battin, Tom J; Besemer, Katharina

    2013-08-01

    While glaciers become increasingly recognised as a habitat for diverse and active microbial communities, effects of their climate change-induced retreat on the microbial ecology of glacier-fed streams remain elusive. Understanding the effect of climate change on microorganisms in these ecosystems is crucial given that microbial biofilms control numerous stream ecosystem processes with potential implications for downstream biodiversity and biogeochemistry. Here, using a space-for-time substitution approach across 26 Alpine glaciers, we show how microbial community composition and diversity, based on 454-pyrosequencing of the 16S rRNA gene, in biofilms of glacier-fed streams may change as glaciers recede. Variations in streamwater geochemistry correlated with biofilm community composition, even at the phylum level. The most dominant phyla detected in glacial habitats were Proteobacteria, Bacteroidetes, Actinobacteria and Cyanobacteria/chloroplasts. Microorganisms from ice had the lowest α diversity and contributed marginally to biofilm and streamwater community composition. Rather, streamwater apparently collected microorganisms from various glacial and non-glacial sources forming the upstream metacommunity, thereby achieving the highest α diversity. Biofilms in the glacier-fed streams had intermediate α diversity and species sorting by local environmental conditions likely shaped their community composition. α diversity of streamwater and biofilm communities decreased with elevation, possibly reflecting less diverse sources of microorganisms upstream in the catchment. In contrast, β diversity of biofilms decreased with increasing streamwater temperature, suggesting that glacier retreat may contribute to the homogenisation of microbial communities among glacier-fed streams.

  3. Microbial biodiversity of Sardinian oleic ecosystems.

    Science.gov (United States)

    Santona, Mario; Sanna, Maria Lina; Multineddu, Chiara; Fancello, Francesco; de la Fuente, Sara Audije; Dettori, Sandro; Zara, Severino

    2018-04-01

    The olives are rich in microorganisms that, during the extraction process may persist in the oils and can influence their physicochemical and sensory characteristics. In this work, and for the first time, we isolated and identified microbial species, yeast and bacteria, present during the production process in four Sardinian (Italy) oleic ecosystems. Among these varieties, we found that Nera di Gonnos was associated to the highest microbial biodiversity, which was followed by Bosana, Nocellara del Belice and Semidana. Among the different microbial species isolated, some are specific of olive ecological niches, such as Cryptococcus spp and Serratia spp; and others to olive oils such as Candida spp and Saccharomyces. Some other species identified in this work were not found before in oleic ecosystems. The enzymatic analyses of yeast and bacteria showed that they have good β-glucosidase activity and yeast also showed good β-glucanase activity. The majority of bacteria presented lipolytic and catalase activities while in yeast were species-specific. Interestingly, yeast and bacteria isolates presented a high resistance to bile acid, and about 65% of the yeast were able to resist at pH 2.5 for 2 h. Finally, bacteria showed no biofilm activity compared to yeast. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Marine biodiversity survey of St. Eustatius, 2015

    NARCIS (Netherlands)

    Hoeksema, B.W.

    2016-01-01

    The Statia Marine Biodiversity Expedition (2015) was organized by Naturalis Biodiversity Center in Leiden (the national museum of natural history of the Netherlands) and ANEMOON Foundation (a Dutch organisation of citizen scientists) in Bennebroek, The Netherlands. This field survey served as a

  5. Entomological survey and biodiversity conservation in the ...

    African Journals Online (AJOL)

    A management program of biodiversity inventory and conservation was recently adopted for the rehabilitation of the Madeleine Island National Park (MINP). Entomological surveys were conducted between 2006 and 2009 to gather biological data on the biodiversity and to point out species of interest. Over 30 species of ...

  6. Marine biodiversity survey of St. Eustatius, 2015

    OpenAIRE

    Hoeksema, B.W.

    2016-01-01

    The Statia Marine Biodiversity Expedition (2015) was organized by Naturalis Biodiversity Center in Leiden (the national museum of natural history of the Netherlands) and ANEMOON Foundation (a Dutch organisation of citizen scientists) in Bennebroek, The Netherlands. This field survey served as a baseline study to explore the marine biota of St. Eustatius, a small island on the boundary between the eastern Caribbean and the West Atlantic. Since 2010, St. Eustatius is part of the Caribbean Nethe...

  7. Functional biodiversity of microbial communities in aerobic selector slaughterhouse wastewater.

    Science.gov (United States)

    Ai-Mutairi, Nayef Z

    2007-06-01

    The biodiversity of the microbial communities of an aerobic selector and a conventional system treating slaughterhouse wastewater were evaluated using the Biolog technique (Biolog Inc., Hayward, California). Principal components analysis of patterns and level of microbial activity indicate that microbial communities statistically differentiate between the selector and conventional system. Biolog data indicated that there was seasonal variation in the structure and function of the microbial community in conventional samples, which may be a useful indicator of wastewater community disturbance and unsteadiness, while, for the selector system, there were no recognizable statistical differences between winter and summer data communities, Biodiversity indices indicated that the selector system maintained a high functional diversity (Shannon-Weaver diversity index [H'] from 3.8 to 4.6) than the conventional system (H' from 1.8 to 2.8). The high values in the selector system were a reflection of the fact that most of the carbon sources were used, contributing to the very high Shannon indices. In addition, the high substrate equitability values (J) obtained for the selector samples indicated that the microbial communities between the summer and winter samples used the carbon sources in the same proportion. In contrast, differences in the equitability of the microbial communities within the conventional system were observed. This indicated a pattern representing unevenness.

  8. Using Metagenomics to Connect Microbial Community Biodiversity and Functions.

    Science.gov (United States)

    Mendes, Lucas William; Braga, Lucas Peres Palma; Navarrete, Acacio Aparecido; Souza, Dennis Goss de; Silva, Genivaldo Gueiros Zacarias; Tsai, Siu Mui

    2017-01-01

    Microbes constitute about a third of the Earth's biomass and are composed by an enormous genetic diversity. In a majority of environments the microbial communities play crucial roles for the ecosystem functioning, where a drastic biodiversity alteration or loss could lead to negative effects on the environment and sustainability. A central goal in microbiome studies is to elucidate the relation between microbial diversity to functions. A better understanding of the relation diversity-function would increase the ability to manipulate that diversity to improve plant and animal health and also setting conservation priorities. The recent advances in genomic methodologies in microbial ecology have provide means to assess highly complex communities in detail, making possible the link between diversity and the functions performed by the microbes. In this work we first explore some advances in bioinformatics tools to connect the microbial community biodiversity to their potential metabolism and after present some examples of how this information can be useful for a better understanding of the microbial role in the environment.

  9. Microbial Cretaceous park: biodiversity of microbial fossils entrapped in amber.

    Science.gov (United States)

    Martín-González, Ana; Wierzchos, Jacek; Gutiérrez, Juan C; Alonso, Jesús; Ascaso, Carmen

    2009-05-01

    Microorganisms are the most ancient cells on this planet and they include key phyla for understanding cell evolution and Earth history, but, unfortunately, their microbial records are scarce. Here, we present a critical review of fossilized prokaryotic and eukaryotic microorganisms entrapped in Cretaceous ambers (but not exclusively from this geological period) obtained from deposits worldwide. Microbiota in ambers are rather diverse and include bacteria, fungi, and protists. We comment on the most important microbial records from the last 25 years, although it is not an exhaustive bibliographic compilation. The most frequently reported eukaryotic microfossils are shells of amoebae and protists with a cell wall or a complex cortex. Likewise, diverse dormant stages (palmeloid forms, resting cysts, spores, etc.) are abundant in ambers. Besides, viral and protist pathogens have been identified inside insects entrapped in amber. The situation regarding filamentous bacteria and fungi is quite confusing because in some cases, the same record was identified consecutively as a member of these phylogenetically distant groups. To avoid these identification errors in the future, we propose to apply a more resolute microscopic and analytical method in amber studies. Also, we discuss the most recent findings about ancient DNA repair and bacterial survival in remote substrates, which support the real possibility of ancient DNA amplification and bacterial resuscitation from Cretaceous resins.

  10. An examination of the biodiversity-ecosystem function relationship in arable soil microbial communities

    NARCIS (Netherlands)

    Griffiths, B.S.; Ritz, K.; Wheatley, R.; Kuan, H.L.; Boag, B.; Christensen, S.; Ekelund, F.; Sorensen, S.J.; Muller, S.; Bloem, J.

    2001-01-01

    Microbial communities differing in biodiversity were established by inoculating sterile agricultural soil with serially diluted soil suspensions prepared from the parent soil. Three replicate communities of each dilution were allowed to establish an equivalent microbial biomass by incubation for 9

  11. [EPS, SMP and microbial biodiversity under the oligotrophic environment].

    Science.gov (United States)

    Huang, Xing; Sun, Bao-Sheng; Sun, Jing-Mei; Zhang, Bin

    2009-05-15

    In order to investigate the extracellular polymeric substances (EPS), soluble microbial product (SMP) and microbial biodiversity of the sludge lacking of nutrition, to provide evidence for optimizing MBR's operation and lessening membrane fouling, a series of experiments were undertaken under the oligotrophic environment using the sludge from the MBR of Tianjin University. The contents of EPS and SMP were determined, and microbial biodiversity was analyzed by PCR-DGGE technology and cloning-sequencing. Furthermore, the sequences were used for homology analysis and then the phylogenetic tree was constructed. In the initial stage, the EPS and SMP contents raised from 15.04 mg/g and 0 mg/g to 17.99 mg/g and 3.29 mg/g, respectively. Along with the experiment progress, the EPS content dropped to 2.40 mg/g; but the SMP content varied around 3.5 mg/g. This indicates that the EPS and SMP possess the buffer action towards the variation of the environment, and the microorganism can utilize the EPS and SMP under the condition of oligotrophic. Because of the utilization of the EPS and SMP, the Shannon index of the sludge raised from 0.81 to 1.09. Then, it began to decline and stabilized at 0.95 finally. The clone and sequence results reflect that the microbial structure is very rich, and most of the dominant species are uncultured bacterium. Some of the bacterium, which are mostly belong to Bacteroidetes, Flavobacterium, Saprospiraceae and Firmicutes, can degrade the EPS and SMP by secreting protein and polysaccharide hydrolyzing enzymes.

  12. Effect of light wavelength on hot spring microbial mat biodiversity.

    Science.gov (United States)

    Nishida, Akifumi; Thiel, Vera; Nakagawa, Mayuko; Ayukawa, Shotaro; Yamamura, Masayuki

    2018-01-01

    Hot spring associated phototrophic microbial mats are purely microbial communities, in which phototrophic bacteria function as primary producers and thus shape the community. The microbial mats at Nakabusa hot springs in Japan harbor diverse photosynthetic bacteria, mainly Thermosynechococcus, Chloroflexus, and Roseiflexus, which use light of different wavelength for energy conversion. The aim of this study was to investigate the effect of the phototrophs on biodiversity and community composition in hot spring microbial mats. For this, we specifically activated the different phototrophs by irradiating the mats with different wavelengths in situ. We used 625, 730, and 890 nm wavelength LEDs alone or in combination and confirmed the hypothesized increase in relative abundance of different phototrophs by 16S rRNA gene sequencing. In addition to the increase of the targeted phototrophs, we studied the effect of the different treatments on chemotrophic members. The specific activation of Thermosynechococcus led to increased abundance of several other bacteria, whereas wavelengths specific to Chloroflexus and Roseiflexus induced a decrease in >50% of the community members as compared to the dark conditions. This suggests that the growth of Thermosynechococcus at the surface layer benefits many community members, whereas less benefit is obtained from an increase in filamentous anoxygenic phototrophs Chloroflexus and Roseiflexus. The increases in relative abundance of chemotrophs under different light conditions suggest a relationship between the two groups. Aerobic chemoheterotrophs such as Thermus sp. and Meiothermus sp. are thought to benefit from aerobic conditions and organic carbon in the form of photosynthates by Thermosynechococcus, while the oxidation of sulfide and production of elemental sulfur by filamentous anoxygenic phototrophs benefit the sulfur-disproportionating Caldimicrobium thiodismutans. In this study, we used an experimental approach under controlled

  13. An examination of the biodiversity-ecosystem function relationship in arable soil microbial communities

    DEFF Research Database (Denmark)

    Griffiths, B.S.; Ritz, Karl; Wheatley, R.

    2001-01-01

    Microbial communities differing in biodiversity were established by inoculating sterile agricultural soil with serially diluted soil suspensions prepared from the parent soil. Three replicate communities of each dilution were allowed to establish an equivalent microbial biomass by incubation for 9...... relates to the numbers and proportions of different microbial species. Biodiversity decreased by ca. 15, 40 and 60% at each successive dilution step. There was no consistent effect of biodiversity on a range of soil processes measured (incorporation of thymidine and leucine, potential nitrification...... months at 15°C, after which the biodiversity-ecosystem function relationship was examined for a range of soil processes. Biodiversity was determined by monitoring cultivable bacterial and fungal morphotypes, directly extracted eubacterial DNA and protozoan taxa. In the context of this study biodiversity...

  14. Wooden Tools: Reservoirs of Microbial Biodiversity in Traditional Cheesemaking.

    Science.gov (United States)

    Lortal, Sylvie; Licitra, Giuseppe; Valence, Florence

    2014-02-01

    Today, wooden shelves are used for the ripening of about 500,000 tons of cheese per year in Europe, including about 350,000 tons in France, such as most of the famous cheeses with the protected designation of origin (PDO), e.g., Comté, Reblochon, Beaufort, Munster, Cantal, and Roquefort. For some PDO cheeses, the use of wooden tools is mandatory. Many cheesemakers believe that wooden tools improve the organoleptic and typical characteristics of their final products. Wood is a natural and sustainable material which has been used for centuries in traditional cheese production in a wide variety of forms (vats, shelves, and packaging). Wood is important in the cheesemaking process, interacting with the milk in vats or with the cheeses placed on shelves for ripening. Wood is viable due to its ability to exchange water but, above all, because it is covered by a rich microbial biofilm. As wood is porous and difficult to clean, the European Commission regularly highlights the question of its safety when in contact with food and calls for deeper scientific investigation. In this review, knowledge about the multiple technological roles of wood in dairy technology is discussed. The crucial role of wood as a reservoir of microbial biodiversity for traditional cheeses is reviewed, along with results of safety assessments. As a conclusion, the numerous questions remaining about this natural inoculating system are discussed.

  15. Preliminary survey of biodiversity in New Chicago Marsh

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — During the late winter and early springs 1995, we conducted a preliminary survey of biodiversity in New Chicago Marsh (NCM), at the south end of San Francisco Bay,...

  16. Microbial biodiversity in arable soils is affected by agricultural practices

    Science.gov (United States)

    Wolińska, Agnieszka; Górniak, Dorota; Zielenkiewicz, Urszula; Goryluk-Salmonowicz, Agata; Kuźniar, Agnieszka; Stępniewska, Zofia; Błaszczyk, Mieczysław

    2017-04-01

    The aim of the study was to examine the differences in microbial community structure as a result of agricultural practices. Sixteen samples of cultivated and the same number of non-cultivated soils were selected. Gel bands were identified using the GelCompar software to create the presence-absence matrix, where each band represented a bacterial operational taxonomic unit. The data were used for principal-component analysis and additionally, the Shannon- Weaver index of general diversity, Simpson index of dominance and Simpson index of diversity were calculated. Denaturing gradient gel electrophoresis profiles clearly indicated differentiation of tested samples into two clusters: cultivated and non-cultivated soils. Greater numbers of dominant operational taxonomic units (65) in non-cultivated soils were noted compared to cultivated soils (47 operational taxonomic units). This implies that there was a reduction of dominant bacterial operational taxonomic units by nearly 30% in cultivated soils. Simpson dominance index expressing the number of species weighted by their abundance amounted to 1.22 in cultivated soils, whereas a 3-fold higher value (3.38) was observed in non-cultivated soils. Land-use practices seemed to be a important factors affected on biodiversity, because more than soil type determined the clustering into groups.

  17. An endangered oasis of aquatic microbial biodiversity in the Chihuahuan desert

    OpenAIRE

    Souza, Valeria; Espinosa-Asuar, Laura; Escalante, Ana E.; Eguiarte, Luis E.; Farmer, Jack; Forney, Larry; Lloret, Lourdes; Rodríguez-Martínez, Juan M.; Soberón, Xavier; Dirzo, Rodolfo; Elser, James J.

    2006-01-01

    The Cuatro Cienegas basin in the Chihuahuan desert is a system of springs, streams, and pools. These ecosystems support >70 endemic species and abundant living stromatolites and other microbial communities, representing a desert oasis of high biodiversity. Here, we combine data from molecular microbiology and geology to document the microbial biodiversity of this unique environment. Ten water samples from locations within the Cuatro Cienegas basin and two neighboring valleys as well as three ...

  18. Spatial and Temporal Variations of Microbial Biodiversity at Hypersaline Microbial Mats

    Science.gov (United States)

    Gulecal, Y.; Unsal, N.; Temel, M.

    2014-12-01

    Hypersaline environments, such as hypersaline lakes are interesting sources with considerable potential for the isolation of extremophile microorganisms adapted to severe conditions. Biodiversity in such lakes (Dead Sea, the Great Salt Lake, the Solar Lake, the Soda Lake) varies due to differences in environmental conditions and specific lake characteristics such as local climate, lake size, water depth and lake water salt composition (Kamekura 1998; Sorokin et al. 2004). In this study area, Acigol Lake is an alkaline (pH:9), hypersaline lake located at Southwest Anatolia in Turkey. The aim of study was to determine the Archaea and Bacteria in microbial mats of hypersaline lacustrine environments. In conclusion, diagnostic biosignatures for methanogens and other archaeal groups within hypersaline microbial mats were identified through genomic DNA and lipid analyses.

  19. Biodiversity and succession of microbial community in a multi-habitat membrane bioreactor.

    Science.gov (United States)

    Tang, Bing; Zhang, Zi; Chen, Xuan; Bin, Liying; Huang, Shaosong; Fu, Fenglian; Yang, Huiwen; Chen, Cuiqun

    2014-07-01

    The present study focused on establishing a multi-habitat membrane bioreactor, as well as exploring its biodiversity and succession of microbial communities. In a long-term operational period (100 days), the dissolved oxygen level of a local zone within the bioreactor decreased consistently from the original oxic state to the final anaerobic state, which led to a continuous succession of the microbial community in the bioreactor. The results revealed that the biodiversity of the microbial community in different zones simultaneously increased, with a similar microbial composition in their final successional stage. The results also indicated that the dominant species during the whole operation were distributed among 6 major phyla. At the initial operational stages, the dominant species in the anoxic-anaerobic and the oxic zones exhibited distinguished difference, whereas at the final operational stage, both zones presented nearly the same dominant microbial species and a rather similar structure in their microbial communities. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Biodiversity and species competition regulate the resilience of microbial biofilm community

    DEFF Research Database (Denmark)

    Feng, Kai; Zhang, Zhaojing; Cai, Weiwei

    2017-01-01

    The relationship between biodiversity and ecosystem stability is poorly understood in microbial communities. Biofilm communities in small bioreactors called microbial electrolysis cells (MEC) contain moderate species numbers and easy tractable functional traits, thus providing an ideal platform...... for verifying ecological theories in microbial ecosystems. Here, we investigated the resilience of biofilm communities with a gradient of diversity, and explored the relationship between biodiversity and stability in response to a pH shock. The results showed that all bioreactors could recover to stable...... of biofilms. The microbial communities with higher diversity tended to be recovered faster, implying biofilms with high biodiversity showed better resilience in response to environmental disturbance. Network analysis revealed that the negative interactions between the two dominant genera of Geobacter...

  1. Biodiversity surveys in the East Usambara Mountains: Preliminary ...

    African Journals Online (AJOL)

    Biodiversity surveys were initiated in the East Usambara Mountains in 1995 to provide baseline information on the biological values of the forests for management planning and monitoring, and to train field staff in the use of biological inventory techniques. They were conducted in ten-week field phases. Vegetation plots ...

  2. Handbook of biodiversity methods: survey, evaluation and monitoring

    National Research Council Canada - National Science Library

    Hill, David A

    2005-01-01

    ... for a comprehensive biodiversity audit. For those needing to undertake such audits, this Handbook provides standard procedures for planning and conducting a survey of any terrestrial or freshwater species or habitat and for evaluating the data so as to determine its local, national and international significance. Organised in three parts, the Handb...

  3. Biodiversity in microbial communities: system scale patterns and mechanisms.

    Science.gov (United States)

    Parnell, J Jacob; Crowl, Todd A; Weimer, Bart C; Pfrender, Michael E

    2009-04-01

    The relationship between anthropogenic impact and the maintenance of biodiversity is a fundamental question in ecology. The emphasis on the organizational level of biodiversity responsible for ecosystem processes is shifting from a species-centred focus to include genotypic diversity. The relationship between biodiversity measures at these two scales remains largely unknown. By stratifying anthropogenic effects between scales of biodiversity of bacterial communities, we show a statistically significant difference in diversity based on taxonomic scale. Communities with intermediate species richness show high genotypic diversity while speciose and species-poor communities do not. We propose that in species-poor communities, generally comprising stable yet harsh conditions, physiological tolerance and competitive trade-offs limit both the number of species that occur and the loss of genotypes due to decreases in already constrained fitness. In species-rich communities, natural environmental conditions result in well-defined community structure and resource partitioning. Disturbance of these communities disrupts niche space, resulting in lower genotypic diversity despite the maintenance of species diversity. Our work provides a model to inform future research about relationships between species and genotypic biodiversity based on determining the biodiversity consequences of changing environmental context.

  4. Text mining tools for extracting information about microbial biodiversity in food

    OpenAIRE

    Deleger, Louise; Bossy, Robert; Nédellec, Claire

    2017-01-01

    Introduction Information on food microbial biodiversity is scattered across millions of scientific papers (2 million references in the PubMed bibliographic database in 2017). It is impossible to manually achieve an exhaustive analysis of these documents. Text-mining and knowledge engineering methods can assist the researcher in finding relevant information. Material & Methods We propose to study bacterial biodiversity using text-mining tools from the Alvis platform. First, w...

  5. Biodiversity of the microbial mat of the Garga hot spring.

    Science.gov (United States)

    Rozanov, Alexey Sergeevich; Bryanskaya, Alla Victorovna; Ivanisenko, Timofey Vladimirovich; Malup, Tatyana Konstantinovna; Peltek, Sergey Evgenievich

    2017-12-28

    Microbial mats are a good model system for ecological and evolutionary analysis of microbial communities. There are more than 20 alkaline hot springs on the banks of the Barguzin river inflows. Water temperature reaches 75 °C and pH is usually 8.0-9.0. The formation of microbial mats is observed in all hot springs. Microbial communities of hot springs of the Baikal rift zone are poorly studied. Garga is the biggest hot spring in this area. In this study, we investigated bacterial and archaeal diversity of the Garga hot spring (Baikal rift zone, Russia) using 16S rRNA metagenomic sequencing. We studied two types of microbial communities: (i) small white biofilms on rocks in the points with the highest temperature (75 °C) and (ii) continuous thick phototrophic microbial mats observed at temperatures below 70 °C. Archaea (mainly Crenarchaeota; 19.8% of the total sequences) were detected only in the small biofilms. The high abundance of Archaea in the sample from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. In the microbial mats, primary products were formed by cyanobacteria of the genus Leptolyngbya. Heterotrophic microorganisms were mostly represented by Actinobacteria and Proteobacteria in all studied samples of the microbial mats. Planctomycetes, Chloroflexi, and Chlorobi were abundant in the middle layer of the microbial mats, while heterotrophic microorganisms represented mostly by Firmicutes (Clostridia, strict anaerobes) dominated in the bottom part. Besides prokaryotes, we detect some species of Algae with help of detection their chloroplasts 16 s rRNA. High abundance of Archaea in samples from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. Metagenomic analysis of microbial communities of the microbial mat of Garga hot spring showed that

  6. Trait-based approaches for understanding microbial biodiversity and ecosystem functioning

    Directory of Open Access Journals (Sweden)

    Sascha eKrause

    2014-05-01

    Full Text Available In ecology, biodiversity-ecosystem functioning (BEF research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEF of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEF using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEF studies are often inadequate to unravel BEF relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEF relationships and thus generating systematic principles in microbial ecology and more generally ecology.

  7. Trait-based approaches for understanding microbial biodiversity and ecosystem functioning

    Science.gov (United States)

    Krause, Sascha; Le Roux, Xavier; Niklaus, Pascal A.; Van Bodegom, Peter M.; Lennon, Jay T.; Bertilsson, Stefan; Grossart, Hans-Peter; Philippot, Laurent; Bodelier, Paul L. E.

    2014-01-01

    In ecology, biodiversity-ecosystem functioning (BEF) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEF of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEF using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEF studies are often inadequate to unravel BEF relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEF relationships and thus generating systematic principles in microbial ecology and more generally ecology. PMID:24904563

  8. Trait-based approaches for understanding microbial biodiversity and ecosystem functioning.

    Science.gov (United States)

    Krause, Sascha; Le Roux, Xavier; Niklaus, Pascal A; Van Bodegom, Peter M; Lennon, Jay T; Bertilsson, Stefan; Grossart, Hans-Peter; Philippot, Laurent; Bodelier, Paul L E

    2014-01-01

    In ecology, biodiversity-ecosystem functioning (BEF) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEF of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEF using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEF studies are often inadequate to unravel BEF relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEF relationships and thus generating systematic principles in microbial ecology and more generally ecology.

  9. Elucidating the impact of microbial community biodiversity on pharmaceutical biotransformation during wastewater treatment.

    Science.gov (United States)

    Stadler, Lauren B; Delgado Vela, Jeseth; Jain, Sunit; Dick, Gregory J; Love, Nancy G

    2017-10-27

    In addition to removing organics and other nutrients, the microorganisms in wastewater treatment plants (WWTPs) biotransform many pharmaceuticals present in wastewater. The objective of this study was to examine the relationship between pharmaceutical biotransformation and biodiversity in WWTP bioreactor microbial communities and identify taxa and functional genes that were strongly associated with biotransformation. Dilution-to-extinction of an activated sludge microbial community was performed to establish cultures with a gradient of microbial biodiversity. Batch experiments were performed using the dilution cultures to determine biotransformation extents of several environmentally relevant pharmaceuticals. With this approach, because the communities were all established from the same original community, and using sequencing of the 16S rRNA and metatranscriptome, we identified candidate taxa and genes whose activity and transcript abundances associated with the extent of individual pharmaceutical biotransformation and were lost across the biodiversity gradient. Metabolic genes such as dehydrogenases, amidases and monooxygenases were significantly associated with pharmaceutical biotransformation, and five genera were identified whose activity significantly associated with pharmaceutical biotransformation. Understanding how biotransformation relates to biodiversity will inform the design of biological WWTPs for enhanced removal of chemicals that negatively impact environmental health. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  10. Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards.

    Science.gov (United States)

    Ten Hoopen, Petra; Pesant, Stéphane; Kottmann, Renzo; Kopf, Anna; Bicak, Mesude; Claus, Simon; Deneudt, Klaas; Borremans, Catherine; Thijsse, Peter; Dekeyzer, Stefanie; Schaap, Dick Ma; Bowler, Chris; Glöckner, Frank Oliver; Cochrane, Guy

    2015-01-01

    Contextual data collected concurrently with molecular samples are critical to the use of metagenomics in the fields of marine biodiversity, bioinformatics and biotechnology. We present here Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards for "Reporting" and "Serving" data. The M2B3 Reporting Standard (1) describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, (2) includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and (3) can easily be adopted by any marine laboratory with minimum sampling resources. The M2B3 Service Standard defines a software interface through which these data can be discovered and explored in data repositories. The M2B3 Standards were developed by the European project Micro B3, funded under 7(th) Framework Programme "Ocean of Tomorrow", and were first used with the Ocean Sampling Day initiative. We believe that these standards have value in broader marine science.

  11. Microbial biodiversity of Tang and Pirgal mud volcanoes and evaluation of bio-emulsifier and bio-demulsifier activities of Capnophile bacteria.

    Science.gov (United States)

    Parsia, Yasaman; Sorooshian, Shahryar

    2017-12-01

    The data presented in this article is related to the Master thesis; entitled "Survey Aerobic Microbial Diversity Mud Volcanoes in Chabahar and Khash Ports in Southern Iran" by the first author of this article, year 2011, Islamic Azad University, Iran (reference number (Parsia, 2011) [1] of this article). This article shows microbial biodiversity and evaluates bio-emulsifier and bio-demulsifier abilities of capnophile isolates, in order to introduce a superior isolate for the Microbial Enhanced Oil Recovery (MEOR) process in the petrochemical industry.

  12. Biodiversity and species competition regulate the resilience of microbial biofilm community.

    Science.gov (United States)

    Feng, Kai; Zhang, Zhaojing; Cai, Weiwei; Liu, Wenzong; Xu, Meiying; Yin, Huaqun; Wang, Aijie; He, Zhili; Deng, Ye

    2017-11-01

    The relationship between biodiversity and ecosystem stability is poorly understood in microbial communities. Biofilm communities in small bioreactors called microbial electrolysis cells (MEC) contain moderate species numbers and easy tractable functional traits, thus providing an ideal platform for verifying ecological theories in microbial ecosystems. Here, we investigated the resilience of biofilm communities with a gradient of diversity, and explored the relationship between biodiversity and stability in response to a pH shock. The results showed that all bioreactors could recover to stable performance after pH disturbance, exhibiting a great resilience ability. A further analysis of microbial composition showed that the rebound of Geobacter and other exoelectrogens contributed to the resilient effectiveness, and that the presence of Methanobrevibacter might delay the functional recovery of biofilms. The microbial communities with higher diversity tended to be recovered faster, implying biofilms with high biodiversity showed better resilience in response to environmental disturbance. Network analysis revealed that the negative interactions between the two dominant genera of Geobacter and Methanobrevibacter increased when the recovery time became longer, implying the internal resource or spatial competition of key functional taxa might fundamentally impact the resilience performances of biofilm communities. This study provides new insights into our understanding of the relationship between diversity and ecosystem functioning. © 2017 John Wiley & Sons Ltd.

  13. Soil functional operating range linked to microbial biodiversity and community composition using denitrifiers as model guild.

    Science.gov (United States)

    Hallin, Sara; Welsh, Allana; Stenström, John; Hallet, Stephanie; Enwall, Karin; Bru, David; Philippot, Laurent

    2012-01-01

    Soil microorganisms are key players in biogeochemical cycles. Yet, there is no consistent view on the significance of microbial biodiversity for soil ecosystem functioning. According to the insurance hypothesis, declines in ecosystem functioning due to reduced biodiversity are more likely to occur under fluctuating, extreme or rapidly changing environmental conditions. Here, we compare the functional operating range, a new concept defined as the complete range of environmental conditions under which soil microbial communities are able to maintain their functions, between four naturally assembled soil communities from a long-term fertilization experiment. A functional trait approach was adopted with denitrifiers involved in nitrogen cycling as our model soil community. Using short-term temperature and salt gradients, we show that the functional operating range was broader and process rates were higher when the soil community was phylogenetically more diverse. However, key bacterial genotypes played an important role for maintaining denitrification as an ecosystem functioning under certain conditions.

  14. Prebiotics, faecal transplants and microbial network units to stimulate biodiversity of the human gut microbiome

    Science.gov (United States)

    Van den Abbeele, Pieter; Verstraete, Willy; El Aidy, Sahar; Geirnaert, Annelies; Van de Wiele, Tom

    2013-01-01

    Summary Accumulating evidence demonstrates the intimate association between human hosts and the gut microbiome. Starting at birth, the sterile gut of the newborn acquires a diverse spectrum of microbes, needed for immunological priming. However, current practices (caesarean sections, use of formula milk) deprive newborns from being exposed to this broad spectrum of microbes. Unnecessary use of antibiotics and excessive hygienic precautions (e.g. natural versus chlorinated drinking water) together with the Western diet further contribute to a decreased microbial diversity in the adult gut. This has been correlated with recurrent Clostridium difficile infection, inflammatory bowel diseases and obesity, among others. A healthy gut microbiome is thus characterized by a diverse network of metabolically interacting microbial members. In this context, we review several existing and novel approaches to manage the gut microbiome. First, prebiotic compounds should be re-defined in the sense that they should enhance the ecological biodiversity rather than stimulating single species. Recent studies highlight that structurally different polysaccharides require specific primary degraders but also enhance a similar network of secondary degraders that benefit from cross-feeding. A faecal transplantation is a second approach to restore biodiversity when the microbiota is severely dysbiosed, with promising results regarding C. difficile-associated disease and obesity-related metabolic syndromes. A final strategy is the introduction of key microbial network units, i.e. pre-organized microbial associations, which strengthen the overall microbial network of the gut microbiome that supports human health. PMID:23594389

  15. A unifying quantitative framework for exploring the multiple facets of microbial biodiversity across diverse scales.

    Science.gov (United States)

    Escalas, Arthur; Bouvier, Thierry; Mouchet, Maud A; Leprieur, Fabien; Bouvier, Corinne; Troussellier, Marc; Mouillot, David

    2013-10-01

    Recent developments of molecular tools have revolutionized our knowledge of microbial biodiversity by allowing detailed exploration of its different facets and generating unprecedented amount of data. One key issue with such large datasets is the development of diversity measures that cope with different data outputs and allow comparison of biodiversity across different scales. Diversity has indeed three components: local (α), regional (γ) and the overall difference between local communities (β). Current measures of microbial diversity, derived from several approaches, provide complementary but different views. They only capture the β component of diversity, compare communities in a pairwise way, consider all species as equivalent or lack a mathematically explicit relationship among the α, β and γ components. We propose a unified quantitative framework based on the Rao quadratic entropy, to obtain an additive decomposition of diversity (γ = α + β), so the three components can be compared, and that integrate the relationship (phylogenetic or functional) among Microbial Diversity Units that compose a microbial community. We show how this framework is adapted to all types of molecular data, and we highlight crucial issues in microbial ecology that would benefit from this framework and propose ready-to-use R-functions to easily set up our approach. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

  16. Microbial Biodiversity: Approaches to Experimental Design and Hypothesis Testing in Primary Scientific Literature from 1975 to 1999

    OpenAIRE

    Morris, Cindy E.; Bardin, Marc; Berge, Odile; Frey-Klett, Pascale; Fromin, Nathalie; Girardin, Hélène; Guinebretière, Marie-Hélène; Lebaron, Philippe; Thiéry, Jean M.; Troussellier, Marc

    2002-01-01

    Research interest in microbial biodiversity over the past 25 years has increased markedly as microbiologists have become interested in the significance of biodiversity for ecological processes and as the industrial, medical, and agricultural applications of this diversity have evolved. One major challenge for studies of microbial habitats is how to account for the diversity of extremely large and heterogeneous populations with samples that represent only a very small fraction of these populat...

  17. Over 150 years of long-term fertilization alters spatial scaling of microbial biodiversity.

    Science.gov (United States)

    Liang, Yuting; Wu, Liyou; Clark, Ian M; Xue, Kai; Yang, Yunfeng; Van Nostrand, Joy D; Deng, Ye; He, Zhili; McGrath, Steve; Storkey, Jonathan; Hirsch, Penny R; Sun, Bo; Zhou, Jizhong

    2015-04-07

    Spatial scaling is a critical issue in ecology, but how anthropogenic activities like fertilization affect spatial scaling is poorly understood, especially for microbial communities. Here, we determined the effects of long-term fertilization on the spatial scaling of microbial functional diversity and its relationships to plant diversity in the 150-year-old Park Grass Experiment, the oldest continuous grassland experiment in the world. Nested samples were taken from plots with contrasting inorganic fertilization regimes, and community DNAs were analyzed using the GeoChip-based functional gene array. The slopes of microbial gene-area relationships (GARs) and plant species-area relationships (SARs) were estimated in a plot receiving nitrogen (N), phosphorus (P), and potassium (K) and a control plot without fertilization. Our results indicated that long-term inorganic fertilization significantly increased both microbial GARs and plant SARs. Microbial spatial turnover rates (i.e., z values) were less than 0.1 and were significantly higher in the fertilized plot (0.0583) than in the control plot (0.0449) (P microbial functional community structure, while soil geochemical variables contributed less. These results indicated that long-term agricultural practice could alter the spatial scaling of microbial biodiversity. Determining the spatial scaling of microbial biodiversity and its response to human activities is important but challenging in microbial ecology. Most studies to date are based on different sites that may not be truly comparable or on short-term perturbations, and hence, the results observed could represent transient responses. This study examined the spatial patterns of microbial communities in response to different fertilization regimes at the Rothamsted Research Experimental Station, which has become an invaluable resource for ecologists, environmentalists, and soil scientists. The current study is the first showing that long-term fertilization has

  18. Lipid biomolecules in silica sinters: indicators of microbial biodiversity.

    Science.gov (United States)

    Pancost, Richard D; Pressley, Sarah; Coleman, Joanna M; Benning, Liane G; Mountain, B W

    2005-01-01

    To explore further the diversity of the microorganisms and their relationship with geothermal sinters, we examined the lipids preserved in six sinters associated with four different hot spring (58-82 degrees C) areas of the Taupo Volcanic Zone (TVZ), New Zealand. These sinters contain microbial remains, but the process of mineralization has rendered them largely unidentifiable. Dominant lipids include free fatty acids, 1,2-diacylglycerophospholipids, 1,2-di-O-alkylglycerols, glycerol dialkylglycerol tetraethers and 1-O-alkylglycerols. These confirm the presence and, in some cases, high abundances of bacteria in all six sinters and archaea in four of the six sinter samples; in addition, the presence of novel macrocyclic diethers and unusual distributions of monoethers and diethers suggest the presence of previously uncharacterized bacteria. The lipid distributions are also markedly dissimilar among the four sites; for example, novel macrocyclic diethers are restricted to the Rotokawa samples while particularly abundant monoethers occur only in the Orakei Korako sample. Thus, biomarkers can provide crucial insight into the complex community structure of thermophilic microorganisms, including both archaea and bacteria, involved with biogenic silica sinter formation.

  19. A natural view of microbial biodiversity within hot spring cyanobacterial mat communities

    Science.gov (United States)

    Ward, D. M.; Ferris, M. J.; Nold, S. C.; Bateson, M. M.

    1998-01-01

    This review summarizes a decade of research in which we have used molecular methods, in conjunction with more traditional approaches, to study hot spring cyanobacterial mats as models for understanding principles of microbial community ecology. Molecular methods reveal that the composition of these communities is grossly oversimplified by microscopic and cultivation methods. For example, none of 31 unique 16S rRNA sequences detected in the Octopus Spring mat, Yellowstone National Park, matches that of any prokaryote previously cultivated from geothermal systems; 11 are contributed by genetically diverse cyanobacteria, even though a single cyanobacterial species was suspected based on morphologic and culture analysis. By studying the basis for the incongruity between culture and molecular samplings of community composition, we are beginning to cultivate isolates whose 16S rRNA sequences are readily detected. By placing the genetic diversity detected in context with the well-defined natural environmental gradients typical of hot spring mat systems, the relationship between gene and species diversity is clarified and ecological patterns of species occurrence emerge. By combining these ecological patterns with the evolutionary patterns inherently revealed by phylogenetic analysis of gene sequence data, we find that it may be possible to understand microbial biodiversity within these systems by using principles similar to those developed by evolutionary ecologists to understand biodiversity of larger species. We hope that such an approach guides microbial ecologists to a more realistic and predictive understanding of microbial species occurrence and responsiveness in both natural and disturbed habitats.

  20. The Biodiversity Changes in the Microbial Population of Soils Contaminated with Crude Oil.

    Science.gov (United States)

    Abbasian, Firouz; Lockington, Robin; Megharaj, Mallavarapu; Naidu, Ravi

    2016-06-01

    Crude oil spills resulting from excavation, transportation and downstream processes can cause intensive damage to living organisms and result in changes in the microbial population of that environment. In this study, we used a pyrosequencing analysis to investigate changes in the microbial population of soils contaminated with crude oil. Crude oil contamination in soil resulted in the creation of a more homogenous population of microorganisms dominated by members of the Actinomycetales, Clostridiales and Bacillales (all belonging to Gram-positive bacteria) as well as Flavobacteriales, Pseudomonadales, Burkholderiales, Rhizobiales and Sphingomonadales (all belonging to Gram-negative bacteria). These changes in the biodiversity decreased the ratios of chemoheterotrophic bacteria at higher concentrations of crude oil contamination, with these being replaced by photoheterotrophic bacteria, mainly Rhodospirillales. Several of the dominant microbial orders in the crude oil contaminated soils are able to degrade crude oil hydrocarbons and therefore are potentially useful for remediation of crude oil in contaminated sites.

  1. Prebiotics, faecal transplants and microbial network units to stimulate biodiversity of the human gut microbiome.

    Science.gov (United States)

    Van den Abbeele, Pieter; Verstraete, Willy; El Aidy, Sahar; Geirnaert, Annelies; Van de Wiele, Tom

    2013-07-01

    Accumulating evidence demonstrates the intimate association between human hosts and the gut microbiome. Starting at birth, the sterile gut of the newborn acquires a diverse spectrum of microbes, needed for immunological priming. However, current practices (caesarean sections, use of formula milk) deprive newborns from being exposed to this broad spectrum of microbes. Unnecessary use of antibiotics and excessive hygienic precautions (e.g. natural versus chlorinated drinking water) together with the Western diet further contribute to a decreased microbial diversity in the adult gut. This has been correlated with recurrent Clostridium difficile infection, inflammatory bowel diseases and obesity, among others. A healthy gut microbiome is thus characterized by a diverse network of metabolically interacting microbial members. In this context, we review several existing and novel approaches to manage the gut microbiome. First, prebiotic compounds should be re-defined in the sense that they should enhance the ecological biodiversity rather than stimulating single species. Recent studies highlight that structurally different polysaccharides require specific primary degraders but also enhance a similar network of secondary degraders that benefit from cross-feeding. A faecal transplantation is a second approach to restore biodiversity when the microbiota is severely dysbiosed, with promising results regarding C. difficile-associated disease and obesity-related metabolic syndromes. A final strategy is the introduction of key microbial network units, i.e. pre-organized microbial associations, which strengthen the overall microbial network of the gut microbiome that supports human health. © 2013 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  2. Phylogenetic and functional metagenomic profiling for assessing microbial biodiversity in environmental monitoring.

    Directory of Open Access Journals (Sweden)

    Veljo Kisand

    Full Text Available Decisions guiding environmental management need to be based on a broad and comprehensive understanding of the biodiversity and functional capability within ecosystems. Microbes are of particular importance since they drive biogeochemical cycles, being both producers and decomposers. Their quick and direct responses to changes in environmental conditions modulate the ecosystem accordingly, thus providing a sensitive readout. Here we have used direct sequencing of total DNA from water samples to compare the microbial communities of two distinct coastal regions exposed to different anthropogenic pressures: the highly polluted Port of Genoa and the protected area of Montecristo Island in the Mediterranean Sea. Analysis of the metagenomes revealed significant differences in both microbial diversity and abundance between the two areas, reflecting their distinct ecological habitats and anthropogenic stress conditions. Our results indicate that the combination of next generation sequencing (NGS technologies and bioinformatics tools presents a new approach to monitor the diversity and the ecological status of aquatic ecosystems. Integration of metagenomics into environmental monitoring campaigns should enable the impact of the anthropogenic pressure on microbial biodiversity in various ecosystems to be better assessed and also predicted.

  3. Phylogenetic and functional metagenomic profiling for assessing microbial biodiversity in environmental monitoring.

    Science.gov (United States)

    Kisand, Veljo; Valente, Angelica; Lahm, Armin; Tanet, Gerard; Lettieri, Teresa

    2012-01-01

    Decisions guiding environmental management need to be based on a broad and comprehensive understanding of the biodiversity and functional capability within ecosystems. Microbes are of particular importance since they drive biogeochemical cycles, being both producers and decomposers. Their quick and direct responses to changes in environmental conditions modulate the ecosystem accordingly, thus providing a sensitive readout. Here we have used direct sequencing of total DNA from water samples to compare the microbial communities of two distinct coastal regions exposed to different anthropogenic pressures: the highly polluted Port of Genoa and the protected area of Montecristo Island in the Mediterranean Sea. Analysis of the metagenomes revealed significant differences in both microbial diversity and abundance between the two areas, reflecting their distinct ecological habitats and anthropogenic stress conditions. Our results indicate that the combination of next generation sequencing (NGS) technologies and bioinformatics tools presents a new approach to monitor the diversity and the ecological status of aquatic ecosystems. Integration of metagenomics into environmental monitoring campaigns should enable the impact of the anthropogenic pressure on microbial biodiversity in various ecosystems to be better assessed and also predicted.

  4. Biodiversity and multifunctionality in a microbial community: a novel theoretical approach to quantify functional redundancy.

    Science.gov (United States)

    Miki, Takeshi; Yokokawa, Taichi; Matsui, Kazuaki

    2014-02-07

    Ecosystems have a limited buffering capacity of multiple ecosystem functions against biodiversity loss (i.e. low multifunctional redundancy). We developed a novel theoretical approach to evaluate multifunctional redundancy in a microbial community using the microbial genome database (MBGD) for comparative analysis. In order to fully implement functional information, we defined orthologue richness in a community, each of which is a functionally conservative evolutionary unit in genomes, as an index of community multifunctionality (MF). We constructed a graph of expected orthologue richness in a community (MF) as a function of species richness (SR), fit the power function to SR (i.e. MF = cSR(a)), and interpreted the higher exponent a as the lower multifunctional redundancy. Through a microcosm experiment, we confirmed that MF defined by orthologue richness could predict the actual multiple functions. We simulated random and non-random community assemblages using full genomic data of 478 prokaryotic species in the MBGD, and determined that the exponent in microbial communities ranged from 0.55 to 0.75. This exponent range provided a quantitative estimate that a 6.6-8.9% loss limit in SR occurred in a microbial community for an MF reduction no greater than 5%, suggesting a non-negligible initial loss effect of microbial diversity on MF.

  5. An endangered oasis of aquatic microbial biodiversity in the Chihuahuan desert.

    Science.gov (United States)

    Souza, Valeria; Espinosa-Asuar, Laura; Escalante, Ana E; Eguiarte, Luis E; Farmer, Jack; Forney, Larry; Lloret, Lourdes; Rodríguez-Martínez, Juan M; Soberón, Xavier; Dirzo, Rodolfo; Elser, James J

    2006-04-25

    The Cuatro Cienegas basin in the Chihuahuan desert is a system of springs, streams, and pools. These ecosystems support >70 endemic species and abundant living stromatolites and other microbial communities, representing a desert oasis of high biodiversity. Here, we combine data from molecular microbiology and geology to document the microbial biodiversity of this unique environment. Ten water samples from locations within the Cuatro Cienegas basin and two neighboring valleys as well as three samples of wet sediments were analyzed. The phylogeny of prokaryotic populations in the samples was determined by characterizing cultured organisms and by PCR amplification and sequencing of 16S rRNA genes from total community DNA. The composition of microbial communities was also assessed by determining profiles of terminal restriction site polymorphisms of 16S rRNA genes in total community DNA. There were 250 different phylotypes among the 350 cultivated strains. Ninety-eight partial 16S rRNA gene sequences were obtained and classified. The clones represented 38 unique phylotypes from ten major lineages of Bacteria and one of Archaea. Unexpectedly, 50% of the phylotypes were most closely related to marine taxa, even though these environments have not been in contact with the ocean for tens of millions of years. Furthermore, terminal restriction site polymorphism profiles and geological data suggest that the aquatic ecosystems of Cuatro Cienegas are hydrologically interconnected with adjacent valleys recently targeted for agricultural intensification. The findings underscore the conservation value of desert aquatic ecosystems and the urgent need for study and preservation of freshwater microbial communities.

  6. Eco-evolutionary Red Queen dynamics regulate biodiversity in a metabolite-driven microbial system.

    Science.gov (United States)

    Bonachela, Juan A; Wortel, Meike T; Stenseth, Nils Chr

    2017-12-15

    The Red Queen Hypothesis proposes that perpetual co-evolution among organisms can result from purely biotic drivers. After more than four decades, there is no satisfactory understanding as to which mechanisms trigger Red Queen dynamics or their implications for ecosystem features such as biodiversity. One reason for such a knowledge gap is that typical models are complicated theories where limit cycles represent an idealized Red Queen, and therefore cannot be used to devise experimental setups. Here, we bridge this gap by introducing a simple model for microbial systems able to show Red Queen dynamics. We explore diverse biotic sources that can drive the emergence of the Red Queen and that have the potential to be found in nature or to be replicated in the laboratory. Our model enables an analytical understanding of how Red Queen dynamics emerge in our setup, and the translation of model terms and phenomenology into general underlying mechanisms. We observe, for example, that in our system the Red Queen offers opportunities for the increase of biodiversity by facilitating challenging conditions for intraspecific dominance, whereas stasis tends to homogenize the system. Our results can be used to design and engineer experimental microbial systems showing Red Queen dynamics.

  7. Microbial Biodiversity in the Subsurface of Carbonate Mounds from the Gulf of Cadiz off Morocco

    Science.gov (United States)

    Templer, S. P.; Stadnitskaia, A.; de Haas, H.; Bernasconi, S.; Vasconcelos, C.; McKenzie, J. A.

    2008-12-01

    The study area, El Arraiche mud volcano field, is situated 35 km offshore the north-western Moroccan margin, on top of the accretionary wedge of the Gulf of Cadiz. An exploratory cruise of R/V Belgica in 2002 off Larache (Morocco) has led to the discovery of small mounds topping ridges and structural heights, respectively on Pen Duick Escarpment, Renard Ridge, Vernadsky Ridge and Al Idrisi Ridge. These mounds are found amidst 9 giant mud volcanoes and occur in a setting where focused fluid seepage is observed. Subsequent cruises have confirmed the colonization by dominantly lifeless cold-water corals and have unveiled extensive fields of seep-related carbonates in off-reef regions. We present the microbial biodiversity of the subsurface of two different carbonate mounds (alpha- and beta-mound) flanked by a giant double- peaked mud volcano in the Pen Duick Mound Province in a water depths of 500-600 m. Most of the sediment comprises pelagic calcite (coccoliths), detrital quartz and authigenic dolomite, often observed encasing coccoliths. Stable carbon isotope values of the bulk carbonate range from -7 to -15 permil indicating the involvement of microbes in the production of bicarbonate ions. Pore water analysis evidences a sharp sulphate-methane-transition (SMT) zone at 3.5 m below the mound top, whereas the depth of no sulfate is much deeper in the surrounding sediments. The horizon characterized by a strong corrosion of the coral fragments is just lying above and at the front of the recent location of the zone of anaerobic methane oxidation (AOM). In order to define the primary microbial community involved in carbonate precipitation, we did direct culturing, DNA isolation and PCR analysis of functional genes, including archaeal and bacterial 16S rRNA gene analysis. In combination with a DGGE approach, we developed a microbial biodiversity profile along the two carbonate mounds.

  8. University of Alaska Museum - Bureau of Land Management biodiversity survey 2002

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — During the summer of 2002 the Department of Ornithology at the University of Alaska Museum conducted biodiversity surveys of BLM land-holdings in three separate...

  9. Revisiting the dilution procedure used to manipulate microbial biodiversity in terrestrial systems.

    Science.gov (United States)

    Yan, Yan; Kuramae, Eiko E; Klinkhamer, Peter G L; van Veen, Johannes A

    2015-07-01

    It is hard to assess experimentally the importance of microbial diversity in soil for the functioning of terrestrial ecosystems. An approach that is often used to make such assessment is the so-called dilution method. This method is based on the assumption that the biodiversity of the microbial community is reduced after dilution of a soil suspension and that the reduced diversity persists after incubation of more or less diluted inocula in soil. However, little is known about how the communities develop in soil after inoculation. In this study, serial dilutions of a soil suspension were made and reinoculated into the original soil previously sterilized by gamma irradiation. We determined the structure of the microbial communities in the suspensions and in the inoculated soils using 454-pyrosequencing of 16S rRNA genes. Upon dilution, several diversity indices showed that, indeed, the diversity of the bacterial communities in the suspensions decreased dramatically, with Proteobacteria as the dominant phylum of bacteria detected in all dilutions. The structure of the microbial community was changed considerably in soil, with Proteobacteria, Bacteroidetes, and Verrucomicrobia as the dominant groups in most diluted samples, indicating the importance of soil-related mechanisms operating in the assembly of the communities. We found unique operational taxonomic units (OTUs) even in the highest dilution in both the suspensions and the incubated soil samples. We conclude that the dilution approach reduces the diversity of microbial communities in soil samples but that it does not allow accurate predictions of the community assemblage during incubation of (diluted) suspensions in soil. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  10. Biodiversity and fermentative activity of caecal microbial communities in wild and farm rabbits from Spain.

    Science.gov (United States)

    Abecia, L; Rodríguez-Romero, N; Yañez-Ruiz, D R; Fondevila, M

    2012-06-01

    In order to study the microbial caecal ecosystem of wild and domestic rabbits through the fermentation characteristics and concentration and diversity of bacterial and archaeal communities, caecal samples from sixteen wild rabbits (WR) were contrasted with two groups (n = 4) of farm rabbits receiving low (LSF) or high (HSF) soluble fibre diets from 28 (weaning) to 51 days of age. DNA was extracted for quantifying bacteria and Archaea by qPCR and for biodiversity analysis of microbial communities by DGGE. Samples from WR had lower caecal pH and ammonia and higher volatile fatty acids concentration than farm animals. Lower acetate and higher butyrate proportions were detected in WR. Bacterial and archaeal DGGE profiles were clearly different between wild and farm rabbits, and diet-affected population of farm rabbits. Similarity index of bacteria was lower than 0.40 among WR, and 0.52 among farm rabbits. In conclusion, caecal fermentation characteristics differ between wild and farm rabbits, which harbour clearly different bacterial and archaeal communities. In farm rabbits, diversity is influenced by the dietary level of soluble fibre. Copyright © 2012 Elsevier Ltd. All rights reserved.

  11. Resource pulses can alleviate the biodiversity-invasion relationship in soil microbial communities.

    Science.gov (United States)

    Mallon, Cyrus A; Poly, Franck; Le Roux, Xavier; Marring, Irene; van Elsas, Jan Dirk; Salles, Joana Falcão

    2015-04-01

    The roles of species richness, resource use, and resource availability are central to many hypotheses explaining the diversity-invasion phenomenon but are generally not investigated together. Here, we created a large diversity gradient of soil microbial communities by either assembling communities of pure bacterial strains or removing the diversity of a natural soil. Using data on the resource-use capacities of the soil communities and an invader that were gathered from 71 carbon sources, we quantified the niches available to both constituents by using the metrics community niche and remaining niche available to the invader. A strong positive relationship between species richness and community niche across both experiments indicated the presence of resource complementarity. Moreover, community niche and the remaining niche available to the invader predicted invader abundance well. This suggested that increased competition in communities of higher diversity limits community invasibility and underscored the importance of resource availability as a key mechanism through which diversity hinders invasions. As a proof of principle, we subjected selected invaded communities to a resource pulse, which progressively uncoupled the link between soil microbial diversity and invasion and allowed the invader to rebound after nearly being eliminated in some communities. Our results thus show that (1) resource competition suppresses invasion, (2) biodiversity increases resource competition and decreases invasion through niche preemption, and (3) resource pulses that cannot be fully used, even by diverse communities, are favorable to invasion.

  12. Biodiversity of genes encoding anti-microbial traits within plant associated microbes

    Directory of Open Access Journals (Sweden)

    Walaa Kamel Mousa

    2015-04-01

    Full Text Available The plant is an attractive versatile home for diverse associated microbes. A subset of these microbes produce a diversity of anti-microbial natural products including polyketides, non-ribosomal peptides, terpenoids, heterocylic nitrogenous compounds, volatile compounds, bacteriocins and lytic enzymes. In recent years, detailed molecular analysis has led to a better understanding of the underlying genetic mechanisms. New genomic and bioinformatic tools have permitted comparisons of orthologous genes between species, leading to predictions of the associated evolutionary mechanisms responsible for diversification at the genetic and corresponding biochemical levels. The purpose of this review is to describe the biodiversity of biosynthetic genes of plant-associated bacteria and fungi that encode selected examples of antimicrobial natural products. For each compound, the target pathogen and biochemical mode of action are described, in order to draw attention to the complexity of these phenomena. We review recent information of the underlying molecular diversity and draw lessons through comparative genomic analysis of the orthologous genes. We conclude by discussing emerging themes and gaps, discuss the metabolic pathways in the context of the phylogeny and ecology of their microbial hosts, and discuss potential evolutionary mechanisms that led to the diversification of biosynthetic gene clusters.

  13. Microbial ecology of mountain glacier ecosystems: biodiversity, ecological connections and implications of a warming climate.

    Science.gov (United States)

    Hotaling, Scott; Hood, Eran; Hamilton, Trinity L

    2017-08-01

    Glacier ecosystems are teeming with life on, beneath, and to a lesser degree, within their icy masses. This conclusion largely stems from polar research, with less attention paid to mountain glaciers that overlap environmentally and ecologically with their polar counterparts in some ways, but diverge in others. One difference lies in the susceptibility of mountain glaciers to the near-term threat of climate change, as they tend to be much smaller in both area and volume. Moreover, mountain glaciers are typically steeper, more dependent upon basal sliding for movement, and experience higher seasonal precipitation. Here, we provide a modern synthesis of the microbial ecology of mountain glacier ecosystems, and particularly those at low- to mid-latitudes. We focus on five ecological zones: the supraglacial surface, englacial interior, subglacial bedrock-ice interface, proglacial streams and glacier forefields. For each, we discuss the role of microbiota in biogeochemical cycling and outline ecological and hydrological connections among zones, underscoring the interconnected nature of these ecosystems. Collectively, we highlight the need to: better document the biodiversity and functional roles of mountain glacier microbiota; describe the ecological implications of rapid glacial retreat under climate change and resolve the relative contributions of ecological zones to broader ecosystem function. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  14. Biodiversity and agriculture in dynamic landscapes: Integrating ground and remotely-sensed baseline surveys.

    Science.gov (United States)

    Gillison, Andrew N; Asner, Gregory P; Fernandes, Erick C M; Mafalacusser, Jacinto; Banze, Aurélio; Izidine, Samira; da Fonseca, Ambrósio R; Pacate, Hermenegildo

    2016-07-15

    Sustainable biodiversity and land management require a cost-effective means of forecasting landscape response to environmental change. Conventional species-based, regional biodiversity assessments are rarely adequate for policy planning and decision making. We show how new ground and remotely-sensed survey methods can be coordinated to help elucidate and predict relationships between biodiversity, land use and soil properties along complex biophysical gradients that typify many similar landscapes worldwide. In the lower Zambezi valley, Mozambique we used environmental, gradient-directed transects (gradsects) to sample vascular plant species, plant functional types, vegetation structure, soil properties and land-use characteristics. Soil fertility indices were derived using novel multidimensional scaling of soil properties. To facilitate spatial analysis, we applied a probabilistic remote sensing approach, analyzing Landsat 7 satellite imagery to map photosynthetically active and inactive vegetation and bare soil along each gradsect. Despite the relatively low sample number, we found highly significant correlations between single and combined sets of specific plant, soil and remotely sensed variables that permitted testable spatial projections of biodiversity and soil fertility across the regional land-use mosaic. This integrative and rapid approach provides a low-cost, high-return and readily transferable methodology that permits the ready identification of testable biodiversity indicators for adaptive management of biodiversity and potential agricultural productivity. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor.

    Science.gov (United States)

    Scheckenbach, Frank; Hausmann, Klaus; Wylezich, Claudia; Weitere, Markus; Arndt, Hartmut

    2010-01-05

    Eukaryotic microbial life at abyssal depths remains "uncharted territory" in eukaryotic microbiology. No phylogenetic surveys have focused on the largest benthic environment on this planet, the abyssal plains. Moreover, knowledge of the spatial patterns of deep-sea community structure is scanty, and what little is known originates primarily from morphology-based studies of foraminiferans. Here we report on the great phylogenetic diversity of microbial eukaryotic communities of all 3 abyssal plains of the southeastern Atlantic Ocean--the Angola, Cape, and Guinea Abyssal Plains--from depths of 5,000 m. A high percentage of retrieved clones had no close representatives in genetic databases. Many clones were affiliated with parasitic species. Furthermore, differences between the communities of the Cape Abyssal Plain and the other 2 abyssal plains point to environmental gradients apparently shaping community structure at the landscape level. On a regional scale, local species diversity showed much less variation. Our study provides insight into the community composition of microbial eukaryotes on larger scales from the wide abyssal sea floor realm and marks a direction for more detailed future studies aimed at improving our understanding of deep-sea microbes at the community and ecosystem levels, as well as the ecological principles at play.

  16. Microbial biodiversity assessment of the European Space Agency's ExoMars 2016 mission.

    Science.gov (United States)

    Koskinen, Kaisa; Rettberg, Petra; Pukall, Rüdiger; Auerbach, Anna; Wink, Lisa; Barczyk, Simon; Perras, Alexandra; Mahnert, Alexander; Margheritis, Diana; Kminek, Gerhard; Moissl-Eichinger, Christine

    2017-10-25

    The ExoMars 2016 mission, consisting of the Trace Gas Orbiter and the Schiaparelli lander, was launched on March 14 2016 from Baikonur, Kazakhstan and reached its destination in October 2016. The Schiaparelli lander was subject to strict requirements for microbial cleanliness according to the obligatory planetary protection policy. To reach the required cleanliness, the ExoMars 2016 flight hardware was assembled in a newly built, biocontrolled cleanroom complex at Thales Alenia Space in Turin, Italy. In this study, we performed microbiological surveys of the cleanroom facilities and the spacecraft hardware before and during the assembly, integration and testing (AIT) activities. Besides the European Space Agency (ESA) standard bioburden assay, that served as a proxy for the microbiological contamination in general, we performed various alternative cultivation assays and utilised molecular techniques, including quantitative PCR and next generation sequencing, to assess the absolute and relative abundance and broadest diversity of microorganisms and their signatures in the cleanroom and on the spacecraft hardware. Our results show that the bioburden, detected microbial contamination and microbial diversity decreased continuously after the cleanroom was decontaminated with more effective cleaning agents and during the ongoing AIT. The studied cleanrooms and change room were occupied by very distinct microbial communities: Overall, the change room harboured a higher number and diversity of microorganisms, including Propionibacterium, which was found to be significantly increased in the change room. In particular, the so called alternative cultivation assays proved important in detecting a broader cultivable diversity than covered by the standard bioburden assay and thus completed the picture on the cleanroom microbiota. During the whole project, the bioburden stayed at acceptable level and did not raise any concern for the ExoMars 2016 mission. The cleanroom complex at

  17. High-throughput identification of the microbial biodiversity of cocoa bean fermentation by MALDI-TOF MS.

    Science.gov (United States)

    Miescher Schwenninger, S; Freimüller Leischtfeld, S; Gantenbein-Demarchi, C

    2016-11-01

    Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a powerful biotyping tool increasingly used for high-throughput identification of clinical microbial isolates, however, in food fermentation research this approach is still not well established. This study examines the microbial biodiversity of cocoa bean fermentation based on the isolation of micro-organisms in cocoa-producing regions, followed by MALDI-TOF MS in Switzerland. A preceding 6-week storage test to mimic lengthy transport of microbial samples from cocoa-producing regions to Switzerland was performed with strains of Lactobacillus plantarum, Acetobacter pasteurianus and Saccharomyces cerevisiae. Weekly MALDI-TOF MS analysis was able to successfully identify microbiota to the species level after storing live cultures on slant agar at mild temperatures (7°C) and/or in 75% aqueous ethanol at differing temperatures (-20, 7 and 30°C). The efficacy of this method was confirmed by on-site recording of the microbial biodiversity in cocoa bean fermentation in Bolivia and Brazil, with a total of 1126 randomly selected isolates. MALDI-TOF MS analyses revealed known dominant cocoa bean fermentation species with Lact. plantarum and Lactobacillus fermentum in the lactic acid bacteria taxon, Hanseniaspora opuntiae and S. cerevisiae in the yeast taxon, and Acet. pasteurianus, Acetobacter fabarum, Acetobacter ghanensis and Acetobacter senegalensis in the acetic acid bacteria taxon. Microbial identification with MALDI-TOF MS has increased the number of samples that can be analysed in a given time, a prerequisite for high-throughput methods. This method is already widely used for the identification of clinical microbial isolates, whereas in food fermentation research, including cocoa bean fermentation, microbiota is mostly identified by time-consuming, biochemical-based phenotyping and molecular approaches. This study presents the use of MALDI-TOF MS for characterizing the

  18. Trait-based approaches for understanding microbial biodiversity and ecosystem functioning

    NARCIS (Netherlands)

    Krause, S.; Le Roux, X.; Niklaus, P.A.; van Bodegom, P.M.; Lennon, J.T.; Bertilsson, S.A.; Grossart, H.P.; Philippot, L.; Bodelier, P.L.E.

    2014-01-01

    In ecology, biodiversity-ecosystem functioning (BEF) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity

  19. [Biodiversity of mesophilic microbial community BYND-8 capability of lignocellulose degradation and its effect on biogas production].

    Science.gov (United States)

    Wang, Wei-Dong; Song, Ya-Bin; Wang, Yan-Jie; Gao, Ya-Mei; Jing, Rui-Yong; Cui, Zong-Jun

    2011-01-01

    The biodiversity of a mesophilic microbial community BYND-8 capable of degrading lignocellulose at 30 degrees C was detected using denaturing gradient gel electrophoresis (DGGE) and the isolation of pure cultures, and the effect of the liquid of rice straw degradation by BYND-8 on biogas production was measured. Six bacterial strains were isolated using peptone cellulose solution medium, and the highest similarities of their 16S rDNA gene sequences to Serratia sp. PSGB 13, S. marcescens strain UFLA-25LS, S. marcescens strain DAP33, Alcaligenes sp. YcX-20, Stenotrophomonas maltophilia strain C6, Bacillus cereus isolate BRL02-71 were 99%, 100%, 96%, 100%, 100% and 99%, respectively. In addition, one band was detected besides six bands of cultured isolates on the DGGE gel, and it showed 100% sequence similarity to uncultured bacterium clone ATB-KS-1446. The cumulative biogas and methane productions of biogas fermentation system added with the liquid of rice straw degraded by BYND-8 were 13 167 mL and 7 248 mL, 44.5% and 95.3% higher than those of the control, respectively, in the early 15 days of fermentation. The results showed that the biodiversity of microbial community BYND-8 was very high, and the time of producing biogas was put forward and biogas production was increased with application of microbial community for rice straw pretreatment during the biogas fermentation.

  20. Microbial biodiversity, quality and shelf life of microfiltered and pasteurized extended shelf life (ESL) milk from Germany, Austria and Switzerland.

    Science.gov (United States)

    Schmidt, Verena S J; Kaufmann, Veronika; Kulozik, Ulrich; Scherer, Siegfried; Wenning, Mareike

    2012-03-01

    Information on factors limiting the shelf life of extended shelf life (ESL) milk produced by microfiltration and subsequent pasteurization is very limited. In this study, three different batches of ESL milk were analyzed at different stages of the production process and during storage at 4 °C, 8 °C and 10 °C in order to evaluate the changes in bacterial cell counts, microbial diversity and enzymatic quality. Additionally, detailed biodiversity analyses of 250 retail ESL milk packages produced by five manufacturers in Germany, Austria and Switzerland were performed at the end of shelf life. It was observed that microfiltration decreased the microbial loads by 5-6 log₁₀ units to lower than 1 CFU/mL. However, bacterial counts at the end of shelf life were extremely variable and ranged between microbial counts were well below 6 log₁₀ CFU/mL. Thirteen B. cereus isolates were characterized for their toxin profiles and psychrotolerance. Hbl, nhe, and cytK toxin genes were detected in ten, thirteen, and four isolates, respectively, whereas the ces gene was always absent. Interestingly, only three of the thirteen isolates could be allocated to psychrotolerant genotypes, as indicated by the major cold shock cspA gene signature. Generally, large discrepancies in microbial loads and biodiversity were observed at the end of shelf life, even among packages of the same production batch. We suggest that such unexpected differences may be due to very low cell counts after ESL treatment, causing stochastic variations of initial species distributions in individual packages. This would result in the development of significantly different bacterial populations during cold storage, including the occasional development of high numbers of pathogenic species such as B. cereus or Acinetobacter. Copyright © 2011 Elsevier B.V. All rights reserved.

  1. Microbial community structure and biodiversity of size-fractionated granules in a partial nitritation-anammox process.

    Science.gov (United States)

    Luo, Jinghuan; Chen, Hui; Han, Xiaoyu; Sun, Yanfang; Yuan, Zhiguo; Guo, Jianhua

    2017-06-01

    The performance of a granule-based partial nitritation-anammox process is expected to be affected by the granule size distribution, but little is known about the impact of granule size on microbial community structure and diversity. To reveal how the microbial composition and diversity vary with granule size, granules from a partial nitritation-anammox reactor were size-fractionated into five classes (1.0 mm). Microbial communities and diversity in these size-fractionated granules were investigated using 16S rRNA gene high-throughput sequencing. It was found that larger granules harbor more diverse microbial communities than small granules. Both quantitative PCR and 16S rRNA gene sequencing indicated that the abundance of anammox bacteria (dominated by Candidatus Brocadia) exhibited an increasing trend with granule size. In contrast, the abundance of ammonia-oxidizing bacteria (Nitrosomonas) decreased with increasing granule size. Moreover, larger granules harbored more diverse anammox bacteria, with four genera found in the largest granules while only two with limited abundance were detected in the smallest granules. The findings highlight an important role for granule size in shaping community structure and biodiversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains.

    Science.gov (United States)

    Doll, Hannah M; Armitage, David W; Daly, Rebecca A; Emerson, Joanne B; Goltsman, Daniela S Aliaga; Yelton, Alexis P; Kerekes, Jennifer; Firestone, Mary K; Potts, Matthew D

    2013-11-15

    Microbial ecologists often employ methods from classical community ecology to analyze microbial community diversity. However, these methods have limitations because microbial communities differ from macro-organismal communities in key ways. This study sought to quantify microbial diversity using methods that are better suited for data spanning multiple domains of life and dimensions of diversity. Diversity profiles are one novel, promising way to analyze microbial datasets. Diversity profiles encompass many other indices, provide effective numbers of diversity (mathematical generalizations of previous indices that better convey the magnitude of differences in diversity), and can incorporate taxa similarity information. To explore whether these profiles change interpretations of microbial datasets, diversity profiles were calculated for four microbial datasets from different environments spanning all domains of life as well as viruses. Both similarity-based profiles that incorporated phylogenetic relatedness and naïve (not similarity-based) profiles were calculated. Simulated datasets were used to examine the robustness of diversity profiles to varying phylogenetic topology and community composition. Diversity profiles provided insights into microbial datasets that were not detectable with classical univariate diversity metrics. For all datasets analyzed, there were key distinctions between calculations that incorporated phylogenetic diversity as a measure of taxa similarity and naïve calculations. The profiles also provided information about the effects of rare species on diversity calculations. Additionally, diversity profiles were used to examine thousands of simulated microbial communities, showing that similarity-based and naïve diversity profiles only agreed approximately 50% of the time in their classification of which sample was most diverse. This is a strong argument for incorporating similarity information and calculating diversity with a range of

  3. Biodiversity at the plant-soil interface: microbial abundance and community structure respond to litter mixing.

    Science.gov (United States)

    Chapman, Samantha K; Newman, Gregory S

    2010-03-01

    The interactive effects of diversity in plants and microbial communities at the litter interface are not well understood. Mixtures of plant litter from different species often decompose differently than when individual species decompose alone. Previously, we found that litter mixtures of multiple conifers decomposed more rapidly than expected, but litter mixtures that included conifer and aspen litter did not. Understanding the mechanisms underlying these diversity effects may help explain existing anomalous decay dynamics and provide a glimpse into the elusive linkage between plant diversity and the fungi and bacteria that carry out decomposition. We examined the microbial communities on litter from individual plant species decomposing both in mixture and alone. We assessed two main hypotheses to explain how the decomposer community could stimulate mixed-litter decomposition above predicted rates: either by being more abundant, or having a different or more diverse community structure than when microbes decompose a single species of litter. Fungal, bacterial and total phospholipid fatty acid microbial biomass increased by over 40% on both conifer and aspen litter types in mixture, and microbial community composition changed significantly when plant litter types were mixed. Microbial diversity also increased with increasing plant litter diversity. While our data provide support for both the increased abundance hypothesis and the altered microbial community hypothesis, microbial changes do not translate to predictably altered litter decomposition and may only produce synergisms when mixed litters are functionally similar.

  4. Monitoring biodiversity using ecosystem assessment surveys and regional ocean models within the California Current

    Science.gov (United States)

    Schroeder, I. D.; Santora, J. A.; Field, J. C.; Hazen, E. L.; Bograd, S. J.

    2016-02-01

    The National Marine Fisheries Service has conducted an annual midwater trawl survey for juvenile rockfish and other pelagic micronekton every May and June from 1983 to the present. Although both the spatial and temporal coverage have varied over time, a "core" region has been sampled continuously for the region that extends from Monterey Bay to just north of San Francisco Bay, California. Stations are located from nearshore waters to the offshore environment, but generally within 60 km from land. The mid-water trawl targets a diverse micronekton community spanning a range of juvenile stages of fishes, adult forage fishes and various invertebrates. Here we use the historical catch data to investigate biodiversity across space and time, specifically through developing indices of richness, diversity and evenness. The interannual variability of these indices is coherent over three unique ecological regions located along the shelf, Monterey Bay submarine canyon, and offshore habitats. Spatiotemporal changes in diversity reflect different taxa such as juvenile groundfish, rockfish and forage fish, and influx of oceanic species to nearshore habitat during anomalous years. Finally, data from CTD casts and from a data-assimilative ROMS model links changes in biodiversity with changing environmental conditions. The results of this project will be used to help inform researchers in the creation of a Marine Biodiversity Observation Network (MBON) in the Monterey Bay National Marine Sanctuary.

  5. Characterization of soil fertility and soil biodiversity with dsDNA as a covariate in a regression estimator for mean microbial biomass C

    NARCIS (Netherlands)

    Bragato, G.; Fornasier, F.; Brus, D.J.

    2016-01-01

    The analytical determination of microbial biomass carbon is time-consuming, which limits its use as a reference biochemical property for characterizing soil fertility and soil biodiversity of soil mapping units (SMUs). This paper explores whether the efficiency of sampling strategies for

  6. Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: an examination of the biodiversity-ecosystem function relationship

    NARCIS (Netherlands)

    Griffiths, B.S.; Ritz, K.; Bardgett, R.D.; Cook, R.; Christensen, S.; Ekelund, F.; Sorensen, S.J.; Bccth, E.; Bloem, J.; Ruiter, de P.C.; Dolfing, J.; Nicolardot, B.

    2000-01-01

    A technique based on progressive fumigation was used to reduce soil microbial biodiversity, and the effects of such reductions upon the stability of key soil processes were measured. Mineral soil samples from a grassland were fumigated with chloroform for up to 24 h and then incubated for 5 months

  7. Eco-evolutionary Red Queen dynamics regulate biodiversity in a metabolite-driven microbial system

    OpenAIRE

    Bonachela, Juan A.; Wortel, Meike T.; Stenseth, Nils Chr.

    2017-01-01

    The Red Queen Hypothesis proposes that perpetual co-evolution among organisms can result from purely biotic drivers. After more than four decades, there is no satisfactory understanding as to which mechanisms trigger Red Queen dynamics or their implications for ecosystem features such as biodiversity. One reason for such a knowledge gap is that typical models are complicated theories where limit cycles represent an idealized Red Queen, and therefore cannot be used to devise experimental setup...

  8. Phylogenetic and Functional Metagenomic Profiling for Assessing Microbial Biodiversity in Environmental Monitoring

    OpenAIRE

    Kisand, Veljo; Valente, Angelica; Lahm, Armin; Tanet, Gerard; Lettieri, Teresa

    2012-01-01

    Decisions guiding environmental management need to be based on a broad and comprehensive understanding of the biodiversity and functional capability within ecosystems. Microbes are of particular importance since they drive biogeochemical cycles, being both producers and decomposers. Their quick and direct responses to changes in environmental conditions modulate the ecosystem accordingly, thus providing a sensitive readout. Here we have used direct sequencing of total DNA from water samples t...

  9. Effect of conductive polymers coated anode on the performance of microbial fuel cells (MFCs) and its biodiversity analysis.

    Science.gov (United States)

    Li, Chao; Zhang, Libin; Ding, Lili; Ren, Hongqiang; Cui, Hao

    2011-06-15

    Conductive polymer, one of the most attractive electrode materials, has been applied to coat anode of MFC to improve its performance recently. In this paper, two conductive polymer materials, polyaniline (PANI) and poly(aniline-co-o-aminophenol) (PAOA) were used to modify carbon felt anode and physical and chemical properties of the modified anodes were studied. The power output and biodiversity of modified anodes, along with unmodified carbon anode were compared in two-chamber MFCs. Results showed that the maximum power density of PANI and PAOA MFC could reach 27.4 mW/m(2) and 23.8 mW/m(2), comparing with unmodified MFC, increased by 35% and 18% separately. Low temperature caused greatly decrease of the maximum voltage by 70% and reduced the sorts of bacteria on anodes in the three MFCs. Anode biofilm analysis showed different bacteria enrichment: a larger mount of bacteria and higher biodiversity were found on the two modified anodes than on the unmodified one. For PANI anode, the two predominant bacteria were phylogenetically closely related to Hippea maritima and an uncultured clone MEC_Bicarb_Ac-008; for PAOA, Clostridiales showed more enrichment. Compare PAOA with PANI, the former introduced phenolic hydroxyl group by copolymerization o-aminophenol with aniline, which led to a different microbial community and the mechanism of group effect was proposed. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Marine Biodiversity in Temperate Western Australia: Multi-Taxon Surveys of Minden and Roe Reefs

    Directory of Open Access Journals (Sweden)

    Zoe Richards

    2016-03-01

    Full Text Available A growing body of evidence indicates that temperate marine ecosystems are being tropicalised due to the poleward extension of tropical species. Such climate mediated changes in species distribution patterns have the potential to profoundly alter temperate communities, as this advance can serve to push temperate taxa, many of which are southern Australian endemics, southward. These changes can lead to cascading effects for the biodiversity and function of coastal ecosystems, including contraction of ranges/habitats of sensitive cool water species. Hence there is growing concern for the future of Australia’s temperate marine biodiversity. Here we examine the diversity and abundance of marine flora and fauna at two reefs near Perth’s metropolitan area—Minden Reef and Roe Reef. We report the presence of 427 species of marine flora and fauna from eight taxon groups occurring in the Perth metropolitan area; at least three species of which appear to be new to science. Our data also extends the known range of 15 species, and in numerous instances, thousands of kilometres south from the Kimberley or Pilbara and verifies that tropicalisation of reef communities in the Perth metropolitan area is occurring. We report the presence of 24 species endemic to south-west Australia that may be at risk of range contractions with continued ocean warming. The results of these surveys add to our knowledge of local nearshore marine environments in the Perth metropolitan area and support the growing body of evidence that indicates a diverse and regionally significant marine fauna occurs in temperate Western Australia. Regular, repeated survey work across seasons is important in order to thoroughly document the status of marine biodiversity in this significant transition zone.

  11. The cryptic role of biodiversity in the emergence of host-microbial mutualisms.

    Science.gov (United States)

    Pillai, Pradeep; Gouhier, Tarik C; Vollmer, Steven V

    2014-11-01

    The persistence of mutualisms in host-microbial - or holobiont - systems is difficult to explain because microbial mutualists, who bear the costs of providing benefits to their host, are always prone to being competitively displaced by non-mutualist 'cheater' species. This disruptive effect of competition is expected to be particularly strong when the benefits provided by the mutualists entail costs such as reduced competitive ability. Using a metacommunity model, we show that competition between multiple cheaters within the host's microbiome, when combined with the spatial structure of host-microbial interactions, can have a constructive rather than a disruptive effect by allowing the emergence and maintenance of mutualistic microorganisms within the host. These results indicate that many of the microorganisms inhabiting a host's microbiome, including those that would otherwise be considered opportunistic or even potential pathogens, play a cryptic yet critical role in promoting the health and persistence of the holobiont across spatial scales. © 2014 John Wiley & Sons Ltd/CNRS.

  12. Biodiversity of benthic microbial communities in bioturbated coastal sediments is controlled by geochemical microniches.

    Science.gov (United States)

    Bertics, Victoria J; Ziebis, Wiebke

    2009-11-01

    We used a combination of field and laboratory approaches to address how the bioturbation activity of two crustaceans, the ghost shrimp Neotrypaea californiensis and the fiddler crab Uca crenulata, affects the microbial diversity in the seabed of a coastal lagoon (Catalina Harbor, Santa Catalina Island, CA, USA). Detailed geochemical analyses, including oxygen microsensor measurements, were performed to characterize environmental parameters. We used a whole-assemblage fingerprinting approach (ARISA: amplified ribosomal intergenic spacer analysis) to compare bacterial diversity along geochemical gradients and in relation to subsurface microniches. The two crustaceans have different burrowing behaviors. The ghost shrimp maintains complex, deep-reaching burrows and permanently lives subterranean, supplying its burrow with oxygen-rich water. In contrast, the fiddler crab constructs simpler, J-shaped burrows, which it does not inhabit permanently and does not actively ventilate. Our goal was to address how varying environmental parameters affect benthic microbial communities. An important question in benthic microbial ecology has been whether burrows support similar or unique communities compared with the sediment surface. Our results showed that sediment surface microbial communities are distinct from subsurface assemblages and that different burrow types support diverse bacterial taxa. Statistical comparisons by canonical correspondence analysis indicated that the availability of oxidants (oxygen, nitrate, ferric iron) play a key role in determining the presence and abundance of different taxa. When geochemical parameters were alike, microbial communities associated with burrows showed significant similarity to sediment surface communities. Our study provides implications on the community structure of microbial communities in marine sediments and the factors controlling their distribution.

  13. New Dimensions in Microbial Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment

    Directory of Open Access Journals (Sweden)

    Johannes F. Imhoff

    2016-05-01

    Full Text Available During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA as target for the green sulfur bacteria and of two reaction center proteins (pufLM for the phototrophic purple bacteria, with genes of adenosine-5′phosphosulfate (APS reductase (aprA, sulfate thioesterase (soxB and dissimilatory sulfite reductase (dsrAB for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK for denitrifying bacteria and with genes

  14. New Dimensions in Microbial Ecology-Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment.

    Science.gov (United States)

    Imhoff, Johannes F

    2016-05-24

    During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5'phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane

  15. "Bugs on Bugs": An Inquiry-Based, Collaborative Activity to Learn Arthropod & Microbial Biodiversity

    Science.gov (United States)

    Lampert, Evan C.; Morgan, Jeanelle M.

    2015-01-01

    Diverse communities of arthropods and microbes provide humans with essential ecosystem goods and services. Arthropods are the most diverse and abundant macroscopic animals on the planet, and many remain to be discovered. Much less is known about microbial diversity, despite their importance as free-living species and as symbionts. We created…

  16. Response of soil microbial activity and biodiversity in soils polluted with different concentrations of cypermethrin insecticide.

    Science.gov (United States)

    Tejada, Manuel; García, Carlos; Hernández, Teresa; Gómez, Isidoro

    2015-07-01

    We performed a laboratory study into the effect of cypermethrin insecticide applied to different concentrations on biological properties in two soils [Typic Xerofluvent (soil A) and Xerollic Calciorthid (soil B)]. Two kg of each soil were polluted with cypermethrin at a rate of 60, 300, 600, and 1,200 g ha(-1) (C1, C2, C3, and C4 treatments). A nonpolluted soil was used as a control (C0 treatment). For all treatments and each experimental soil, soil dehydrogenase, urease, β-glucosidase, phosphatase, and arylsulphatase activities and soil microbial community were analysed by phospholipid fatty acids, which were measured at six incubation times (3, 7, 15, 30, 60, and 90 days). The behavior of the enzymatic activities and microbial population were dependent on the dose of insecticide applied to the soil. Compared with the C0 treatment, in soil A, the maximum inhibition of the enzymatic activities was at 15, 30, 45, and 90 days for the C1, C2, C3, and C4 treatments, respectively. However, in soil B, the maximum inhibition occurred at 7, 15, 30, and 45 days for the C1, C2, C3, and C4 treatments, respectively. These results suggest that the cypermethrin insecticide caused a negative effect on soil enzymatic activities and microbial diversity. This negative impact was greater when a greater dose of insecticide was used; this impact was also greater in soil with lower organic matter content. For both soils, and from these respective days onward, the enzymatic activities and microbial populations progressively increased by the end of the experimental period. This is possibly due to the fact that the insecticide or its breakdown products and killed microbial cells, subsequently killed by the insecticide, are being used as a source of energy or as a carbon source for the surviving microorganisms for cell proliferation.

  17. Commercial product exploitation from marine microbial biodiversity: some legal and IP issues.

    Science.gov (United States)

    Tichet, Camille; Nguyen, Hong Khanh; Yaakoubi, Sefia El; Bloch, Jean-François

    2010-09-01

    The biodiversity found in the marine environment is remarkable and yet largely unknown compared with the terrestrial one. The associated genetic resource, also wide and unrevealed, has raised a strong interest from the scientific and industrial community. However, despite this growing interest, the discovery of new compounds extracted from marine organisms, more precisely from microorganisms, is ruled by a complex legislation. The access and transfer of genetic resource are ruled by the Convention on Biological Diversity. One of the three core objectives of this convention is to ensure the fair and equitable sharing of benefits generated by the use of genetic resources and to split these benefits between the different stakeholders. From the discovery of a microorganism to the commercialization of a product, three main stakeholders are involved: providers of microorganisms, e.g. academic institutes, the scientists who will perform R&D on biodiversity, and the industrial companies which will commercialize the final product arising from the R&D results. This article describes how difficult and complex it might be to ensure a fair distribution of benefits of this research between the parties. © 2010 The Authors; Journal compilation © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

  18. Microbial biodiversity in cheese consortia and comparative Listeria growth on surfaces of uncooked pressed cheeses.

    Science.gov (United States)

    Callon, Cécile; Retureau, Emilie; Didienne, Robert; Montel, Marie-Christine

    2014-03-17

    The study set out to determine how changes in the microbial diversity of a complex antilisterial consortium from the surface of St-Nectaire cheese modify its antilisterial activities. On the basis of the microbial composition of a natural complex consortium named TR15 (Truefood consortium 15), three new consortia of different species and strain compositions were defined: TR15-SC (58 isolates from TR15 collection), TR15-M (pools of isolates from selective counting media) and TR15-BHI (pools of isolates from BHI medium). Their antilisterial activities on the surfaces of uncooked pressed cheese made with pasteurised milk were compared with the activity of complex consortium TR15 and a control cheese inoculated only with starter culture (Streptococcus thermophilus, Lactobacillus delbrueckii). The natural consortium TR15 was the most inhibitory, followed by reconstituted consortium TR15-BHI. The dynamics of the cheese rind microbial flora were monitored by counting on media and by isolate identification using 16S rDNA sequencing and direct 16S rDNA Single Strand Conformation Polymorphism analysis. The combination of these methods showed that rind with natural consortium TR15 had greater microbial diversity and different microbial dynamics than cheese rinds with reconstituted consortia. Cheese rind with the natural consortium showed higher citrate consumption and the highest concentrations of lactic and acetic acids, connected with high levels of lactic acid bacteria such as Carnobacterium maltaromaticum, Vagococcus fluvialis, Enterococcus gilvus, Leuconostoc mesenteroides, Brochothrix thermosphacta and Lactococcus lactis, ripening bacteria such as Arthrobacter nicotianae/arilaitensis, and Gram negative bacteria (Pseudomonas psychrophila and Enterobacter spp.). The highest L. monocytogenes count was on rind with TR15-M and was positively associated with the highest pH value, high succinic and citric acid contents, and the highest levels of Marinilactibacillus

  19. Microbial biodiversity in a Malaysian oil field and a systematic comparison with oil reservoirs worldwide.

    Science.gov (United States)

    Li, Dongmei; Midgley, David J; Ross, Jason P; Oytam, Yalchin; Abell, Guy C J; Volk, Herbert; Daud, Wan Ata Wan; Hendry, Philip

    2012-06-01

    Microbial diversity within formation water and oil from two compartments in Bokor oil reservoir from a Malaysian petroleum oil field was examined. A total of 1,056 16S rRNA gene clones were screened from each location by amplified ribosomal DNA restriction analysis. All samples were dominated by clones affiliated with Marinobacter, some novel Deferribacteraceae genera and various clones allied to the Methanococci. In addition, either Marinobacterium- or Pseudomonas-like operational taxonomic units were detected from either compartment. A systematic comparison with the existing pertinent studies was undertaken by analysing the microbial amplicons detected and the PCR primers used. The analyses demonstrated that bacterial communities were site specific, while Archaea co-occurred more frequently. Amplicons related to Marinobacter, Marinobacterium and Pseudomonas were detected in a number of the studies examined, suggesting they may be ubiquitous members in oil reservoirs. Further analysis of primers used in those studies suggested that most primer pairs had fairly broad but low matches across the bacterial and archaeal domains, while a minority had selective matches to certain taxa or low matches to all the microbial taxa tested. Thus, it indicated that primers may play an important role in determining which taxa would be detected.

  20. Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach.

    Science.gov (United States)

    Rocca-Serra, Philippe; Walls, Ramona; Parnell, Jacob; Gallery, Rachel; Zheng, Jie; Sansone, Susanna-Assunta; Gonzalez-Beltran, Alejandra

    2015-01-01

    The advent of affordable sequencing technology provides for a new generation of explorers who probe the world's microbial diversity. Projects such as Tara Oceans, Moorea Biocode Project and Gut Microbiome rely on sequencing technologies to probe community diversity. Either targeted gene surveys (also known as community surveys) or complete metagenomes are evaluated. The former, being the less costly of the two methods, relies on the identification of specific genomic regions, which can be used as a proxy to estimate genetic distance between related species in a Phylum. For instance, 16 S ribosomal RNA gene surveys are used to probe bacterial communities while internal transcribed spacer surveys, for example, can be used for probing fungal communities. With the explosion of projects and frenzy to explore new domains of life, scientists in the field have issued guidelines to report minimal information (following a checklist), ensuring that information is contextualized in a meaningful way. Yet the semantics of a checklist are not explicit. We demonstrate here how a tabular template can be used to collect information on microbial diversity using an explicit representation in the Resource Description Framework that is consistent with community agreed-upon knowledge representation patterns found in the Ontology for Biomedical Investigations. © The Author(s) 2015. Published by Oxford University Press.

  1. Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics.

    Science.gov (United States)

    Llorens-Marès, Tomàs; Yooseph, Shibu; Goll, Johannes; Hoffman, Jeff; Vila-Costa, Maria; Borrego, Carles M; Dupont, Chris L; Casamayor, Emilio O

    2015-07-01

    Stratified sulfurous lakes are appropriate environments for studying the links between composition and functionality in microbial communities and are potentially modern analogs of anoxic conditions prevailing in the ancient ocean. We explored these aspects in the Lake Banyoles karstic area (NE Spain) through metagenomics and in silico reconstruction of carbon, nitrogen and sulfur metabolic pathways that were tightly coupled through a few bacterial groups. The potential for nitrogen fixation and denitrification was detected in both autotrophs and heterotrophs, with a major role for nitrogen and carbon fixations in Chlorobiaceae. Campylobacterales accounted for a large percentage of denitrification genes, while Gallionellales were putatively involved in denitrification, iron oxidation and carbon fixation and may have a major role in the biogeochemistry of the iron cycle. Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium. The very low abundance of genes for nitrification, the minor presence of anammox genes, the high potential for nitrogen fixation and mineralization and the potential for chemotrophic CO2 fixation and CO oxidation all provide potential clues on the anoxic zones functioning. We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments. Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems.

  2. Microbial biodiversity of the liquid fraction of rumen content from lactating cows.

    Science.gov (United States)

    Sandri, M; Manfrin, C; Pallavicini, A; Stefanon, B

    2014-04-01

    Host and dietary interactions with the rumen microbiome can affect the efficacy of supplements, and their effect on the composition of the bacterial population is still unknown. A 16S rRNA metagenomic approach and Next-Generation Sequencing (NGS) technology were used to investigate the bacterial microbiome composition in the liquid fraction of the rumen content collected via stomach tubing. To investigate biodiversity, samples were taken from three groups of four lactating dairy cows given a supplement of either 50 g of potato protein (Ctrl group), or 50 g of lyophilized Saccharomyces cerevisiae (LY group) or 50 g of dried S. cerevisiae (DY group) in a potato protein support. Rumen samples were collected after 15 days of dietary treatments and milk production was similar between the three groups. Taxonomic distribution analysis revealed a prevalence of the Firmicutes phylum in all cows (79.76%) and a significantly (P<0.05) higher presence of the genus Bacillus in the DY group. Volatile fatty-acid concentration was not significantly different between groups, possibly because of relatively high inter-animal variability or limited effect of the treatments or both, and the correlation analysis with bacterial taxa showed significant associations, in particular between many Firmicutes genera and butyrate. Limited differences were observed between dietary treatments, but the lack of microbiome data before yeast administration does not allow to draw firm conclusions on the effect of dietary treatments.

  3. Biodiversity of Soil Microbial Communities Following Woody Plant Invasion of Grassland: An Assessment Using Molecular Methods

    Science.gov (United States)

    Kantola, I. B.; Gentry, T. J.; Filley, T. R.; Boutton, T. W.

    2012-12-01

    Woody plants have encroached into grasslands, savannas, and other grass-dominated ecosystems throughout the world during the last century. This dramatic vegetation change is likely driven by livestock grazing, altered fire frequencies, elevated atmospheric CO2 concentrations, and/or changes in atmospheric deposition patterns. Woody invasion often results in significant changes in ecosystem function, including alterations in above- and belowground primary productivity, soil C, N, and P storage and turnover, and the size and activity of the soil microbial biomass pool. The purpose of this study was to examine the relationships and interactions between plant communities and soil microbial communities in the Rio Grande Plains region of southern Texas where grasslands have been largely replaced by woodlands. Research was conducted along a successional chronosequence representing the stages of woody plant encroachment from open grassland to closed-canopy woodland. To characterize soil microbial community composition, soil samples (0-7.5 cm) were collected in remnant grasslands (representing time 0) and near the centers of woody plant clusters, groves, and drainage woodlands ranging in age from 10 to 130 yrs. Ages of woody plant stands were determined by dendrochronology. Community DNA was extracted from each soil sample with a MoBio PowerMax Soil DNA isolation kit. The DNA concentrations were quantified on a NanoDrop ND-1000 spectrophotometer and diluted to a standard concentration. Pyrosequencing was performed by the Research and Testing Laboratory (Lubbock, TX) according to Roche 454 Titanium chemistry protocols. Samples were amplified with primers 27F and 519R for bacteria, and primers ITS1F and ITS4 for fungi. Sequences were aligned using BioEdit and the RDP Pipeline and analyzed in MOTHUR. Non-metric multidimensional scaling of the operational taxonomic units identified by pyrosequencing revealed that both bacterial and fungal community composition were

  4. [Effects of vegetable cultivation years on microbial biodiversity and abundance of nitrogen cycling in greenhouse soils].

    Science.gov (United States)

    Wang, Ya-Nan; Zeng, Xi-Bai; Wang, Yu-Zhong; Bai, Ling-Yu; Su, Shi-Ming; Wu, Cui-Xia; Li, Lian-Fang; Duan, Ran

    2014-04-01

    The effects of facility vegetable cultivation years (three, nine, fourteen or seventeen years) on biodiversity and abundance of soil microorganisms, such as bacteria, ammonia oxidizing bacteria (AOB) and nirK type denitrifying bacteria, in the greenhouse soils in Wuwei of Gansu Province, China were determined by the combined analyses of terminal restriction fragment length polymorphism (T-RFLP) and real-time quantitative PCR. The results showed that the dominant population structure and abundance of bacteria, AOB, nirK type denitrifying bacteria in the soils were significantly different from those in the farmland fields. The dominant population also changed with the cultivation years. With the increase of vegetable cultivation years, the abundance of 16S rRNA and nirK gene in the 0-20 cm soil layer first increased and then decreased, with the maximum values of 9.67 x 10(9) and 2.30 x 10(7) copies x g(-1) soil at year 14 and year 9, being as 1.51 and 1.52 times of that of the 3-year, respectively. However, the abundance of amoA gene showed an opposite trend. The amoA gene copy number in the 14-year sample was 3.28 x 10(7) copies x g(-1) soil, which was only 45.7% of that of the 3-year. These results illustrated that the ecological adaptation mechanisms of the different functional microorganisms involved in nitrogen cycling had significant differences in the facility vegetable soils, and provided a base for further researches on exploring and explaining the characteristics and adaptation mechanisms of microorganisms in greenhouse soil.

  5. Novel lineage patterns from an automated water sampler to probe marine microbial biodiversity with ships of opportunity

    Science.gov (United States)

    Stern, Rowena F.; Picard, Kathryn T.; Hamilton, Kristina M.; Walne, Antony; Tarran, Glen A.; Mills, David; McQuatters-Gollop, Abigail; Edwards, Martin

    2015-09-01

    There is a paucity of data on long-term, spatially resolved changes in microbial diversity and biogeography in marine systems, and yet these organisms underpin fundamental ecological processes in the oceans affecting socio-economic values of the marine environment. We report results from a new autonomous Water and Microplankton Sampler (WaMS) that is carried within the Continuous Plankton Recorder (CPR). Whilst the CPR with its larger mesh size (270 μm), is designed to capture larger plankton, the WaMS was designed as an additional device to capture plankton below 50 μm and delicate larger species, often destroyed by net sampling methods. A 454 pyrosequencing and flow cytometric investigation of eukaryotic microbes using the partial 18S rDNA from thirteen WaMS samples collected over three months in the English Channel revealed a wide diversity of organisms. Alveolates, Fungi, and picoplanktonic Chlorophytes were the most common lineages captured despite the small sample volumes (200-250 ml). The survey also identified Cercozoa and MAST heterotrophic Stramenopiles, normally missed in microscopic-based plankton surveys. The most common was the likely parasitic LKM11 Rozellomycota lineage which comprised 43.2% of all reads and are rarely observed in marine pelagic surveys. An additional 9.5% of reads belonged to other parasitic lineages including marine Syndiniales and Ichthyosporea. Sample variation was considerable, indicating that microbial diversity is spatially or temporally patchy. Our study has shown that the WaMS sampling system is autonomous, versatile and robust, and due to its deployment on the established CPR network, is a cost-effective monitoring tool for microbial diversity for the detection of smaller and delicate taxa.

  6. [Effects of cadmium stress on the microbial biodiversity in purple soil and alluvial soil potted with a poplar (Populus deltoides x Populus nigra)].

    Science.gov (United States)

    Wang, Ao; Wu, Fu-Zhong; Yang, Wan-Qin; Zhou, Li-Qiang; Wang, Xu-Xi; Han, Yu

    2011-07-01

    Effects of current Cd contamination levels on microbial biodiversity were studied under the typical Cd contaminated soils in the Yangtze Basin. Purple soil and alluvial soil potted with a poplar (Populus deltoides x Populus nigra) were selected, and the culturable soil microbial amounts by flat method, microbial biomass and bacterial community structure by PCR-DGGE were investigated. Cd supplies significantly increased the culturable amounts of bacteria and actinomyces in purple soil, but decreased the culturable amounts of fungi and the content of microbial biomass N. Fingerprint of DGGE also showed that bacterial community structure have obviously changed under different Cd supplies. In contrast, the lower Cd supplies slightly increased the culturable amounts of bacteria and fungi in alluvial soil, but higher Cd supply treatment decreased the culturable amounts of bacteria, actinomyces and fungi, and the content of microbial biomass N. However, only a slight change was observed under different Cd supplies by DGGE fingerprint. Additionally, there were few effects of Cd supplies on the content of microbial biomass C in both purple soil and alluvial soil. The results provided basic data to understand the effects of present Cd contamination levels on soil microbial characteristics.

  7. [Microbial communities on the monuments of Moscow and St. Petersburg: biodiversity and trophic relations].

    Science.gov (United States)

    Gorbushina, A A; Lialikova, N N; Vlasov, D Iu; Khizhniak, T V

    2002-01-01

    Stone monuments situated in the Alexander Nevsky Abbey, the Summer Garden, and the Smolenskoe Cemetery, St. Petersburg, and marble and limestone sculptures and tombstones situated in the Novodevichy Convent and the Donskoy Monastery, Moscow, were investigated for their microbial contamination. The architectural objects studied date to the 12th century. The monuments in the Alexander Nevsky Abbey were found to be severely contaminated with micromycetes belonging to 24 genera (primarily of the class Deuteromycetes). The analysis of the samples taken from the monuments of the Donskoy Monastery by the serial dilution technique showed that they were contaminated with bacteria at a density of (1-1.7) x 10(5) cells/g. This value, however, turned out to be 1 to 2 orders greater when the bacterial population was evaluated by the luciferin-luciferase method. We succeeded in identifying 12 bacterial genera; however, this number may be increased in the course of further studies. Some preventive measures to control the biodeterioration of stone heritage are discussed.

  8. Microbial biodiversity in saline shallow lakes of the Monegros Desert, Spain.

    Science.gov (United States)

    Casamayor, Emilio O; Triadó-Margarit, Xavier; Castañeda, Carmen

    2013-09-01

    The Monegros Desert contains one of the largest sets of inland saline lakes in Europe constituting a threatened landscape of great scientific and ecological value with large number of reported endemisms. We analyzed bacteria, archaea, and microbial eukaryotes from 11 saline lakes in winter and spring by rRNA gene fingerprinting and sequencing covering large salinity (2.7-22.1%) and temperature ranges (1.5-35.3 °C). The highest ecological diversity (Shannon-Weaver index) was found in protists and the lowest in Archaea. Eukaryotes showed higher ecological diversity at intermediate salinities, whereas Bacteria and Archaea did not. The genetic diversity was broad and with remarkable novelty. The highest novelty was found in Archaea at the lowest saline concentrations, whereas for bacteria and protists, no differences were observed along the gradient. Euryarchaeota of the enigmatic group DHVEG-6 and phylotypes distantly related to well-known haloarchaea were present in several sites. Recurrent presence of bacterial phylotypes distantly related to Psychroflexus and Cryomorphaceae initially isolated from polar marine habitats was observed. Saline lakes contained chlorophyta, among other new groups, substantially different from green algae previously reported in marine or freshwater. The great scientific and ecological value found for macroorganisms can be extended to the idiosyncratic microorganisms inhabiting such unique habitat in Europe. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  9. Biodiversity within hot spring microbial mat communities: molecular monitoring of enrichment cultures

    Science.gov (United States)

    Ward, D. M.; Santegoeds, C. M.; Nold, S. C.; Ramsing, N. B.; Ferris, M. J.; Bateson, M. M.

    1997-01-01

    We have begun to examine the basis for incongruence between hot spring microbial mat populations detected by cultivation or by 16S rRNA methods. We used denaturing gradient gel electrophoresis (DGGE) to monitor enrichments and isolates plated therefrom. At near extincting inoculum dilutions we observed Chloroflexus-like and cyanobacterial populations whose 16S rRNA sequences have been detected in the 'New Pit' Spring Chloroflexus mat and the Octopus Spring cyanobacterial mat. Cyanobacterial populations enriched from 44 to 54 degrees C and 56 to 63 degrees C samples at near habitat temperatures were similar to those previously detected in mat samples of comparable temperatures. However, a lower temperature enrichment from the higher temperature sample selected for the populations found in the lower temperature sample. Three Thermus populations detected by both DGGE and isolation exemplify even more how enrichment may bias our view of community structure. The most abundant population was adapted to the habitat temperature (50 degrees C), while populations adapted to 65 degrees C and 70 degrees C were 10(2)- and 10(4)-fold less abundant, respectively. However, enrichment at 70 degrees C favored the least abundant strain. Inoculum dilution and incubation at the habitat temperature favored the more numerically relevant populations. We enriched many other aerobic chemoorganotrophic populations at various inoculum dilutions and substrate concentrations, most of whose 16S rRNA sequences have not been detected in mats. A common feature of numerically relevant cyanobacterial, Chloroflexus-like and aerobic chemorganotrophic populations, is that they grow poorly and resist cultivation on solidified medium, suggesting plating bias, and that the medium composition and incubation conditions may not reflect the natural microenvironments these populations inhabit.

  10. ASSESSMENT OF THE BIODIVERSITY OF SAMPLES USED FOR ISOLATION OF MICROBIAL STRAINS CAPABLE OF CONVERTING STRAW DESTINED AS A SUBSTRATE FOR BIOGAS PLANT

    Directory of Open Access Journals (Sweden)

    Krystyna Cybulska

    2016-01-01

    Full Text Available In biogas plants, almost any type of organic matter can be used as a substrate to produce biogas. To make the process of methane fermentation more effective, these materials are pretreated. This applies in particular to a group of difficult substrates. Straw, due to its hemicellulose structure and saturation, is hardly fermented by biogas reactor microorganisms. The methods of post-harvest residue preparation for anaerobic digestion being applied so far are expensive, while their application has a negative effect on methanoegenic bacteria. Therefore, the microorganisms being able to degrade straw hemicellulose structure, utilisation of which could precede the proper fermentation process, have been searched for. This paper presents the results of microbial biodiversity analysis in the environmental samples being lupin, cereal, rape and maize straw as well as hay and haylage at different degradation stages. The analysis of biodiversity will help at a further stage of study to isolate active microbial strains showing cellulolytic, hemicellulolytic or ligninolytic activity which are desirable in the process of straw biodegradation. Analysis of the microbial count was performed by the method of deep inoculation on different microbiological culture media. The conducted tests include determination of the number of fungi, bacteria and actinomycetes. The results obtained confirm the usefulness of the analysed samples for isolation of microbial strains capable of converting straw preceding the biogas production.

  11. Species undersampling in tropical bat surveys: effects on emerging biodiversity patterns.

    Science.gov (United States)

    Meyer, Christoph F J; Aguiar, Ludmilla M S; Aguirre, Luis F; Baumgarten, Julio; Clarke, Frank M; Cosson, Jean-François; Estrada Villegas, Sergio; Fahr, Jakob; Faria, Deborah; Furey, Neil; Henry, Mickaël; Jenkins, Richard K B; Kunz, Thomas H; Cristina MacSwiney González, M; Moya, Isabel; Pons, Jean-Marc; Racey, Paul A; Rex, Katja; Sampaio, Erica M; Stoner, Kathryn E; Voigt, Christian C; von Staden, Dietrich; Weise, Christa D; Kalko, Elisabeth K V

    2015-01-01

    Undersampling is commonplace in biodiversity surveys of species-rich tropical assemblages in which rare taxa abound, with possible repercussions for our ability to implement surveys and monitoring programmes in a cost-effective way. We investigated the consequences of information loss due to species undersampling (missing subsets of species from the full species pool) in tropical bat surveys for the emerging patterns of species richness (SR) and compositional variation across sites. For 27 bat assemblage data sets from across the tropics, we used correlations between original data sets and subsets with different numbers of species deleted either at random, or according to their rarity in the assemblage, to assess to what extent patterns in SR and composition in data subsets are congruent with those in the initial data set. We then examined to what degree high sample representativeness (r ≥ 0·8) was influenced by biogeographic region, sampling method, sampling effort or structural assemblage characteristics. For SR, correlations between random subsets and original data sets were strong (r ≥ 0·8) with moderate (ca. 20%) species loss. Bias associated with information loss was greater for species composition; on average ca. 90% of species in random subsets had to be retained to adequately capture among-site variation. For nonrandom subsets, removing only the rarest species (on average c. 10% of the full data set) yielded strong correlations (r > 0·95) for both SR and composition. Eliminating greater proportions of rare species resulted in weaker correlations and large variation in the magnitude of observed correlations among data sets. Species subsets that comprised ca. 85% of the original set can be considered reliable surrogates, capable of adequately revealing patterns of SR and temporal or spatial turnover in many tropical bat assemblages. Our analyses thus demonstrate the potential as well as limitations for reducing survey effort and streamlining

  12. Biodiversity inventories in high gear: DNA barcoding facilitates a rapid biotic survey of a temperate nature reserve.

    Science.gov (United States)

    Telfer, Angela C; Young, Monica R; Quinn, Jenna; Perez, Kate; Sobel, Crystal N; Sones, Jayme E; Levesque-Beaudin, Valerie; Derbyshire, Rachael; Fernandez-Triana, Jose; Rougerie, Rodolphe; Thevanayagam, Abinah; Boskovic, Adrian; Borisenko, Alex V; Cadel, Alex; Brown, Allison; Pages, Anais; Castillo, Anibal H; Nicolai, Annegret; Glenn Mockford, Barb Mockford; Bukowski, Belén; Wilson, Bill; Trojahn, Brock; Lacroix, Carole Ann; Brimblecombe, Chris; Hay, Christoper; Ho, Christmas; Steinke, Claudia; Warne, Connor P; Garrido Cortes, Cristina; Engelking, Daniel; Wright, Danielle; Lijtmaer, Dario A; Gascoigne, David; Hernandez Martich, David; Morningstar, Derek; Neumann, Dirk; Steinke, Dirk; Marco DeBruin, Donna DeBruin; Dobias, Dylan; Sears, Elizabeth; Richard, Ellen; Damstra, Emily; Zakharov, Evgeny V; Laberge, Frederic; Collins, Gemma E; Blagoev, Gergin A; Grainge, Gerrie; Ansell, Graham; Meredith, Greg; Hogg, Ian; McKeown, Jaclyn; Topan, Janet; Bracey, Jason; Guenther, Jerry; Sills-Gilligan, Jesse; Addesi, Joseph; Persi, Joshua; Layton, Kara K S; D'Souza, Kareina; Dorji, Kencho; Grundy, Kevin; Nghidinwa, Kirsti; Ronnenberg, Kylee; Lee, Kyung Min; Xie, Linxi; Lu, Liuqiong; Penev, Lyubomir; Gonzalez, Mailyn; Rosati, Margaret E; Kekkonen, Mari; Kuzmina, Maria; Iskandar, Marianne; Mutanen, Marko; Fatahi, Maryam; Pentinsaari, Mikko; Bauman, Miriam; Nikolova, Nadya; Ivanova, Natalia V; Jones, Nathaniel; Weerasuriya, Nimalka; Monkhouse, Norman; Lavinia, Pablo D; Jannetta, Paul; Hanisch, Priscila E; McMullin, R Troy; Ojeda Flores, Rafael; Mouttet, Raphaëlle; Vender, Reid; Labbee, Renee N; Forsyth, Robert; Lauder, Rob; Dickson, Ross; Kroft, Ruth; Miller, Scott E; MacDonald, Shannon; Panthi, Sishir; Pedersen, Stephanie; Sobek-Swant, Stephanie; Naik, Suresh; Lipinskaya, Tatsiana; Eagalle, Thanushi; Decaëns, Thibaud; Kosuth, Thibault; Braukmann, Thomas; Woodcock, Tom; Roslin, Tomas; Zammit, Tony; Campbell, Victoria; Dinca, Vlad; Peneva, Vlada; Hebert, Paul D N; deWaard, Jeremy R

    2015-01-01

    Comprehensive biotic surveys, or 'all taxon biodiversity inventories' (ATBI), have traditionally been limited in scale or scope due to the complications surrounding specimen sorting and species identification. To circumvent these issues, several ATBI projects have successfully integrated DNA barcoding into their identification procedures and witnessed acceleration in their surveys and subsequent increase in project scope and scale. The Biodiversity Institute of Ontario partnered with the rare Charitable Research Reserve and delegates of the 6th International Barcode of Life Conference to complete its own rapid, barcode-assisted ATBI of an established land trust in Cambridge, Ontario, Canada. The existing species inventory for the rare Charitable Research Reserve was rapidly expanded by integrating a DNA barcoding workflow with two surveying strategies - a comprehensive sampling scheme over four months, followed by a one-day bioblitz involving international taxonomic experts. The two surveys resulted in 25,287 and 3,502 specimens barcoded, respectively, as well as 127 human observations. This barcoded material, all vouchered at the Biodiversity Institute of Ontario collection, covers 14 phyla, 29 classes, 117 orders, and 531 families of animals, plants, fungi, and lichens. Overall, the ATBI documented 1,102 new species records for the nature reserve, expanding the existing long-term inventory by 49%. In addition, 2,793 distinct Barcode Index Numbers (BINs) were assigned to genus or higher level taxonomy, and represent additional species that will be added once their taxonomy is resolved. For the 3,502 specimens, the collection, sequence analysis, taxonomic assignment, data release and manuscript submission by 100+ co-authors all occurred in less than one week. This demonstrates the speed at which barcode-assisted inventories can be completed and the utility that barcoding provides in minimizing and guiding valuable taxonomic specialist time. The final product is

  13. Could the canopy structure of bryophytes serve as an indicator of microbial biodiversity? A test for testate amoebae and microcrustaceans from a subtropical cloud forest in Dominican Republic.

    Science.gov (United States)

    Acosta-Mercado, D; Cancel-Morales, N; Chinea, J D; Santos-Flores, C J; De Jesús, I Sastre

    2012-07-01

    The mechanisms that ultimately regulate the diversity of microbial eukaryotic communities in bryophyte ecosystems remain a contentious topic in microbial ecology. Although there is robust consensus that abiotic factors, such as water chemistry of the bryophyte and pH, explain a significant proportion of protist and microcrustacean diversity, there is no systematic assessment of the role of bryophyte habitat complexity on such prominent microbial groups. Water-holding capacity is correlated with bryophyte morphology and canopy structure. Similarly, canopy structure explains biodiversity dynamics of the macrobiota suggesting that canopy structure may also be a potential parameter for understanding microbial diversity. Canopy roughness of the dominant bryophyte species within the Bahoruco Cloud Forest, Cachote, Dominican Republic, concomitant with their associated diversity of testate amoebae and microcrustaceans was estimated to determine whether canopy structure could be added to the list of factors explaining microbial biodiversity in bryophytes. We hypothesized that smooth (with high moisture content) canopies will have higher species richness, density, and biomass of testate amoebae and higher richness and density of microcrustaceans than rough (desiccation-prone) canopies. For testate amoebae, we found 83 morphospecies with relative low abundances. Species richness and density differed among bryophytes with different bryophyte canopy structures and based on non-metric multidimensional scaling, canopy roughness explained 25% of the variation in species composition although not as predicted. Acroporium pungens (low roughness, LR) had the lowest species richness (2 ± 0.61 SD per gram dry weight bryophyte), and density (2.1 ± 0.61 SD individual per gram of dry weight bryophyte); whereas Thuidium urceolatum (high roughness) had the highest richness (24 ± 10.82 SD) and density (94 ± 64.30 SD). The fact that the bryophyte with the highest roughness had the highest

  14. Microbial survey of a full-scale, biologically active filter for treatment of drinking water.

    Science.gov (United States)

    White, Colin P; Debry, Ronald W; Lytle, Darren A

    2012-09-01

    The microbial community of a full-scale, biologically active drinking water filter was surveyed using molecular techniques. Nitrosomonas, Nitrospira, Sphingomonadales, and Rhizobiales dominated the clone libraries. The results elucidate the microbial ecology of biological filters and demonstrate that biological treatment of drinking water should be considered a viable alternative to physicochemical methods.

  15. The Hawaiian freshwater algae biodiversity survey (2009–2014): systematic and biogeographic trends with an emphasis on the macroalgae

    Science.gov (United States)

    2014-01-01

    Background A remarkable range of environmental conditions is present in the Hawaiian Islands due to their gradients of elevation, rainfall and island age. Despite being well known as a location for the study of evolutionary processes and island biogeography, little is known about the composition of the non-marine algal flora of the archipelago, its degree of endemism, or affinities with other floras. We conducted a biodiversity survey of the non-marine macroalgae of the six largest main Hawaiian Islands using molecular and microscopic assessment techniques. We aimed to evaluate whether endemism or cosmopolitanism better explain freshwater algal distribution patterns, and provide a baseline data set for monitoring future biodiversity changes in the Hawaiian Islands. Results 1,786 aquatic and terrestrial habitats and 1,407 distinct collections of non-marine macroalgae were collected from the islands of Kauai, Oahu, Molokai, Maui, Lanai and Hawaii from the years 2009–2014. Targeted habitats included streams, wet walls, high elevation bogs, taro fields, ditches and flumes, lakes/reservoirs, cave walls and terrestrial areas. Sites that lacked freshwater macroalgae were typically terrestrial or wet wall habitats that were sampled for diatoms and other microalgae. Approximately 50% of the identifications were of green algae, with lesser proportions of diatoms, red algae, cyanobacteria, xanthophytes and euglenoids. 898 DNA sequences were generated representing eight different markers, which enabled an assessment of the number of taxonomic entities for genera collected as part of the survey. Forty-four well-characterized taxa were assessed for global distribution patterns. This analysis revealed no clear biogeographic affinities of the flora, with 27.3% characterized as “cosmopolitan”, 11.4% “endemic”, and 61.3% as intermediate. Conclusions The Hawaiian freshwater algal biodiversity survey represents the first comprehensive effort to characterize the non

  16. Microbial survey of fish ponds and mineral composition of Clarias ...

    African Journals Online (AJOL)

    This work reports on the microbial composition of stagnant fish ponds and mineral & metal composition of Clarias gariepinus from the fish ponds in Ilorin, Kwara State, Nigeria. The fishes apparently thrived well in the fish ponds. Microbiological analysis of the different fish ponds as well as the mineral composition of the fish ...

  17. Long-term effect of irrigation with water from sewage treatment plant on AMF biodiversity and microbial activities.

    Science.gov (United States)

    Alguacil, M. M.; Torrecillas, E.; Lozano, Z.; Torres, M. P.; Garcia-Orenes, F.; Roldan, A.

    2012-04-01

    Shortage of water is one of the most important environmental problem in the Mediterranean areas that implicates the search for strategies for saving good quality water. The use of treated waste water for the irrigation of agricultural land can be a good solution for this problem because it reduces the utilization of fresh water and potentially could improve soil key parameters, but can modify physical-chemical and biological properties of the same. The aim of this work was to study the effect of long-term irrigation with treated waste water on microbial diversity, mainly arbuscular mycorrhizal fungi (AMF) of the soil and other properties related with the microbial community. The experiment was developed in an agricultural area with Citrus orchard, located in Alicante in the southeast Spain. Here, we tested whether the communities of AMF as well as soil microbial properties were affected by irrigation with water coming from sewage treatment plant during 40 years in a soil. To carry out this study the soil properties (dehydrogenase, urease, protease-BAA, acid phosphatase, β-glucosidase, glomalin related soil protein, microbial biomass C and aggregate stability) and AMF diversity (the AM fungal small sub-unit (SSU) rRNA genes were subjected to PCR, cloning, sequencing and phylogenetic analyses) were analysed in the soil from two different plots with the same soil but with different type of irrigation (irrigated with fresh water and irrigated with treated water). The first results did not show significant differences in some soil properties between soil irrigated with water treated or not.

  18. Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar.

    Science.gov (United States)

    Bletz, Molly C; Archer, Holly; Harris, Reid N; McKenzie, Valerie J; Rabemananjara, Falitiana C E; Rakotoarison, Andolalao; Vences, Miguel

    2017-01-01

    Host-associated microbiotas of vertebrates are diverse and complex communities that contribute to host health. In particular, for amphibians, cutaneous microbial communities likely play a significant role in pathogen defense; however, our ecological understanding of these communities is still in its infancy. Here, we take advantage of the fully endemic and locally species-rich amphibian fauna of Madagascar to investigate the factors structuring amphibian skin microbiota on a large scale. Using amplicon-based sequencing, we evaluate how multiple host species traits and site factors affect host bacterial diversity and community structure. Madagascar is home to over 400 native frog species, all of which are endemic to the island; more than 100 different species are known to occur in sympatry within multiple rainforest sites. We intensively sampled frog skin bacterial communities, from over 800 amphibians from 89 species across 30 sites in Madagascar during three field visits, and found that skin bacterial communities differed strongly from those of the surrounding environment. Richness of bacterial operational taxonomic units (OTUs) and phylogenetic diversity differed among host ecomorphs, with arboreal frogs exhibiting lower richness and diversity than terrestrial and aquatic frogs. Host ecomorphology was the strongest factor influencing microbial community structure, with host phylogeny and site parameters (latitude and elevation) explaining less but significant portions of the observed variation. Correlation analysis and topological congruency analyses revealed little to no phylosymbiosis for amphibian skin microbiota. Despite the observed geographic variation and low phylosymbiosis, we found particular OTUs that were differentially abundant between particular ecomorphs. For example, the genus Pigmentiphaga (Alcaligenaceae) was significantly enriched on arboreal frogs, Methylotenera (Methylophilaceae) was enriched on aquatic frogs, and Agrobacterium (Rhizobiaceae

  19. Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar

    Directory of Open Access Journals (Sweden)

    Molly C. Bletz

    2017-08-01

    Full Text Available Host-associated microbiotas of vertebrates are diverse and complex communities that contribute to host health. In particular, for amphibians, cutaneous microbial communities likely play a significant role in pathogen defense; however, our ecological understanding of these communities is still in its infancy. Here, we take advantage of the fully endemic and locally species-rich amphibian fauna of Madagascar to investigate the factors structuring amphibian skin microbiota on a large scale. Using amplicon-based sequencing, we evaluate how multiple host species traits and site factors affect host bacterial diversity and community structure. Madagascar is home to over 400 native frog species, all of which are endemic to the island; more than 100 different species are known to occur in sympatry within multiple rainforest sites. We intensively sampled frog skin bacterial communities, from over 800 amphibians from 89 species across 30 sites in Madagascar during three field visits, and found that skin bacterial communities differed strongly from those of the surrounding environment. Richness of bacterial operational taxonomic units (OTUs and phylogenetic diversity differed among host ecomorphs, with arboreal frogs exhibiting lower richness and diversity than terrestrial and aquatic frogs. Host ecomorphology was the strongest factor influencing microbial community structure, with host phylogeny and site parameters (latitude and elevation explaining less but significant portions of the observed variation. Correlation analysis and topological congruency analyses revealed little to no phylosymbiosis for amphibian skin microbiota. Despite the observed geographic variation and low phylosymbiosis, we found particular OTUs that were differentially abundant between particular ecomorphs. For example, the genus Pigmentiphaga (Alcaligenaceae was significantly enriched on arboreal frogs, Methylotenera (Methylophilaceae was enriched on aquatic frogs, and Agrobacterium

  20. A Molecular Survey of the Diversity of Microbial Communities in Different Amazonian Agricultural Model Systems

    Directory of Open Access Journals (Sweden)

    Acácio A. Navarrete

    2010-05-01

    Full Text Available The processes of land conversion and agricultural intensification are a significant cause of biodiversity loss, with consequent negative effects both on the environment and the sustainability of food production.The anthrosols associated with pre-Colombian settlements in the Amazonian region are examples of how anthropogenic activities may sustain the native populations against harsh tropical environments for human establishment, even without a previous intentionality of anthropic soil formation. In a case study (Model I—“Slash-and-Burn” the community structures detected by automated ribosomal intergenic spacer analysis (ARISA revealed that soil archaeal, bacterial and fungal communities are heterogeneous and each capable of responding differently to environmental characteristics. ARISA data evidenced considerable difference in structure existing between microbial communities in forest and agricultural soils. In a second study (Model II—“Anthropogenic Soil”, the bacterial community structures revealed by terminal restriction fragment length polymorphism (T-RFLP differed among an Amazonian Dark Earth (ADE, black carbon (BC and its adjacent non-anthropogenic oxisoil. The bacterial 16S rRNA gene (OTU richness estimated by pyrosequencing was higher in ADE than BC. The most abundant bacterial phyla in ADE soils and BC were Proteobacteria—24% ADE, 15% BC; Acidobacteria—10% ADE, 21% BC; Actinobacteria—7% ADE, 12% BC; Verrucomicrobia, 8% ADE; 9% BC; Firmicutes—3% ADE, 8% BC. Overall, unclassified bacteria corresponded to 36% ADE, and 26% BC. Regardless of current land uses, our data suggest that soil microbial community structures may be strongly influenced by the historical soil management and that anthrosols in Amazonia, of anthropogenic origins, in addition to their capacity of enhancing crop yields, may also improve microbial diversity, with the support of the black carbon, which may sustain a particular and unique habitat for the

  1. A survey of Opportunities for Microbial Conversion of Biomass to Hydrocarbon Compatible Fuels

    Energy Technology Data Exchange (ETDEWEB)

    Jovanovic, Iva; Jones, Susanne B.; Santosa, Daniel M.; Dai, Ziyu; Ramasamy, Karthikeyan K.; Zhu, Yunhua

    2010-09-01

    Biomass is uniquely able to supply renewable and sustainable liquid transportation fuels. In the near term, the Biomass program has a 2012 goal of cost competitive cellulosic ethanol. However, beyond 2012, there will be an increasing need to provide liquid transportation fuels that are more compatible with the existing infrastructure and can supply fuel into all transportation sectors, including aviation and heavy road transport. Microbial organisms are capable of producing a wide variety of fuel and fuel precursors such as higher alcohols, ethers, esters, fatty acids, alkenes and alkanes. This report surveys liquid fuels and fuel precurors that can be produced from microbial processes, but are not yet ready for commercialization using cellulosic feedstocks. Organisms, current research and commercial activities, and economics are addressed. Significant improvements to yields and process intensification are needed to make these routes economic. Specifically, high productivity, titer and efficient conversion are the key factors for success.

  2. A molecular systematic survey of cultured microbial associates of deep-water marine invertebrates.

    Science.gov (United States)

    Sfanos, Karen; Harmody, Dedra; Dang, Phat; Ledger, Angela; Pomponi, Shirley; McCarthy, Peter; Lopez, Jose

    2005-04-01

    A taxonomic survey was conducted to determine the microbial diversity held within the Harbor Branch Oceanographic Marine Microbial Culture Collection (HBMMCC). The collection consists of approximately 17,000 microbial isolates, with 11,000 from a depth of greater than 150 ft seawater. A total of 2273 heterotrophic bacterial isolates were inventoried using the DNA fingerprinting technique amplified rDNA restriction analysis on approximately 750-800 base pairs (bp) encompassing hypervariable regions in the 5' portion of the small subunit (SSU) 16S rRNA gene. Restriction fragment length polymorphism patterns obtained from restriction digests with RsaI, HaeIII, and HhaI were used to infer taxonomic similarity. SSU 16S rDNA fragments were sequenced from a total of 356 isolates for more definitive taxonomic analysis. Sequence results show that this subset of the HBMMCC contains 224 different phylotypes from six major bacterial clades (Proteobacteria (Alpha, Beta, Gamma), Cytophaga, Flavobacteria, and Bacteroides (CFB), Gram + high GC content, Gram + low GC content). The 2273 microorganisms surveyed encompass 834 alpha-Proteobacteria (representing 60 different phylotypes), 25 beta-Proteobacteria (3 phylotypes), 767 gamma-Proteobacteria (77 phylotypes), 122 CFB (17 phylotypes), 327 Gram + high GC content (43 phylotypes), and 198 Gram + low GC content isolates (24 phylotypes). Notably, 11 phylotypes were < or =93% similar to the closest sequence match in the GenBank database even after sequencing a larger portion of the 16S rRNA gene (approximately 1400 bp), indicating the likely discovery of novel microbial taxa. Furthermore, previously reported "uncultured" microbes, such as sponge-specific isolates, are part of the HBMMCC. The results of this research will be available online as a searchable taxonomic database (www.hboi.edu/dbmr/dbmr_hbmmd.html).

  3. Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals

    Directory of Open Access Journals (Sweden)

    Shan-Hua Yang

    2017-06-01

    Full Text Available The coral holobiont is the assemblage of coral host and its microbial symbionts, which functions as a unit and is responsive to host species and environmental factors. Although monitoring surveys have been done to determine bacteria associated with coral, none have persisted for >1 year. Therefore, potential variations in minor or dominant community members that occur over extended intervals have not been characterized. In this study, 16S rRNA gene amplicon pyrosequencing was used to investigate the relationship between bacterial communities in healthy Stylophora pistillata in tropical and subtropical Taiwan over 2 years, apparently one of the longest surveys of coral-associated microbes. Dominant bacterial genera in S. pistillata had disparate changes in different geographical setups, whereas the constitution of minor bacteria fluctuated in abundance over time. We concluded that dominant bacteria (Acinetobacter, Propionibacterium, and Pseudomonas were stable in composition, regardless of seasonal and geographical variations, whereas Endozoicomonas had a geographical preference. In addition, by combining current data with previous studies, we concluded that a minor bacteria symbiont, Ralstonia, was a keystone species in coral. Finally, we concluded that long-term surveys for coral microbial communities were necessary to detect compositional shifts, especially for minor bacterial members in corals.

  4. Undergraduate Students' Attitudes toward Biodiversity

    Science.gov (United States)

    Huang, Hui-Ju; Lin, Yu-Teh Kirk

    2014-01-01

    The study investigated American and Taiwan undergraduate students' attitudes toward biodiversity. The survey questionnaire consisted of statements prompted by the question "To what extent do you agree with the following statements about problems with the biodiversity issues." Students indicated strongly disagree, disagree, agree,…

  5. Biodiversity and Climate Change

    African Journals Online (AJOL)

    NWUuser

    preventing and mitigating the impacts of climate change and biodiversity loss. As should be evident from the above very brief survey of the content of the book, it is vast in its substantive breadth and rich in its diversity of approach and perspective. This is naturally one of its strength but as with many books comprising.

  6. Biodiversity and Biological Degradation of Soil

    Indian Academy of Sciences (India)

    ... Journals; Resonance – Journal of Science Education; Volume 9; Issue 1. Biodiversity and Biological Degradation of Soil. Upasana Mishra Dolly Wattal Dhar. General Article Volume 9 Issue 1 January 2004 pp 26-33 ... Keywords. Microbial biodiversity; soil science; biogeochemical cycles; sustainable agriculture; ecology ...

  7. Functional diversity of terrestrial microbial decomposers and their substrates.

    Science.gov (United States)

    Hättenschwiler, Stephan; Fromin, Nathalie; Barantal, Sandra

    2011-05-01

    The relationship between biodiversity and biogeochemical processes gained much interest in light of the rapidly decreasing biodiversity worldwide. In this article, we discuss the current status, challenges and prospects of functional concepts to plant litter diversity and microbial decomposer diversity. We also evaluate whether these concepts permit a better understanding of how biodiversity is linked to litter decomposition as a key ecosystem process influencing carbon and nutrient cycles. Based on a literature survey, we show that plant litter and microbial diversity matters for decomposition, but that considering numbers of taxonomic units appears overall as little relevant and less useful than functional diversity. However, despite easily available functional litter traits and the well-established theoretical framework for functional litter diversity, the impact of functional litter diversity on decomposition is not yet well enough explored. Defining functional diversity of microorganisms remains one of the biggest challenges for functional approaches to microbial diversity. Recent developments in microarray and metagenomics technology offer promising possibilities in the assessment of the functional structure of microbial communities. This might allow significant progress in measuring functional microbial diversity and ultimately in our ability to predict consequences of biodiversity loss in the decomposer system for biogeochemical processes. Copyright © 2011 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  8. Differential efficiencies of dip-net sampling versus sampling surface-floating pupal exuviae in a biodiversity survey of Chironomidae

    Directory of Open Access Journals (Sweden)

    Leonard Charles Ferrington Jr

    2014-12-01

    Full Text Available Relative efficiencies of standard dip-net sampling (SDN versus collections of surface-floating pupal exuviae (SFPE were determined for detecting Chironomidae at catchment and site scales and at subfamily/tribe-, genus- and species-levels based on simultaneous, equal-effort sampling on a monthly basis for one year during a biodiversity assessment of Bear Run Nature Reserve. Results showed SFPE was more efficient than SDN at catchment scales for detecting both genera and species. At site scales, SDN sampling was more efficient for assessment of a first-order site. No consistent pattern, except for better efficiency of SFPE to detect Orthocladiinae genera, was observed at genus-level for two second-order sites. However, SFPE was consistently more efficient at detecting species of Orthocladiinae, Chironomini and Tanytarsini at the second order sites. SFPE was more efficient at detecting both genera and species at two third-order sites. The differential efficiencies of the two methods are concluded to be related to stream order and size, substrate size, flow and water velocity, depth and habitat heterogeneity, and differential ability to discriminate species among pupal exuviae specimens versus larval specimens. Although both approaches are considered necessary for comprehensive biodiversity assessments of Chironomidae, our results suggest that there is an optimal, but different, allocation of sampling effort for detecting Chironomidae across stream orders and at differing spatial and taxonomic scales.Article submitted 13. August 2014, accepted 31. October 2014, published 22. December 2014.

  9. Conservation of biodiversity in the Sango Bay area, southern Uganda

    African Journals Online (AJOL)

    A series of biodiversity and socio-economic surveys carried out in the Sango Bay area of southern Uganda revealed high biodiversity values for some taxa in some sites. Use of this biodiversity and reliance on it by local communities was widespread. Biodiversity scores were given to all species and these were coupled with ...

  10. Teaching Biodiversity

    Indian Academy of Sciences (India)

    Madhav Gadgil1 2. Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560 012, India. Biodiversity Unit, Jowaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O. Jakkur, Bangalore 560064, India. Resonance – Journal of Science Education. Current Issue : Vol. 23, Issue 2 · Current Issue

  11. Biodiversity Conservation in Asia

    OpenAIRE

    Dale Squires

    2014-01-01

    Asian's remarkable economic growth brought many benefits but also fuelled threats to its ecosystems and biodiversity. Economic growth brings biodiversity threats but also conservation opportunities. Continued biodiversity loss is inevitable, but the types, areas and rates of biodiversity loss are not. Prioritising biodiversity conservation, tempered by what is tractable, remains a high priority. Policy and market distortions and failures significantly underprice biodiversity, undermine ecosys...

  12. Metaproteomic survey of six aquatic habitats: discovering the identities of microbial populations active in biogeochemical cycling.

    Science.gov (United States)

    Hanson, Buck T; Hewson, Ian; Madsen, Eugene L

    2014-04-01

    Our goal is to strengthen the foundations of metaproteomics as a microbial community analysis tool that links the functional identity of actively expressed gene products with host phylogeny. We used shotgun metaproteomics to survey waters in six disparate aquatic habitats (Cayuga Lake, NY; Oneida Lake, NY; Gulf of Maine; Chesapeake Bay, MD; Gulf of Mexico; and the South Pacific). Peptide pools prepared from filter-gathered microbial biomass, analyzed by nano-liquid chromatography-mass spectrometry (MS/MS) generating 9,693 ± 1,073 mass spectra identified 326 ± 107 bacterial proteins per sample. Distribution of proteobacterial (Alpha and Beta) and cyanobacterial (Prochlorococcus and Synechococcus spp.) protein hosts across all six samples was consistent with the previously published biogeography for these microorganisms. Marine samples were enriched in transport proteins (TRAP-type for dicarboxylates and ATP binding cassette (ABC)-type for amino acids and carbohydrates) compared with the freshwater samples. We were able to match in situ expression of many key proteins catalyzing C-, N-, and S-cycle processes with their bacterial hosts across all six habitats. Pelagibacter was identified as the host of ABC-type sugar-, organic polyanion-, and glycine betaine-transport proteins; this extends previously published studies of Pelagibacter's in situ biogeochemical role in marine C- and N-metabolism. Proteins matched to Ruegeria confirmed these organism's role in marine waters oxidizing both carbon monoxide and sulfide. By documenting both processes expressed in situ and the identity of host cells, metaproteomics tested several existing hypotheses about ecophysiological processes and provided fodder for new ones.

  13. How to Show the Real Microbial Biodiversity? A Comparison of Seven DNA Extraction Methods for Bacterial Population Analyses in Matrices Containing Highly Charged Natural Nanoparticles.

    Science.gov (United States)

    Kaden, Rene; Krolla-Sidenstein, Peter

    2015-10-20

    A DNA extraction that comprises the DNA of all available taxa in an ecosystem is an essential step in population analysis, especially for next generation sequencing applications. Many nanoparticles as well as naturally occurring clay minerals contain charged surfaces or edges that capture negatively charged DNA molecules after cell lysis within DNA extraction. Depending on the methodology of DNA extraction, this phenomenon causes a shift in detection of microbial taxa in ecosystems and a possible misinterpretation of microbial interactions. With the aim to describe microbial interactions and the bio-geo-chemical reactions during a clay alteration experiment, several methods for the detection of a high number of microbial taxa were examined in this study. Altogether, 13 different methods of commercially available DNA extraction kits provided by seven companies as well as the classical phenol-chloroform DNA extraction were compared. The amount and the quality of nucleic acid extracts were determined and compared to the amplifiable amount of DNA. The 16S rRNA gene fragments of several taxa were separated using denaturing gradient gel electrophoresis (DGGE) to determine the number of different species and sequenced to get the information about what kind of species the microbial population consists of. A total number of 13 species was detected in the system. Up to nine taxa could be detected with commercially available DNA extraction kits while phenol-chloroform extraction lead to three detected species. In this paper, we describe how to combine several DNA extraction methods for the investigation of microbial community structures in clay.

  14. The biodiversity and species composition of the spider community of Marion Island, a recent survey (Arachnida: Araneae

    Directory of Open Access Journals (Sweden)

    T.T. Khoza

    2005-12-01

    Full Text Available Marion Island, the larger of the Prince Edward Islands, lies in the sub-Antarctic biogeographic region in the southern Indian Ocean. From previous surveys, four spider species are known from Marion. The last survey was undertaken in 1968. During this study a survey was undertaken over a period of four weeks on the island to determine the present spider diversity and to record information about the habitat preferences and general behaviour of the species present. Three collection methods (active search, Tullgren funnels and pitfall traps were used, and spiders were sampled from six habitat sites. A total of 430 spiders represented by four families were collected, Myro kerguelenesis crozetensis Enderlein, 1909 and M. paucispinosus Berland, 1947 (Desidae, Prinerigone vagans (Audouin, 1826 (Linyphiidae, Cheiracanthium furculatum Karsch, 1879 (Miturgidae and an immature Salticidae. The miturgid and salticid are first records. Neomaso antarticus (Hickman, 1939 (Linyphiidae was absent from samples, confirming that the species might have been an erroneous record.

  15. Assessing stock and change in land cover and biodiversity in GB: an introduction to Countryside Survey 2000.

    Science.gov (United States)

    Firbank, L G; Barr, C J; Bunce, R G H; Furse, M T; Haines-Young, R; Hornung, M; Howard, D C; Sheail, J; Sier, A; Smart, S M

    2003-03-01

    Countryside Survey 2000 (CS2000) is the latest in a series of surveys designed to measure and evaluate stock and change of land cover, landscape features, freshwaters, habitats and the vegetation of Great Britain. The ideas behind CS2000 developed during the 1960s and 1970s and culminated in the first survey of vegetation and land cover in 1978. One kilometer sample squares were selected at random using an environmental stratification. Subsequent surveys took place in 1984, 1990 and 1998, revisiting the original sample locations, whilst progressively expanding in scope and sample size; CS2000 included soils, breeding birds, remotely sensed imagery, freshwater biota and hydromorphology. Countryside Survey data may be interpreted using the pressure-state-response model, by selecting indicators of process and quality, and by identifying models of expected responses to different pressures. Thus, results showing losses of hedgerows between 1984 and 1990 stimulated new protection for these features. Ideally, CS2000 data should be used to stimulate experiments to distinguish between different pressures, in order to ensure that policy and management responses are both appropriate and achievable.The experience from CS2000 may prove helpful for the design and management of other large scale monitoring programmes of ecosystems. In particular, the scope of the survey, and the use to which the data are applied, have evolved through time, and yet continuity was essential for change to be detected efficiently. These objectives were reconciled by collecting the data in a disaggregated form, allowing a high degree of flexibility in both analysis and reporting.

  16. Biodiversity, community structure and function of biofilms in stream ecosystems.

    Science.gov (United States)

    Besemer, Katharina

    2015-12-01

    Multi-species, surface-attached biofilms often dominate microbial life in streams and rivers, where they contribute substantially to biogeochemical processes. The microbial diversity of natural biofilms is huge, and may have important implications for the functioning of aquatic environments and the ecosystem services they provide. Yet the causes and consequences of biofilm biodiversity remain insufficiently understood. This review aims to give an overview of current knowledge on the distribution of stream biofilm biodiversity, the mechanisms generating biodiversity patterns and the relationship between biofilm biodiversity and ecosystem functioning. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  17. Forest soil microbial communities: Using metagenomic approaches to survey permanent plots

    Science.gov (United States)

    Amy L. Ross-Davis; Jane E. Stewart; John W. Hanna; John D. Shaw; Andrew T. Hudak; Theresa B. Jain; Robert J. Denner; Russell T. Graham; Deborah S. Page-Dumroese; Joanne M. Tirocke; Mee-Sook Kim; Ned B. Klopfenstein

    2014-01-01

    Forest soil ecosystems include some of the most complex microbial communities on Earth (Fierer et al. 2012). These assemblages of archaea, bacteria, fungi, and protists play essential roles in biogeochemical cycles (van der Heijden et al. 2008) and account for considerable terrestrial biomass (Nielsen et al. 2011). Yet, determining the microbial composition of forest...

  18. Marine biodiversity of the coastal area of the Berau region, East Kalimantan, Indonesia : progress report East Kalimantan program, pilot phase (October 2003) : preliminary results of a field survey performed by an Indonesian-Dutch biodiversity research team

    NARCIS (Netherlands)

    Hoeksema, B.W.

    2004-01-01

    The coastal waters of East Kalimantan are part of the western boundary of the Indo-West Pacific centre of maximum marine biodiversity. During the pilot phase of the East Kalimantan Program (EKP) this has been tested by various specialists who used model taxa to test this hypothesis. Emphasis has

  19. Microbial cytochromes P450: biodiversity and biotechnology. Where do cytochromes P450 come from, what do they do and what can they do for us?

    Science.gov (United States)

    Kelly, Steven L.; Kelly, Diane E.

    2013-01-01

    The first eukaryote genome revealed three yeast cytochromes P450 (CYPs), hence the subsequent realization that some microbial fungal genomes encode these proteins in 1 per cent or more of all genes (greater than 100) has been surprising. They are unique biocatalysts undertaking a wide array of stereo- and regio-specific reactions and so hold promise in many applications. Based on ancestral activities that included 14α-demethylation during sterol biosynthesis, it is now seen that CYPs are part of the genes and metabolism of most eukaryotes. In contrast, Archaea and Eubacteria often do not contain CYPs, while those that do are frequently interesting as producers of natural products undertaking their oxidative tailoring. Apart from roles in primary and secondary metabolism, microbial CYPs are actual/potential targets of drugs/agrochemicals and CYP51 in sterol biosynthesis is exhibiting evolution to resistance in the clinic and the field. Other CYP applications include the first industrial biotransformation for corticosteroid production in the 1950s, the diversion into penicillin synthesis in early mutations in fungal strain improvement and bioremediation using bacteria and fungi. The vast untapped resource of orphan CYPs in numerous genomes is being probed and new methods for discovering function and for discovering desired activities are being investigated. PMID:23297358

  20. A survey of phytotoxic microbial and plant metabolites as potential natural products for pest management

    Science.gov (United States)

    Phytotoxic microbial metabolites produced by certain phytopathogenic fungi and bacteria and a group of a phytotoxic plant metabolites including Amayllidaceae alkaloids and some derivatives of these compounds were evaluated for algicide, bactericide, insecticide, fungicide, and herbicide activities i...

  1. Biodiversity Information Serving Our Nation (BISON)

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The USGS Biodiversity Information Serving Our Nation (BISON) project is an online mapping information system consisting of a large collection of species occurrence...

  2. The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist.

    Science.gov (United States)

    Gilbert, Jack A; O'Dor, Ronald; King, Nicholas; Vogel, Timothy M

    2011-06-14

    Scientific discovery is incremental. The Merriam-Webster definition of 'Scientific Method' is "principles and procedures for the systematic pursuit of knowledge involving the recognition and formulation of a problem, the collection of data through observation and experiment, and the formulation and testing of hypotheses". Scientists are taught to be excellent observers, as observations create questions, which in turn generate hypotheses. After centuries of science we tend to assume that we have enough observations to drive science, and enable the small steps and giant leaps which lead to theories and subsequent testable hypotheses. One excellent example of this is Charles Darwin's Voyage of the Beagle, which was essentially an opportunistic survey of biodiversity. Today, obtaining funding for even small-scale surveys of life on Earth is difficult; but few argue the importance of the theory that was generated by Darwin from his observations made during this epic journey. However, these observations, even combined with the parallel work of Alfred Russell Wallace at around the same time have still not generated an indisputable 'law of biology'. The fact that evolution remains a 'theory', at least to the general public, suggests that surveys for new data need to be taken to a new level.

  3. Hydroecological Connections: Hyporheic Zone Weathering of Silicate Minerals Controls Diatom Biodiversity in Microbial Mats in Glacial Meltwater Streams of the McMurdo Dry Valleys, Antarctica

    Science.gov (United States)

    McKnight, D. M.; Dyson, I.; Esposito, R. M.; Gooseff, M. N.; Lyons, W. B.; Welch, K. A.

    2015-12-01

    The McMurdo Dry Valleys of Antarctica is comprised of alpine and terminal glaciers, large expanses of patterned ground, and ice-covered lakes in the valley floors, which are linked by glacial meltwater streams that flow during the austral summer. As part of the McMurdo Dry Valleys Long-Term Ecological research project, we have observed stream ecosystem response to a sustained 18 year cool period with low flows, which has been recently interrupted by three "flood events" during sunny, warm summers. Many of these streams contain thriving microbial mats comprised of cyanobacteria and endemic diatoms, the most diverse group of eukaryotic organisms in the valleys. Of the 45 diatom taxa, some common taxa are heavily silicified, Hantzschia amphioxys f. muelleri, while others are only lightly silicified. By comparing diatom communities in streams which flow every summer with those in streams that only flow during flood events, we found that hydrologic flow regime acts as a strong environmental filter on diatom community composition. Following the first flood event in 2001/02, mat biomass was two-fold lower due to scouring and recovered over several years, with lesser declines following the subsequent floods. In the longer streams, the diatom community composition remained stable through the flood events, whereas in two of the shorter streams, Green and Bowles Creeks, the diatom community shifted after the first flood event to a greater abundance of lightly silicified taxa. Water quality monitoring and reactive transport modeling have shown that rapid weathering of silicate minerals in the hyporheic zone accounts for the downstream increases in Si concentration which are observed in the longer streams. One mechanism driving this greater abundance of lightly silicified diatoms in shorter streams could be the greater dilution of the Si supply from hyporheic weathering in shorter streams under high flows. Given that the stream diatom community is well preserved in the 40

  4. Biodiversity of the microbial community in a Spanish farmhouse cheese as revealed by culture-dependent and culture-independent methods.

    Science.gov (United States)

    Abriouel, Hikmate; Martín-Platero, Antonio; Maqueda, Mercedes; Valdivia, Eva; Martínez-Bueno, Manuel

    2008-10-31

    The microbial diversity within Alberquilla cheese, made from a spontaneously fermented mixture of raw goats' and sheep's milk in the Alpujarra mountains (Granada, south-east Spain), has been studied by the classical culturing method and also by molecular analysis of community DNA. A collection of 206 isolates was obtained from the cheese on different selective/differential media, which were then re-grouped to 52 after randomly amplified polymorphic DNA (RAPD)-PCR analyses. Isolates on Man-Rogosa and Sharpe-agar (MRS), M17-glucose agar and Kenner Fecal (KF)-agar medium were identified by specific PCR or 16S rRNA gene sequencing and belonged mainly to the lactic-acid bacteria group. The predominant genus was Lactobacillus, which accounted for more than 50% of the isolates, the most abundant species being Lactobacillus paracasei, followed by considerably less quantities of Lb. plantarum and Lb. brevis. Other lactic-acid bacteria identified were Pediococcus urinaequi, Leuconostoc pseudomesenteroides, Leuc. mesenteroides, Lactococcus lactis and even the enterococci Enterococcus faecium and E. devriesei. Cluster analyses of RAPD-PCR patterns revealed a high degree of diversity among the lactobacilli. The Gram-negative bacterial strains belonged mainly to Hafnia alvei species. The microbes occurring in Alberquilla cheese were also studied by PCR temporal temperature-gradient gel electrophoresis (TTGE) of the 16S rRNA V3 region and partial 16S rRNA sequencing of the TTGE bands. The results showed a major presence of lactic-acid bacteria closely related to Lc. lactis, Lb. paracasei, Lb. plantarum, Lb. brevis, Lb. acidophilus and Enterococcus sp. The non-lactic-acid bacterium detected was identified as Escherichia coli. All the Enterococcus strains showed great susceptibility to the most clinically relevant antibiotics, harbouring only the virulence gene efaAfm. On the basis of their antimicrobial activity against Listeria monocytogenes we chose two strains of Ln

  5. 16S rRNA gene survey of microbial communities in Winogradsky columns.

    Directory of Open Access Journals (Sweden)

    Ethan A Rundell

    Full Text Available A Winogradsky column is a clear glass or plastic column filled with enriched sediment. Over time, microbial communities in the sediment grow in a stratified ecosystem with an oxic top layer and anoxic sub-surface layers. Winogradsky columns have been used extensively to demonstrate microbial nutrient cycling and metabolic diversity in undergraduate microbiology labs. In this study, we used high-throughput 16s rRNA gene sequencing to investigate the microbial diversity of Winogradsky columns. Specifically, we tested the impact of sediment source, supplemental cellulose source, and depth within the column, on microbial community structure. We found that the Winogradsky columns were highly diverse communities but are dominated by three phyla: Proteobacteria, Bacteroidetes, and Firmicutes. The community is structured by a founding population dependent on the source of sediment used to prepare the columns and is differentiated by depth within the column. Numerous biomarkers were identified distinguishing sample depth, including Cyanobacteria, Alphaproteobacteria, and Betaproteobacteria as biomarkers of the soil-water interface, and Clostridia as a biomarker of the deepest depth. Supplemental cellulose source impacted community structure but less strongly than depth and sediment source. In columns dominated by Firmicutes, the family Peptococcaceae was the most abundant sulfate reducer, while in columns abundant in Proteobacteria, several Deltaproteobacteria families, including Desulfobacteraceae, were found, showing that different taxonomic groups carry out sulfur cycling in different columns. This study brings this historical method for enrichment culture of chemolithotrophs and other soil bacteria into the modern era of microbiology and demonstrates the potential of the Winogradsky column as a model system for investigating the effect of environmental variables on soil microbial communities.

  6. Biodiversity and landscape

    Science.gov (United States)

    Bridgewater, P. B.

    1988-12-01

    Biodiversity and landscape pattern and process are inextricably linked. Maximum biodiversity occurs where landscape patterns and processes are most heterogeneous. Human use of landscapes in Australia and New Zealand has changed biodiversity patterns. European settlement introduced many species from Europe, America, Africa and Asia to the landscapes of Australia and New Zealand. These species have caused a decline in native biodiversity of much greater significance than their addition to the biodiversity. Future landscape management should seek to maintain maximum landscape heterogeneity, thereby ensuring the maximum persistence of biodiversity.

  7. A Literature Survey and Data Base Assessment: Microbial Fate of Diesel Fuel and Fog Oils,

    Science.gov (United States)

    1986-04-01

    were mostly aerobic NocardLa species and fungi. Cladosporum resinae , which has been repeatedly found as a contaminant of jet fuels and has been...1,13 2 Glucose metabolism is subject to inhibition or repression by hydrocarbon in a Candida strain 1 3 3 and Cladosporium resinae .1 3 ,1 5 Microbial...microorganisms isolated from soil. Can. J. Microbiol. 14:403. 93. Cooney, J.J. and J.D. Walker. 1973. Hydrocarbon utilization by Cladosporium resinae

  8. The Survey of Microbial Quality of the Dry Sample, Extract and Brewing of some Medicinal Plants

    Directory of Open Access Journals (Sweden)

    Razieh VALIASILL

    2014-12-01

    Full Text Available Medicinal plants may be exposed to a wide range of microbial contamination during pre- and post- harvest stages and they can present high microbial counts. In this study, the microbial quality of 44 samples of dry herbs namely: mint (Menthaspp., lemon balm (Melissa officinalis, summer savory (Satureja hortensis, zataria (Zataria multiflora, Indian valerian (Valeriana wallichii, their brewing and extracts were analyzed. Total count using plate count agar medium (PCA, coliform count by Violet Red Bile Agar (VRBL, Enterobacteriacea by Violet Red Bile Glucose (VRBG were evaluated. Medium Baird-Parker agar (BP medium and Tryptone Bile X-Gluc (TBX medium were used for the isolation and enumeration of Staphylococcus aurous and E. coli spp. respectively. Furthermore, Xylose Lysine Deoxycholate agar medium (XLD and Bismuth Sulfite Agar medium(BSA were used for detection of Salmonella spp. Fungal and mold contamination was assessed using yeast extract glucose chloramphenicol agar. The results showed that the contamination of the samples with total count (100% and Enterobacteriaceae (85%, total coliform (83%, mold and yeast (98% and E. coli ssp. (2.27 were detected, including in the study samples the absence of pathogenic bacteria like Staphylococcus aurous, Salmonella spp. Moreover, the extract had a lower microbial load in comparison to dry herb samples. Also, the lowest and the highest of contamination rates were observed for Indian valerian and zataria, respectively. According to the results, there is a need to control the environmental conditions and improve hygiene in the production process; even more, it is recommended to choose a suitable decontamination method for disinfection during packing medicinal plants and during post-packing manipulation and transport.

  9. Livestock biodiversity and sustainability

    NARCIS (Netherlands)

    Hoffmann, I.

    2011-01-01

    Sustainable development equally includes environmental protection including biodiversity, economic growth and social equity, both within and between generations. The paper first reviews different aspects related to the sustainable use of livestock biodiversity and property regimes that influence

  10. Evaluating Temporal Consistency in Marine Biodiversity Hotspots

    Science.gov (United States)

    Barner, Allison K.; Benkwitt, Cassandra E.; Boersma, Kate S.; Cerny-Chipman, Elizabeth B.; Ingeman, Kurt E.; Kindinger, Tye L.; Lindsley, Amy J.; Nelson, Jake; Reimer, Jessica N.; Rowe, Jennifer C.; Shen, Chenchen; Thompson, Kevin A.; Heppell, Selina S.

    2015-01-01

    With the ongoing crisis of biodiversity loss and limited resources for conservation, the concept of biodiversity hotspots has been useful in determining conservation priority areas. However, there has been limited research into how temporal variability in biodiversity may influence conservation area prioritization. To address this information gap, we present an approach to evaluate the temporal consistency of biodiversity hotspots in large marine ecosystems. Using a large scale, public monitoring dataset collected over an eight year period off the US Pacific Coast, we developed a methodological approach for avoiding biases associated with hotspot delineation. We aggregated benthic fish species data from research trawls and calculated mean hotspot thresholds for fish species richness and Shannon’s diversity indices over the eight year dataset. We used a spatial frequency distribution method to assign hotspot designations to the grid cells annually. We found no areas containing consistently high biodiversity through the entire study period based on the mean thresholds, and no grid cell was designated as a hotspot for greater than 50% of the time-series. To test if our approach was sensitive to sampling effort and the geographic extent of the survey, we followed a similar routine for the northern region of the survey area. Our finding of low consistency in benthic fish biodiversity hotspots over time was upheld, regardless of biodiversity metric used, whether thresholds were calculated per year or across all years, or the spatial extent for which we calculated thresholds and identified hotspots. Our results suggest that static measures of benthic fish biodiversity off the US West Coast are insufficient for identification of hotspots and that long-term data are required to appropriately identify patterns of high temporal variability in biodiversity for these highly mobile taxa. Given that ecological communities are responding to a changing climate and other

  11. Evaluating Temporal Consistency in Marine Biodiversity Hotspots.

    Science.gov (United States)

    Piacenza, Susan E; Thurman, Lindsey L; Barner, Allison K; Benkwitt, Cassandra E; Boersma, Kate S; Cerny-Chipman, Elizabeth B; Ingeman, Kurt E; Kindinger, Tye L; Lindsley, Amy J; Nelson, Jake; Reimer, Jessica N; Rowe, Jennifer C; Shen, Chenchen; Thompson, Kevin A; Heppell, Selina S

    2015-01-01

    With the ongoing crisis of biodiversity loss and limited resources for conservation, the concept of biodiversity hotspots has been useful in determining conservation priority areas. However, there has been limited research into how temporal variability in biodiversity may influence conservation area prioritization. To address this information gap, we present an approach to evaluate the temporal consistency of biodiversity hotspots in large marine ecosystems. Using a large scale, public monitoring dataset collected over an eight year period off the US Pacific Coast, we developed a methodological approach for avoiding biases associated with hotspot delineation. We aggregated benthic fish species data from research trawls and calculated mean hotspot thresholds for fish species richness and Shannon's diversity indices over the eight year dataset. We used a spatial frequency distribution method to assign hotspot designations to the grid cells annually. We found no areas containing consistently high biodiversity through the entire study period based on the mean thresholds, and no grid cell was designated as a hotspot for greater than 50% of the time-series. To test if our approach was sensitive to sampling effort and the geographic extent of the survey, we followed a similar routine for the northern region of the survey area. Our finding of low consistency in benthic fish biodiversity hotspots over time was upheld, regardless of biodiversity metric used, whether thresholds were calculated per year or across all years, or the spatial extent for which we calculated thresholds and identified hotspots. Our results suggest that static measures of benthic fish biodiversity off the US West Coast are insufficient for identification of hotspots and that long-term data are required to appropriately identify patterns of high temporal variability in biodiversity for these highly mobile taxa. Given that ecological communities are responding to a changing climate and other

  12. Microbial quality of hemodialysis water, a survey of six centers in Lagos, Nigeria.

    Science.gov (United States)

    Braimoh, Rotimi Williams; Mabayoje, Monica Omolara; Amira, Christiana Oluwatoyin; Bello, Babawale Taslim

    2014-01-01

    Patients with end-stage kidney disease (ESRD) on maintenance hemodialysis (HD) are usually exposed to large volumes of dialysate, which is separated from patients' blood only by thin membrane of dialyzer. It is therefore essential to frequently monitor the quality of HD water to ensure that it meets the recommended standards. The objective of this study was to evaluate the microbial quality of HD water in Lagos, Nigeria. Four sets of pre- and post-treatment water samples, 20 mL each, were collected from six HD centers in Lagos and tested for microbial contamination using the molten Tryptic soy agar in accordance with Association for Advancement of Medical Instrumentation (AAMI) and European Best Practice Guidelines (EBPG). Pyrogen tests were also conducted on pre- and post-treatment samples using standard technique. Information on water treatment modalities, maintenance practices and quality control measures in each center were obtained using a questionnaire. All centers use treated water for HD purpose. None of the HD centers met EBPG/AAMI guidelines for microbial contaminants as the mean levels of Escherichia coli in both feed and treated water were 441.7 ± 87.90 and 168.5 ± 64.03, respectively. E. coli was the commonest organism isolated in both feed and treated water in all the centers. HD water quality is still a neglected problem in our environment and more efforts are required to ensure good water quality for HD purpose. © 2013 International Society for Hemodialysis.

  13. Biodiversity and globalization

    OpenAIRE

    Heal, Geoffrey

    2002-01-01

    Reduction of the earth’s biodiversity as a result of human activities is a matter of great concern to prominent scientists. What are the economic aspects of this loss? In economic terms, what is biodiversity and why might it matter? And is the loss of biodiversity in any way connected with globalization of the economy?

  14. Knowing Agricultural Biodiversity

    OpenAIRE

    Mulvany, P.

    2001-01-01

    The term "agricultural biodiversity" is relatively recent, perhaps post-CBD. Although, the specific nature of the biodiversity used by people was recognised for a long time, the overwhelming emphasis in the CBD was on general biodiversity, mainly 'wild' flora and fauna that inhabit this fragile biosphere in which people also live.

  15. Biodeterioration of epoxy resin: a microbial survey through culture-independent and culture-dependent approaches.

    Science.gov (United States)

    Pangallo, Domenico; Bučková, Maria; Kraková, Lucia; Puškárová, Andrea; Šaková, Nikoleta; Grivalský, Tomaš; Chovanová, Katarina; Zemánková, Milina

    2015-02-01

    During the 20th century, synthetic polymers were greatly used in the field of art. In particular, the epoxy resins were used for both conservation and for creating sculptures. The biodeterioration of these polymers has not been adequately studied. The aim of this investigation was to examine the microflora responsible for the deterioration of an epoxy statue exposed to outdoor conditions. Fungal and bacterial microflora were isolated from the art object, clustered by fluorescence-ITS (internal transcribed spacer), identified by ITS and 16S rRNA sequencing and tested for their lipolytic abilities by three agar assays. Different algal, bacterial, cyanobacterial and fungal clone libraries were constructed. The surrounding airborne microflora was analyzed using culture-dependent and culture-independent approaches. The results indicated the presence, on the statue surface, of an interesting and differentiate microbial community composed of rock-inhabiting members, algal photobionts (Trebouxia spp., Chloroidium ellipsoideum and Chlorella angustoellipsoidea), Cyanobacteria (Leptolyngbya sp., Phormidium sp., Cylindrospermum stagnale, Hassallia byssoidea and Geitlerinema sp.), black yeasts related to the species Friedmanniomyces endolithicus, Pseudotaeniolina globosa, Phaeococcomyces catenatus and Catenulostroma germanicum and several plant-associated fungi. This investigation provides new information on the potential microfloral inhabitants of epoxy resin discovering a new ecological niche, occupied mainly by several members of rock-colonizing microbial species. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  16. Production of Microbial Protease from Selected Soil Fungal Isolates

    African Journals Online (AJOL)

    Dr Oseni

    establishing the industrial and biotechnological importance of this microbial enzyme. The harvested mycelia of the fungi ... Keywords: Soil microorganism, fungal isolate, incubation period, microbial enzyme. Correspondence: ..... highlands, Sarawak. ASEAN Review of Biodiversity and Environmental Conservation (ARBEC).

  17. Survey of physicochemical characteristics and microbial contamination in selected food locally vended in Morogoro Municipality, Tanzania.

    Science.gov (United States)

    Nonga, Hezron Emmanuel; Ngowi, Helena Aminiel; Mdegela, Robinson Hammerthon; Mutakyawa, Eliud; Nyahinga, Gabriel Busungu; William, Robert; Mwadini, Mtumwa Mohd

    2015-11-26

    Raw milk, raw fruit juice and raw fish are enriched with essential nutrients for human diet but are prone to microbial contamination along the value chain. This cross sectional study was conducted to assess physicochemical characteristics and microbial quality of raw milk, fruit juice and fish from food vendors in Morogoro Municipality, Tanzania. The physicochemical assessment of food samples was done by smell, colour, presence of debris, turbidity, consistence, pH and clot on alcohol test. Hygiene of food containers, personnel and the vending environment was also assessed. Qualitative and quantitative microbial assessment of food was done using standard laboratory protocols as described by Tanzania Bureau of Standards and International Systems of Standards. Raw milk sold in Morogoro was of poor quality since was adulterated with water, contained sediments and clotted on alcohol test. Up to 63 % of the milk samples were contaminated with Escherichia coli and 60 % had higher total viable count (TVC) than the recommended values. Raw fruit juice was stored in dirty containers and sold under unhygienic environment. Seventy-three percent of juice samples had TVC beyond the recommendations while E. coli contamination rate was 63.3 %. The raw fish samples had started spoiling as depicted through sensory evaluation. E. coli contamination rate was 55 % and that of Campylobacter jejuni was 0.5 %. The mean TVC of raw fish was 8.1 (Log cfu/g) and 96.2 % of the fish samples had TVC beyond the recommended limits of 5.0 Log cfu/g. The physicochemical characteristics of food vended in Morogoro Municipality were of poor quality. The food had high bacterial contaminations. This situation poses health risks to the public and losses to food vendors due to spoilage. Stakeholders in food value chain should be educated on safe production and good hygienic practices. Routine quality and safety assessment of locally vended food, inspection of selling premises and regular health check-up of

  18. Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platform (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    Energy Technology Data Exchange (ETDEWEB)

    Tremblay, Julien

    2012-06-01

    Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  19. Biodiversity of Jinggangshan Mountain: the importance of topography and geographical location in supporting higher biodiversity.

    Science.gov (United States)

    Zhou, Ting; Chen, Bao-Ming; Liu, Gang; Huang, Fang-Fang; Liu, Jin-Gang; Liao, Wen-Bo; Wang, Ying-Yong; Ren, Si-Jie; Chen, Chun-Quan; Peng, Shao-Lin

    2015-01-01

    Diversity is mainly determined by climate and environment. In addition, topography is a complex factor, and the relationship between topography and biodiversity is still poorly understood. To understand the role of topography, i.e., altitude and slope, in biodiversity, we selected Jinggangshan Mountain (JGM), an area with unique topography, as the study area. We surveyed plant and animal species richness of JGM and compared the biodiversity and the main geographic characteristics of JGM with the adjacent 4 mountains. Gleason's richness index was calculated to assess the diversity of species. In total, 2958 spermatophyte species, 418 bryophyte species, 355 pteridophyte species and 493 species of vertebrate animals were recorded in this survey. In general, the JGM biodiversity was higher than that of the adjacent mountains. Regarding topographic characteristics, 77% of JGM's area was in the mid-altitude region and approximately 40% of JGM's area was in the 10°-20° slope range, which may support more vegetation types in JGM area and make it a biodiversity hotspot. It should be noted that although the impact of topography on biodiversity was substantial, climate is still a more general factor driving the formation and maintenance of higher biodiversity. Topographic conditions can create microclimates, and both climatic and topographic conditions contribute to the formation of high biodiversity in JGM.

  20. Biodiversity of Jinggangshan Mountain: the importance of topography and geographical location in supporting higher biodiversity.

    Directory of Open Access Journals (Sweden)

    Ting Zhou

    Full Text Available Diversity is mainly determined by climate and environment. In addition, topography is a complex factor, and the relationship between topography and biodiversity is still poorly understood. To understand the role of topography, i.e., altitude and slope, in biodiversity, we selected Jinggangshan Mountain (JGM, an area with unique topography, as the study area. We surveyed plant and animal species richness of JGM and compared the biodiversity and the main geographic characteristics of JGM with the adjacent 4 mountains. Gleason's richness index was calculated to assess the diversity of species. In total, 2958 spermatophyte species, 418 bryophyte species, 355 pteridophyte species and 493 species of vertebrate animals were recorded in this survey. In general, the JGM biodiversity was higher than that of the adjacent mountains. Regarding topographic characteristics, 77% of JGM's area was in the mid-altitude region and approximately 40% of JGM's area was in the 10°-20° slope range, which may support more vegetation types in JGM area and make it a biodiversity hotspot. It should be noted that although the impact of topography on biodiversity was substantial, climate is still a more general factor driving the formation and maintenance of higher biodiversity. Topographic conditions can create microclimates, and both climatic and topographic conditions contribute to the formation of high biodiversity in JGM.

  1. Survey and documentation of the potential and actual invasive alien plant species and other biological threats to biodiversity in Awash National Park, Ethiopia

    Directory of Open Access Journals (Sweden)

    Sebsebe DEMISSEW

    2011-01-01

    Full Text Available The study was conducted at the Awash National Park (ANP Ethiopia, todocument Invasive Alien Species (IAS and to assess the spread of Prosopis juliflora (Sw. DC. A total of 64 sample plots were laid systematically along the altitudinal gradient of 750 to 1916 m.Potential IAS were recorded. IAS which may threaten biodiversity of the park includes species such as Prosopis juliflora, Parthenium hysterophorus L., Cryptostegia grandiflora Roxb. ex R. Br., Parkinsonia aculeata L., Senna occidentalis (L. Link, Datura ferox L. and Xanthium strumarium L. Except P. juliflora and P. hysterophorus, all others were not recorded in Ethiopia as IAS. P.juliflora was recorded in three plots with cover of 1% to 10%. P. juliflora was also found spread in different parts of the park particularly following the route of cattle movement. P. hysterophoruswas recorded in and around nine sample plots. Plot 46, 47 and 48 werehighly infested by P. hysterophorus which covered more than 60, 70 and 80% of the ground layer respectively. C. grandiflora was recorded in 11 plots with cover ranging from 1% to 35%. In view of all the natural as well as anthropogenic threats to the biodiversity of the Park, the ANP is at high risk. The rich biodiversity needsimmediate management intervention.

  2. Molecular epidemiology of dermatophytes in Tehran, Iran, a clinical and microbial survey

    NARCIS (Netherlands)

    Rezaei-Matehkolaei, A.; Makimura, K.; de Hoog, S.; Shidfar, M.R.; Zaini, F.; Eshraghian, M.; Naghan, P.A.; Mirhendi, H.

    2013-01-01

    In the framework of a survey on dermatophytoses, 14,619 clinical specimens taken from outpatients with symptoms suggestive of tinea and referred to a Medical Mycology laboratory in Tehran, Iran, were analyzed by direct microscopy and culture. In total, 777 dermatophyte strains recovered in culture

  3. Business and biodiversity

    DEFF Research Database (Denmark)

    Andersen, Rasmus Meyer; Lehmann, Martin; Christensen, Per

    Despite the overall importance of biodiversity, the quality measures of biodiversity show worrying figures. Numerous human impacts on nature impose serious hazard to its inherent diversity. This expansion of human activities leaves the battle against loss of biodiversity to be a great challenge......, but the effort has until now considered biodiversity actions relatively little, compared to other areas such as e.g. climate related actions. Nevertheless, the opportunity for businesses to meet their responsibilities and lift a share of the challenge is far from being just a romantic thought. Nor...... is the challenge of engaging businesses in responsible actions. The core challenge is to create awareness of the environmental phenomenon biodiversity, inform about the significance of business involvement, and encourage the business world to participate in this process of protecting biodiversity as the valuable...

  4. Deep Water Survey Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The deep water biodiversity surveys explore and describe the biodiversity of the bathy- and bentho-pelagic nekton using Midwater and bottom trawls centered in the...

  5. In silico substrate dependence increases community productivity but threatens biodiversity

    Science.gov (United States)

    Daly, Aisling J.; Baetens, Jan M.; De Baets, Bernard

    2016-04-01

    The critical role that biodiversity plays in ecosystem functioning has motivated many studies of the mechanisms that sustain biodiversity, a notable example being cyclic competition. We extend existing models of communities with cyclic competition by incorporating variable community evenness and resource dependence in demographic processes, two features that have generally been neglected. In this way, we align previous approaches more closely with real-world microbial ecosystems. We demonstrate the existence of a trade-off between increasing biomass production and maintaining biodiversity. This supports experimental observations of a net negative biodiversity effect on biomass productivity, due to competition effects suffered by highly productive species in diverse communities. Our results also support the important role assigned by microbial ecologists to evenness in maintaining ecosystem stability, thus far largely overlooked in in silico approaches.

  6. Soil biodiversity in artificial black pine stands one year after selective silvicultural treatments

    Science.gov (United States)

    Mocali, Stefano; Fabiani, Arturo; Landi, Silvia; Bianchetto, Elisa; Montini, Piergiuseppe; Samaden, Stefano; Cantiani, Paolo

    2017-04-01

    The decay of forest cover and soil erosion is a consequence of continual intensive forest exploitation, such as grazing and wild fires over the centuries. From the end of the eighteenth century up to the mid-1900s, black pine plantations were established throughout the Apennines' range in Italy, to improve forest soil quality. The main aim of this silvicultural treatment was to re-establish the pine as a first cover and pioneer species. A series of thinning activities were therefore planned by foresters when these plantations were designed. The project Selpibiolife (LIFE13 BIO/IT/000282) has the main objective to demonstrate the potential of an innovative silvicultural treatment to enhance soil and flora biodiversity and under black pine stands. The monitoring will be carried out by comparing selective and traditional thinning methods (selecting trees from below leaving well-spaced, highest-quality trees) to areas without any silvicultural treatments (e.g. weeding, cleaning, liberation cutting). The monitoring survey was carried out in Pratomagno and Amiata Val D'Orcia areas on the Appennines (Italy) and involved different biotic levels: microorganisms, mesofauna, nematodes and macrofauna (Coleoptera) and flora. The microbial (bacteria and fungi) diversity was assessed by both biochemical (microbial biomass, microbial respiration, metabolic quotient) and molecular (microbiota) approaches whereas QBS (Soil Biological Quality) index and diversity indexes were determined for mesofauna and other organisms, respectively, including flora. The overall results highlighted different a composition and activity of microbial communities within the two areas before thinning, and revealed a significant difference between the overall biodiversity of the two areas. Even though silvicultural treatments provided no significant differences at floristic level, microbial and mesofaunal parameters revealed to be differently affected by treatments. In particular, little but significant

  7. PLANT CLASSIFICATION AND BIODIVERSITY WHAT RELATIONSHIP IN TEXTBOOKS OF MOROCCO

    OpenAIRE

    MASKOUR, Lhoussaine; ALAMI, Anouar; ZAKI, Moncef; AGORRAM, Boujemaa

    2016-01-01

    Biodiversity is rapidly declining worldwide. The main causeof the loss of biodiversity can be attributed to the influence of human beingson the world’s. To protect biodiversity we need to understand it. An informedunderstanding of plant diversity and resources has never been more important.Environmental surveys and effective conservation strategies depend upondetailed knowledge of plants. To communicate such knowledge accurately andeffectively, training is required in plant taxonomy, the disc...

  8. Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato)

    Science.gov (United States)

    2013-01-01

    Background Research to understand and control microbiological risks associated with the consumption of fresh fruits and vegetables has examined many environments in the farm to fork continuum. An important data gap however, that remains poorly studied is the baseline description of microflora that may be associated with plant anatomy either endemically or in response to environmental pressures. Specific anatomical niches of plants may contribute to persistence of human pathogens in agricultural environments in ways we have yet to describe. Tomatoes have been implicated in outbreaks of Salmonella at least 17 times during the years spanning 1990 to 2010. Our research seeks to provide a baseline description of the tomato microbiome and possibly identify whether or not there is something distinctive about tomatoes or their growing ecology that contributes to persistence of Salmonella in this important food crop. Results DNA was recovered from washes of epiphytic surfaces of tomato anatomical organs; leaves, stems, roots, flowers and fruits of Solanum lycopersicum (BHN602), grown at a site in close proximity to commercial farms previously implicated in tomato-Salmonella outbreaks. DNA was amplified for targeted 16S and 18S rRNA genes and sheared for shotgun metagenomic sequencing. Amplicons and metagenomes were used to describe “native” bacterial microflora for diverse anatomical parts of Virginia-grown tomatoes. Conclusions Distinct groupings of microbial communities were associated with different tomato plant organs and a gradient of compositional similarity could be correlated to the distance of a given plant part from the soil. Unique bacterial phylotypes (at 95% identity) were associated with fruits and flowers of tomato plants. These include Microvirga, Pseudomonas, Sphingomonas, Brachybacterium, Rhizobiales, Paracocccus, Chryseomonas and Microbacterium. The most frequently observed bacterial taxa across aerial plant regions were Pseudomonas and Xanthomonas

  9. MICROBIAL BIOFILMS AS INDICATORS OF ESTUARINE CONDITION

    Science.gov (United States)

    Microbial biofilms are complex communities of bacteria, protozoa, microalgae, and micrometazoa which exist in a polymer matrix on submerged surfaces. Their development is integrative of environmental conditions and is affected by local biodiversity, the availability of organic ma...

  10. Biodiversity intactness index

    CSIR Research Space (South Africa)

    Scholes, RJ

    2005-03-03

    Full Text Available The nations of the world have set themselves a target of reducing the rate of biodiversity loss by 2010. Here, we propose a biodiversity intactness index (BII) for assessing progress towards this target that is simple and practical - but sensitive...

  11. Essential Biodiversity Variables

    NARCIS (Netherlands)

    Pereira, H.M.; Ferrier, S.; Walters, M.; Geller, G.; Jongman, R.H.G.; Scholes, R.J.; Bruford, M.W.; Brummitt, N.; Butchart, S.H.M.; Cardoso, A.C.; Coops, N.C.; Dulloo, E.; Faith, D.P.; Freyhof, J.; Gregory, R.D.; Heip, C.; Höft, R.; Hurtt, G.; Jetz, W.; Karp, D.; McGeoch, M.A.; Obura, D.; Onoda, Y.; Pettorelli, N.; Reyers, B.; Sayre, R.; Scharlemann, J.P.W.; Stuart, S.N.; Turak, E.; Walpole, M.; Wegmann, M.

    2013-01-01

    Reducing the rate of biodiversity loss and averting dangerous biodiversity change are international goals, reasserted by the Aichi Targets for 2020 by Parties to the United Nations (UN) Convention on Biological Diversity (CBD) after failure to meet the 2010 target (1, 2). However, there is no

  12. Microbial analysis and survey test of gamma-irradiated freeze-dried fruits for patient's food

    Science.gov (United States)

    Park, Jae-Nam; Sung, Nak-Yun; Byun, Eui-Hong; Byun, Eui-Baek; Song, Beom-Seok; Kim, Jae-Hun; Lee, Kyung-A.; Son, Eun-Joo; Lyu, Eun-Soon

    2015-06-01

    This study examined the microbiological and organoleptic qualities of gamma-irradiated freeze-dried apples, pears, strawberries, pineapples, and grapes, and evaluated the organoleptic acceptability of the sterilized freeze-dried fruits for hospitalized patients. The freeze-dried fruits were gamma-irradiated at 0, 1, 2, 3, 4, 5, 10, 12, and 15 kGy, and their quality was evaluated. Microorganisms were not detected in apples after 1 kGy, in strawberries and pears after 4 kGy, in pineapples after 5 kGy, and in grapes after 12 kGy of gamma irradiation. The overall acceptance score, of the irradiated freeze-dried fruits on a 7-point scale at the sterilization doses was 5.5, 4.2, 4.0, 4.1, and 5.1 points for apples, strawberries, pears, pineapples, and grapes, respectively. The sensory survey of the hospitalized cancer patients (N=102) resulted in scores of 3.8, 3.7, 3.9, 3.9, and 3.7 on a 5-point scale for the gamma-irradiated freeze-dried apples, strawberries, pears, pineapples, and grapes, respectively. The results suggest that freeze-dried fruits can be sterilized with a dose of 5 kGy, except for grapes, which require a dose of 12 kGy, and that the organoleptic quality of the fruits is acceptable to immuno-compromised patients. However, to clarify the microbiological quality and safety of freeze-dried fruits should be verified by plating for both aerobic and anaerobic microorganisms.

  13. Monitoring biodiversity in libraries: a pilot study and perspectives for indoor air quality.

    Science.gov (United States)

    Valeriani, F; Cianfanelli, C; Gianfranceschi, G; Santucci, S; Romano Spica, V; Mucci, N

    2017-09-01

    Indoor Air Quality (IAQ) in libraries is influenced by the presence of specific factors which can impact on both paper storage as well as people health. Microclimatic conditions induce and support a biodiversity pattern involving environmental and anthropic microorganisms. We used a multidisciplinary monitoring model to characterize microflora biodiversity by Next Generation Sequencing (NGS). Biodiversity indexes were adapted to evaluate anthropic vs environmental pollution by combining Shannon mean index (H), species representativeness (E H ), human/environmental pollution ratio (SA) to better characterize the NGS output and acquire synthetic information on Indoor Air Microbial Biodiversity (IAMB). Results indicate a frequently low microbial load (IGCM/m 3 < 1000) characterized by different species (n = 102), including several cellulose metabolizing bacteria. Workers and visitors appeared a relevant source of microbial contamination. Air biodiversity assayed by NGS seems a promising marker for studying IAQ.

  14. Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity.

    Science.gov (United States)

    Maury, Mylène M; Tsai, Yu-Huan; Charlier, Caroline; Touchon, Marie; Chenal-Francisque, Viviane; Leclercq, Alexandre; Criscuolo, Alexis; Gaultier, Charlotte; Roussel, Sophie; Brisabois, Anne; Disson, Olivier; Rocha, Eduardo P C; Brisse, Sylvain; Lecuit, Marc

    2016-03-01

    Microbial pathogenesis studies are typically performed with reference strains, thereby overlooking within-species heterogeneity in microbial virulence. Here we integrated human epidemiological and clinical data with bacterial population genomics to harness the biodiversity of the model foodborne pathogen Listeria monocytogenes and decipher the basis of its neural and placental tropisms. Taking advantage of the clonal structure of this bacterial species, we identify clones epidemiologically associated either with food or with human central nervous system (CNS) or maternal-neonatal (MN) listeriosis. The latter clones are also most prevalent in patients without immunosuppressive comorbidities. Strikingly, CNS- and MN-associated clones are hypervirulent in a humanized mouse model of listeriosis. By integrating epidemiological data and comparative genomics, we have uncovered multiple new putative virulence factors and demonstrate experimentally the contribution of the first gene cluster mediating L. monocytogenes neural and placental tropisms. This study illustrates the exceptional power in harnessing microbial biodiversity to identify clinically relevant microbial virulence attributes.

  15. Indigenous Angiosperm biodiversity of Olabisi Onabanjo University ...

    African Journals Online (AJOL)

    The conservation of the genetic variability of the indigenous angiosperm community is a sine qua non. A survey of indigenous angiosperm biodiversity of the Olabisi Onabanjo University permanent site was undertaken. Plants collected were dried, poisoned and mounted on herbarium sheets, proper identification and ...

  16. Birds as biodiversity surrogates

    DEFF Research Database (Denmark)

    Larsen, Frank Wugt; Bladt, Jesper Stentoft; Balmford, Andrew

    2012-01-01

    1. Most biodiversity is still unknown, and therefore, priority areas for conservation typically are identified based on the presence of surrogates, or indicator groups. Birds are commonly used as surrogates of biodiversity owing to the wide availability of relevant data and their broad popular...... and applications.?Good surrogates of biodiversity are necessary to help identify conservation areas that will be effective in preventing species extinctions. Birds perform fairly well as surrogates in cases where birds are relatively speciose, but overall effectiveness will be improved by adding additional data...... from other taxa, in particular from range-restricted species. Conservation solutions with focus on birds as biodiversity surrogate could therefore benefit from also incorporating species data from other taxa....

  17. Biodiversity and global change

    National Research Council Canada - National Science Library

    Solbrig, Otto Thomas; Emden, H. M. van; Oordt, P. G. W. J. van; Solbrig, Otto T

    1992-01-01

    The IUBS symposium "Biodiversity and Global Change" held during the 24th General Assembly, 1-6 September, 1991, in Amsterdam, the Netherlands, represented the first attempt to address the issue of bio...

  18. Quantifying biodiversity and asymptotics for a sequence of random strings.

    Science.gov (United States)

    Koyano, Hitoshi; Kishino, Hirohisa

    2010-06-01

    We present a methodology for quantifying biodiversity at the sequence level by developing the probability theory on a set of strings. Further, we apply our methodology to the problem of quantifying the population diversity of microorganisms in several extreme environments and digestive organs and reveal the relation between microbial diversity and various environmental parameters.

  19. [Metagenomics and biodiversity of sphagnum bogs].

    Science.gov (United States)

    Rusin, L Yu

    2016-01-01

    Biodiversity of sphagnum bogs is one of the richest and less studied, while these ecosystems are among the top ones in ecological, conservation, and economic value. Recent studies focused on the prokaryotic consortia associated with sphagnum mosses, and revealed the factors that maintain sustainability and productivity of bog ecosystems. High-throughput sequencing technologies provided insight into functional diversity of moss microbial communities (microbiomes), and helped to identify the biochemical pathways and gene families that facilitate the spectrum of adaptive strategies and largely foster the very successful colonization of the Northern hemisphere by sphagnum mosses. Rich and valuable information obtained on microbiomes of peat bogs sets off the paucity of evidence on their eukaryotic diversity. Prospects and expectations of reliable assessment of taxonomic profiles, relative abundance of taxa, and hidden biodiversity of microscopic eukaryotes in sphagnum bog ecosystems are briefly outlined in the context of today's metagenomics.

  20. CALICE: Calibrating Plant Biodiversity in Glacier Ice

    Science.gov (United States)

    Festi, Daniela; Cristofori, Antonella; Vernesi, Cristiano; Zerbe, Stefan; Wellstein, Camilla; Maggi, Valter; Oeggl, Klaus

    2017-04-01

    The objective of the project is to reconstruct plant biodiversity and its trend archived in Alpine glacier ice by pollen and eDNA (environmental DNA) during the last five decades by analyzing a 40 m ice core. For our study we chose the Adamello glacier (Trentino - Südtirol, Lombardia) because of i) the good preservation conditions for pollen and eDNA in ice, ii) the thickness of the ice cap (270m) and iii) the expected high time resolution. The biodiversity estimates gained by pollen analysis and eDNA will be validated by historical biodiversity assessments mainly based on vegetation maps, aerial photos and vegetation surveys in the catchment area of the Adamello glacier for the last five decades. This historical reconstruction of biodiversity trends will be performed on a micro-, meso- and macro-scale (5, 20-50 and 50-100 Km radius, respectively). The results will serve as a calibration data set on biodiversity for future studies, such as the second step of the coring by the POLLiCE research consortium (pollice.fmach.it). In fact, arrangements are currently been made to drill the complete ice cap and retrieve a 270 m thick core which has the potential to cover a time span of minimum 400 years up to several millennia. This second stage will extend the time scale and enable the evaluation of dissimilarity/similarity of modern biodiversity in relation to Late Holocene trends. Finally, we believe this case study has the potential to be applied in other glaciated areas to evaluate biodiversity for large regions (e.g. central Asian mountain ranges, Tibet and Tian Shan or the Andes).

  1. Dormancy contributes to the maintenance of microbial diversity.

    Science.gov (United States)

    Jones, Stuart E; Lennon, Jay T

    2010-03-30

    Dormancy is a bet-hedging strategy used by a variety of organisms to overcome unfavorable environmental conditions. By entering a reversible state of low metabolic activity, dormant individuals become members of a seed bank, which can determine community dynamics in future generations. Although microbiologists have documented dormancy in both clinical and natural settings, the importance of seed banks for the diversity and functioning of microbial communities remains untested. Here, we develop a theoretical model demonstrating that microbial communities are structured by environmental cues that trigger dormancy. A molecular survey of lake ecosystems revealed that dormancy plays a more important role in shaping bacterial communities than eukaryotic microbial communities. The proportion of dormant bacteria was relatively low in productive ecosystems but accounted for up to 40% of taxon richness in nutrient-poor systems. Our simulations and empirical data suggest that regional environmental cues and dormancy synchronize the composition of active communities across the landscape while decoupling active microbes from the total community at local scales. Furthermore, we observed that rare bacterial taxa were disproportionately active relative to common bacterial taxa, suggesting that microbial rank-abundance curves are more dynamic than previously considered. We propose that repeated transitions to and from the seed bank may help maintain the high levels of microbial biodiversity that are observed in nearly all ecosystems.

  2. Biodiversity in marine ecosystems – European developments towards robust assessments

    Directory of Open Access Journals (Sweden)

    Anna-Stiina Heiskanen

    2016-09-01

    Full Text Available Sustainability of marine ecosystems and their services are dependent on marine biodiversity, which is threatened worldwide. Biodiversity protection is a major target of the EU Marine Strategy Framework Directive, requiring assessment of the status of biodiversity on the level of species, habitats, and ecosystems including genetic diversity and the role of biodiversity in food web functioning and structure. This paper provides a summary of the development of new indicators and refinement of existing ones in order to address some of the observed gaps in indicator availability for marine biodiversity assessments considering genetic, species, habitat, and ecosystem levels. Promising new indicators are available addressing genetic diversity of microbial and benthic communities. Novel indicators to assess biodiversity and food webs associated with habitats formed by keystone species (such as macroalgae as well as to map benthic habitats (such as biogenic reefs using high resolution habitat characterization were developed. We also discuss the advances made on indicators for detecting impacts of non-native invasive species and assessing the structure and functioning of marine food-webs. The latter are based on indicators showing the effects of fishing on trophic level and size distribution of fish and elasmobranch communities well as phytoplankton and zooplankton community structure as food web indicators. New and refined indicators are ranked based on quality criteria. Their applicability for various EU and global biodiversity assessments and the need for further development of new indicators and refinement of the existing ones is discussed.

  3. Biodiversity in urban habitat patches.

    Science.gov (United States)

    Angold, P G; Sadler, J P; Hill, M O; Pullin, A; Rushton, S; Austin, K; Small, E; Wood, B; Wadsworth, R; Sanderson, R; Thompson, K

    2006-05-01

    We examined the biodiversity of urban habitats in Birmingham (England) using a combination of field surveys of plants and carabid beetles, genetic studies of four species of butterflies, modelling the anthropochorous nature of the floral communities and spatially explicit modelling of selected mammal species. The aim of the project was to: (i) understand the ecological characteristics of the biota of cities model, (ii) examine the effects of habitat fragment size and connectivity upon the ecological diversity and individual species distributions, (iii) predict biodiversity in cities, and (iv) analyse the extent to which the flora and fauna utilise the 'urban greenways' both as wildlife corridors and as habitats in their own right. The results suggest that cities provide habitats for rich and diverse range of plants and animals, which occur sometimes in unlikely recombinant communities. The studies on carabids and butterflies illustrated the relative importance of habitat quality on individual sites as opposed to site location within the conurbation. This suggests that dispersal for most of our urban species is not a limiting factor in population persistence, although elements of the woodland carabid fauna did appear to have some geographical structuring. Theoretical models suggested that dormice and water voles may depend on linear habitats for dispersal. The models also indicated that other groups, such as small and medium sized mammals, may use corridors, although field-based research did not provide any evidence to suggest that plants or invertebrates use urban greenways for dispersal. This finding indicates the importance of identifying a target species or group of species for urban greenways intended as dispersal routeways rather than as habitat in their own right. Their importance for most groups is rather that greenways provide a chain of different habitats permeating the urban environment. We suggest that planners can have a positive impact on urban

  4. A biodiversity indicators dashboard: addressing challenges to monitoring progress towards the Aichi biodiversity targets using disaggregated global data.

    Directory of Open Access Journals (Sweden)

    Xuemei Han

    Full Text Available Recognizing the imperiled status of biodiversity and its benefit to human well-being, the world's governments committed in 2010 to take effective and urgent action to halt biodiversity loss through the Convention on Biological Diversity's "Aichi Targets". These targets, and many conservation programs, require monitoring to assess progress toward specific goals. However, comprehensive and easily understood information on biodiversity trends at appropriate spatial scales is often not available to the policy makers, managers, and scientists who require it. We surveyed conservation stakeholders in three geographically diverse regions of critical biodiversity concern (the Tropical Andes, the African Great Lakes, and the Greater Mekong and found high demand for biodiversity indicator information but uneven availability. To begin to address this need, we present a biodiversity "dashboard"--a visualization of biodiversity indicators designed to enable tracking of biodiversity and conservation performance data in a clear, user-friendly format. This builds on previous, more conceptual, indicator work to create an operationalized online interface communicating multiple indicators at multiple spatial scales. We structured this dashboard around the Pressure-State-Response-Benefit framework, selecting four indicators to measure pressure on biodiversity (deforestation rate, state of species (Red List Index, conservation response (protection of key biodiversity areas, and benefits to human populations (freshwater provision. Disaggregating global data, we present dashboard maps and graphics for the three regions surveyed and their component countries. These visualizations provide charts showing regional and national trends and lay the foundation for a web-enabled, interactive biodiversity indicators dashboard. This new tool can help track progress toward the Aichi Targets, support national monitoring and reporting, and inform outcome-based policy-making for the

  5. A biodiversity indicators dashboard: addressing challenges to monitoring progress towards the Aichi biodiversity targets using disaggregated global data.

    Science.gov (United States)

    Han, Xuemei; Smyth, Regan L; Young, Bruce E; Brooks, Thomas M; Sánchez de Lozada, Alexandra; Bubb, Philip; Butchart, Stuart H M; Larsen, Frank W; Hamilton, Healy; Hansen, Matthew C; Turner, Will R

    2014-01-01

    Recognizing the imperiled status of biodiversity and its benefit to human well-being, the world's governments committed in 2010 to take effective and urgent action to halt biodiversity loss through the Convention on Biological Diversity's "Aichi Targets". These targets, and many conservation programs, require monitoring to assess progress toward specific goals. However, comprehensive and easily understood information on biodiversity trends at appropriate spatial scales is often not available to the policy makers, managers, and scientists who require it. We surveyed conservation stakeholders in three geographically diverse regions of critical biodiversity concern (the Tropical Andes, the African Great Lakes, and the Greater Mekong) and found high demand for biodiversity indicator information but uneven availability. To begin to address this need, we present a biodiversity "dashboard"--a visualization of biodiversity indicators designed to enable tracking of biodiversity and conservation performance data in a clear, user-friendly format. This builds on previous, more conceptual, indicator work to create an operationalized online interface communicating multiple indicators at multiple spatial scales. We structured this dashboard around the Pressure-State-Response-Benefit framework, selecting four indicators to measure pressure on biodiversity (deforestation rate), state of species (Red List Index), conservation response (protection of key biodiversity areas), and benefits to human populations (freshwater provision). Disaggregating global data, we present dashboard maps and graphics for the three regions surveyed and their component countries. These visualizations provide charts showing regional and national trends and lay the foundation for a web-enabled, interactive biodiversity indicators dashboard. This new tool can help track progress toward the Aichi Targets, support national monitoring and reporting, and inform outcome-based policy-making for the protection of

  6. A Biodiversity Indicators Dashboard: Addressing Challenges to Monitoring Progress towards the Aichi Biodiversity Targets Using Disaggregated Global Data

    Science.gov (United States)

    Han, Xuemei; Smyth, Regan L.; Young, Bruce E.; Brooks, Thomas M.; Sánchez de Lozada, Alexandra; Bubb, Philip; Butchart, Stuart H. M.; Larsen, Frank W.; Hamilton, Healy; Hansen, Matthew C.; Turner, Will R.

    2014-01-01

    Recognizing the imperiled status of biodiversity and its benefit to human well-being, the world's governments committed in 2010 to take effective and urgent action to halt biodiversity loss through the Convention on Biological Diversity's “Aichi Targets”. These targets, and many conservation programs, require monitoring to assess progress toward specific goals. However, comprehensive and easily understood information on biodiversity trends at appropriate spatial scales is often not available to the policy makers, managers, and scientists who require it. We surveyed conservation stakeholders in three geographically diverse regions of critical biodiversity concern (the Tropical Andes, the African Great Lakes, and the Greater Mekong) and found high demand for biodiversity indicator information but uneven availability. To begin to address this need, we present a biodiversity “dashboard” – a visualization of biodiversity indicators designed to enable tracking of biodiversity and conservation performance data in a clear, user-friendly format. This builds on previous, more conceptual, indicator work to create an operationalized online interface communicating multiple indicators at multiple spatial scales. We structured this dashboard around the Pressure-State-Response-Benefit framework, selecting four indicators to measure pressure on biodiversity (deforestation rate), state of species (Red List Index), conservation response (protection of key biodiversity areas), and benefits to human populations (freshwater provision). Disaggregating global data, we present dashboard maps and graphics for the three regions surveyed and their component countries. These visualizations provide charts showing regional and national trends and lay the foundation for a web-enabled, interactive biodiversity indicators dashboard. This new tool can help track progress toward the Aichi Targets, support national monitoring and reporting, and inform outcome-based policy-making for the

  7. Funding begets biodiversity

    DEFF Research Database (Denmark)

    Ahrends, Antje; Burgess, Neil David; Gereau, Roy E.

    2011-01-01

    . Location Eastern Arc Mountains, Tanzania. Methods We analysed time series data (1980–2007) of funding (n = 134 projects) and plant species records (n = 75,631) from a newly compiled database. Perceived plant diversity, over three decades, is regressed against funding and environmental factors......, and variances decomposed in partial regressions. Cross-correlations are used to assess whether perceived biodiversity drives funding or vice versa. Results Funding explained 65% of variation in perceived biodiversity patterns – six times more variation than accounted for by 34 candidate environmental factors...... facilitating further research that results in more species discoveries. Here, we test whether there is circularity between funding and perceived biodiversity, which may reinforce the conservation status of areas already perceived to be important while other areas with less initial funding may remain overlooked...

  8. Loss of soil microbial diversity may increase insecticide uptake by crop

    Science.gov (United States)

    Belowground biodiversity is essential for soil functioning, but the effect of belowground biodiversity loss on food safety is unknown. We investigated the loss of soil microbial diversity on insecticides accumulation in Brassica. We manipulated soil biodiversity using the dilution-to-extinction appr...

  9. Biodiversity and productivity

    Science.gov (United States)

    M.R. Willig

    2011-01-01

    Researchers predict that human activities especially landscape modification and climate change will have a considerable impact on the distribution and abundance of species at local, regional, and global scales in the 21st century ( 1, 2). This is a concern for a number of reasons, including the potential loss of goods and services that biodiversity provides to people...

  10. When Leeches reveal Biodiversity

    DEFF Research Database (Denmark)

    Schnell, Ida Bærholm

    to provide information about vertebrate biodiversity. This thesis covers the development of a monitoring method based on iDNA extracted from terrestrial haematophagous leeches, a continuation of the work presented in Schnell et al., 2012. The chapters investigate and/or discuss different subjects regarding...

  11. Resolving the biodiversity paradox

    Science.gov (United States)

    James S. Clark; Mike Dieta; Sukhendu Chakraborty; Pankaj K.Ibeanez Agarwal; Shannon LaDeau; Mike Wolosin

    2007-01-01

    The paradox of biodiversity involves three elements, (i) mathematical models predict that species must differ in specific ways in order to coexist as stable ecological communities, (ii) such differences are difficult to identify, yet (iii) there is widespread evidence of stability in natural communities.

  12. The Biodiversity Informatics Potential Index

    OpenAIRE

    Ariño Arturo H; Chavan Vishwas; King Nick

    2011-01-01

    Abstract Background Biodiversity informatics is a relatively new discipline extending computer science in the context of biodiversity data, and its development to date has not been uniform throughout the world. Digitizing effort and capacity building are costly, and ways should be found to prioritize them rationally. The proposed 'Biodiversity Informatics Potential (BIP) Index' seeks to fulfill such a prioritization role. We propose that the potential for biodiversity informatics be assessed ...

  13. Caribbean landscapes and their biodiversity

    Science.gov (United States)

    A. E. Lugo; E. H. Helmer; E. Santiago Valentín

    2012-01-01

    Both the biodiversity and the landscapes of the Caribbean have been greatly modified as a consequence of human activity. In this essay we provide an overview of the natural landscapes and biodiversity of the Caribbean and discuss how human activity has affected both. Our Caribbean geographic focus is on the insular Caribbean and the biodiversity focus is on the flora,...

  14. Mining Hot Springs for Biodiversity and Novel Enzymes

    DEFF Research Database (Denmark)

    Islin, Sóley Ruth

    The existence of microbial life at extreme environments, such as hot springs, has been known for a few decades. The remarkable ability of microorganisms to withstand the extreme conditions of their habitats, has astounded scientist and pushed the limits of what was considered possible. Thermophilic...... the biodiversity within the environment. By comparing several metagenomic data sets from hot spring from around the world, we could analyze community structures of cellular microorganisms as well as the biodiversity of viral sequences. We found that crenarchaeal viruses are dominant in these environments...

  15. Biodiversity enhances reef fish biomass and resistance to climate change.

    Science.gov (United States)

    Duffy, J Emmett; Lefcheck, Jonathan S; Stuart-Smith, Rick D; Navarrete, Sergio A; Edgar, Graham J

    2016-05-31

    Fishes are the most diverse group of vertebrates, play key functional roles in aquatic ecosystems, and provide protein for a billion people, especially in the developing world. Those functions are compromised by mounting pressures on marine biodiversity and ecosystems. Because of its economic and food value, fish biomass production provides an unusually direct link from biodiversity to critical ecosystem services. We used the Reef Life Survey's global database of 4,556 standardized fish surveys to test the importance of biodiversity to fish production relative to 25 environmental drivers. Temperature, biodiversity, and human influence together explained 47% of the global variation in reef fish biomass among sites. Fish species richness and functional diversity were among the strongest predictors of fish biomass, particularly for the large-bodied species and carnivores preferred by fishers, and these biodiversity effects were robust to potentially confounding influences of sample abundance, scale, and environmental correlations. Warmer temperatures increased biomass directly, presumably by raising metabolism, and indirectly by increasing diversity, whereas temperature variability reduced biomass. Importantly, diversity and climate interact, with biomass of diverse communities less affected by rising and variable temperatures than species-poor communities. Biodiversity thus buffers global fish biomass from climate change, and conservation of marine biodiversity can stabilize fish production in a changing ocean.

  16. Engaging the public in biodiversity issues

    OpenAIRE

    Novacek, Michael J.

    2008-01-01

    To engage people in biodiversity and other environmental issues, one must provide the opportunity for enhanced understanding that empowers individuals to make choices and take action based on sound science and reliable recommendations. To this end, we must acknowledge some real challenges. Recent surveys show that, despite growing public concern, environmental issues still rank below many other problems, such as terrorism, health care, the economy, and (in the U.S.) family values. Moreover, m...

  17. The rich and the poor: environmental biodiversity protecting from allergy.

    Science.gov (United States)

    Ruokolainen, Lasse; Fyhrquist, Nanna; Haahtela, Tari

    2016-10-01

    It has been proposed that biodiversity loss leads to reduced interaction between environmental and human microbiotas. This, in turn, may lead to immune dysfunction and impaired tolerance mechanisms in humans. That is, contact with environmental biodiversity is expected to protect from allergies. However, direct evidence linking contact with biodiversity and risk of allergy has been lacking. In this review, we consider the latest research on the biodiversity hypothesis of allergy. It is becoming clear that what you eat, drink, inhale, and touch all contribute to the grand scheme of host-microbial crosstalk that is needed for a balanced, healthy immune system to develop and maintain a healthy recognition between harmful and harmless invasions. Microbes can either communicate directly with host immune cells or affect the host via metabolism that can even lead to epigenetic modifications. Our living environment plays a key role in this process. Although especially, early exposure to diverse, beneficial microbiota from the environment is repeatedly found crucial, studies on immigrants demonstrate that condition in later life can also be decisive. We are still lacking a more detailed understanding of the interaction between natural, environmental biodiversity, and health, which calls for new innovative and more long-term investigations. The outcomes should be utilized in policy and urban planning efforts, promoting human interaction with natural biodiversity, and supporting a healthy lifestyle.

  18. An End-to-End DNA Taxonomy Methodology for Benthic Biodiversity Survey in the Clarion-Clipperton Zone, Central Pacific Abyss

    Directory of Open Access Journals (Sweden)

    Adrian G. Glover

    2015-12-01

    Full Text Available Recent years have seen increased survey and sampling expeditions to the Clarion-Clipperton Zone (CCZ, central Pacific Ocean abyss, driven by commercial interests from contractors in the potential extraction of polymetallic nodules in the region. Part of the International Seabed Authority (ISA regulatory requirements are that these contractors undertake environmental research expeditions to their CCZ exploration claims following guidelines approved by the ISA Legal and Technical Commission (ISA, 2010. Section 9 (e of these guidelines instructs contractors to “…collect data on the sea floor communities specifically relating to megafauna, macrofauna, meiofauna, microfauna, nodule fauna and demersal scavengers”. There are a number of methodological challenges to this, including the water depth (4000–5000 m, extremely warm surface waters (~28 °C compared to bottom water (~1.5 °C and great distances to ports requiring a large and long seagoing expedition with only a limited number of scientists. Both scientists and regulators have recently realized that a major gap in our knowledge of the region is the fundamental taxonomy of the animals that live there; this is essential to inform our knowledge of the biogeography, natural history and ultimately our stewardship of the region. Recognising this, the ISA is currently sponsoring a series of taxonomic workshops on the CCZ fauna and to assist in this process we present here a series of methodological pipelines for DNA taxonomy (incorporating both molecular and morphological data of the macrofauna and megafauna from the CCZ benthic habitat in the recent ABYSSLINE cruise program to the UK-1 exploration claim. A major problem on recent CCZ cruises has been the collection of high-quality samples suitable for both morphology and DNA taxonomy, coupled with a workflow that ensures these data are made available. The DNA sequencing techniques themselves are relatively standard, once good samples have been

  19. Evaluation of microbial diversity of the microbial mat from the extremely acidic Lake Robule (Bor, Serbia)

    OpenAIRE

    Stanković Srđan; Vasiljević Branka; Jeremić Sanja; Cvetković Vladica; Morić Ivana

    2017-01-01

    Extremely acidic environments are frequently formed in areas impacted by mining activities, and Lake Robule is such an ecosystem. Although an extreme environment, Lake Robule is inhabited by acidophilic microorganisms. We investigated biodiversity of the macroscopic structure known as a microbial mat formed on the lake bottom in shallow waters. Microbial mats are common in acidic environments, but their composition can differ significantly from site to site. Microbial diversity of the mat fro...

  20. Optimal fire histories for biodiversity conservation.

    Science.gov (United States)

    Kelly, Luke T; Bennett, Andrew F; Clarke, Michael F; McCarthy, Michael A

    2015-04-01

    Fire is used as a management tool for biodiversity conservation worldwide. A common objective is to avoid population extinctions due to inappropriate fire regimes. However, in many ecosystems, it is unclear what mix of fire histories will achieve this goal. We determined the optimal fire history of a given area for biological conservation with a method that links tools from 3 fields of research: species distribution modeling, composite indices of biodiversity, and decision science. We based our case study on extensive field surveys of birds, reptiles, and mammals in fire-prone semi-arid Australia. First, we developed statistical models of species' responses to fire history. Second, we determined the optimal allocation of successional states in a given area, based on the geometric mean of species relative abundance. Finally, we showed how conservation targets based on this index can be incorporated into a decision-making framework for fire management. Pyrodiversity per se did not necessarily promote vertebrate biodiversity. Maximizing pyrodiversity by having an even allocation of successional states did not maximize the geometric mean abundance of bird species. Older vegetation was disproportionately important for the conservation of birds, reptiles, and small mammals. Because our method defines fire management objectives based on the habitat requirements of multiple species in the community, it could be used widely to maximize biodiversity in fire-prone ecosystems. © 2014 Society for Conservation Biology.

  1. Beyond biodiversity: fish metagenomes.

    Directory of Open Access Journals (Sweden)

    Alba Ardura

    Full Text Available Biodiversity and intra-specific genetic diversity are interrelated and determine the potential of a community to survive and evolve. Both are considered together in Prokaryote communities treated as metagenomes or ensembles of functional variants beyond species limits.Many factors alter biodiversity in higher Eukaryote communities, and human exploitation can be one of the most important for some groups of plants and animals. For example, fisheries can modify both biodiversity and genetic diversity (intra specific. Intra-specific diversity can be drastically altered by overfishing. Intense fishing pressure on one stock may imply extinction of some genetic variants and subsequent loss of intra-specific diversity. The objective of this study was to apply a metagenome approach to fish communities and explore its value for rapid evaluation of biodiversity and genetic diversity at community level. Here we have applied the metagenome approach employing the barcoding target gene coi as a model sequence in catch from four very different fish assemblages exploited by fisheries: freshwater communities from the Amazon River and northern Spanish rivers, and marine communities from the Cantabric and Mediterranean seas.Treating all sequences obtained from each regional catch as a biological unit (exploited community we found that metagenomic diversity indices of the Amazonian catch sample here examined were lower than expected. Reduced diversity could be explained, at least partially, by overexploitation of the fish community that had been independently estimated by other methods.We propose using a metagenome approach for estimating diversity in Eukaryote communities and early evaluating genetic variation losses at multi-species level.

  2. Defining biodiversity resources

    OpenAIRE

    Gadgil, Madhav

    2000-01-01

    The scope of the Biological Diversity Bill, tabled in the monsoon 2000 session of the Indian Parliament is excessively wide covering all biological resources. Instead it should focus on diversity related end-uses such as drugs, industrial enzymes, cosmetics, dyestuffs, plant growth regulators, emulsifiers, oleoresins and genes used for improving crops and livestock through breeding and genetic intervention. It should seek to regulate collection and movement of such biodiversity resources and ...

  3. The value of biodiversity

    Directory of Open Access Journals (Sweden)

    CJR. Alho

    Full Text Available In addition to its intrinsic value (nature working as it is; species are the product of a long history of continuing evolution by means of ecological processes, and so they have the right to continued existence, biodiversity also plays a fundamental role as ecosystem services in the maintenance of natural ecological processes. The economic or utilitarian values of biodiversity rely upon the dependence of man on biodiversity; products that nature can provide: wood, food, fibers to make paper, resins, chemical organic products, genes as well as knowledge for biotechnology, including medicine and cosmetic sub-products. It also encompasses ecosystem services, such as climate regulation, reproductive and feeding habitats for commercial fish, some organisms that can create soil fertility through complex cycles and interactions, such as earthworms, termites and bacteria, in addition to fungi responsible for cycling nutrients like nitrogen, phosphorus and sulfur and making them available to plant absorption. These services are the benefits that people indirectly receive from natural ecosystem functions (air quality maintenance, regional climate, water quality, nutrient cycling, reproductive habitats of commercial fish, etc. with their related economic values.

  4. Biodiversity, globalisation and poverty.

    Science.gov (United States)

    Olorode, Omotoye

    2007-06-10

    The erosion of the stock of biodiversity on earth developed historically with the so-called voyages of discovery (and their antecedents), colonial conquests and the accompanying movements of natural products and peoples, i.e. movements of populations and genetic materials. These events happened with the development of technology and the so-called conquest, by man, of his environment and the appertaining development of specialization not only in industry but also in agriculture and environmental management. The development of specialization resulted in the homogenization of processes, products, inputs and input industries; this increased homogenization had the corollary of arrested heterogeneity across the board; what they call globalization is part of this process. The efficiency of homogenization, however, engendered new problems of fragility of human environment and of production and social relations and processes. The effects of this complex situation, in general terms and in terms of biodiversity in particular, have been more devastating for the more vulnerable regions, classes of people, and peoples of the world. A continuous rethinking of the epistemology and the social and political bases of existing policies on environment in general, and of biodiversity conservation in particular, has become imperative.

  5. The vintage effect overcomes the terroir effect: a three year survey on the wine yeast biodiversity in Franciacorta and Oltrepò Pavese, two northern Italian vine-growing areas.

    Science.gov (United States)

    Vigentini, Ileana; De Lorenzis, Gabriella; Fabrizio, Vincenzo; Valdetara, Federica; Faccincani, Monica; Panont, Carlo Alberto; Picozzi, Claudia; Imazio, Serena; Failla, Osvaldo; Foschino, Roberto

    2015-02-01

    A three year survey on the dominant yeast populations in samples of air, must and wine in different vineyards and cellars of two northern Italian vine-growing territories (six sites in Franciacorta and eight sites in Oltrepò Pavese areas) was carried out. A total of 505 isolates were ascribed to 31 different species by RFLP analysis of the ITS1-5.8SrRNA-ITS2 region and partial sequence analysis of the 26S rRNA gene. The most commonly found species were Saccharomyces cerevisiae (frequency, F' = 58.7%; incidence, I' = 53.5%), Hanseniaspora uvarum (F' = 14.3%; I' = 5.3%), Metschnikowia fructicola (F' = 11.1%; I' = 5.0%) and Torulaspora delbrueckii (F' = 10.3%; I' = 3.8%). Among 270 S. cerevisiae new isolates, 156 (57.8%) revealed a different genetic pattern through polymorphism analysis of the interdelta regions by capillary electrophoresis, while 47 isolates (17.4 %) were clones of starter cultures. By considering the Shannon-Wiener index and results of principal component analysis (PCA) analyses, the year of isolation (vintage) proved to be a factor that significantly affected the biodiversity of the yeast species, whereas the geographical site (terroir) was not. Seventy-five per cent of S. cerevisiae isolates gathered in a unique cluster at a similarity level of 82%, while the remaining 25% were separated into minor groups without any evident relationship between δ-PCR profile and territory, year or source of isolation. However, in six cases a similar strain appeared at the harvesting time both in Franciacorta and Oltrepò Pavese areas, whereas surprisingly no strain was reisolated in the same vineyard or cellar for consecutive years. © 2015 The Authors.

  6. Agricultural Informatics Contributions to Biodiversity Science and Biodiversity Assessments

    OpenAIRE

    Kampmeier,Gail; Parr, Cynthia; Macklin, James

    2017-01-01

    Agricultural biodiversity has long been ignored by the traditional biodiversity community and the aggregators of their data. The Arnaud et al. (2016) GBIF "Final Report of the Task Group on GBIF Data Fitness for Use in Agrobiodiversity," provided recommendations primarily regarding crops and their wild relatives, but did not address wider issues of crop pests (plant diseases and their vectors, arthropods) and management systems that affect the greater biodiversity of those crops. The Biodiver...

  7. Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing.

    Science.gov (United States)

    Mhuantong, Wuttichai; Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Eurwilaichitr, Lily; Tangphatsornruang, Sithichoke; Boonchayaanant, Benjaporn; Limpiyakorn, Tawan; Pattaragulwanit, Kobchai; Punmatharith, Thantip; McEvoy, John; Khan, Eakalak; Rachakornkij, Manaskorn; Champreda, Verawat

    2015-01-01

    The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas.

  8. Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Wuttichai Mhuantong

    Full Text Available The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas.

  9. Backbones of evolutionary history test biodiversity theory for microbes.

    Science.gov (United States)

    O'Dwyer, James P; Kembel, Steven W; Sharpton, Thomas J

    2015-07-07

    Identifying the ecological and evolutionary mechanisms that determine biological diversity is a central question in ecology. In microbial ecology, phylogenetic diversity is an increasingly common and relevant means of quantifying community diversity, particularly given the challenges in defining unambiguous species units from environmental sequence data. We explore patterns of phylogenetic diversity across multiple bacterial communities drawn from different habitats and compare these data to evolutionary trees generated using theoretical models of biodiversity. We have two central findings. First, although on finer scales the empirical trees are highly idiosyncratic, on coarse scales the backbone of these trees is simple and robust, consistent across habitats, and displays bursts of diversification dotted throughout. Second, we find that these data demonstrate a clear departure from the predictions of standard neutral theories of biodiversity and that an alternative family of generalized models provides a qualitatively better description. Together, these results lay the groundwork for a theoretical framework to connect ecological mechanisms to observed phylogenetic patterns in microbial communities.

  10. Towards understanding, managing and protecting microbial ecosystems

    Directory of Open Access Journals (Sweden)

    Paul eBodelier

    2011-04-01

    Full Text Available Microbial communities are at the very basis of life on earth, catalysing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper indentifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology.

  11. Toward understanding, managing, and protecting microbial ecosystems.

    Science.gov (United States)

    Bodelier, Paul L E

    2011-01-01

    Microbial communities are at the very basis of life on earth, catalyzing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity-conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper identifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology.

  12. Predicting the responsiveness of soil biodiversity to deforestation: a cross-biome study.

    Science.gov (United States)

    Crowther, Thomas W; Maynard, Daniel S; Leff, Jonathan W; Oldfield, Emily E; McCulley, Rebecca L; Fierer, Noah; Bradford, Mark A

    2014-09-01

    The consequences of deforestation for aboveground biodiversity have been a scientific and political concern for decades. In contrast, despite being a dominant component of biodiversity that is essential to the functioning of ecosystems, the responses of belowground biodiversity to forest removal have received less attention. Single-site studies suggest that soil microbes can be highly responsive to forest removal, but responses are highly variable, with negligible effects in some regions. Using high throughput sequencing, we characterize the effects of deforestation on microbial communities across multiple biomes and explore what determines the vulnerability of microbial communities to this vegetative change. We reveal consistent directional trends in the microbial community response, yet the magnitude of this vegetation effect varied between sites, and was explained strongly by soil texture. In sandy sites, the difference in vegetation type caused shifts in a suite of edaphic characteristics, driving substantial differences in microbial community composition. In contrast, fine-textured soil buffered microbes against these effects and there were minimal differences between communities in forest and grassland soil. These microbial community changes were associated with distinct changes in the microbial catabolic profile, placing community changes in an ecosystem functioning context. The universal nature of these patterns allows us to predict where deforestation will have the strongest effects on soil biodiversity, and how these effects could be mitigated. © 2014 John Wiley & Sons Ltd.

  13. Targeted Metagenomic Survey of the Fe-Cycling Microbial Community at Chocolate Pots Hot Springs, Yellowstone National Park

    Science.gov (United States)

    Fortney, N. W.; He, S.; Kulkarni, A.; Friedrich, M. W.; Boyd, E. S.; Roden, E. E.

    2016-12-01

    Chocolate Pots hot springs (CP) is a circumneutral pH, Fe-rich geothermal feature located in Yellowstone National Park. Fe-based metabolic processes are deeply rooted in the tree of life and studying environments like CP are important for us to study to gain insight into ancient Earth ecosystems. Recently identified features on Mars are indicative of near-surface hydrothermal environments and studies of modern Earth systems like CP allow us a glimpse into how life may have potentially arisen on other rocky worlds. Previous enrichment culture studies of the microbial community present at CP identified close relatives of dissimilatory Fe-reducing bacteria (DIRB), including Geobacter metallireducens and Melioribacter roseus. However, the question still remains as to the composition and activity of the microbial community in situ. Here we used 13C stable isotope probing to gain an understanding of the Fe cycling microbial community at CP. Fe-Si oxide sediments collected from near the hot spring vent were incubated under in situ conditions and amended with 13C-acetate or -bicarbonate to target DIRB and Fe-oxidizing bacteria, respectively. 16S rRNA gene amplicon libraries along with shotgun metagenomic libraries were obtained from both sets of incubations. Differential read coverage mapping of metagenomic reads identified a set of taxonomic bins that showed a response to the incubation treatments. We searched the Fe-reducing incubation bins for homologues of genes involved in known extracellular electron transfer (EET) systems such as Pcc and MtrAB, as well as putative porins proximal to multiheme cytochrome c genes. We also searched bins from the Fe-oxidizing incubations for these EET systems in addition to homologues of the outer membrane cytochrome c Cyc2. The Fe-oxidizing bins were also examined for genes encoding RuBisCo to identify potential chemolithoautotrophs. Our targeted metagenomic analysis will identify which organisms are likely to be part of an active Fe

  14. Soil biodiversity and human health

    Science.gov (United States)

    Wall, Diana H.; Nielsen, Uffe N.; Six, Johan

    2015-12-01

    Soil biodiversity is increasingly recognized as providing benefits to human health because it can suppress disease-causing soil organisms and provide clean air, water and food. Poor land-management practices and environmental change are, however, affecting belowground communities globally, and the resulting declines in soil biodiversity reduce and impair these benefits. Importantly, current research indicates that soil biodiversity can be maintained and partially restored if managed sustainably. Promoting the ecological complexity and robustness of soil biodiversity through improved management practices represents an underutilized resource with the ability to improve human health.

  15. Millennium Ecosystem Assessment: MA Biodiversity

    Data.gov (United States)

    National Aeronautics and Space Administration — The Millennium Ecosystem Assessment: MA Biodiversity provides data and information on amphibians, disease agents (extent and distribution of infectious and parasitic...

  16. Protistan Diversity in the Arctic: A Case of Paleoclimate Shaping Modern Biodiversity?

    OpenAIRE

    Stoeck, Thorsten; Kasper, Jennifer; Bunge, John; Leslin, Chesley; Ilyin, Valya; Epstein, Slava

    2007-01-01

    BACKGROUND: The impact of climate on biodiversity is indisputable. Climate changes over geological time must have significantly influenced the evolution of biodiversity, ultimately leading to its present pattern. Here we consider the paleoclimate data record, inferring that present-day hot and cold environments should contain, respectively, the largest and the smallest diversity of ancestral lineages of microbial eukaryotes. METHODOLOGY/PRINCIPAL FINDINGS: We investigate this hypothesis by an...

  17. Net present biodiversity value and the design of biodiversity offsets.

    Science.gov (United States)

    Overton, Jacob McC; Stephens, R T Theo; Ferrier, Simon

    2013-02-01

    There is an urgent need to develop sound theory and practice for biodiversity offsets to provide a better basis for offset multipliers, to improve accounting for time delays in offset repayments, and to develop a common framework for evaluating in-kind and out-of-kind offsets. Here, we apply concepts and measures from systematic conservation planning and financial accounting to provide a basis for determining equity across type (of biodiversity), space, and time. We introduce net present biodiversity value (NPBV) as a theoretical and practical measure for defining the offset required to achieve no-net-loss. For evaluating equity in type and space we use measures of biodiversity value from systematic conservation planning. Time discount rates are used to address risk of non-repayment, and loss of utility. We illustrate these concepts and measures with two examples of biodiversity impact-offset transactions. Considerable further work is required to understand the characteristics of these approaches.

  18. Linking soil biodiversity and agricultural soil management

    NARCIS (Netherlands)

    Thiele-Bruhn, S.; Bloem, J.; de Vries, F.T.; Kalbitz, K.; Wagg, C.

    2012-01-01

    Soil biodiversity vastly exceeds aboveground biodiversity, and is prerequisite for ecosystem stability and services. This review presents recent findings in soil biodiversity research focused on interrelations with agricultural soil management. Richness and community structure of soil biota depend

  19. Belowground biodiversity and ecosystem functioning

    NARCIS (Netherlands)

    Bardgett, R.D.; van der Putten, W.H.

    2014-01-01

    Belowground biodiversity is largely out of sight and mind, but there is mounting evidence to show that the vast diversity of subterranean microorganisms and animals that live belowground contribute significantly to shaping the overall biodiversity and and terrestrial ecosystem function. In this

  20. Place prioritization for biodiversity content

    Indian Academy of Sciences (India)

    The prioritization of places on the basis of biodiversity content is part of any systematic biodiversity conservation planning process. The place prioritization procedure implemented in the ResNet software package is described. This procedure is primarily based on the principles of rarity and complementarity. Application of the ...

  1. Soil biodiversity for agricultural sustainability

    NARCIS (Netherlands)

    Brussaard, L.; Ruiter, de P.C.; Brown, G.G.

    2007-01-01

    We critically highlight some evidence for the importance of soil biodiversity to sustaining (agro-)ecosystem functioning and explore directions for future research. We first deal with resistance and resilience against abiotic disturbance and stress. There is evidence that soil biodiversity does

  2. Operationalizing biodiversity for conservation planning

    Indian Academy of Sciences (India)

    The relative concept of biodiversity built into the definition of complementarity has the level of precision needed to undertake conservation planning. ... Biodiversity and Biocultural Conservation Laboratory, Program in the History and Philosophy of Science and the Department of Philosophy, University of Texas at Austin, ...

  3. Biodiversity: Who Knows, Who Cares?

    Science.gov (United States)

    Zemits, Birut

    2006-01-01

    Biodiversity is an abstract concept, attracting various responses from different people according to where they have come from and what ecosystems they have been closely linked to. In theory, most people would agree that protecting biodiversity is an important process, but in practice, few people commit to actions on a local level. This paper…

  4. Temporal variability of available P, microbial P and some ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-12-15

    Dec 15, 2009 ... phytase activities decreased continuously, but microbial P, alkaline and acid phosphatase activities fluctuated during incubation. ... Key words: Soil water potential, available P, microbial P, phosphomonoesterase, incubation. ...... biodiversity of cultivated and uncultivated a horizons of vertisols in. NW New ...

  5. Phylogenic inference using alignment-free methods for applications in microbial community surveys using 16s rRNA gene.

    Directory of Open Access Journals (Sweden)

    Yifei Zhang

    Full Text Available The diversity of microbiota is best explored by understanding the phylogenetic structure of the microbial communities. Traditionally, sequence alignment has been used for phylogenetic inference. However, alignment-based approaches come with significant challenges and limitations when massive amounts of data are analyzed. In the recent decade, alignment-free approaches have enabled genome-scale phylogenetic inference. Here we evaluate three alignment-free methods: ACS, CVTree, and Kr for phylogenetic inference with 16s rRNA gene data. We use a taxonomic gold standard to compare the accuracy of alignment-free phylogenetic inference with that of common microbiome-wide phylogenetic inference pipelines based on PyNAST and MUSCLE alignments with FastTree and RAxML. We re-simulate fecal communities from Human Microbiome Project data to evaluate the performance of the methods on datasets with properties of real data. Our comparisons show that alignment-free methods are not inferior to alignment-based methods in giving accurate and robust phylogenic trees. Moreover, consensus ensembles of alignment-free phylogenies are superior to those built from alignment-based methods in their ability to highlight community differences in low power settings. In addition, the overall running times of alignment-based and alignment-free phylogenetic inference are comparable. Taken together our empirical results suggest that alignment-free methods provide a viable approach for microbiome-wide phylogenetic inference.

  6. Microbial metropolis.

    Science.gov (United States)

    Wimpenny, Julian

    2009-01-01

    Microorganisms can form tightly knit communities such as biofilms. Many others include marine snow, anaerobic digester granules, the ginger beer plant and bacterial colonies. This chapter is devoted to a survey of the main properties of these communities, with an emphasis on biofilms. We start with attachment to surfaces and the nature of adhesion. The growing community then forms within a matrix, generally of organic macromolecules. Inevitably the environment within such a matrix is different from that outside. Organisms respond by forming crowd-detection and response units; these quorum sensing systems act as switches between planktonic life and the dramatically altered conditions found inside microbial aggregates. The community then matures and changes and may even fail and disappear. Antimicrobial resistance is discussed as an example of multicellular behavior. The multicellular lifestyle has been modeled mathematically and responded to powerful molecular biological techniques. Latterly, microbial systems have been used as models for fundamental evolutionary processes, mostly because of their high rates of reproduction and the ease of genetic manipulation. The life of most microbes is a duality between the yin of the community and the yang of planktonic existence. Sadly far less research has been devoted to adaptation to free-living forms than in the opposite direction. Copyright © 2009 Elsevier Ltd. All rights reserved.

  7. Genomic Approaches in Marine Biodiversity and Aquaculture

    Directory of Open Access Journals (Sweden)

    Jorge A Huete-Pérez

    2013-01-01

    Full Text Available Recent advances in genomic and post-genomic technologies have now established the new standard in medical and biotechnological research. The introduction of next-generation sequencing, NGS,has resulted in the generation of thousands of genomes from all domains of life, including the genomes of complex uncultured microbial communities revealed through metagenomics. Although the application of genomics to marine biodiversity remains poorly developed overall, some noteworthy progress has been made in recent years. The genomes of various model marine organisms have been published and a few more are underway. In addition, the recent large-scale analysis of marine microbes, along with transcriptomic and proteomic approaches to the study of teleost fishes, mollusks and crustaceans, to mention a few, has provided a better understanding of phenotypic variability and functional genomics. The past few years have also seen advances in applications relevant to marine aquaculture and fisheries. In this review we introduce several examples of recent discoveries and progress made towards engendering genomic resources aimed at enhancing our understanding of marine biodiversity and promoting the development of aquaculture. Finally, we discuss the need for auspicious science policies to address challenges confronting smaller nations in the appropriate oversight of this growing domain as they strive to guarantee food security and conservation of their natural resources.

  8. Fungal Biodiversity in the Alpine Tarfala Valley.

    Science.gov (United States)

    Coleine, Claudia; Selbmann, Laura; Ventura, Stefano; D'Acqui, Luigi Paolo; Onofri, Silvano; Zucconi, Laura

    2015-10-10

    Biological soil crusts (BSCs) are distributed worldwide in all semiarid and arid lands, where they play a determinant role in element cycling and soil development. Although much work has concentrated on BSC microbial communities, free-living fungi have been hitherto largely overlooked. The aim of this study was to examine the fungal biodiversity, by cultural-dependent and cultural-independent approaches, in thirteen samples of Arctic BSCs collected at different sites in the Alpine Tarfala Valley, located on the slopes of Kebnekaise, the highest mountain in northern Scandinavia. Isolated fungi were identified by both microscopic observation and molecular approaches. Data revealed that the fungal assemblage composition was homogeneous among the BSCs analyzed, with low biodiversity and the presence of a few dominant species; the majority of fungi isolated belonged to the Ascomycota, and Cryptococcus gilvescens and Pezoloma ericae were the most frequently-recorded species. Ecological considerations for the species involved and the implication of our findings for future fungal research in BSCs are put forward.

  9. Fungal Biodiversity in the Alpine Tarfala Valley

    Directory of Open Access Journals (Sweden)

    Claudia Coleine

    2015-10-01

    Full Text Available Biological soil crusts (BSCs are distributed worldwide in all semiarid and arid lands, where they play a determinant role in element cycling and soil development. Although much work has concentrated on BSC microbial communities, free-living fungi have been hitherto largely overlooked. The aim of this study was to examine the fungal biodiversity, by cultural-dependent and cultural-independent approaches, in thirteen samples of Arctic BSCs collected at different sites in the Alpine Tarfala Valley, located on the slopes of Kebnekaise, the highest mountain in northern Scandinavia. Isolated fungi were identified by both microscopic observation and molecular approaches. Data revealed that the fungal assemblage composition was homogeneous among the BSCs analyzed, with low biodiversity and the presence of a few dominant species; the majority of fungi isolated belonged to the Ascomycota, and Cryptococcus gilvescens and Pezoloma ericae were the most frequently-recorded species. Ecological considerations for the species involved and the implication of our findings for future fungal research in BSCs are put forward.

  10. HYDROLOGY AND BIODIVERSITY

    OpenAIRE

    OSUJI, CORNELIUS I.

    2014-01-01

    Temperature is the main controller of in-stream progression when it relates to metabolism of plants and animals, microbial decomposition of organic matter, solubility of air and water exchange of gases (Thyssen, 1987). However there are so many factors that could bring about low and high stream temperatures that lead to significant ecological variation in running waters. The major drivers as observed from the experiments conducted reveals that as water travels downstream, the temperature i...

  11. Engaging the public in biodiversity issues

    Science.gov (United States)

    Novacek, Michael J.

    2008-01-01

    To engage people in biodiversity and other environmental issues, one must provide the opportunity for enhanced understanding that empowers individuals to make choices and take action based on sound science and reliable recommendations. To this end, we must acknowledge some real challenges. Recent surveys show that, despite growing public concern, environmental issues still rank below many other problems, such as terrorism, health care, the economy, and (in the U.S.) family values. Moreover, much of the recent upswing in interest in the environment is due to the marked shift in attention to global warming away from other environmental problems such as destruction of ecosystems, water pollution, overpopulation, and biodiversity loss. Such a change in public focus often comes with a tendency to decouple various environmental problems and ignore their synergistic effects. Exacerbating this problem are arguments from the media and other sources that discourage public interest in environmental topics by characterizing the science behind them as overly complex, immersed in debate and controversy, and detached from human interests. Educational programming, media, exhibitions, and other means of public outreach should build on the welcome increase in public interest in global warming by demonstrating the interplay of various environmental disruptions. In the case of biodiversity, the importance of species in providing ecosystem services, natural beauty and pleasure, and sustaining human lives is a message that requires constant attention and recrafting to impact diverse audiences. PMID:18695244

  12. Ciliate communities and hidden biodiversity in freshwater biotopes of the Pistoia province (Tuscany, Italy).

    Science.gov (United States)

    Rossi, Alessia; Boscaro, Vittorio; Carducci, Daniela; Serra, Valentina; Modeo, Letizia; Verni, Franco; Fokin, Sergei I; Petroni, Giulio

    2016-04-01

    Ciliates are essential components of aquatic environments, playing a pivotal role in microbial loops. Thus, the composition and dynamics of ciliate communities have been subjected to intense studying. Morphological methods have been traditionally employed, until the development of next-generation sequencing recently allowed to explore the topic with exclusively molecular techniques. However, the results of the two approaches are hardly comparable, and the pictures they offer can be quite different. This may be due, among other reasons, to two factors: (1) morphological descriptions may miss a large portion of "hidden biodiversity" (including rare species and resistance forms) that is detected instead by molecular methods; (2) identification errors may arise due to difficulties in recognizing microbial taxa without in-depth analyses. In this survey of freshwater systems of the Pistoia province (Tuscany, Italy) we address both issues, trying to quantify the hidden diversity through prolonged observations of differentially treated sample aliquots, combining morphological identification with Sanger sequencing. We provide the first insights into the ciliate fauna of this area presenting results that are suitable for future comparisons thanks to their multidisciplinary origin, and supply the first molecular data on well-known taxa such as Linostomella and Disematostoma. Copyright © 2015 Elsevier GmbH. All rights reserved.

  13. Biodiversity in Benthic Ecology

    DEFF Research Database (Denmark)

    Friberg, Nikolai; Carl, J. D.

    Foreword: This proceeding is based on a set of papers presented at the second Nordic Benthological Meeting held in Silkeborg, November 13-14, 1997. The main theme of the meeting was biodiversity in benthic ecology and the majority of contributions touch on this subject. In addition, the proceeding...... contains papers which cover other themes thus continuing with the spirit of the meetings in the Nordic Benthological Society (NORBS) by being an open forum for exchanging knowledge on all aspects of benthic ecology. Overall, we feel the proceeding contains a wide selection of very interesting papers...... representing the state-of-the-art of benthic ecology research within, and to a lesser degree, outside the Nordic countries. We wish to thank all the authors for their inspirational contributions to the proceeding, but we feel that a special thanks is due to the invited speakers for their readiness to produce...

  14. Status of Biodiversity and Its Conservation in the Kobadak River Basin of Maheshpur Upazila, Jhenaidah, Bangladesh

    Science.gov (United States)

    Uddin, Jashim Md.

    2015-01-01

    This research project represents the Status of Biodiversity and Its Conservation of Kobadak River basin of Maheshpur Upazila. The study was designed to develop a set of information about the present condition of biodiversity of the study area. Both primary and secondary data have been used to fulfill the survey successfully. Primary data have been…

  15. A comparison of proxy performance in coral biodiversity monitoring

    Science.gov (United States)

    Richards, Zoe T.

    2013-03-01

    The productivity and health of coral reef habitat is diminishing worldwide; however, the effect that habitat declines have on coral reef biodiversity is not known. Logistical and financial constraints mean that surveys of hard coral communities rarely collect data at the species level; hence it is important to know if there are proxy metrics that can reliably predict biodiversity. Here, the performances of six proxy metrics are compared using regression analyses on survey data from a location in the northern Great Barrier Reef. Results suggest generic richness is a strong explanatory variable for spatial patterns in species richness (explaining 82 % of the variation when measured on a belt transect). The most commonly used metric of reef health, percentage live coral cover, is not positively or linearly related to hard coral species richness. This result raises doubt as to whether management actions based on such reefscape information will be effective for the conservation of coral biodiversity.

  16. The Biodiversity Informatics Potential Index

    Science.gov (United States)

    2011-01-01

    Background Biodiversity informatics is a relatively new discipline extending computer science in the context of biodiversity data, and its development to date has not been uniform throughout the world. Digitizing effort and capacity building are costly, and ways should be found to prioritize them rationally. The proposed 'Biodiversity Informatics Potential (BIP) Index' seeks to fulfill such a prioritization role. We propose that the potential for biodiversity informatics be assessed through three concepts: (a) the intrinsic biodiversity potential (the biological richness or ecological diversity) of a country; (b) the capacity of the country to generate biodiversity data records; and (c) the availability of technical infrastructure in a country for managing and publishing such records. Methods Broadly, the techniques used to construct the BIP Index were rank correlation, multiple regression analysis, principal components analysis and optimization by linear programming. We built the BIP Index by finding a parsimonious set of country-level human, economic and environmental variables that best predicted the availability of primary biodiversity data accessible through the Global Biodiversity Information Facility (GBIF) network, and constructing an optimized model with these variables. The model was then applied to all countries for which sufficient data existed, to obtain a score for each country. Countries were ranked according to that score. Results Many of the current GBIF participants ranked highly in the BIP Index, although some of them seemed not to have realized their biodiversity informatics potential. The BIP Index attributed low ranking to most non-participant countries; however, a few of them scored highly, suggesting that these would be high-return new participants if encouraged to contribute towards the GBIF mission of free and open access to biodiversity data. Conclusions The BIP Index could potentially help in (a) identifying countries most likely to

  17. The Biodiversity Informatics Potential Index.

    Science.gov (United States)

    Ariño, Arturo H; Chavan, Vishwas; King, Nick

    2011-01-01

    Biodiversity informatics is a relatively new discipline extending computer science in the context of biodiversity data, and its development to date has not been uniform throughout the world. Digitizing effort and capacity building are costly, and ways should be found to prioritize them rationally. The proposed 'Biodiversity Informatics Potential (BIP) Index' seeks to fulfill such a prioritization role. We propose that the potential for biodiversity informatics be assessed through three concepts: (a) the intrinsic biodiversity potential (the biological richness or ecological diversity) of a country; (b) the capacity of the country to generate biodiversity data records; and (c) the availability of technical infrastructure in a country for managing and publishing such records. Broadly, the techniques used to construct the BIP Index were rank correlation, multiple regression analysis, principal components analysis and optimization by linear programming. We built the BIP Index by finding a parsimonious set of country-level human, economic and environmental variables that best predicted the availability of primary biodiversity data accessible through the Global Biodiversity Information Facility (GBIF) network, and constructing an optimized model with these variables. The model was then applied to all countries for which sufficient data existed, to obtain a score for each country. Countries were ranked according to that score. Many of the current GBIF participants ranked highly in the BIP Index, although some of them seemed not to have realized their biodiversity informatics potential. The BIP Index attributed low ranking to most nonparticipant countries; however, a few of them scored highly, suggesting that these would be high-return new participants if encouraged to contribute towards the GBIF mission of free and open access to biodiversity data. The BIP Index could potentially help in (a) identifying countries most likely to contribute to filling gaps in digitized

  18. Urban biodiversity: patterns and mechanisms.

    Science.gov (United States)

    Faeth, Stanley H; Bang, Christofer; Saari, Susanna

    2011-03-01

    The patterns of biodiversity changes in cities are now fairly well established, although diversity changes in temperate cities are much better studied than cities in other climate zones. Generally, plant species richness often increases in cities due to importation of exotic species, whereas animal species richness declines. Abundances of some groups, especially birds and arthropods, often increase in urban areas despite declines in species richness. Although several models have been proposed for biodiversity change, the processes underlying the patterns of biodiversity in cities are poorly understood. We argue that humans directly control plants but relatively few animals and microbes-the remaining biological community is determined by this plant "template" upon which natural ecological and evolutionary processes act. As a result, conserving or reconstructing natural habitats defined by vegetation within urban areas is no guarantee that other components of the biological community will follow suit. Understanding the human-controlled and natural processes that alter biodiversity is essential for conserving urban biodiversity. This urban biodiversity will comprise a growing fraction of the world's repository of biodiversity in the future. © 2011 New York Academy of Sciences.

  19. Indicators for Monitoring Soil Biodiversity

    DEFF Research Database (Denmark)

    Bispo, A.; Cluzeau, D.; Creamer, R.

    2009-01-01

    is made for a set of suitable indicators for monitoring the decline in soil biodiversity (Bispo et al. 2007). These indicators were selected both from a literature review and an inventory of national monitoring programmes. Decline in soil biodiversity was defined as the reduction of forms of life living...... indicators are actually measured.   For monitoring application it was considered in ENVASSO that only three key indicators per soil stress were practical. For indicating biodiversity decline it was difficult to arrive at a small set of indicators due to the complexity of soil biota and functions. Therefore...

  20. Biodiversity and ethnobotanical potentials of plant species of ...

    African Journals Online (AJOL)

    Plant biodiversity and ethnobotanical potentials of University of Agriculture Makurdi (UAM) Wildlife Park and Ikwe Games Reserve, Benue State, Nigeria, were investigated in this study. Floristic survey was conducted in the two reserves using stratified sampling technique based on the three identified microhabitats in each of ...

  1. Preliminary Assessment of Sponge Biodiversity on Saba Bank, Netherlands Antilles

    NARCIS (Netherlands)

    Thacker, R.W.; Díaz, M.C.; de Voogd, N.J.; van Soest, R.W.M.; Freeman, C.J.; Mobley, A.S.; LaPietra, J.; Cope, K.; McKenna, S.

    2010-01-01

    Background Saba Bank Atoll, Netherlands Antilles, is one of the three largest atolls on Earth and provides habitat for an extensive coral reef community. To improve our knowledge of this vast marine resource, a survey of biodiversity at Saba Bank included a multi-disciplinary team that sampled

  2. Protecting the Endangered Biodiversity in The Gilgel-Gibe Rivers ...

    African Journals Online (AJOL)

    The major objectives of the survey were: To ascertain the degree of endangering the biodiversity in the basins; to inform the professionals and farmers how their activities contribute to environmental degradation; to encourage the communities to initiate mitigating measures to arrest environmental degradation; to influence ...

  3. Fungal biodiversity to biotechnology.

    Science.gov (United States)

    Chambergo, Felipe S; Valencia, Estela Y

    2016-03-01

    Fungal habitats include soil, water, and extreme environments. With around 100,000 fungus species already described, it is estimated that 5.1 million fungus species exist on our planet, making fungi one of the largest and most diverse kingdoms of eukaryotes. Fungi show remarkable metabolic features due to a sophisticated genomic network and are important for the production of biotechnological compounds that greatly impact our society in many ways. In this review, we present the current state of knowledge on fungal biodiversity, with special emphasis on filamentous fungi and the most recent discoveries in the field of identification and production of biotechnological compounds. More than 250 fungus species have been studied to produce these biotechnological compounds. This review focuses on three of the branches generally accepted in biotechnological applications, which have been identified by a color code: red, green, and white for pharmaceutical, agricultural, and industrial biotechnology, respectively. We also discuss future prospects for the use of filamentous fungi in biotechnology application.

  4. Getting the measure of biodiversity.

    Science.gov (United States)

    Purvis, A; Hector, A

    2000-05-11

    The term 'biodiversity' is a simple contraction of 'biological diversity', and at first sight the concept is simple too: biodiversity is the sum total of all biotic variation from the level of genes to ecosystems. The challenge comes in measuring such a broad concept in ways that are useful. We show that, although biodiversity can never be fully captured by a single number, study of particular facets has led to rapid, exciting and sometimes alarming discoveries. Phylogenetic and temporal analyses are shedding light on the ecological and evolutionary processes that have shaped current biodiversity. There is no doubt that humans are now destroying this diversity at an alarming rate. A vital question now being tackled is how badly this loss affects ecosystem functioning. Although current research efforts are impressive, they are tiny in comparison to the amount of unknown diversity and the urgency and importance of the task.

  5. MCBS Sites of Biodiversity Significance

    Data.gov (United States)

    Minnesota Department of Natural Resources — This data layer represents areas with varying levels of native biodiversity that may contain high quality native plant communities, rare plants, rare animals, and/or...

  6. Economic inequality predicts biodiversity loss.

    Directory of Open Access Journals (Sweden)

    Gregory M Mikkelson

    Full Text Available Human activity is causing high rates of biodiversity loss. Yet, surprisingly little is known about the extent to which socioeconomic factors exacerbate or ameliorate our impacts on biological diversity. One such factor, economic inequality, has been shown to affect public health, and has been linked to environmental problems in general. We tested how strongly economic inequality is related to biodiversity loss in particular. We found that among countries, and among US states, the number of species that are threatened or declining increases substantially with the Gini ratio of income inequality. At both levels of analysis, the connection between income inequality and biodiversity loss persists after controlling for biophysical conditions, human population size, and per capita GDP or income. Future research should explore potential mechanisms behind this equality-biodiversity relationship. Our results suggest that economic reforms would go hand in hand with, if not serving as a prerequisite for, effective conservation.

  7. Biodiversity of the Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Parulekar, A.H.

    stream_size 2 stream_content_type text/plain stream_name Biodiversity_Western_Ghats_Inf_Kit_1994_3.1_1.pdf.txt stream_source_info Biodiversity_Western_Ghats_Inf_Kit_1994_3.1_1.pdf.txt Content-Encoding ISO-8859-1 Content-Type text.../plain; charset=ISO-8859-1 ...

  8. Arctic Terrestrial Biodiversity Monitoring Plan

    DEFF Research Database (Denmark)

    Christensen, Tom; Payne, J.; Doyle, M.

    The Conservation of Arctic Flora and Fauna (CAFF), the biodiversity working group of the Arctic Council, established the Circumpolar Biodiversity Monitoring Program (CBMP) to address the need for coordinated and standardized monitoring of Arctic environments. The CBMP includes an international ne....... Where are the areas of high ecological importance including, for example, resilient and vulnerable areas (related to the FECs) and where are drivers having the greatest impact?...

  9. Mid-Atlantic Ridge Deepwater Biodiversity Exploration (HB0902, EK60)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Objectives: With the overall goal of surveying and describing the biodiversity of the bathypelagic fauna near the Mid-Atlantic Ridge, a team of biological...

  10. Biodiversity of Intestinal Lactic Acid Bacteria in the Healthy Population.

    Science.gov (United States)

    Mikelsaar, Marika; Sepp, Epp; Štšepetova, Jelena; Songisepp, Epp; Mändar, Reet

    2016-01-01

    The complex ecosystem of the gastrointestinal tract involves tight interrelations among host cells, diet, and billions of microbes, both beneficial and opportunistic pathogens. In spite of advanced genomic, metagenomic, and metabonomic approaches, knowledge is still quite limited regarding the biodiversity of beneficial microbiota, including Lactobacillus spp., and its impact on the main biomarkers of general health. In this paper, Lactobacillus biodiversity is demonstrated through its taxonomy, function, and host-microbial interactions. Its prevalence, composition, abundance, intertwined metabolic properties, and relation to host age, genotype, and socioeconomic factors are reviewed based on the literature and original research experience. The species richness, e.g., the biodiversity of gut microbiota, provides the host with a variety of metabolically active species and strains that predict their response for different health conditions and extrinsic interventions. Metabolically active and safe Lactobacillus species and specific strains with particular functional properties increase the biodiversity of the whole intestinal microbiota. The elaborated principles for effective application of probiotics are discussed, aimed at regulating the composition of microbiota simultaneously with blood and urine biomarkers at the borderline of normality. This approach targets the impact of probiotic strains to maintenance of health with anti-infectious, cardiovascular, and metabolic support.

  11. Livestock ownership and microbial contamination of drinking-water: Evidence from nationally representative household surveys in Ghana, Nepal and Bangladesh.

    Science.gov (United States)

    Wardrop, Nicola A; Hill, Allan G; Dzodzomenyo, Mawuli; Aryeetey, Genevieve; Wright, Jim A

    2018-01-01

    Current priorities for diarrhoeal disease prevention include use of sanitation and safe water. There have been few attempts to quantify the importance of animal faeces in drinking-water contamination, despite the presence of potentially water-borne zoonotic pathogens in animal faeces. This study aimed to quantify the relationship between livestock ownership and point-of-consumption drinking-water contamination. Data from nationally representative household surveys in Nepal, Bangladesh, and Ghana, each with associated water quality assessments, were used. Multinomial regression adjusting for confounders was applied to assess the relationship between livestock ownership and the level of drinking-water contamination with E. coli. Ownership of five or more large livestock (e.g. cattle) was significantly associated with drinking-water contamination in Ghana (RRR=7.9, 95% CI=1.6 to 38.9 for medium levels of contamination with 1-31cfu/100ml; RRR=5.2, 95% CI=1.1-24.5 for high levels of contamination with >31cfu/100ml) and Bangladesh (RRR=2.4, 95% CI=1.3-4.5 for medium levels of contamination; non-significant for high levels of contamination). Ownership of eight or more poultry (chickens, guinea fowl, ducks or turkeys) was associated with drinking-water contamination in Bangladesh (RRR=1.5, 95% CI=1.1-2.0 for medium levels of contamination, non-significant for high levels of contamination). These results suggest that livestock ownership is a significant risk factor for the contamination of drinking-water at the point of consumption. This indicates that addressing human sanitation without consideration of faecal contamination from livestock sources will not be sufficient to prevent drinking-water contamination. Copyright © 2017 The Authors. Published by Elsevier GmbH.. All rights reserved.

  12. Biodiversity impact assessment (BIA+) - methodological framework for screening biodiversity.

    Science.gov (United States)

    Winter, Lisa; Pflugmacher, Stephan; Berger, Markus; Finkbeiner, Matthias

    2017-11-10

    For the past 20 years, the life cycle assessment (LCA) community has sought to integrate impacts on biodiversity into the LCA framework. However, existing impact assessment methods still fail to do so comprehensively because they quantify only a few impacts related to specific species and regions. This paper proposes a methodological framework that will allow LCA practitioners to assess currently missing impacts on biodiversity on a global scale. Building on existing models that seek to quantify the impacts of human activities on biodiversity, the herein proposed methodological framework consists of 2 components: a habitat factor for 14 major habitat types and the impact on the biodiversity status in those major habitat types. The habitat factor is calculated by means of indicators that characterize each habitat. The biodiversity status depends on parameters from impact categories. The impact functions, relating these different parameters to a given response in the biodiversity status, rely on expert judgments. To ensure the applicability for LCA practitioners, the components of the framework can be regionalized on a country scale for which LCA inventory data is more readily available. The weighting factors for the 14 major habitat types range from 0.63 to 1.82. By means of area weighting of the major habitat types in a country, country-specific weighting factors are calculated. In order to demonstrate the main part of the framework, examples of impact functions are given for the categories "freshwater eutrophication" and "freshwater ecotoxicity" in 1 major habitat type. The results confirm suitability of the methodological framework. The major advantages are the framework's user-friendliness, given that data can be used from LCA databases directly, and the complete inclusion of all levels of biodiversity (genetic, species, and ecosystem). It is applicable for the whole world and a wide range of impact categories. Integr Environ Assess Manag 2017;00:000-000.

  13. SURVEY

    DEFF Research Database (Denmark)

    SURVEY er en udbredt metode og benyttes inden for bl.a. samfundsvidenskab, humaniora, psykologi og sundhedsforskning. Også uden for forskningsverdenen er der mange organisationer som f.eks. konsulentfirmaer og offentlige institutioner samt marketingsafdelinger i private virksomheder, der arbejder...

  14. Biodiversity and the Role of Microbial Resource Centres

    OpenAIRE

    Sly, Lindsay I.

    2010-01-01

    Micro-organisms were the first forms of life on earth and have evolved into the most ecologically, genetically and metabolically diverse species known. Micro-organisms belong to all three Domains of life: The Bacteria, Archaea and Eukarya as well as the Viruses. They have shaped the evolution of the planet and continue to nurture and sustain the environment, plants and animals on which human society depends. While we continue to face difficulties posed by emerging animal, plant and human path...

  15. Motivations for conserving urban biodiversity.

    Science.gov (United States)

    Dearborn, Donald C; Kark, Salit

    2010-04-01

    In a time of increasing urbanization, the fundamental value of conserving urban biodiversity remains controversial. How much of a fixed budget should be spent on conservation in urban versus nonurban landscapes? The answer should depend on the goals that drive our conservation actions, yet proponents of urban conservation often fail to specify the motivation for protecting urban biodiversity. This is an important shortcoming on several fronts, including a missed opportunity to make a stronger appeal to those who believe conservation biology should focus exclusively on more natural, wilder landscapes. We argue that urban areas do offer an important venue for conservation biology, but that we must become better at choosing and articulating our goals. We explored seven possible motivations for urban biodiversity conservation: preserving local biodiversity, creating stepping stones to nonurban habitat, understanding and facilitating responses to environmental change, conducting environmental education, providing ecosystem services, fulfilling ethical responsibilities, and improving human well-being. To attain all these goals, challenges must be faced that are common to the urban environment, such as localized pollution, disruption of ecosystem structure, and limited availability of land. There are, however, also challenges specific only to particular goals, meaning that different goals will require different approaches and actions. This highlights the importance of specifying the motivations behind urban biodiversity conservation. If the goals are unknown, progress cannot be assessed.

  16. Evolution, plant breeding and biodiversity

    Directory of Open Access Journals (Sweden)

    Salvatore Ceccarelli

    2011-11-01

    Full Text Available This paper deals with changes in biodiversity during the course of evolution, plant domestication and plant breeding. It shows than man has had a strong influence on the progressive decrease of biodiversity, unconscious at first and deliberate in modern times. The decrease in biodiversity in the agricultures of the North causes a severe threat to food security and is in contrasts with the conservation of biodiversity which is part of the culture of several populations in the South. The concluding section of the paper shows that man could have guided evolution in a different way and shows an example of participatory plant breeding, a type of breeding which is done in collaboration with farmers and is based on selection for specific adaptation. Even though participatory plant breeding has been practiced for only about 20 years and by relatively few groups, the effects on both biodiversity and crop production are impressive. Eventually the paper shows how participatory plant breeding can be developed into ‘evolutionary plant breeding’ to cope in a dynamic way with climate changes.

  17. European Atlas of Soil Biodiversity

    DEFF Research Database (Denmark)

    Krogh (contributor), Paul Henning

    a normal atlas. Produced by leading soil scientists from Europe and other parts of the world under the auspice of the International Year of Biodiversity 2010, this unique document presents an interpretation of an often neglected biome that surrounds and affects us all. The European Atlas of Soil...... world. The first part of the book provides an overview of the below ground environment, soil biota in general, the ecosystem functions that soil organism perform, the important value it has for human activities and relevance for global biogeochemical cycles. The second part is an 'Encyclopedia of Soil...... Biodiversity is an essential reference to the many and varied aspects of soil. The overall goal of this work is to convey the fundamental necessity to safeguard soil biodiversity in order to guarantee life on this planet....

  18. Urban lifestyle and urban biodiversity

    DEFF Research Database (Denmark)

    Petersen, L. K.; Lyytimäki, J.; Normander, B.

    2007-01-01

    biodiversity, recreational, educational and other needs. However, uncovered and unsealed space is constantly under pressure for building and infrastructure development in the urban landscape, and the design and usages of urban green structure is a matter of differing interests and expectations. Integrating......This report is concerned with the relations between lifestyles of urban populations on one hand and protection of biodiversity in urban areas on the other. Urban areas are of importance for the general protection of biodiversity. In the surroundings of cities and within urban sprawls there can...... be important habitats and valuable corridors for both common and less common species. At the same time a comprehensive, functional and viable green structure is important for urban populations to whom it serves many functions and offers a whole range of benefits. Urban green structure should serve both...

  19. Biodiversity and industry ecosystem management

    Science.gov (United States)

    Coleman, William G.

    1996-11-01

    The term biodiversity describes the array of interacting, genetically distinct populations and species in a region, the communities they comprise, and the variety of ecosystems of which they are functioning parts. Ecosystem health, a closely related concept, is described in terms of a process identifying biological indicators, end points, and values. The decline of populations or species, an accelerating trend worldwide, can lead to simplification of ecosystem processes, thus threatening the stability and sustainability of ecosystem services directly relevant to human welfare in the chain of economic and ecological relationships. The challenge of addressing issues of such enormous scope and complexity has highlighted the limitations of ecology-as-science. Additionally, biosphere-scale conflicts seem to lie beyond the scope of conventional economics, leading to differences of opinion about the commodity value of biodiversity and of the services that intact ecosystems provide. In the face of these uncertainties, many scientists and economists have adopted principles that clearly assign burdens of proof to those who would promote the loss of biodiversity and that also establish “near-trump” (preeminent) status for ecological integrity. Electric utility facilities and operations impact biodiversity whenever construction, operation, or maintenance of generation, delivery, and support facilities alters landscapes and habitats and thereby impacts species. Although industry is accustomed to dealing with broad environmental concerns (such as global warming or acid rain), the biodiversity issue invokes hemisphere-wide, regional, local, and site-specific concerns all at the same time. Industry can proactively address these issues of scope and scale in two main ways: first, by aligning strategically with the broad research agenda put forth by informed scientists and institutions; and second, by supporting focused management processes whose results will contribute

  20. Measuring temporal trends in biodiversity

    OpenAIRE

    Buckland, S. T.; Yuan, Y.; Marcon, Eric

    2017-01-01

    Yuan was part-funded by EPSRC/NERC Grant EP/1000917/1 and Marcon by ANR-10-LABX-25-01. In 2002, nearly 200 nations signed up to the 2010 target of the Convention for Biological Diversity, ‘to significantly reduce the rate of biodiversity loss by 2010’. In order to assess whether the target was met, it became necessary to quantify temporal trends in measures of diversity. This resulted in a marked shift in focus for biodiversity measurement. We explore the developments in measuring biodiver...

  1. Data intensive computing for biodiversity

    CERN Document Server

    Dhillon, Sarinder K

    2013-01-01

    This book is focused on the development of a data integration framework for retrieval of biodiversity information from heterogeneous and distributed data sources. The data integration system proposed in this book links remote databases in a networked environment, supports heterogeneous databases and data formats, links databases hosted on multiple platforms, and provides data security for database owners by allowing them to keep and maintain their own data and to choose information to be shared and linked. The book is a useful guide for researchers, practitioners, and graduate-level students interested in learning state-of-the-art development for data integration in biodiversity.

  2. PYCNOIB: biodiversity and biogeography of Iberian pycnogonids.

    Science.gov (United States)

    Soler-Membrives, Anna; Munilla, Tomás

    2015-01-01

    Biodiversity and biogeographic studies comparing the distribution patterns of benthic marine organisms across the Iberian Atlantic and Mediterranean waters are scarce. The Pycnogonida (sea spiders) are a clear example of both endemicity and diversity, and are considered a key taxon to study and monitor biogeographic and biodiversity patterns. This is the first review that compiles data about abundance and diversity of Iberian pycnogonids and examines their biogeographic patterns and bathymetric constraints using GIS tools. A total of 17,762 pycnogonid records from 343 localities were analyzed and were found to contain 65 species, 21 genera and 12 families. Achelia echinata and Ammothella longipes (family Acheliidae) were the most abundant comprising ~80% of the total records. The Acheliidae is also the most speciose in Iberian waters with 15 species. In contrast, the family Nymphonidae has 7 species but is significantly less abundant (Mediterranean region may be richer than that of the Atlantic. The Strait of Gibraltar and the Alboran Sea are recognized as species-rich areas that act as buffer zones between the Atlantic and Mediterranean boundaries. The deep waters surrounding the Iberian Peninsula are poorly surveyed, with only 15% of the sampling sites located below 1000 m. Further deep-water sampling is needed mainly on the Iberian Mediterranean side.

  3. PYCNOIB: biodiversity and biogeography of Iberian pycnogonids.

    Directory of Open Access Journals (Sweden)

    Anna Soler-Membrives

    Full Text Available Biodiversity and biogeographic studies comparing the distribution patterns of benthic marine organisms across the Iberian Atlantic and Mediterranean waters are scarce. The Pycnogonida (sea spiders are a clear example of both endemicity and diversity, and are considered a key taxon to study and monitor biogeographic and biodiversity patterns. This is the first review that compiles data about abundance and diversity of Iberian pycnogonids and examines their biogeographic patterns and bathymetric constraints using GIS tools. A total of 17,762 pycnogonid records from 343 localities were analyzed and were found to contain 65 species, 21 genera and 12 families. Achelia echinata and Ammothella longipes (family Acheliidae were the most abundant comprising ~80% of the total records. The Acheliidae is also the most speciose in Iberian waters with 15 species. In contrast, the family Nymphonidae has 7 species but is significantly less abundant (<1% of the total records than Acheliidae. Species accumulation curves indicate that further sampling would increase the number of Iberian species records. Current sampling effort suggests that the pycnogonid fauna of the Mediterranean region may be richer than that of the Atlantic. The Strait of Gibraltar and the Alboran Sea are recognized as species-rich areas that act as buffer zones between the Atlantic and Mediterranean boundaries. The deep waters surrounding the Iberian Peninsula are poorly surveyed, with only 15% of the sampling sites located below 1000 m. Further deep-water sampling is needed mainly on the Iberian Mediterranean side.

  4. Building a discovery partnership with Sarawak Biodiversity Centre: a gateway to access natural products from the rainforests.

    Science.gov (United States)

    Yeo, Tiong Chia; Naming, Margarita; Manurung, Rita

    2014-03-01

    The Sarawak Biodiversity Centre (SBC) is a state government agency which regulates research and promotes the sustainable use of biodiversity. It has a program on documentation of traditional knowledge (TK) and is well-equipped with facilities for natural product research. SBC maintains a Natural Product Library (NPL) consisting of local plant and microbial extracts for bioprospecting. The NPL is a core discovery platform for screening of bioactive compounds by researchers through a formal agreement with clear benefit sharing obligations. SBC aims to develop partnerships with leading institutions and the industries to explore the benefits of biodiversity.

  5. Global biodiversity monitoring: from data sources to essential biodiversity variables

    Science.gov (United States)

    Proenca, Vania; Martin, Laura J.; Pereira, Henrique M.; Fernandez, Miguel; McRae, Louise; Belnap, Jayne; Böhm, Monika; Brummitt, Neil; Garcia-Moreno, Jaime; Gregory, Richard D.; Honrado, Joao P; Jürgens, Norbert; Opige, Michael; Schmeller, Dirk S.; Tiago, Patricia; van Sway, Chris A

    2016-01-01

    Essential Biodiversity Variables (EBVs) consolidate information from varied biodiversity observation sources. Here we demonstrate the links between data sources, EBVs and indicators and discuss how different sources of biodiversity observations can be harnessed to inform EBVs. We classify sources of primary observations into four types: extensive and intensive monitoring schemes, ecological field studies and satellite remote sensing. We characterize their geographic, taxonomic and temporal coverage. Ecological field studies and intensive monitoring schemes inform a wide range of EBVs, but the former tend to deliver short-term data, while the geographic coverage of the latter is limited. In contrast, extensive monitoring schemes mostly inform the population abundance EBV, but deliver long-term data across an extensive network of sites. Satellite remote sensing is particularly suited to providing information on ecosystem function and structure EBVs. Biases behind data sources may affect the representativeness of global biodiversity datasets. To improve them, researchers must assess data sources and then develop strategies to compensate for identified gaps. We draw on the population abundance dataset informing the Living Planet Index (LPI) to illustrate the effects of data sources on EBV representativeness. We find that long-term monitoring schemes informing the LPI are still scarce outside of Europe and North America and that ecological field studies play a key role in covering that gap. Achieving representative EBV datasets will depend both on the ability to integrate available data, through data harmonization and modeling efforts, and on the establishment of new monitoring programs to address critical data gaps.

  6. Children prioritize virtual exotic biodiversity over local biodiversity.

    Directory of Open Access Journals (Sweden)

    Jean-Marie Ballouard

    Full Text Available Environmental education is essential to stem current dramatic biodiversity loss, and childhood is considered as the key period for developing awareness and positive attitudes toward nature. Children are strongly influenced by the media, notably the internet, about biodiversity and conservation issues. However, most media focus on a few iconic, appealing, and usually exotic species. In addition, virtual activities are replacing field experiences. This situation may curb children knowledge and concerns about local biodiversity. Focusing our analyses on local versus exotic species, we examined the level of knowledge and the level of diversity of the animals that French schoolchildren are willing to protect, and whether these perceptions are mainly guided by information available in the internet. For that, we collected and compared two complementary data sets: 1 a questionnaire was administered to schoolchildren to assess their knowledge and consideration to protect animals, 2 an internet content analysis (i.e. Google searching sessions using keywords was performed to assess which animals are the most often represented. Our results suggest that the knowledge of children and their consideration to protect animal are mainly limited to internet contents, represented by a few exotic and charismatic species. The identification rate of local animals by schoolchildren was meager, suggesting a worrying disconnection from their local environment. Schoolchildren were more prone to protect "virtual" (unseen, exotic rather than local animal species. Our results reinforce the message that environmental education must also focus on outdoor activities to develop conservation consciousness and concerns about local biodiversity.

  7. The microbial temperature sensitivity to warming is controlled by thermal adaptation and is independent of C-quality across a pan-continental survey

    Science.gov (United States)

    Berglund, Eva; Rousk, Johannes

    2017-04-01

    Climate models predict that warming will result in an increased loss of soil organic matter (SOM). However, field experiments suggest that although warming results in an immediate increase in SOM turnover, the effect diminishes over time. Although the use and subsequent turnover of SOM is dominated by the soil microbial community, the underlying physiology underpinning warming responses are not considered in current climate models. It has been suggested that a reduction in the perceived quality of SOM to the microbial community, and changes in the microbial thermal adaptation, could be important feed-backs to soil warming. Thus, studies distinguishing between temperature relationships and how substrate quality influences microbial decomposition are a priority. We examined microbial communities and temperature sensitivities along a natural climate gradient including 56 independent samples from across Europe. The gradient included mean annual temperatures (MAT) from ca -4 to 18 ˚ C, along with wide spans of environmental factors known to influence microbial communities, such as pH (4.0 to 8.8), nutrients (C/N from 7 to 50), SOM (from 4 to 94%), and plant communities, etc. The extensive ranges of environmental conditions resulted in wide ranges of substrate quality, indexed as microbial respiration per unit SOM, from 5-150 μg CO2g-1 SOM g-1 h-1. We hypothesised microbial communities to (1) be adapted to the temperature of their climate, leading to warm adapted bacterial communities that were more temperature sensitive (higher Q10s) at higher MAT; (2) have temperature sensitivities affected by the quality of SOM, with higher Q10s for lower quality SOM. To determine the microbial use of SOM and its dependence on temperature, we characterized microbial temperature dependences of bacterial growth (leu inc), fungal growth (ac-in-erg) and soil respiration in all 56 sites. Temperature dependences were determined using brief (ca. 1-2 h at 25˚ C) laboratory incubation

  8. Surveys for Pathogens of Monoecious Hydrilla 2014

    Science.gov (United States)

    2016-06-01

    Woolfolk. 2007. Microfungi from bark of healthy and damaged American beech, Fraser fir, and Eastern hemlock trees during an all taxa biodiversity ...Biocontrol Science and Technology 12:75-82. Charudattan, R. 2010. Microbial control of weeds. Symposium: Microbial biocontrol of arthropods, weeds and

  9. Monetary valuation of biodiversity: sense or nonsense?

    NARCIS (Netherlands)

    Nunes, P.A.L.D.; van den Bergh, J.C.J.M.

    2001-01-01

    This paper critically evaluates the notion and application of economic, monetary valuation of biological diversity, or biodiversity. For this purpose four levels of diversity are considered: genes, species, ecosystems and functions. Different perspectives on biodiversity value can be characterized

  10. Antarctica and the strategic plan for biodiversity

    National Research Council Canada - National Science Library

    Steven L Chown; Cassandra M Brooks; Aleks Terauds; Céline Le Bohec; Céline van Klaveren-Impagliazzo; Jason D Whittington; Stuart H M Butchart; Bernard W T Coetzee; Ben Collen; Peter Convey; Kevin J Gaston; Neil Gilbert; Mike Gill; Robert Höft; Sam Johnston; Mahlon C Kennicutt II; Hannah J Kriesell; Yvon Le Maho; Heather J Lynch; Maria Palomares; Roser Puig-Marcó; Peter Stoett; Melodie A McGeoch

    2017-01-01

    The Strategic Plan for Biodiversity, adopted under the auspices of the Convention on Biological Diversity, provides the basis for taking effective action to curb biodiversity loss across the planet...

  11. Microbial pesticides

    Science.gov (United States)

    Michael L. McManus

    1991-01-01

    Interest in the use of microbial pesticides has intensified because of public concern about the safety of chemical pesticides and their impact in the environment. Characteristics of the five groups of entomopathogens that have potential as microbial pesticides are briefly discussed and an update is provided on research and development activities underway to enhance the...

  12. Synthesis of knowledge on marine biodiversity in European Seas: from census to sustainable management.

    Science.gov (United States)

    Narayanaswamy, Bhavani E; Coll, Marta; Danovaro, Roberto; Davidson, Keith; Ojaveer, Henn; Renaud, Paul E

    2013-01-01

    The recently completed European Census of Marine Life, conducted within the framework of the global Census of Marine Life programme (2000-2010), markedly enhanced our understanding of marine biodiversity in European Seas, its importance within ecological systems, and the implications for human use. Here we undertake a synthesis of present knowledge of biodiversity in European Seas and identify remaining challenges that prevent sustainable management of marine biodiversity in one of the most exploited continents of the globe. Our analysis demonstrates that changes in faunal standing stock with depth depends on the size of the fauna, with macrofaunal abundance only declining with increasing water depth below 1000 m, whilst there was no obvious decrease in meiofauna with increasing depth. Species richness was highly variable for both deep water macro- and meio- fauna along latitudinal and longitudinal gradients. Nematode biodiversity decreased from the Atlantic into the Mediterranean whilst latitudinal related biodiversity patterns were similar for both faunal groups investigated, suggesting that the same environmental drivers were influencing the fauna. While climate change and habitat degradation are the most frequently implicated stressors affecting biodiversity throughout European Seas, quantitative understanding, both at individual and cumulative/synergistic level, of their influences are often lacking. Full identification and quantification of species, in even a single marine habitat, remains a distant goal, as we lack integrated data-sets to quantify these. While the importance of safeguarding marine biodiversity is recognised by policy makers, the lack of advanced understanding of species diversity and of a full survey of any single habitat raises huge challenges in quantifying change, and facilitating/prioritising habitat/ecosystem protection. Our study highlights a pressing requirement for more complete biodiversity surveys to be undertaken within

  13. Synthesis of Knowledge on Marine Biodiversity in European Seas: From Census to Sustainable Management

    Science.gov (United States)

    Narayanaswamy, Bhavani E.

    2013-01-01

    The recently completed European Census of Marine Life, conducted within the framework of the global Census of Marine Life programme (2000–2010), markedly enhanced our understanding of marine biodiversity in European Seas, its importance within ecological systems, and the implications for human use. Here we undertake a synthesis of present knowledge of biodiversity in European Seas and identify remaining challenges that prevent sustainable management of marine biodiversity in one of the most exploited continents of the globe. Our analysis demonstrates that changes in faunal standing stock with depth depends on the size of the fauna, with macrofaunal abundance only declining with increasing water depth below 1000 m, whilst there was no obvious decrease in meiofauna with increasing depth. Species richness was highly variable for both deep water macro- and meio- fauna along latitudinal and longitudinal gradients. Nematode biodiversity decreased from the Atlantic into the Mediterranean whilst latitudinal related biodiversity patterns were similar for both faunal groups investigated, suggesting that the same environmental drivers were influencing the fauna. While climate change and habitat degradation are the most frequently implicated stressors affecting biodiversity throughout European Seas, quantitative understanding, both at individual and cumulative/synergistic level, of their influences are often lacking. Full identification and quantification of species, in even a single marine habitat, remains a distant goal, as we lack integrated data-sets to quantify these. While the importance of safeguarding marine biodiversity is recognised by policy makers, the lack of advanced understanding of species diversity and of a full survey of any single habitat raises huge challenges in quantifying change, and facilitating/prioritising habitat/ecosystem protection. Our study highlights a pressing requirement for more complete biodiversity surveys to be undertaken within

  14. DNA barcoding to map the microbial communities: current advances and future directions.

    Science.gov (United States)

    Chakraborty, Chiranjib; Doss, C George Priya; Patra, Bidhan C; Bandyopadhyay, Sanghamitra

    2014-04-01

    During the last two decades, the DNA barcode development towards microbial community has increased dramatically. DNA barcode development is related to error-free and quick species identification which aid in understanding the microbial biodiversity, as well as the diseases related to microbial species. Here, we seek to evaluate the so-called barcoding initiatives for the microbial communities and the emerging trends in this field. In this paper, we describe the development of DNA marker-based DNA barcoding system, comparison between routine species identification and DNA barcode, and microbial biodiversity and DNA barcode for microbial communities. Two major topics, such as the molecular diversity of viruses and barcode for viruses have been discussed at the same time. We demonstrate the current status and the maker of DNA barcode for bacteria, algae, fungi, and protozoa. Furthermore, we argue about the promises, limitations, and present and future challenges of microbial barcode development.

  15. Place prioritization for biodiversity content

    Indian Academy of Sciences (India)

    Unknown

    diversity value and to devise management strategies to conserve biodiversity in these places. Traditionally, an implicit place prioritization was routinely performed when places were selected as managed forests, game reserves, national parks, etc. However, this process has almost always involved either the use of intuitive ...

  16. Trading biodiversity for pest problems

    Science.gov (United States)

    Recent shifts in agricultural practices have resulted in increased pesticide use, land use intensification, and landscape simplification, all of which threaten biodiversity in and near farms. Pests are major challenges to food security, and responses to pests can represent unintended socioeconomic a...

  17. Business Meets Biodiversity Conference 2012

    NARCIS (Netherlands)

    Vollaard, B.; Man, M. de; Verweij, P.A.

    2012-01-01

    How can companies successfully integrate the sustainable management of ecosystems and biodiversity into their business models? This was the central question at the international conference ‘Business Meets Biodiversity’ held in Utrecht, The Netherlands, on June 27th 2012. The organizing committee,

  18. Biodiversity in Word and Meaning

    Science.gov (United States)

    Slingsby, David

    2010-01-01

    This article argues that we need to abandon the word "biodiversity", to rediscover the biology that it obscures and to rethink how to introduce this biology to young people. We cannot go back to the systematics that once made up a large part of a biology A-level course (ages 16-18), so we need to find alternative ways of introducing the…

  19. Nitrogen deposition and terrestrial biodiversity

    Science.gov (United States)

    Christopher M. Clark; Yongfei Bai; William D. Bowman; Jane M. Cowles; Mark E. Fenn; Frank S. Gilliam; Gareth K. Phoenix; Ilyas Siddique; Carly J. Stevens; Harald U. Sverdrup; Heather L. Throop

    2013-01-01

    Nitrogen deposition, along with habitat losses and climate change, has been identified as a primary threat to biodiversity worldwide (Butchart et al., 2010; MEA, 2005; Sala et al., 2000). The source of this stressor to natural systems is generally twofold: burning of fossil fuels and the use of fertilizers in modern intensive agriculture. Each of these human...

  20. The Early Years: Exploring Biodiversity

    Science.gov (United States)

    Ashbrook, Peggy

    2017-01-01

    The importance of biodiversity to human life and the benefits of a diverse ecosystem are not often obvious to young children. This column discusses resources and science topics related to students in grades preK to 2. The objective in this month's issue is to introduce children to the diversity of plant life in a given area through a plant…

  1. Wilderness, biodiversity, and human health

    Science.gov (United States)

    Daniel L. Dustin; Keri A. Schwab; Kelly S. Bricker

    2015-01-01

    This paper illustrates how wilderness, biodiversity, and human health are intertwined. Proceeding from the assumption that humankind is part of, rather than apart from, nature, health is re-imagined as a dynamic relationship that can best be conceived in broad ecological terms. Health, from an ecological perspective, is a measure of the wellness of the individual and...

  2. Relationship Between Biodiversity and Agricultural Production

    OpenAIRE

    Brunetti, Ilaria; Tidball, Mabel; Couvet, Denis

    2018-01-01

    Agriculture is one of the main causes of biodiversity loss. In this work we model the interdependent relationship between biodiversity and agriculture on a farmed land, supposing that, while agriculture has a negative impact on biodiversity, the latter can increase agricultural production. Farmers act as myopic agents, who maximize their instantaneous profit without considering the negative effects of their practice on the evolution of biodiversity. We find that a tax on inputs can have a pos...

  3. Evaluating the contribution of zoos and aquariums to Aichi Biodiversity Target 1.

    Science.gov (United States)

    Moss, Andrew; Jensen, Eric; Gusset, Markus

    2015-04-01

    The United Nations Strategic Plan for Biodiversity 2011-2020 is a key initiative within global efforts to halt and eventually reverse the loss of biodiversity. The very first target of this plan states that "by 2020, at the latest, people are aware of the values of biodiversity and the steps they can take to conserve and use it sustainably." Zoos and aquariums worldwide, attracting more than 700 million visits every year, could potentially make a positive contribution to this target. However, a global evaluation of the educational impacts of visits to zoos and aquariums is entirely lacking in the existing literature. To address this gap, we conducted a large-scale impact evaluation study. We used a pre- and postvisit repeated-measures survey design to evaluate biodiversity literacy-understanding of biodiversity and knowledge of actions to help protect it-of zoo and aquarium visitors worldwide. Ours was the largest and most international study of zoo and aquarium visitors ever conducted. In total, 5661 visitors to 26 zoos and aquariums from 19 countries around the globe participated in the study. Aggregate biodiversity understanding and knowledge of actions to help protect biodiversity both significantly increased over the course of zoo and aquarium visits. There was an increase from previsit (69.8%) to postvisit (75.1%) in respondents demonstrating at least some positive evidence of biodiversity understanding. Similarly, there was an increase from previsit (50.5%) to postvisit (58.8%) in respondents who could identify actions to help protect biodiversity that could be achieved at an individual level. Our results are the most compelling evidence to date that zoo and aquarium visits contribute to increasing the number of people who understand biodiversity and know actions they can take to help protect biodiversity. © 2014 Society for Conservation Biology.

  4. Systematic temporal patterns in the relationship between housing development and forest bird biodiversity.

    Science.gov (United States)

    Pidgeon, Anna M; Flather, Curtis H; Radeloff, Volker C; Lepczyk, Christopher A; Keuler, Nicholas S; Wood, Eric M; Stewart, Susan I; Hammer, Roger B

    2014-10-01

    As people encroach increasingly on natural areas, one question is how this affects avian biodiversity. The answer to this is partly scale-dependent. At broad scales, human populations and biodiversity concentrate in the same areas and are positively associated, but at local scales people and biodiversity are negatively associated with biodiversity. We investigated whether there is also a systematic temporal trend in the relationship between bird biodiversity and housing development. We used linear regression to examine associations between forest bird species richness and housing growth in the conterminous United States over 30 years. Our data sources were the North American Breeding Bird Survey and the 2000 decennial U.S. Census. In the 9 largest forested ecoregions, housing density increased continually over time. Across the conterminous United States, the association between bird species richness and housing density was positive for virtually all guilds except ground nesting birds. We found a systematic trajectory of declining bird species richness as housing increased through time. In more recently developed ecoregions, where housing density was still low, the association with bird species richness was neutral or positive. In ecoregions that were developed earlier and where housing density was highest, the association of housing density with bird species richness for most guilds was negative and grew stronger with advancing decades. We propose that in general the relationship between human settlement and biodiversity over time unfolds as a 2-phase process. The first phase is apparently innocuous; associations are positive due to coincidence of low-density housing with high biodiversity. The second phase is highly detrimental to biodiversity, and increases in housing density are associated with biodiversity losses. The long-term effect on biodiversity depends on the final housing density. This general pattern can help unify our understanding of the relationship

  5. Achieving Aichi Biodiversity Target 11 to improve the performance of protected areas and conserve freshwater biodiversity

    Science.gov (United States)

    Diego Juffe-Bignoli; Ian Harrison; Stuart HM Butchart; Rebecca Flitcroft; Virgilio Hermoso; Harry Jonas; Anna Lukasiewicz; Michele Thieme; Eren Turak; Heather Bingham; James Dalton; William Darwall; Marine Deguignet; Nigel Dudley; Royal Gardner; Jonathan Higgins; Ritesh Kumar; Simon Linke; G Randy Milton; Jamie Pittock; Kevin G Smith; Arnout van Soesbergen

    2016-01-01

    1. The Strategic Plan for Biodiversity (2011–2020), adopted at the 10th meeting of the Conference of the Parties to the Convention on Biological Diversity, sets 20 Aichi Biodiversity Targets to be met by 2020 to address biodiversity loss and ensure its sustainable and equitable use. Aichi Biodiversity Target 11 describes what an improved conservation network would look...

  6. Evaluation of microbial diversity of the microbial mat from the extremely acidic Lake Robule (Bor, Serbia

    Directory of Open Access Journals (Sweden)

    Stanković Srđan

    2017-04-01

    Full Text Available Extremely acidic environments are frequently formed in areas impacted by mining activities, and Lake Robule is such an ecosystem. Although an extreme environment, Lake Robule is inhabited by acidophilic microorganisms. We investigated biodiversity of the macroscopic structure known as a microbial mat formed on the lake bottom in shallow waters. Microbial mats are common in acidic environments, but their composition can differ significantly from site to site. Microbial diversity of the mat from Lake Robule was investigated using both cultivation-dependent and metagenomic approaches. The results showed the mat to be mostly inhabited by heterotrophic acidophilic bacteria. When compared to the microbial community of Lake Robule’s surface water, the microbial mat proved to be a more complex community. A biogeochemical model of the mat of Lake Robule is proposed on the basis of our results and available published data.

  7. Biodiversity offsetting – en vogue in Madagascar?

    African Journals Online (AJOL)

    So how exactly is biodiversity offsetting working? Biodiversity offsets are conservation measures imple- mented to compensate for the residual biodiversity losses caused by development activities. This entails 'adequate' compensation in form of upgrading the environmental value of other sites. The 'successful' upgrading or ...

  8. Biology Student Teachers' Conceptual Frameworks regarding Biodiversity

    Science.gov (United States)

    Dikmenli, Musa

    2010-01-01

    In recent years, biodiversity has received a great deal of attention worldwide, especially in environmental education. The reasons for this attention are the increase of human activities on biodiversity and environmental problems. The purpose of this study is to investigate biology student teachers' conceptual frameworks regarding biodiversity.…

  9. Soil biodiversity and human health

    Science.gov (United States)

    Six, Johan; Pereg, Lily; Brevik, Eric

    2017-04-01

    Biodiversity is important for the maintenance of soil quality. Healthy, biodiverse soils are crucial for human health and wellbeing from several reasons, for example: biodiversity has been shown to be important in controlling populations of pathogens; healthy, well-covered soils can reduce disease outbreaks; carbon-rich soils may also reduce outbreaks of human and animal parasites; exposure to soil microbes can reduce allergies; soils have provided many of our current antibiotics; soil organisms can provide biological disease and pest control agents, healthy soils mean healthier and more abundant foods; soil microbes can enhance crop plant resilience; healthy soils promote good clean air quality, less prone to wind and water erosion; and healthy soils provide clean and safe water through filtration, decontamination by microbes and removal of pollutants. Soil microbes and other biota provide many benefits to human health. Soil microbes are a source of medicines, such as antibiotics, anticancer drugs and many more. Organisms that affect soil health and thus human health include those involved in nutrient cycling, decomposition of organic matter and determining soil structure (e.g. aggregation). Again these are related to food security but also affect human health in other ways. Many beneficial organisms have been isolated from soil - plant growth promoting and disease suppressive microbes used as inoculants, foliar inoculants for improvement of ruminant digestion systems and inoculants used in bioremediation of toxic compounds in the environment. Soil biodiversity is highly recognised now as an important feature of healthy soil and imbalances have been shown to give advantage to harmful over beneficial organisms. This presentation will highlight the many connections of biodiversity to soil quality and human health.

  10. Phage Life Cycles Behind Bacterial Biodiversity.

    Science.gov (United States)

    Olszak, Tomasz; Latka, Agnieszka; Roszniowski, Bartosz; Valvano, Miguel A; Drulis-Kawa, Zuzanna

    2017-11-24

    Bacteriophages (phages or bacterial viruses) are the most abundant biological entities in our planet; their influence reaches far beyond the microorganisms they parasitize. Phages are present in every environment and shape up every bacterial population in both active and passive ways. They participate in the circulation of organic matter and drive the evolution of microorganisms by horizontal gene transfer at unprecedented scales. The mass flow of genetic information in the microbial world influences the biosphere and poses challenges for science and medicine. The genetic flow, however, depends on the fate of the viral DNA injected into the bacterial cell. The archetypal notion of phages only engaging in predatorprey relationships is slowly fading. Because of their varied development cycles, environmental conditions, and the diversity of microorganisms they parasitize, phages form a dense and highly complex web of dependencies, which has important consequences for life on Earth. The sophisticated phage-bacteria interplay includes both aggressive action (bacterial lysis) and "diplomatic negotiations" (prophage domestication). Here, we review the most important mechanisms of interactions between phages and bacteria and their evolutionary consequences influencing their biodiversity. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  11. Helsinki alert of biodiversity and health.

    Science.gov (United States)

    von Hertzen, Leena; Beutler, Bruce; Bienenstock, John; Blaser, Martin; Cani, Patrice D; Eriksson, Johan; Färkkilä, Martti; Haahtela, Tari; Hanski, Ilkka; Jenmalm, Maria C; Kere, Juha; Knip, Mikael; Kontula, Kimmo; Koskenvuo, Markku; Ling, Charlotte; Mandrup-Poulsen, Thomas; von Mutius, Erika; Mäkelä, Mika J; Paunio, Tiina; Pershagen, Göran; Renz, Harald; Rook, Graham; Saarela, Maria; Vaarala, Outi; Veldhoen, Marc; de Vos, Willem M

    2015-05-01

    Urban living in built environments, combined with the use of processed water and food, may not provide the microbial stimulation necessary for a balanced development of immune function. Many chronic inflammatory disorders, including allergic, autoimmune, metabolic, and even some behavioural disorders, are linked to alteration in the human commensal microbiota. Sedentary lifestyle is associated with reduced exposure to a broad spectrum of environmental micro-organisms and surplus energy balance, both risk factors of chronic inflammatory disorders. According to the Biodiversity Hypothesis, an environment with diverse macrobiota and microbiota modifies and enriches the human microbiota, which in turn is crucial in the development and maintenance of appropriate immune function. These issues were discussed in the symposium 'Chronic Inflammation, Lifestyle and Environment', held in Helsinki, 20-22 August 2014, under the sponsorship of the Yrjö Jahnsson Foundation. This paper briefly outlines the recent findings in the context of the environment, lifestyle, and health; discusses the forces that undermine immune tolerance in urban environments; and highlights the possibilities to restore broken immune tolerance among urban dwellers, summarizing the main messages in four statements and calling for actions to combat major public health threats.

  12. Scaling biodiversity responses to hydrological regimes.

    Science.gov (United States)

    Rolls, Robert J; Heino, Jani; Ryder, Darren S; Chessman, Bruce C; Growns, Ivor O; Thompson, Ross M; Gido, Keith B

    2017-11-08

    Of all ecosystems, freshwaters support the most dynamic and highly concentrated biodiversity on Earth. These attributes of freshwater biodiversity along with increasing demand for water mean that these systems serve as significant models to understand drivers of global biodiversity change. Freshwater biodiversity changes are often attributed to hydrological alteration by water-resource development and climate change owing to the role of the hydrological regime of rivers, wetlands and floodplains affecting patterns of biodiversity. However, a major gap remains in conceptualising how the hydrological regime determines patterns in biodiversity's multiple spatial components and facets (taxonomic, functional and phylogenetic). We synthesised primary evidence of freshwater biodiversity responses to natural hydrological regimes to determine how distinct ecohydrological mechanisms affect freshwater biodiversity at local, landscape and regional spatial scales. Hydrological connectivity influences local and landscape biodiversity, yet responses vary depending on spatial scale. Biodiversity at local scales is generally positively associated with increasing connectivity whereas landscape-scale biodiversity is greater with increasing fragmentation among locations. The effects of hydrological disturbance on freshwater biodiversity are variable at separate spatial scales and depend on disturbance frequency and history and organism characteristics. The role of hydrology in determining habitat for freshwater biodiversity also depends on spatial scaling. At local scales, persistence, stability and size of habitat each contribute to patterns of freshwater biodiversity yet the responses are variable across the organism groups that constitute overall freshwater biodiversity. We present a conceptual model to unite the effects of different ecohydrological mechanisms on freshwater biodiversity across spatial scales, and develop four principles for applying a multi-scaled understanding of

  13. Current and future patterns of global marine mammal biodiversity.

    Science.gov (United States)

    Kaschner, Kristin; Tittensor, Derek P; Ready, Jonathan; Gerrodette, Tim; Worm, Boris

    2011-01-01

    Quantifying the spatial distribution of taxa is an important prerequisite for the preservation of biodiversity, and can provide a baseline against which to measure the impacts of climate change. Here we analyse patterns of marine mammal species richness based on predictions of global distributional ranges for 115 species, including all extant pinnipeds and cetaceans. We used an environmental suitability model specifically designed to address the paucity of distributional data for many marine mammal species. We generated richness patterns by overlaying predicted distributions for all species; these were then validated against sightings data from dedicated long-term surveys in the Eastern Tropical Pacific, the Northeast Atlantic and the Southern Ocean. Model outputs correlated well with empirically observed patterns of biodiversity in all three survey regions. Marine mammal richness was predicted to be highest in temperate waters of both hemispheres with distinct hotspots around New Zealand, Japan, Baja California, the Galapagos Islands, the Southeast Pacific, and the Southern Ocean. We then applied our model to explore potential changes in biodiversity under future perturbations of environmental conditions. Forward projections of biodiversity using an intermediate Intergovernmental Panel for Climate Change (IPCC) temperature scenario predicted that projected ocean warming and changes in sea ice cover until 2050 may have moderate effects on the spatial patterns of marine mammal richness. Increases in cetacean richness were predicted above 40° latitude in both hemispheres, while decreases in both pinniped and cetacean richness were expected at lower latitudes. Our results show how species distribution models can be applied to explore broad patterns of marine biodiversity worldwide for taxa for which limited distributional data are available.

  14. Current and Future Patterns of Global Marine Mammal Biodiversity

    Science.gov (United States)

    Kaschner, Kristin; Tittensor, Derek P.; Ready, Jonathan; Gerrodette, Tim; Worm, Boris

    2011-01-01

    Quantifying the spatial distribution of taxa is an important prerequisite for the preservation of biodiversity, and can provide a baseline against which to measure the impacts of climate change. Here we analyse patterns of marine mammal species richness based on predictions of global distributional ranges for 115 species, including all extant pinnipeds and cetaceans. We used an environmental suitability model specifically designed to address the paucity of distributional data for many marine mammal species. We generated richness patterns by overlaying predicted distributions for all species; these were then validated against sightings data from dedicated long-term surveys in the Eastern Tropical Pacific, the Northeast Atlantic and the Southern Ocean. Model outputs correlated well with empirically observed patterns of biodiversity in all three survey regions. Marine mammal richness was predicted to be highest in temperate waters of both hemispheres with distinct hotspots around New Zealand, Japan, Baja California, the Galapagos Islands, the Southeast Pacific, and the Southern Ocean. We then applied our model to explore potential changes in biodiversity under future perturbations of environmental conditions. Forward projections of biodiversity using an intermediate Intergovernmental Panel for Climate Change (IPCC) temperature scenario predicted that projected ocean warming and changes in sea ice cover until 2050 may have moderate effects on the spatial patterns of marine mammal richness. Increases in cetacean richness were predicted above 40° latitude in both hemispheres, while decreases in both pinniped and cetacean richness were expected at lower latitudes. Our results show how species distribution models can be applied to explore broad patterns of marine biodiversity worldwide for taxa for which limited distributional data are available. PMID:21625431

  15. Current and future patterns of global marine mammal biodiversity.

    Directory of Open Access Journals (Sweden)

    Kristin Kaschner

    Full Text Available Quantifying the spatial distribution of taxa is an important prerequisite for the preservation of biodiversity, and can provide a baseline against which to measure the impacts of climate change. Here we analyse patterns of marine mammal species richness based on predictions of global distributional ranges for 115 species, including all extant pinnipeds and cetaceans. We used an environmental suitability model specifically designed to address the paucity of distributional data for many marine mammal species. We generated richness patterns by overlaying predicted distributions for all species; these were then validated against sightings data from dedicated long-term surveys in the Eastern Tropical Pacific, the Northeast Atlantic and the Southern Ocean. Model outputs correlated well with empirically observed patterns of biodiversity in all three survey regions. Marine mammal richness was predicted to be highest in temperate waters of both hemispheres with distinct hotspots around New Zealand, Japan, Baja California, the Galapagos Islands, the Southeast Pacific, and the Southern Ocean. We then applied our model to explore potential changes in biodiversity under future perturbations of environmental conditions. Forward projections of biodiversity using an intermediate Intergovernmental Panel for Climate Change (IPCC temperature scenario predicted that projected ocean warming and changes in sea ice cover until 2050 may have moderate effects on the spatial patterns of marine mammal richness. Increases in cetacean richness were predicted above 40° latitude in both hemispheres, while decreases in both pinniped and cetacean richness were expected at lower latitudes. Our results show how species distribution models can be applied to explore broad patterns of marine biodiversity worldwide for taxa for which limited distributional data are available.

  16. Mosquitoes of eastern Amazonian Ecuador: biodiversity, bionomics and barcodes

    OpenAIRE

    Yvonne-Marie Linton; Pecor, James E; Porter,Charles H; Luke Brett Mitchell; Andres Garzon-Moreno; Foley, Desmond H.; David Brooks Pecor; Wilkerson, Richard C

    2013-01-01

    Two snapshot surveys to establish the diversity and ecological preferences of mosquitoes (Diptera: Culicidae) in the terra firme primary rain forest surrounding the Tiputini Biodiversity Station in the UNESCO Yasuní Biosphere Reserve of eastern Amazonian Ecuador were carried out in November 1998 and May 1999. The mosquito fauna of this region is poorly known; the focus of this study was to obtain high quality link-reared specimens that could be used to unequivocally confirm species level...

  17. Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

    DEFF Research Database (Denmark)

    Froslev, Tobias Guldberg; Kjoller, Rasmus; Bruun, Hans Henrik

    2017-01-01

    DNA metabarcoding is promising for cost-effective biodiversity monitoring, but reliable diversity estimates are difficult to achieve and validate. Here we present and validate a method, called LULU, for removing erroneous molecular operational taxonomic units (OTUs) from community data derived...... soil from 130 sites in Denmark spanning major environmental gradients. OTU tables are produced with several different OTU definition algorithms and subsequently curated with LULU, and validated against field survey data. LULU curation consistently improves α-diversity estimates and other biodiversity...... metrics, and does not require a sequence reference database; thus, it represents a promising method for reliable biodiversity estimation....

  18. Speciation gradients and the distribution of biodiversity.

    Science.gov (United States)

    Schluter, Dolph; Pennell, Matthew W

    2017-05-31

    Global patterns of biodiversity are influenced by spatial and environmental variations in the rate at which new species form. We relate variations in speciation rates to six key patterns of biodiversity worldwide, including the species-area relationship, latitudinal gradients in species and genetic diversity, and between-habitat differences in species richness. Although they sometimes mirror biodiversity patterns, recent rates of speciation, at the tip of the tree of life, are often highest where species richness is low. Speciation gradients therefore shape, but are also shaped by, biodiversity gradients and are often more useful for predicting future patterns of biodiversity than for interpreting the past.

  19. Options for promoting high-biodiversity REDD+

    Energy Technology Data Exchange (ETDEWEB)

    Swan, Steve; Mcnally, Richard; Grieg-Gran, Maryanne; Roe, Dilys; Mohammed, Essam Yassin

    2011-11-15

    International climate and biodiversity conventions agree that to be effective in the long term, strategies to reduce emissions from deforestation, forest degradation, conservation and enhancement of forest carbon stocks, and sustainable forest management (REDD+), must not undermine biodiversity. But how do countries achieve 'high-biodiversity REDD+' in practice? At a global level, options include immediate policy strengthening in international negotiations; promotion of co-benefit standards; and financial incentives and preferences for buying countries. At a national level, developing countries can also promote high-biodiversity REDD+ through more coherent policies; integrated planning; regulatory and economic instruments; and improved monitoring of biodiversity impacts.

  20. Rocky road in the Rockies: Challenges to biodiversity

    Science.gov (United States)

    Tomback, Diana F.; Kendall, Katherine C.

    2002-01-01

    degree of natural ecosystem processes and preserve natural biodiversity in light of these challenges, Americans and Canadians are faced with the need for intensive, hands-on management of both ecosystems and selected plant and animal populations. In this chapter, we first discuss the primary issues regarding the biodiversity of the Rocky Mountains, including the Rocky Mountain portions of Arizona, Colorado, Idaho, Montana, New Mexico, Utah, Wyoming, British Columbia, and Alberta. Next, we survey groups of organisms to examine their status and special problems. Finally, we touch on major challenges to biodiversity that loom in the near future. Given that entire books may be written on these issues, the discussion is brief and general, but with case histories for more detailed examples.

  1. A study on the biodiversity of benthic invertebrates in the waters of Seogwipo, Jeju Island, Korea

    OpenAIRE

    In-Young Cho; Dong-Won Kang; Jisoon Kang; Hosung Hwang; Jeong-Hye Won; Woon Kee Paek; Su-Yuan Seo

    2014-01-01

    The biodiversity of benthic invertebrates in the intertidal and subtidal regions of Gapado, Beomseom, and Munseom islets was surveyed twice in May and September 2013 to study the state of biodiversity in Seogwipo, Jeju Island. As a result, a total of 77 species, 46 families, 25 orders, 14 classes, and nine phyla of benthic invertebrates were found. The species which were found, by taxon, consisted of the following: 26 species of Cnidaria (34%), 24 species of Mollusca (31%), seven species of C...

  2. Why evolutionary biologists should get seriously involved in ecological monitoring and applied biodiversity assessment programs

    OpenAIRE

    Brodersen, Jakob; Seehausen, Ole

    2014-01-01

    While ecological monitoring and biodiversity assessment programs are widely implemented and relatively well developed to survey and monitor the structure and dynamics of populations and communities in many ecosystems, quantitative assessment and monitoring of genetic and phenotypic diversity that is important to understand evolutionary dynamics is only rarely integrated. As a consequence, monitoring programs often fail to detect changes in these key components of biodiversity until after majo...

  3. Combining internal and external motivations in multi-actor governance arrangements for biodiversity and ecosystem services

    OpenAIRE

    Dedeurwaerdere, Tom; Admiraal, Jeroen; Beringer, Almut; Bonaiuto, Flavia; Cicero, Lavinia; Fernandez-Wulff, Paula; Hagens, Janneke; Hiedanpää, Juha; Knights, Paul; Molinario, Erica; Melindi-Ghidi, Paolo; Popa, Florin; Šilc, Urban; Soethe, Nathalie; Soininen, Tina

    2016-01-01

    This paper analyses the possibility of building a mutually supportive dynamics between internally and externally motivated behaviour for biodiversity conservation and ecosystem services provision. To this purpose a face to face survey amongst 169 key actors of 34 highly successful and prominent biodiversity arrangements in seven EU countries was conducted. The main finding of the paper is the feasibility of combining inherently intrinsically motivated behaviours (providing enjoyment, pleasure...

  4. Scaling laws predict global microbial diversity.

    Science.gov (United States)

    Locey, Kenneth J; Lennon, Jay T

    2016-05-24

    Scaling laws underpin unifying theories of biodiversity and are among the most predictively powerful relationships in biology. However, scaling laws developed for plants and animals often go untested or fail to hold for microorganisms. As a result, it is unclear whether scaling laws of biodiversity will span evolutionarily distant domains of life that encompass all modes of metabolism and scales of abundance. Using a global-scale compilation of ∼35,000 sites and ∼5.6⋅10(6) species, including the largest ever inventory of high-throughput molecular data and one of the largest compilations of plant and animal community data, we show similar rates of scaling in commonness and rarity across microorganisms and macroscopic plants and animals. We document a universal dominance scaling law that holds across 30 orders of magnitude, an unprecedented expanse that predicts the abundance of dominant ocean bacteria. In combining this scaling law with the lognormal model of biodiversity, we predict that Earth is home to upward of 1 trillion (10(12)) microbial species. Microbial biodiversity seems greater than ever anticipated yet predictable from the smallest to the largest microbiome.

  5. Biodiversity in the Anthropocene: prospects and policy.

    Science.gov (United States)

    Seddon, Nathalie; Mace, Georgina M; Naeem, Shahid; Tobias, Joseph A; Pigot, Alex L; Cavanagh, Rachel; Mouillot, David; Vause, James; Walpole, Matt

    2016-12-14

    Meeting the ever-increasing needs of the Earth's human population without excessively reducing biological diversity is one of the greatest challenges facing humanity, suggesting that new approaches to biodiversity conservation are required. One idea rapidly gaining momentum-as well as opposition-is to incorporate the values of biodiversity into decision-making using economic methods. Here, we develop several lines of argument for how biodiversity might be valued, building on recent developments in natural science, economics and science-policy processes. Then we provide a synoptic guide to the papers in this special feature, summarizing recent research advances relevant to biodiversity valuation and management. Current evidence suggests that more biodiverse systems have greater stability and resilience, and that by maximizing key components of biodiversity we maximize an ecosystem's long-term value. Moreover, many services and values arising from biodiversity are interdependent, and often poorly captured by standard economic models. We conclude that economic valuation approaches to biodiversity conservation should (i) account for interdependency and (ii) complement rather than replace traditional approaches. To identify possible solutions, we present a framework for understanding the foundational role of hard-to-quantify 'biodiversity services' in sustaining the value of ecosystems to humanity, and then use this framework to highlight new directions for pure and applied research. In most cases, clarifying the links between biodiversity and ecosystem services, and developing effective policy and practice for managing biodiversity, will require a genuinely interdisciplinary approach. © 2016 The Author(s).

  6. Mangrove microbial diversity and the impact of trophic contamination

    OpenAIRE

    Bouchez, A.; Pascault, N.; Chardon, C.; Bouvy, Marc; Cecchi, Philippe; Lambs, L.; Herteman, M.; Fromard, F.; Got, Patrice; Leboulanger, Christophe

    2013-01-01

    International audience; Mangroves are threatened ecosystems that provide numerous ecosystem services, especially through their wide biodiversity, and their bioremediation capacity is a challenging question in tropical areas. In a mangrove in Mayotte, we studied the potential role of microbial biofilm communities in removing nutrient loads from pre-treated wastewater. Microbial community samples were collected from tree roots, sediments, water, and from a colonization device, and their structu...

  7. Microbial biotechnology addressing the plastic waste disaster

    OpenAIRE

    Narancic, Tanja; O'Connor, Kevin E.

    2017-01-01

    Oceans are a major source of biodiversity, they provide livelihood, and regulate the global ecosystem by absorbing heat and CO 2. However, they are highly polluted with plastic waste. We are discussing here microbial biotechnology advances with the view to improve the start and the end of life of biodegradable polymers, which could contribute to the sustainable use of marine and coastal ecosystems (UN Sustainability development goal 14).

  8. Accounting for biodiversity in the dairy industry.

    Science.gov (United States)

    Sizemore, Grant C

    2015-05-15

    Biodiversity is an essential part of properly functioning ecosystems, yet the loss of biodiversity currently occurs at rates unparalleled in the modern era. One of the major causes of this phenomenon is habitat loss and modification as a result of intensified agricultural practices. This paper provides a starting point for considering biodiversity within dairy production, and, although focusing primarily on the United States, findings are applicable broadly. Biodiversity definitions and assessments (e.g., indicators, tools) are proposed and reviewed. Although no single indicator or tool currently meets all the needs of comprehensive assessment, many sustainable practices are readily adoptable as ways to conserve and promote biodiversity. These practices, as well as potential funding opportunities are identified. Given the state of uncertainty in addressing the complex nature of biodiversity assessments, the adoption of generally sustainable environmental practices may be the best currently available option for protecting biodiversity on dairy lands. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Poor prospects for avian biodiversity in Amazonian oil palm.

    Science.gov (United States)

    Lees, Alexander C; Moura, Nárgila G; de Almeida, Arlete Silva; Vieira, Ima C G

    2015-01-01

    Expansion of oil palm plantations across the humid tropics has precipitated massive loss of tropical forest habitats and their associated speciose biotas. Oil palm plantation monocultures have been identified as an emerging threat to Amazonian biodiversity, but there are no quantitative studies exploring the impact of these plantations on the biome's biota. Understanding these impacts is extremely important given the rapid projected expansion of oil palm cultivation in the basin. Here we investigate the biodiversity value of oil palm plantations in comparison with other dominant regional land-uses in Eastern Amazonia. We carried out bird surveys in oil palm plantations of varying ages, primary and secondary forests, and cattle pastures. We found that oil palm plantations retained impoverished avian communities with a similar species composition to pastures and agrarian land-uses and did not offer habitat for most forest-associated species, including restricted range species and species of conservation concern. On the other hand, the forests that the oil palm companies are legally obliged to protect hosted a relatively species-rich community including several globally-threatened bird species. We consider oil palm to be no less detrimental to regional biodiversity than other agricultural land-uses and that political pressure exerted by large landowners to allow oil palm to count as a substitute for native forest vegetation in private landholdings with forest restoration deficits would have dire consequences for regional biodiversity.

  10. Observations of Everyday Biodiversity: a New Perspective for Conservation?

    Directory of Open Access Journals (Sweden)

    Alix Cosquer

    2012-12-01

    Full Text Available Public involvement is one of the keys to achieving biodiversity conservation goals. Increasing public involvement in conservation activities requires investigation into what makes people more aware of nature, especially in an ordinary and local context, in their everyday lives. Among the initiatives developed to increase the public's awareness of conservation issues and individual environmental practices, citizen-science programs are based on an invitation to observe and survey nature. In our study, we examined the consequences of participation in a participative citizen-science program that takes place in an everyday-life context on individuals' knowledge and beliefs about biodiversity. This program, the French Garden Butterflies Watch, is addressed to the non-scientifically literate public and is run by the French National Museum of Natural History (MNHN. We examined the ways increased knowledge or strengthened beliefs or ideas about biodiversity can foster pro-conservation attitudes and behavior. We explored how repeated interactions with nature influence the development of knowledge in this area, and how these repeated observations of biodiversity become integrated into complex cognitive processes over time and space. We showed that repeated observations of nature can increase individual knowledge and beliefs. Our results brought out three important conclusions: (1 conservation issues must be integrated into a wider network of social relationships; (2 observing everyday nature often makes people consider its functional and evolutionary characteristics; and (3 scientific knowledge seems necessary to help people to develop their own position on ecosystems.

  11. [From biodiversity to biodiversification: a new economy of nature?].

    Science.gov (United States)

    Höhler, Sabine

    2014-03-01

    This paper explores the relations between economy and ecology in the last quarter of the 20th century with the example of biodiversity. From its definition in the 1980s, the concept of biodiversity responded not only to conservational concerns but also to hopes and demands of economic profitability. The paper argues that archival systems of inventorying and surveying nature, the biodiversity database and the biodiversity portfolio, changed the view on nature from a resource to an investment. The paper studies the alliances of ecologists and environmental economists in managing nature according to economic principles of successful asset management, "diversification", with the aim to distribute risk, minimize ecological loss and maximize overall ecosystem performance. Finally, the paper discusses the assumptions and the consequences of transferring principles from financial risk management to landscape management. How has the substitution of the existential values of nature by shareholder value affected the relations between ecology, environment, and ecosystem conservation? Who gains and who looses in exchanging natural capital and financial capital, yields, and profits?

  12. Microbial ecology: new insights into the great wide-open culture independent sea

    Science.gov (United States)

    Microbial communities are the basis for most, if not all, biochemical or biogeochemical functions in the environment. These environments are vastly different with respect to matrix, function, and biodiversity, and as such, present minute to stark differences in their respective microbial communities...

  13. Intellectual Property and biodiversity: interplay.

    Science.gov (United States)

    Bhola, Ravi; Dave, Shreya

    2017-05-01

    Potentially divergent objectives and thereby obligations under the Convention on Biodiversity and Trade-Related Aspects of Intellectual Property Rights Agreement are also reflected in respective domestic legislations in India. The review article focuses on Biological Diversity Act, 2002 vis-à-vis Patents Act, 1970 of India with intricacies involved thereunder. Authors have analyzed the obligations under these domestic legislations. The article goes on to make a few suggestions to aid effective implementation of both the statutes. The scope of this review article is limited in two aspects; first, it speaks only about Indian landscape and second, it discusses about interplay of biodiversity law only with respect to patent law instead of all the domestic Intellectual Property enactments of India.

  14. Medicinal plants, human health and biodiversity: a broad review.

    Science.gov (United States)

    Sen, Tuhinadri; Samanta, Samir Kumar

    2015-01-01

    Biodiversity contributes significantly towards human livelihood and development and thus plays a predominant role in the well being of the global population. According to WHO reports, around 80 % of the global population still relies on botanical drugs; today several medicines owe their origin to medicinal plants. Natural substances have long served as sources of therapeutic drugs, where drugs including digitalis (from foxglove), ergotamine (from contaminated rye), quinine (from cinchona), and salicylates (willow bark) can be cited as some classical examples.Drug discovery from natural sources involve a multifaceted approach combining botanical, phytochemical, biological, and molecular techniques. Accordingly, medicinal-plant-based drug discovery still remains an important area, hitherto unexplored, where a systematic search may definitely provide important leads against various pharmacological targets.Ironically, the potential benefits of plant-based medicines have led to unscientific exploitation of the natural resources, a phenomenon that is being observed globally. This decline in biodiversity is largely the result of the rise in the global population, rapid and sometimes unplanned industrialization, indiscriminate deforestation, overexploitation of natural resources, pollution, and finally global climate change.Therefore, it is of utmost importance that plant biodiversity be preserved, to provide future structural diversity and lead compounds for the sustainable development of human civilization at large. This becomes even more important for developing nations, where well-planned bioprospecting coupled with nondestructive commercialization could help in the conservation of biodiversity, ultimately benefiting mankind in the long run.Based on these findings, the present review is an attempt to update our knowledge about the diverse therapeutic application of different plant products against various pharmacological targets including cancer, human brain

  15. Biodiversity Effects on Plant Stoichiometry

    OpenAIRE

    Maike Abbas; Anne Ebeling; Yvonne Oelmann; Robert Ptacnik; Christiane Roscher; Alexandra Weigelt; Wolfgang W Weisser; Wolfgang Wilcke; Helmut Hillebrand

    2013-01-01

    In the course of the biodiversity-ecosystem functioning debate, the issue of multifunctionality of species communities has recently become a major focus. Elemental stoichiometry is related to a variety of processes reflecting multiple plant responses to the biotic and abiotic environment. It can thus be expected that the diversity of a plant assemblage alters community level plant tissue chemistry. We explored elemental stoichiometry in aboveground plant tissue (ratios of carbon, nitrogen, ph...

  16. Island biodiversity conservation needs palaeoecology

    DEFF Research Database (Denmark)

    Nogué, Sandra; de Nascimento, Lea; Froyd, Cynthia A.

    2017-01-01

    to human activities. Consequently, even the most degraded islands are a focus for restoration, eradication, and monitoring programmes to protect the remaining endemic and/or relict populations. Here, we build a framework that incorporates an assessment of the degree of change from multiple baseline...... and the introduction of non-native species. We provide exemplification of how such approaches can provide valuable information for biodiversity conservation managers of island ecosystems....

  17. Seeing global biodiversity in a new light

    Science.gov (United States)

    Pavlick, R.

    2016-12-01

    Earth's biodiversity is experiencing rapid and widespread decline and alterations due to multiple interacting anthropogenic drivers. Mounting evidence synthesized from many biodiversity manipulation experiments, conducted primarily at the field and lab scale, indicate that biodiversity changes threaten ecosystem services essential for human well-being. However, at regional and global scales, relatively little is known quantitatively about how much and what kinds of biodiversity can be lost before key aspects of ecosystem functioning are eroded . The extent and rate at which biodiversity losses are pushing ecosystems towards critical tipping points in to undesirable and irreversibly degraded states with decreased functioning and dangerous reductions to ecosystem services remains a major gap in Earth system knowledge High-resolution and timely global data on Earth's biodiversity are crucial for understanding and predicting changes to Earth's life support systems, yet existing data sources are sorely lacking in spatial coverage, are nonsystematic, and arriving too slowly to keep pace with accelerating environmental changes. Fortunately, parallel developments in biodiversity science and spectroscopic remote sensing could enable frequent global monitoring of one key dimension of biodiversity, the functional diversity of terrestrial and aquatic plants, corals, and phytoplankton.Here we report on a series of NASA-funded activities, wherein a diverse teams of biodiversity scientists and remote sensing experts have come together to propose a global biodiversity observing system which integrates repeated global functional diversity maps from spectroscopic satellite missions with in situ biodiversity observations. We also report on an initial draft plan for a potential NASA biodiversity airborne campaign utilizing AVIRIS-NG, PRISM, HyTES spectrometers, and the LVIS lidar on the ER-2 aircraft, along with an assessment of current biodiversity remote sensing algorithms.

  18. Biolog for the determination of diversity in microbial communities ...

    African Journals Online (AJOL)

    Molecular methods have been used to determine diversity of microbial communities, but indicate the genetic complexity within a community. An alternative approach is to examine components of functional biodiversity (i.e. substrate utilisation), for which there exists a reasonable chance of detecting patterns, which could be ...

  19. Patterns and Processes of Microbial Community Assembly

    Science.gov (United States)

    Schmidt, Steven K.; Fukami, Tadashi; O'Neill, Sean P.; Bilinski, Teresa M.; Stanish, Lee F.; Knelman, Joseph E.; Darcy, John L.; Lynch, Ryan C.; Wickey, Phillip; Ferrenberg, Scott

    2013-01-01

    SUMMARY Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183–206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity. PMID:24006468

  20. Enhancing the Biodiversity of Ditches in Intensively Managed UK Farmland

    Science.gov (United States)

    Shaw, Rosalind F.; Johnson, Paul J.; Macdonald, David W.; Feber, Ruth E.

    2015-01-01

    Drainage ditches, either seasonally flooded or permanent, are commonly found on intensively managed lowland farmland in the UK. They are potentially important for wetland biodiversity but, despite their ubiquity, information on their biodiversity and management in the wider countryside is scarce. We surveyed 175 ditches for their physical and chemical characteristics, spatial connectivity, plant communities and aquatic invertebrates in an area of intensively managed farmland in Oxfordshire, UK and collected information on ditch management from farmer interviews. Water depth and shade had a small impact on the diversity of plant and invertebrate communities in ditches. Increased shade over the ditch channel resulted in reduced taxonomic richness of both channel vegetation and aquatic invertebrates and channel vegetation cover was lower at shaded sites. Invertebrate taxonomic richness was higher when water was deeper. Spatial connectivity had no detectable impact on the aquatic invertebrate or plant communities found in ditches. The number of families within the orders Ephemeroptera, Plecoptera and Trichoptera (EPT), which contain many pollution-sensitive species, declined with decreasing pH of ditch water. As time since dredging increased, the number of EPT families increased in permanent ditches but decreased in temporary ditches. Whether or not a ditch was in an agri-environment scheme had little impact on the reported management regime or biodiversity value of the ditch. Measures for increasing the amount of water in ditches, by increasing the water depth or promoting retention of water in ditches, could increase the biodiversity value of ditches in agricultural land. Some temporary ditches for specialised species should be retained. Reducing the amount of shade over narrow ditches by managing adjacent hedgerows is also likely to increase the species diversity of plant and invertebrate communities within the ditch. We recommend that to preserve or enhance the

  1. Enhancing the Biodiversity of Ditches in Intensively Managed UK Farmland.

    Science.gov (United States)

    Shaw, Rosalind F; Johnson, Paul J; Macdonald, David W; Feber, Ruth E

    2015-01-01

    Drainage ditches, either seasonally flooded or permanent, are commonly found on intensively managed lowland farmland in the UK. They are potentially important for wetland biodiversity but, despite their ubiquity, information on their biodiversity and management in the wider countryside is scarce. We surveyed 175 ditches for their physical and chemical characteristics, spatial connectivity, plant communities and aquatic invertebrates in an area of intensively managed farmland in Oxfordshire, UK and collected information on ditch management from farmer interviews. Water depth and shade had a small impact on the diversity of plant and invertebrate communities in ditches. Increased shade over the ditch channel resulted in reduced taxonomic richness of both channel vegetation and aquatic invertebrates and channel vegetation cover was lower at shaded sites. Invertebrate taxonomic richness was higher when water was deeper. Spatial connectivity had no detectable impact on the aquatic invertebrate or plant communities found in ditches. The number of families within the orders Ephemeroptera, Plecoptera and Trichoptera (EPT), which contain many pollution-sensitive species, declined with decreasing pH of ditch water. As time since dredging increased, the number of EPT families increased in permanent ditches but decreased in temporary ditches. Whether or not a ditch was in an agri-environment scheme had little impact on the reported management regime or biodiversity value of the ditch. Measures for increasing the amount of water in ditches, by increasing the water depth or promoting retention of water in ditches, could increase the biodiversity value of ditches in agricultural land. Some temporary ditches for specialised species should be retained. Reducing the amount of shade over narrow ditches by managing adjacent hedgerows is also likely to increase the species diversity of plant and invertebrate communities within the ditch. We recommend that to preserve or enhance the

  2. Enhancing the Biodiversity of Ditches in Intensively Managed UK Farmland.

    Directory of Open Access Journals (Sweden)

    Rosalind F Shaw

    Full Text Available Drainage ditches, either seasonally flooded or permanent, are commonly found on intensively managed lowland farmland in the UK. They are potentially important for wetland biodiversity but, despite their ubiquity, information on their biodiversity and management in the wider countryside is scarce. We surveyed 175 ditches for their physical and chemical characteristics, spatial connectivity, plant communities and aquatic invertebrates in an area of intensively managed farmland in Oxfordshire, UK and collected information on ditch management from farmer interviews. Water depth and shade had a small impact on the diversity of plant and invertebrate communities in ditches. Increased shade over the ditch channel resulted in reduced taxonomic richness of both channel vegetation and aquatic invertebrates and channel vegetation cover was lower at shaded sites. Invertebrate taxonomic richness was higher when water was deeper. Spatial connectivity had no detectable impact on the aquatic invertebrate or plant communities found in ditches. The number of families within the orders Ephemeroptera, Plecoptera and Trichoptera (EPT, which contain many pollution-sensitive species, declined with decreasing pH of ditch water. As time since dredging increased, the number of EPT families increased in permanent ditches but decreased in temporary ditches. Whether or not a ditch was in an agri-environment scheme had little impact on the reported management regime or biodiversity value of the ditch. Measures for increasing the amount of water in ditches, by increasing the water depth or promoting retention of water in ditches, could increase the biodiversity value of ditches in agricultural land. Some temporary ditches for specialised species should be retained. Reducing the amount of shade over narrow ditches by managing adjacent hedgerows is also likely to increase the species diversity of plant and invertebrate communities within the ditch. We recommend that to preserve

  3. Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics.

    Science.gov (United States)

    Bokulich, Nicholas A; Collins, Thomas S; Masarweh, Chad; Allen, Greg; Heymann, Hildegarde; Ebeler, Susan E; Mills, David A

    2016-06-14

    Regionally distinct wine characteristics (terroir) are an important aspect of wine production and consumer appreciation. Microbial activity is an integral part of wine production, and grape and wine microbiota present regionally defined patterns associated with vineyard and climatic conditions, but the degree to which these microbial patterns associate with the chemical composition of wine is unclear. Through a longitudinal survey of over 200 commercial wine fermentations, we demonstrate that both grape microbiota and wine metabolite profiles distinguish viticultural area designations and individual vineyards within Napa and Sonoma Counties, California. Associations among wine microbiota and fermentation characteristics suggest new links between microbiota, fermentation performance, and wine properties. The bacterial and fungal consortia of wine fermentations, composed from vineyard and winery sources, correlate with the chemical composition of the finished wines and predict metabolite abundances in finished wines using machine learning models. The use of postharvest microbiota as an early predictor of wine chemical composition is unprecedented and potentially poses a new paradigm for quality control of agricultural products. These findings add further evidence that microbial activity is associated with wine terroir Wine production is a multi-billion-dollar global industry for which microbial control and wine chemical composition are crucial aspects of quality. Terroir is an important feature of consumer appreciation and wine culture, but the many factors that contribute to terroir are nebulous. We show that grape and wine microbiota exhibit regional patterns that correlate with wine chemical composition, suggesting that the grape microbiome may influence terroir In addition to enriching our understanding of how growing region and wine properties interact, this may provide further economic incentive for agricultural and enological practices that maintain regional

  4. Global biodiversity: indicators of recent declines.

    Science.gov (United States)

    Butchart, Stuart H M; Walpole, Matt; Collen, Ben; van Strien, Arco; Scharlemann, Jörn P W; Almond, Rosamunde E A; Baillie, Jonathan E M; Bomhard, Bastian; Brown, Claire; Bruno, John; Carpenter, Kent E; Carr, Geneviève M; Chanson, Janice; Chenery, Anna M; Csirke, Jorge; Davidson, Nick C; Dentener, Frank; Foster, Matt; Galli, Alessandro; Galloway, James N; Genovesi, Piero; Gregory, Richard D; Hockings, Marc; Kapos, Valerie; Lamarque, Jean-Francois; Leverington, Fiona; Loh, Jonathan; McGeoch, Melodie A; McRae, Louise; Minasyan, Anahit; Hernández Morcillo, Monica; Oldfield, Thomasina E E; Pauly, Daniel; Quader, Suhel; Revenga, Carmen; Sauer, John R; Skolnik, Benjamin; Spear, Dian; Stanwell-Smith, Damon; Stuart, Simon N; Symes, Andy; Tierney, Megan; Tyrrell, Tristan D; Vié, Jean-Christophe; Watson, Reg

    2010-05-28

    In 2002, world leaders committed, through the Convention on Biological Diversity, to achieve a significant reduction in the rate of biodiversity loss by 2010. We compiled 31 indicators to report on progress toward this target. Most indicators of the state of biodiversity (covering species' population trends, extinction risk, habitat extent and condition, and community composition) showed declines, with no significant recent reductions in rate, whereas indicators of pressures on biodiversity (including resource consumption, invasive alien species, nitrogen pollution, overexploitation, and climate change impacts) showed increases. Despite some local successes and increasing responses (including extent and biodiversity coverage of protected areas, sustainable forest management, policy responses to invasive alien species, and biodiversity-related aid), the rate of biodiversity loss does not appear to be slowing.

  5. Biodiversity Monitoring in Changing Tropical Forests: A Review of Approaches and New Opportunities

    Directory of Open Access Journals (Sweden)

    Kalkidan Ayele Mulatu

    2017-10-01

    Full Text Available Tropical forests host at least two-thirds of the world’s flora and fauna diversity and store 25% of the terrestrial above and belowground carbon. However, biodiversity decline due to deforestation and forest degradation of tropical forest is increasing at an alarming rate. Biodiversity dynamics due to natural and anthropogenic disturbances are mainly monitored using established field survey approaches. However, such approaches appear to fall short at addressing complex disturbance factors and responses. We argue that the integration of state-of-the-art monitoring approaches can improve the detection of subtle biodiversity disturbances and responses in changing tropical forests, which are often data-poor. We assess the state-of-the-art technologies used to monitor biodiversity dynamics of changing tropical forests, and how their potential integration can increase the detail and accuracy of biodiversity monitoring. Moreover, the relevance of these biodiversity monitoring techniques in support of the UNCBD Aichi targets was explored using the Essential Biodiversity Variables (EBVs as a framework. Our review indicates that although established field surveys were generally the dominant monitoring systems employed, the temporal trend of monitoring approaches indicates the increasing application of remote sensing and in -situ sensors in detecting disturbances related to agricultural activities, logging, hunting and infrastructure. The relevance of new technologies (i.e., remote sensing, in situ sensors, and DNA barcoding in operationalising EBVs (especially towards the ecosystem structure, ecosystem function, and species population classes and the Aichi targets has been assessed. Remote sensing application is limited for EBV classes such as genetic composition and species traits but was found most suitable for ecosystem structure class. The complementarity of remote sensing and emerging technologies were shown in relation to EBV candidates such as

  6. Yeast biodiversity in Slovenian wine regions: Case amino acids in spontaneous and induced fermentations of Malvasia

    OpenAIRE

    Raspor Peter I.; Zagorc Tatjana I.; Povhe-Jemec Katja R.; Čadež Neža I.

    2009-01-01

    Microbial biodiversity can also be reflected in final product composition. The work described in this paper investigates the differences in the amino acid composition of 14 Malvasia musts/wines fermented with local and commercial starter yeasts, comparing all to the spontaneous fermentations of must of the same origin. We tried to ascertain whether the changes were dependent upon different initiations of fermentations. A comparative study of free and total amino acid evolution was prepared. T...

  7. Exploring fungal biodiversity for the production of water-soluble pigments as potential natural food colorants

    DEFF Research Database (Denmark)

    Mapari, Sameer Shamsuddin; Nielsen, Kristian Fog; Larsen, Thomas Ostenfeld

    2005-01-01

    be produced in high yields. The recent authorization of a fungal food colorant has fuelled research to explore the extraordinary chemical diversity and biodiversity of fungi for the biotechnological production of pigments as natural food colorants. These studies require an appropriate use of chernotaxonomic...... technology, in the future it should be possible to employ metabolic engineering to create microbial cell factories for the production of food colorants....

  8. Circumpolar Biodiversity Monitoring Programme coastal biodiversity monitoring background paper

    Science.gov (United States)

    McLennan, Donald; Anderson, Rebecca D.; Wegeberg, S.; Pettersvik Arvnes, Maria; Sergienko, Liudmila; Behe, Carolina; Moss-Davies, Pitseolak; Fritz, S.; Markon, Carl J.; Christensen, T.; Barry, T.; Price, C.

    2016-01-01

    In 2014, the United States (U.S.) and Canada agreed to act as co-lead countries for the initial development of the Coastal Expert Monitoring Group (CEMG) as part of the Circumpolar Biodiversity Monitoring Program (CBMP, www. cbmp.is) under the Arctic Council’s Conservation of Arctic Flora and Fauna (CAFF, www.caff.is) working group. The CAFF Management Board approved Terms of Reference for the CEMG in the spring of 2014. The primary goal of the CEMG is to develop a long term, integrated, multi-disciplinary, circumpolar Arctic Coastal Biodiversity Monitoring Plan (the Coastal Plan) that relies on science and Traditional Knowledge, and has direct and relevant application for communities, industry, government decision makers, and other users. In addition to the monitoring plan, the CAFF working group has asked the CBMP, and thus the CEMG, to develop an implementation plan that identifies timeline, costs, organizational structure and partners. This background paper provides a platform for the guidance for the development of the Coastal Plan and is produced by the CEMG with assistance from a number of experts in multiple countries.

  9. Bridging the gap between biodiversity data and policy reporting needs: An essential biodiversity variables perspective

    CSIR Research Space (South Africa)

    Geijzendorffer, IR

    2016-01-01

    Full Text Available Political commitment and policy instruments to halt biodiversity loss require robust data and a diverse indicator set to monitor and report on biodiversity trends. Gaps in data availability and narrow-based indicator sets are significant information...

  10. Marine biodiversity in Japanese waters.

    Directory of Open Access Journals (Sweden)

    Katsunori Fujikura

    Full Text Available To understand marine biodiversity in Japanese waters, we have compiled information on the marine biota in Japanese waters, including the number of described species (species richness, the history of marine biology research in Japan, the state of knowledge, the number of endemic species, the number of identified but undescribed species, the number of known introduced species, and the number of taxonomic experts and identification guides, with consideration of the general ocean environmental background, such as the physical and geological settings. A total of 33,629 species have been reported to occur in Japanese waters. The state of knowledge was extremely variable, with taxa containing many inconspicuous, smaller species tending to be less well known. The total number of identified but undescribed species was at least 121,913. The total number of described species combined with the number of identified but undescribed species reached 155,542. This is the best estimate of the total number of species in Japanese waters and indicates that more than 70% of Japan's marine biodiversity remains un-described. The number of species reported as introduced into Japanese waters was 39. This is the first attempt to estimate species richness for all marine species in Japanese waters. Although its marine biota can be considered relatively well known, at least within the Asian-Pacific region, considering the vast number of different marine environments such as coral reefs, ocean trenches, ice-bound waters, methane seeps, and hydrothermal vents, much work remains to be done. We expect global change to have a tremendous impact on marine biodiversity and ecosystems. Japan is in a particularly suitable geographic situation and has a lot of facilities for conducting marine science research. Japan has an important responsibility to contribute to our understanding of life in the oceans.

  11. Biodiversity

    CSIR Research Space (South Africa)

    Scholes, RJ

    2006-01-01

    Full Text Available are enjoyed by foreign owners and middlemen in the tourism market chain. In best practice examples, the costs to local people are minimized by negotiated access, and the benefits are spread by joint ownership, profit-sharing, preferential employment... and others 1994), which is an exceptionally high proportion by global standards. More recent studies suggest that these figures for species richness and endemism in Madagascar may be underestimates (Goodman 2004). Southern Africa has a rich and varied...

  12. Filling in biodiversity threat gaps

    DEFF Research Database (Denmark)

    Joppa, L. N.; O'Connor, Brian; Visconti, Piero

    2016-01-01

    he diversity of life on Earth—which provides vital services to humanity (1)—stems from the difference between rates of evolutionary diversification and extinction. Human activities have shifted the balance (2): Species extinction rates are an estimated 1000 times the “background” rate (3) and cou...... into the United Nations' 2030 Agenda for Sustainable Development and its 17 Sustainable Development Goals (SDGs). We identify major gaps in data available for assessing global biodiversity threats and suggest mechanisms for closing them....

  13. Constructing a biodiversity terminological inventory.

    Directory of Open Access Journals (Sweden)

    Nhung T H Nguyen

    Full Text Available The increasing growth of literature in biodiversity presents challenges to users who need to discover pertinent information in an efficient and timely manner. In response, text mining techniques offer solutions by facilitating the automated discovery of knowledge from large textual data. An important step in text mining is the recognition of concepts via their linguistic realisation, i.e., terms. However, a given concept may be referred to in text using various synonyms or term variants, making search systems likely to overlook documents mentioning less known variants, which are albeit relevant to a query term. Domain-specific terminological resources, which include term variants, synonyms and related terms, are thus important in supporting semantic search over large textual archives. This article describes the use of text mining methods for the automatic construction of a large-scale biodiversity term inventory. The inventory consists of names of species, amongst which naming variations are prevalent. We apply a number of distributional semantic techniques on all of the titles in the Biodiversity Heritage Library, to compute semantic similarity between species names and support the automated construction of the resource. With the construction of our biodiversity term inventory, we demonstrate that distributional semantic models are able to identify semantically similar names that are not yet recorded in existing taxonomies. Such methods can thus be used to update existing taxonomies semi-automatically by deriving semantically related taxonomic names from a text corpus and allowing expert curators to validate them. We also evaluate our inventory as a means to improve search by facilitating automatic query expansion. Specifically, we developed a visual search interface that suggests semantically related species names, which are available in our inventory but not always in other repositories, to incorporate into the search query. An assessment of

  14. Antarctica and the strategic plan for biodiversity.

    Science.gov (United States)

    Chown, Steven L; Brooks, Cassandra M; Terauds, Aleks; Le Bohec, Céline; van Klaveren-Impagliazzo, Céline; Whittington, Jason D; Butchart, Stuart H M; Coetzee, Bernard W T; Collen, Ben; Convey, Peter; Gaston, Kevin J; Gilbert, Neil; Gill, Mike; Höft, Robert; Johnston, Sam; Kennicutt, Mahlon C; Kriesell, Hannah J; Le Maho, Yvon; Lynch, Heather J; Palomares, Maria; Puig-Marcó, Roser; Stoett, Peter; McGeoch, Melodie A

    2017-03-01

    The Strategic Plan for Biodiversity, adopted under the auspices of the Convention on Biological Diversity, provides the basis for taking effective action to curb biodiversity loss across the planet by 2020-an urgent imperative. Yet, Antarctica and the Southern Ocean, which encompass 10% of the planet's surface, are excluded from assessments of progress against the Strategic Plan. The situation is a lost opportunity for biodiversity conservation globally. We provide such an assessment. Our evidence suggests, surprisingly, that for a region so remote and apparently pristine as the Antarctic, the biodiversity outlook is similar to that for the rest of the planet. Promisingly, however, much scope for remedial action exists.

  15. Antarctica and the strategic plan for biodiversity.

    Directory of Open Access Journals (Sweden)

    Steven L Chown

    2017-03-01

    Full Text Available The Strategic Plan for Biodiversity, adopted under the auspices of the Convention on Biological Diversity, provides the basis for taking effective action to curb biodiversity loss across the planet by 2020-an urgent imperative. Yet, Antarctica and the Southern Ocean, which encompass 10% of the planet's surface, are excluded from assessments of progress against the Strategic Plan. The situation is a lost opportunity for biodiversity conservation globally. We provide such an assessment. Our evidence suggests, surprisingly, that for a region so remote and apparently pristine as the Antarctic, the biodiversity outlook is similar to that for the rest of the planet. Promisingly, however, much scope for remedial action exists.

  16. Circular linkages between soil biodiversity, fertility and plant productivity are limited to topsoil at the continental scale.

    Science.gov (United States)

    Delgado-Baquerizo, Manuel; Powell, Jeff R; Hamonts, Kelly; Reith, Frank; Mele, Pauline; Brown, Mark V; Dennis, Paul G; Ferrari, Belinda C; Fitzgerald, Anna; Young, Andrew; Singh, Brajesh K; Bissett, Andrew

    2017-08-01

    The current theoretical framework suggests that tripartite positive feedback relationships between soil biodiversity, fertility and plant productivity are universal. However, empirical evidence for these relationships at the continental scale and across different soil depths is lacking. We investigate the continental-scale relationships between the diversity of microbial and invertebrate-based soil food webs, fertility and above-ground plant productivity at 289 sites and two soil depths, that is 0-10 and 20-30 cm, across Australia. Soil biodiversity, fertility and plant productivity are strongly positively related in surface soils. Conversely, in the deeper soil layer, the relationships between soil biodiversity, fertility and plant productivity weaken considerably, probably as a result of a reduction in biodiversity and fertility with depth. Further modeling suggested that strong positive associations among soil biodiversity-fertility and fertility-plant productivity are limited to the upper soil layer (0-10 cm), after accounting for key factors, such as distance from the equator, altitude, climate and physicochemical soil properties. These findings highlight the importance of surface soil biodiversity for soil fertility, and suggest that any loss of surface soil could potentially break the links between soil biodiversity-fertility and/or fertility-plant productivity, which can negatively impact nutrient cycling and food production, upon which future generations depend. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  17. Sites for priority biodiversity conservation in the Caribbean Islands Biodiversity Hotspot

    OpenAIRE

    V. Anadon-Irizarry; D.C. Wege; A. Upgren; Young, R; Boom, B.; Leon, Y.M.; Y Arias; Koenig, K.; Morales, A.L.; Burke, W

    2012-01-01

    The Caribbean Islands Biodiversity Hotspot is exceptionally important for global biodiversity conservation due to high levels of species endemism and threat. A total of 755 Caribbean plant and vertebrate species are considered globally threatened, making it one of the top Biodiversity Hotspots in terms of threat levels. In 2009, Key Biodiversity Areas (KBAs) were identified for the Caribbean Islands through a regional-level analysis of accessible data and literature, followed by extensive nat...

  18. Biodiversity of soil bacteria exposed to sub-lethal concentrations of phosphonium-based ionic liquids: Effects of toxicity and biodegradation

    DEFF Research Database (Denmark)

    Sydow, Mateusz; Owsianiak, Mikołaj; Framski, Grzegorz

    2018-01-01

    Little is known about the effect of ionic liquids (ILs) on the structure of soil microbial communities and resulting biodiversity. Therefore, we studied the influence of six trihexyl(tetradecyl)phosphonium ILs (with either bromide or various organic anions) at sublethal concentrations...... on the structure of microbial community present in an urban park soil in 100-day microcosm experiments. The biodiversity decreased in all samples (Shannon's index decreased from 1.75 down to 0.74 and OTU's number decreased from 1399 down to 965) with the largest decrease observed in the microcosms spiked with ILs...... where biodegradation extent was higher than 80%. (i.e. [P66614][Br] and [P66614][2,4,4]). Despite this general decrease in biodiversity, which can be explained by ecotoxic effect of the ILs, the microbial community in the microcosms was enriched with Gram-negative hydrocarbon-degrading genera e...

  19. Towards global interoperability for supporting biodiversity research on Essential Biodiversity Variables (EBVs)

    NARCIS (Netherlands)

    Kissling, W.D.; Hardisty, A.; García, E.A.; Santamaria, M.; De Leo, F.; Pesole, G.; Freyhof, J.; Manset, D.; Wissel, S.; Konijn, J.; Los, W.

    2015-01-01

    Essential biodiversity variables (EBVs) have been proposed by the Group on Earth Observations Biodiversity Observation Network (GEO BON) to identify a minimum set of essential measurements that are required for studying, monitoring and reporting biodiversity and ecosystem change. Despite the initial

  20. BIOMETORE Project - Studying the Biodiversity in the Northeastern Atlantic Seamounts

    Science.gov (United States)

    Dos Santos, A.; Biscoito, M.; Campos, A.; Tuaty Guerra, M.; Meneses, G.; Santos, A. M. P. A.

    2016-02-01

    Understanding the deep-sea ecosystem functioning is a key issue in the study of ocean sciences. Bringing together researchers from several scientific domains, the BIOMETORE project aims to the increase knowledge on deep-sea ecosystems and biodiversity at the Atlantic seamounts of the Madeira-Tore and Great Meteor geological complexes. The project outputs will provide important information for the understanding and sustainable management of the target seamount ecosystems, thus contributing to fulfill knowledge gaps on their biodiversity, from bacteria to mammals, and food webs, as well as to promote future sustainable fisheries and sea-floor integrity. The plan includes the realization of eight multidisciplinary surveys, four done during the summer of 2015 and another four planned for the same season of 2016, in target seamounts: the Gorringe bank, the Josephine, and others in the Madeira-Tore, and selected ones in the Greta Meteor (northeastern Atlantic Ocean). The surveys cover a number of scientific areas in the domains of oceanography, ecology, integrative taxonomy, geology, fisheries and spatial mapping. We present and discuss BIOMETORE developments, the preliminary results from the four 2015 summer surveys, and the planning of the next four surveys.

  1. Soil microbial biomass and function are altered by 12 years of crop rotation

    Science.gov (United States)

    McDaniel, Marshall D.; Grandy, A. Stuart

    2016-11-01

    Declines in plant diversity will likely reduce soil microbial biomass, alter microbial functions, and threaten the provisioning of soil ecosystem services. We examined whether increasing temporal plant biodiversity in agroecosystems (by rotating crops) can partially reverse these trends and enhance soil microbial biomass and function. We quantified seasonal patterns in soil microbial biomass, respiration rates, extracellular enzyme activity, and catabolic potential three times over one growing season in a 12-year crop rotation study at the W. K. Kellogg Biological Station LTER. Rotation treatments varied from one to five crops in a 3-year rotation cycle, but all soils were sampled under a corn year. We hypothesized that crop diversity would increase microbial biomass, activity, and catabolic evenness (a measure of functional diversity). Inorganic N, the stoichiometry of microbial biomass and dissolved organic C and N varied seasonally, likely reflecting fluctuations in soil resources during the growing season. Soils from biodiverse cropping systems increased microbial biomass C by 28-112 % and N by 18-58 % compared to low-diversity systems. Rotations increased potential C mineralization by as much as 53 %, and potential N mineralization by 72 %, and both were related to substantially higher hydrolase and lower oxidase enzyme activities. The catabolic potential of the soil microbial community showed no, or slightly lower, catabolic evenness in more diverse rotations. However, the catabolic potential indicated that soil microbial communities were functionally distinct, and microbes from monoculture corn preferentially used simple substrates like carboxylic acids, relative to more diverse cropping systems. By isolating plant biodiversity from differences in fertilization and tillage, our study illustrates that crop biodiversity has overarching effects on soil microbial biomass and function that last throughout the growing season. In simplified agricultural systems

  2. Biodiversity of soil bacteria exposed to sub-lethal concentrations of phosphonium-based ionic liquids: Effects of toxicity and biodegradation.

    Science.gov (United States)

    Sydow, Mateusz; Owsianiak, Mikołaj; Framski, Grzegorz; Woźniak-Karczewska, Marta; Piotrowska-Cyplik, Agnieszka; Ławniczak, Łukasz; Szulc, Alicja; Zgoła-Grześkowiak, Agnieszka; Heipieper, Hermann J; Chrzanowski, Łukasz

    2018-01-01

    Little is known about the effect of ionic liquids (ILs) on the structure of soil microbial communities and resulting biodiversity. Therefore, we studied the influence of six trihexyl(tetradecyl)phosphonium ILs (with either bromide or various organic anions) at sublethal concentrations on the structure of microbial community present in an urban park soil in 100-day microcosm experiments. The biodiversity decreased in all samples (Shannon's index decreased from 1.75 down to 0.74 and OTU's number decreased from 1399 down to 965) with the largest decrease observed in the microcosms spiked with ILs where biodegradation extent was higher than 80%. (i.e. [P 66614 ][Br] and [P 66614 ][2,4,4]). Despite this general decrease in biodiversity, which can be explained by ecotoxic effect of the ILs, the microbial community in the microcosms was enriched with Gram-negative hydrocarbon-degrading genera e.g. Sphingomonas. It is hypothesized that, in addition to toxicity, the observed decrease in biodiversity and change in the microbial community structure may be explained by the primary biodegradation of the ILs or their metabolites by the mentioned genera, which outcompeted other microorganisms unable to degrade ILs or their metabolites. Thus, the introduction of phosphonium-based ILs into soils at sub-lethal concentrations may result not only in a decrease in biodiversity due to toxic effects, but also in enrichment with ILs-degrading bacteria. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Managing Agricultural Biodiversity for Nutrition, Health, Livelihoods ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Managing Agricultural Biodiversity for Nutrition, Health, Livelihoods and Sustainable Production Systems (Sub-Saharan Africa) ... Project status. Closed ... Managing agricultural biodiversity for better nutrition and health, improved livelihoods and more sustainable production systems in sub-Saharan Africa : case studies from ...

  4. Biodiversity and marginality: Dilemma of economic development

    OpenAIRE

    Piniero, M.C.

    2002-01-01

    This study investigates the impact of economic development on women and biodiversity in two rural communities in Ecuador. The level of womens integration into the development process as influenced by age, ethnicity, and socioeconomic status, are analyzed. The effects of the economic change on biodiversity using homegardens as its indicators are also evaluated.

  5. Intentional systems management: managing forests for biodiversity.

    Science.gov (United States)

    A.B. Carey; B.R. Lippke; J. Sessions

    1999-01-01

    Conservation of biodiversity provides for economic, social, and environmental sustainability. Intentional management is designed to manage conflicts among groups with conflicting interests. Our goal was to ascertain if intentional management and principles of conservation of biodiversity could be combined into upland and riparian forest management strategies that would...

  6. Does biodiversity protect humans against infectious disease?

    Science.gov (United States)

    Wood, Chelsea L; Lafferty, Kevin D; DeLeo, Giulio; Young, Hillary S; Hudson, Peter J; Kuris, Armand M

    2014-04-01

    Control of human infectious disease has been promoted as a valuable ecosystem service arising from the conservation of biodiversity. There are two commonly discussed mechanisms by which biodiversity loss could increase rates of infectious disease in a landscape. First, loss of competitors or predators could facilitate an increase in the abundance of competent reservoir hosts. Second, biodiversity loss could disproportionately affect non-competent, or less competent reservoir hosts, which would otherwise interfere with pathogen transmission to human populations by, for example, wasting the bites of infected vectors. A negative association between biodiversity and disease risk, sometimes called the "dilution effect hypothesis," has been supported for a few disease agents, suggests an exciting win-win outcome for the environment and society, and has become a pervasive topic in the disease ecology literature. Case studies have been assembled to argue that the dilution effect is general across disease agents. Less touted are examples in which elevated biodiversity does not affect or increases infectious disease risk for pathogens of public health concern. In order to assess the likely generality of the dilution effect, we review the association between biodiversity and public health across a broad variety of human disease agents. Overall, we hypothesize that conditions for the dilution effect are unlikely to be met for most important diseases of humans. Biodiversity probably has little net effect on most human infectious diseases but, when it does have an effect, observation and basic logic suggest that biodiversity will be more likely to increase than to decrease infectious disease risk.

  7. Assessment of biodiversity based on morphological characteristics ...

    African Journals Online (AJOL)

    Jane

    2011-10-03

    Oct 3, 2011 ... of biodiversity. Wild native resources are adapted to specific and diverse environmental conditions and therefore, these adaptive features can be introduced into modern cultivars either through ... contribute to further loss of biodiversity through ... identification and measuring of diversity (Maryum, 2000).

  8. Biodiversity and Tourism : Impacts and Interventions

    NARCIS (Netherlands)

    Duim, van der V.R.; Caalders, J.D.A.D.

    2002-01-01

    This paper sets a framework for intervention in the relationship between biodiversity and tourism against the background of the Convention on Biological Diversity. It is argued that intervention cannot and should not only be based on considerations of measurable impacts of tourism on biodiversity

  9. Plantation forests and biodiversity: oxymoron or opportunity?

    Science.gov (United States)

    Eckehard G. Brockerhoff; Hervé Jactel; John A. Parrotta; Christopher Quine; Jeffrey Sayer

    2008-01-01

    Losses of natural and semi-natural forests, mostly to agriculture, are a significant concern for biodiversity. Against this trend, the area of intensively managed plantation forests increases, and there is much debate about the implications for biodiversity. We provide a comprehensive review of the function of plantation forests as habitat compared with other land...

  10. Species Assortment and Biodiversity Conservation in Homegardens ...

    African Journals Online (AJOL)

    user

    that the urban gardens are a storehouse of biodiversity including species that run the risk of disappearance in the natural habitat. ... Species assortment and biodiversity conservation in homegardens of Bahir Dar. [33] consumption, and significantly ... Nile River and the Mediterranean Sea. The topography of the City is ...

  11. A new sampling formula for neutral biodiversity

    NARCIS (Netherlands)

    Etienne, R.S.

    2005-01-01

    The neutral model of biodiversity, proposed by Hubbell (The Unified Neutral Theory of Biodiversity and Biogeography, Princeton University Press, Princeton, NJ, 2001) to explain the diversity of functionally equivalent species, has been subject of hot debate in community ecology. Whereas Hubbell

  12. Biodiversity offsetting – en vogue in Madagascar?

    African Journals Online (AJOL)

    This entails 'adequate' compensation in form of upgrading the environmental value of other sites. The 'successful' ... used to quantify biodiversity values in such a context (Hirsch et al. 2011). However, biodiversity trade - offs ... (such as industrial mining) and to enhance global reputation. (“we are practicing conservation and ...

  13. Bussiness Cases for Biodiversity: the smallholders' perspective

    NARCIS (Netherlands)

    Vollaard, B.; Verweij, P.A.

    2011-01-01

    Market-based instruments are increasingly being promoted as a promising measure to face the twin challenge of biodiversity conservation and development. In the realm of market-based approaches, an important instrument is the creation of biodiversity business: ‘commercial enterprises that generate

  14. African Traditional Knowledge Systems and Biodiversity Management

    African Journals Online (AJOL)

    There is a link between African Traditional Knowledge Systems and the management of Biodiversity. These have been passed over from one generation to the next through oral tradition. The lack of documentation of these systems of managing biodiversity has led to the existence of a gap between the scientifi cally based ...

  15. Digital Geogames to Foster Local Biodiversity

    Science.gov (United States)

    Schaal, Sonja; Schaal, Steffen; Lude, Armin

    2015-01-01

    The valuing of biodiversity is considered to be a first step towards its conservation. Therefore, the aim of the BioDiv2Go project is to combine sensuous experiences discovering biodiversity with mobile technology and a game-based learning approach. Following the competence model for environmental education (Roczen et al, 2014), Geogames (location…

  16. Identifying Indicators for Monitoring Farmland Biodiversity

    NARCIS (Netherlands)

    Herzog, F.; Balázs, K.; Dennis, P.; Dyman, T.; Fjellstad, W.; Friedel, J.; Garchi, S.; Jeanneret, P.; Jongman, R.H.G.; Kainz, M.; Moreno, G.; Nkwiine, C.; Paoletti, M.; Pointerreau, P.; Sarthou, J.P.; Stoyanova, S.; Viaggi, D.

    2011-01-01

    Farmland biodiversity is an important component of Europe’s biodiversity. More than half the continent is occupied by agricultural lands. They host specific habitats and species, which – in addition to their conservation values they provide – perform vital ecological functions. Indicators are needed

  17. Norms and the Conservation of Biodiversity

    Indian Academy of Sciences (India)

    user

    Austin and Professor in the. Section of Integrative. Biology, the Department of. Philosophy and the. Department of Geography and the Environment. Keywords ... behind biodiversity. Introduction. Twenty years ago, the neologism biodiversity was introduced as a contraction for biological diversity to describe the intended.

  18. Species Assortment and Biodiversity Conservation in Homegardens ...

    African Journals Online (AJOL)

    user

    that the urban gardens are a storehouse of biodiversity including species that run the risk of disappearance in the ... Consequently, enhancement of biodiversity in urban homegardens is very crucial which its composition ..... Several factors such as agro-ecological conditions and socio-cultural factors can play role in species ...

  19. Forest Resilience, Biodiversity, and Climate Change

    Science.gov (United States)

    I. Thompson; B. Mackey; S. McNulty; A. Mosseler

    2009-01-01

    This paper reviews the concepts of ecosystem resilience, resistance, and stability in forests and their relationship to biodiversity, with particular reference to climate change. The report is a direct response to a request by the ninth meeting of the Conference of the Parties to the CBD, in decision IX/51, to explore the links between biodiversity, forest ecosystem...

  20. Assessing National Biodiversity Trends for Rocky and Coral Reefs through the Integration of Citizen Science and Scientific Monitoring Programs

    Science.gov (United States)

    Stuart-Smith, Rick D.; Edgar, Graham J.; Barrett, Neville S.; Bates, Amanda E.; Baker, Susan C.; Bax, Nicholas J.; Becerro, Mikel A.; Berkhout, Just; Blanchard, Julia L.; Brock, Daniel J.; Clark, Graeme F.; Cooper, Antonia T.; Davis, Tom R.; Day, Paul B.; Duffy, J. Emmett; Holmes, Thomas H.; Howe, Steffan A.; Jordan, Alan; Kininmonth, Stuart; Knott, Nathan A.; Lefcheck, Jonathan S.; Ling, Scott D.; Parr, Amanda; Strain, Elisabeth; Sweatman, Hugh; Thomson, Russell

    2017-01-01

    Abstract Reporting progress against targets for international biodiversity agreements is hindered by a shortage of suitable biodiversity data. We describe a cost-effective system involving Reef Life Survey citizen scientists in the systematic collection of quantitative data covering multiple phyla that can underpin numerous marine biodiversity indicators at high spatial and temporal resolution. We then summarize the findings of a continental- and decadal-scale State of the Environment assessment for rocky and coral reefs based on indicators of ecosystem state relating to fishing, ocean warming, and invasive species and describing the distribution of threatened species. Fishing impacts are widespread, whereas substantial warming-related change affected some regions between 2005 and 2015. Invasive species are concentrated near harbors in southeastern Australia, and the threatened-species index is highest for the Great Australian Bight and Tasman Sea. Our approach can be applied globally to improve reporting against biodiversity targets and enhance public and policymakers’ understanding of marine biodiversity trends. PMID:28596615

  1. A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage-specific barcode markers in microbial ecology.

    Science.gov (United States)

    Stoeck, Thorsten; Breiner, Hans-Werner; Filker, Sabine; Ostermaier, Veronika; Kammerlander, Barbara; Sonntag, Bettina

    2014-02-01

    Analyses of high-throughput environmental sequencing data have become the 'gold-standard' to address fundamental questions of microbial diversity, ecology and biogeography. Findings that emerged from sequencing are, e.g. the discovery of the extensive 'rare microbial biosphere' and its potential function as a seed-bank. Even though applied since several years, results from high-throughput environmental sequencing have hardly been validated. We assessed how well pyrosequenced amplicons [the hypervariable eukaryotic V4 region of the small subunit ribosomal RNA (SSU rRNA) gene] reflected morphotype ciliate plankton. Moreover, we assessed if amplicon sequencing had the potential to detect the annual ciliate plankton stock. In both cases, we identified significant quantitative and qualitative differences. Our study makes evident that taxon abundance distributions inferred from amplicon data are highly biased and do not mirror actual morphotype abundances at all. Potential reasons included cell losses after fixation, cryptic morphotypes, resting stages, insufficient sequence data availability of morphologically described species and the unsatisfying resolution of the V4 SSU rRNA fragment for accurate taxonomic assignments. The latter two underline the necessity of barcoding initiatives for eukaryotic microbes to better and fully exploit environmental amplicon data sets, which then will also allow studying the potential of seed-bank taxa as a buffer for environmental changes. © 2013 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  2. Biodiversity and models of evolution

    Directory of Open Access Journals (Sweden)

    S. L. Podvalny

    2016-01-01

    Full Text Available Summary. The paper discusses the evolutionary impact of biodiversity, the backbone of noosphere, which status has been fixed by a UN convention. The examples and role of such diversity are considered the various levels of life arrangement. On the level of standalone organisms, the diversity in question manifests itself in the differentiation and separation of the key physiologic functions which significantly broaden the eco-niche for the species with the consummate type of such separation. However, the organismic level of biodiversity does not work for building any developmental models since the starting point of genetic inheritance and variability processes emerges on the minimum structural unit of the living world only, i.e. the population. It is noted that the sufficient gene pool for species development may accumulate in fairly large populations only, where the general rate of mutation does not yield to the rate of ambient variations. The paper shows that the known formal models of species development based on the Fisher theorem about the impact of genodispersion on species adjustment are not in keeping with the actual existence of the species due to the conventionally finite and steady number of genotypes within a population. On the ecosystem level of life arrangement, the key role pertains to the taxonomic diversity supporting the continuous food chain in the system against any adverse developmental conditions of certain taxons. Also, the progressive evolution of an ecosystem is largely stabilized by its multilayer hierarchic structure and the closed circle of matter and energy. The developmental system models based on the Lotka-Volterra equations describing the interaction of the open-loop ecosystem elements only insufficiently represent the position of biodiversity in the evolutionary processes. The paper lays down the requirements to such models which take into account the mass balance within a system; its trophic structure; the

  3. Colloquium paper: engaging the public in biodiversity issues.

    Science.gov (United States)

    Novacek, Michael J

    2008-08-12

    To engage people in biodiversity and other environmental issues, one must provide the opportunity for enhanced understanding that empowers individuals to make choices and take action based on sound science and reliable recommendations. To this end, we must acknowledge some real challenges. Recent surveys show that, despite growing public concern, environmental issues still rank below many other problems, such as terrorism, health care, the economy, and (in the U.S.) family values. Moreover, much of the recent upswing in interest in the environment is due to the marked shift in attention to global warming away from other environmental problems such as destruction of ecosystems, water pollution, overpopulation, and biodiversity loss. Such a change in public focus often comes with a tendency to decouple various environmental problems and ignore their synergistic effects. Exacerbating this problem are arguments from the media and other sources that discourage public interest in environmental topics by characterizing the science behind them as overly complex, immersed in debate and controversy, and detached from human interests. Educational programming, media, exhibitions, and other means of public outreach should build on the welcome increase in public interest in global warming by demonstrating the interplay of various environmental disruptions. In the case of biodiversity, the importance of species in providing ecosystem services, natural beauty and pleasure, and sustaining human lives is a message that requires constant attention and recrafting to impact diverse audiences.

  4. Biodiversity redistribution under climate change

    DEFF Research Database (Denmark)

    Pecl, Gretta T.; Bastos, Miguel; Bell, Johann D.

    2017-01-01

    Distributions of Earth’s species are changing at accelerating rates, increasingly driven by humanmediated climate change. Such changes are already altering the composition of ecological communities, but beyond conservation of natural systems, how and why does this matter? We review evidence...... that climate-driven species redistribution at regional to global scales affects ecosystem functioning, human well-being, and the dynamics of climate change itself. Production of natural resources required for food security, patterns of disease transmission, and processes of carbon sequestration are all altered...... by changes in species distribution. Consideration of these effects of biodiversity redistribution is critical yet lacking in most mitigation and adaptation strategies, including the United Nation’s Sustainable Development Goals....

  5. Cycad diversification and tropical biodiversity

    Directory of Open Access Journals (Sweden)

    Rull, V.

    2012-12-01

    Full Text Available The recent unexpected discovery that living Cycadales are not Jurassic-Cretaceous (200– 65 Mya relicts, as all their extant genera began to diversify during the Late Miocene (12 Mya, has challenged a classical evolutionary myth. This brief note shows how this finding may also provide new clues on the shaping of the high tropical biodiversity

    El reciente e inesperado descubrimiento de que las Cycadales actuales no son relictos Jurásico-Cretácicos (200-65 Mya, ya que todos sus géneros iniciaron su diversificación durante el Mioceno Tardío (12 Mya, ha puesto en entredicho un mito evolutivo clásico. En esta nota se expone como este hallazgo puede, además, proporcionar nuevas pistas sobre el origen de la elevada biodiversidad tropical.

  6. Environmental biodiversity, human microbiota, and allergy are interrelated

    National Research Council Canada - National Science Library

    Ilkka Hanski; Leena von Hertzen; Nanna Fyhrquist; Kaisa Koskinen; Kaisa Torppa; Tiina Laatikainen; Piia Karisola; Petri Auvinen; Lars Paulin; Mika J. Mäkelä; Erkki Vartiainen; Timo U. Kosunen; Harri Alenius; Tari Haahtela

    2012-01-01

    .... According to the "biodiversity hypothesis," reduced contact of people with natural environmental features and biodiversity may adversely affect the human commensal microbiota and its immunomodulatory capacity...

  7. Phylogenetic survey of metabolically active microbial communities associated with the deep-sea coral Lophelia pertusa from the Apulian plateau, Central Mediterranean Sea

    Science.gov (United States)

    Yakimov, Michail M.; Cappello, Simone; Crisafi, Ermanno; Tursi, Angelo; Savini, Alessandra; Corselli, Cesare; Scarfi, Simona; Giuliano, Laura

    2006-01-01

    Living deep-water coral assemblages were discovered recently inhabiting the Mediterranean Sea between the depths of 300 and 1000 m off the Cape of Santa Maria di Leuca (Apulian platform, Ionian Sea). This living assemblage was dominated by two colonial scleractinian corals, Lophelia pertusa and Madrepora oculata. Two other corals, Desmophyllum crystagalli and Stenocyathus vermiformis were also recovered from this site, but were much less common. The composition of the metabolically active fraction of the microbial community associated with living specimens of L. pertusa was determined. Dead corals, proximal sediments and overlying seawater were also sampled and analyzed. Complementary 16S ribosomal DNA (crDNA) was obtained from total RNA extracted from all samples that had been subjected to reverse transcription-PCR amplification. Domain-specific 16S PCR primers were used to construct four different 16S crDNA libraries containing 45 Archaea and 201 Bacteria clones. Using Archaea-specific primers, no amplification products were obtained from any coral samples (live and dead). Living specimens of L. pertusa seem to possess a specific microbial community different from that of dead coral and sediment samples. The majority of all coral-associated riboclones was related to the Holophaga-Acidobacterium and Nitrospira divisions (80%). Moreover, more than 12% of all coral-associated riboclones formed a separate deep-branching cluster within the α- Proteobacteria with no known close relatives. The metabolically active fraction of the bacterial community colonizing the dead corals was dominated by Proteobacteria related to the gamma and epsilon subdivisions (74% and 26% of all clones, respectively). Phylogenetic analysis of the Archaea clone library retrieved from proximal sediments indicated an exclusive dominance by the members of Crenarchaea Marine Group I (MGI), a lineage of unculturable microorganisms, widely distributed in marine habitats. In contrast, bacterial

  8. Saving Saba bank: policy implications of biodiversity studies.

    Directory of Open Access Journals (Sweden)

    Paul C Hoetjes

    Full Text Available Saba Bank has always been an area of special importance to the neighboring island of Saba in the Netherlands Antilles. Sabans traditionally fished on the Bank as far back as 1907, but increasing foreign fishing pressures on the Bank in the 1970s and 1980s forced many Saban fishermen out. Concerns were compounded by the suspicion that shipping was also damaging the benthic habitat of the bank. Fishery legislation, enacted in 1996, brought an end to unlicensed fishing and established Coast Guard enforcement on the Bank, but also led to protests from neighboring countries that previously fished on the Bank.Research was necessary to support the need for protection. Review of available research of Saba Bank and rapid biological assessments and fisheries surveys since 1996 emphasized the richness of Saba Bank's biodiversity and the need for protection of fisheries stocks. The national nature policy plan recognized this and encouraged further research to base conservation measures on.Recent biological surveys of corals, fishes, and algae presented in this collection of articles emphasized habitat heterogeneity and the relative richness of the marine flora and fauna. These assessments formed the basis for a management plan to protect Saba Bank's biodiversity and a draft proposal to the International Maritime Organization (IMO seeking Particularly Sensitive Sea Area (PSSA status for the Bank. The intention of the PSSA proposal is to protect the benthic habitat on Saba Bank from anchor damage. This paper serves to provide the context for the results of the recent biodiversity surveys of Saba Bank. It is hoped that this collection will serve as a knowledge baseline and engender further research in the area.

  9. Counterintuitive proposals for trans-boundary ecological compensation under "No Net Loss" biodiversity policy

    DEFF Research Database (Denmark)

    Bull, Joseph William; Abatayo, Anna Lou; Strange, Niels

    2017-01-01

    to stakeholders when they are not experts? We surveyed 691 students with limited or no knowledge of NNL policy across three countries, eliciting perceptions of what constitutes sufficient ecological compensation for forest habitat losses from infrastructure development. NNL policies assume that biodiversity...... compensation should be: close to development impacts; greater than losses; smaller, given a background trend of biodiversity decline; and, smaller when gains have co-benefits for biodiversity. However, survey participant proposals violated all four principles. Participants proposed substantial forest...... could deserve consideration. The findings also support proposals to incorporate social considerations into compensation ratios for NNL. Wherever the rationale underlying NNL is discovered to be counterintuitive insofar as relevant stakeholders are concerned, careful communication of policy intentions...

  10. The biodiversity hypothesis and allergic disease: world allergy organization position statement.

    Science.gov (United States)

    Haahtela, Tari; Holgate, Stephen; Pawankar, Ruby; Akdis, Cezmi A; Benjaponpitak, Suwat; Caraballo, Luis; Demain, Jeffrey; Portnoy, Jay; von Hertzen, Leena

    2013-01-31

    Biodiversity loss and climate change secondary to human activities are now being associated with various adverse health effects. However, less attention is being paid to the effects of biodiversity loss on environmental and commensal (indigenous) microbiotas. Metagenomic and other studies of healthy and diseased individuals reveal that reduced biodiversity and alterations in the composition of the gut and skin microbiota are associated with various inflammatory conditions, including asthma, allergic and inflammatory bowel diseases (IBD), type1 diabetes, and obesity. Altered indigenous microbiota and the general microbial deprivation characterizing the lifestyle of urban people in affluent countries appear to be risk factors for immune dysregulation and impaired tolerance. The risk is further enhanced by physical inactivity and a western diet poor in fresh fruit and vegetables, which may act in synergy with dysbiosis of the gut flora. Studies of immigrants moving from non-affluent to affluent regions indicate that tolerance mechanisms can rapidly become impaired in microbe-poor environments. The data on microbial deprivation and immune dysfunction as they relate to biodiversity loss are evaluated in this Statement of World Allergy Organization (WAO). We propose that biodiversity, the variability among living organisms from all sources are closely related, at both the macro- and micro-levels. Loss of the macrodiversity is associated with shrinking of the microdiversity, which is associated with alterations of the indigenous microbiota. Data on behavioural means to induce tolerance are outlined and a proposal made for a Global Allergy Plan to prevent and reduce the global allergy burden for affected individuals and the societies in which they live.

  11. The biodiversity hypothesis and allergic disease: world allergy organization position statement

    Science.gov (United States)

    2013-01-01

    Biodiversity loss and climate change secondary to human activities are now being associated with various adverse health effects. However, less attention is being paid to the effects of biodiversity loss on environmental and commensal (indigenous) microbiotas. Metagenomic and other studies of healthy and diseased individuals reveal that reduced biodiversity and alterations in the composition of the gut and skin microbiota are associated with various inflammatory conditions, including asthma, allergic and inflammatory bowel diseases (IBD), type1 diabetes, and obesity. Altered indigenous microbiota and the general microbial deprivation characterizing the lifestyle of urban people in affluent countries appear to be risk factors for immune dysregulation and impaired tolerance. The risk is further enhanced by physical inactivity and a western diet poor in fresh fruit and vegetables, which may act in synergy with dysbiosis of the gut flora. Studies of immigrants moving from non-affluent to affluent regions indicate that tolerance mechanisms can rapidly become impaired in microbe-poor environments. The data on microbial deprivation and immune dysfunction as they relate to biodiversity loss are evaluated in this Statement of World Allergy Organization (WAO). We propose that biodiversity, the variability among living organisms from all sources are closely related, at both the macro- and micro-levels. Loss of the macrodiversity is associated with shrinking of the microdiversity, which is associated with alterations of the indigenous microbiota. Data on behavioural means to induce tolerance are outlined and a proposal made for a Global Allergy Plan to prevent and reduce the global allergy burden for affected individuals and the societies in which they live. PMID:23663440

  12. Preliminary assessment of sponge biodiversity on Saba Bank, Netherlands Antilles.

    Directory of Open Access Journals (Sweden)

    Robert W Thacker

    Full Text Available BACKGROUND: Saba Bank Atoll, Netherlands Antilles, is one of the three largest atolls on Earth and provides habitat for an extensive coral reef community. To improve our knowledge of this vast marine resource, a survey of biodiversity at Saba Bank included a multi-disciplinary team that sampled fishes, mollusks, crustaceans, macroalgae, and sponges. METHODOLOGY/PRINCIPAL FINDINGS: A single member of the dive team conducted surveys of sponge biodiversity during eight dives at six locations, at depths ranging from 15 to 30 m. This preliminary assessment documented the presence of 45 species pooled across multiple locations. Rarefaction analysis estimated that only 48 to 84% of species diversity was sampled by this limited effort, clearly indicating a need for additional surveys. An analysis of historical collections from Saba and Saba Bank revealed an additional 36 species, yielding a total of 81 sponge species recorded from this area. CONCLUSIONS/SIGNIFICANCE: This observed species composition is similar to that found on widespread Caribbean reefs, indicating that the sponge fauna of Saba Bank is broadly representative of the Caribbean as a whole. A robust population of the giant barrel sponge, Xestospongia muta, appeared healthy with none of the signs of disease or bleaching reported from other Caribbean reefs; however, more recent reports of anchor chain damage to these sponges suggests that human activities can have dramatic impacts on these communities. Opportunities to protect this extremely large habitat should be pursued, as Saba Bank may serve as a significant reservoir of sponge species diversity.

  13. Microbial iron cycling in acidic geothermal springs of yellowstone national park: integrating molecular surveys, geochemical processes, and isolation of novel fe-active microorganisms.

    Science.gov (United States)

    Kozubal, Mark A; Macur, Richard E; Jay, Zackary J; Beam, Jacob P; Malfatti, Stephanie A; Tringe, Susannah G; Kocar, Benjamin D; Borch, Thomas; Inskeep, William P

    2012-01-01

    Geochemical, molecular, and physiological analyses of microbial isolates were combined to study the geomicrobiology of acidic iron oxide mats in Yellowstone National Park. Nineteen sampling locations from 11 geothermal springs were studied ranging in temperature from 53 to 88°C and pH 2.4 to 3.6. All iron oxide mats exhibited high diversity of crenarchaeal sequences from the Sulfolobales, Thermoproteales, and Desulfurococcales. The predominant Sulfolobales sequences were highly similar to Metallosphaera yellowstonensis str. MK1, previously isolated from one of these sites. Other groups of archaea were consistently associated with different types of iron oxide mats, including undescribed members of the phyla Thaumarchaeota and Euryarchaeota. Bacterial sequences were dominated by relatives of Hydrogenobaculum spp. above 65-70°C, but increased in diversity below 60°C. Cultivation of relevant iron-oxidizing and iron-reducing microbial isolates included Sulfolobus str. MK3, Sulfobacillus str. MK2, Acidicaldus str. MK6, and a new candidate genus in the Sulfolobales referred to as Sulfolobales str. MK5. Strains MK3 and MK5 are capable of oxidizing ferrous iron autotrophically, while strain MK2 oxidizes iron mixotrophically. Similar rates of iron oxidation were measured for M. yellowstonensis str. MK1 and Sulfolobales str. MK5. Biomineralized phases of ferric iron varied among cultures and field sites, and included ferric oxyhydroxides, K-jarosite, goethite, hematite, and scorodite depending on geochemical conditions. Strains MK5 and MK6 are capable of reducing ferric iron under anaerobic conditions with complex carbon sources. The combination of geochemical and molecular data as well as physiological observations of isolates suggests that the community structure of acidic Fe mats is linked with Fe cycling across temperatures ranging from 53 to 88°C.

  14. Microbial iron cycling in acidic geothermal springs of Yellowstone National Park: Integrating molecular surveys, geochemical processes and isolation of novel Fe-active microorganisms

    Directory of Open Access Journals (Sweden)

    Mark A Kozubal

    2012-03-01

    Full Text Available Geochemical, molecular, and physiological analyses of microbial isolates were combined to study the geomicrobiology of acidic iron oxide mats in Yellowstone National Park (YNP. Nineteen sampling locations from 11 geothermal springs were studied ranging in temperature from 53 to 84 °C and pH 2.4 to 3.6. All iron-oxide mats exhibited high diversity of crenarchaeal sequences from the Sulfolobales, Thermoproteales, and Desulfurococcales. The predominant Sulfolobales sequences were highly similar to Metallosphaera yellowstonensis str. MK1, previously isolated from one of these sites. Other groups of archaea were consistently associated with different types of iron oxide mats, including undescribed members of the phyla Thaumarchaeota and Euryarchaeota. Bacterial sequences were dominated by relatives of Hydrogenobaculum spp. above 65-70 °C, but increased in diversity below 60 °C. Cultivation of relevant iron-oxidizing and iron-reducing microbial isolates included Sulfolobus str. MK3, Sulfobacillus str. MK2, Acidicaldus str. MK6, and a new candidate genus in the Sulfolobales referred to as Sulfolobales str. MK5. Strains MK3 and MK5 are capable of oxidizing ferrous iron autotrophically, while strain MK2 oxidizes iron mixotrophically. Similar rates of iron oxidation were observed for M. yellowstonensis str. MK1 and Sulfolobales str. MK5 cultures, and these rates are close to those measured in situ. Biomineralized phases of ferric iron varied among cultures and field sites, and included ferric oxyhydroxides, K-jarosite, goethite, hematite, and scorodite depending on geochemical conditions. Strains MK5 and MK6 are capable of reducing ferric iron under anaerobic conditions with complex carbon sources. The combination of geochemical and molecular data as well as physiological observations of isolates suggests that the community structure of acidic Fe mats is linked with Fe cycling across temperatures ranging from 53 to 88 oC.

  15. Microbial Iron Cycling in Acidic Geothermal Springs of Yellowstone National Park: Integrating Molecular Surveys, Geochemical Processes, and Isolation of Novel Fe-Active Microorganisms

    Science.gov (United States)

    Kozubal, Mark A.; Macur, Richard E.; Jay, Zackary J.; Beam, Jacob P.; Malfatti, Stephanie A.; Tringe, Susannah G.; Kocar, Benjamin D.; Borch, Thomas; Inskeep, William P.

    2012-01-01

    Geochemical, molecular, and physiological analyses of microbial isolates were combined to study the geomicrobiology of acidic iron oxide mats in Yellowstone National Park. Nineteen sampling locations from 11 geothermal springs were studied ranging in temperature from 53 to 88°C and pH 2.4 to 3.6. All iron oxide mats exhibited high diversity of crenarchaeal sequences from the Sulfolobales, Thermoproteales, and Desulfurococcales. The predominant Sulfolobales sequences were highly similar to Metallosphaera yellowstonensis str. MK1, previously isolated from one of these sites. Other groups of archaea were consistently associated with different types of iron oxide mats, including undescribed members of the phyla Thaumarchaeota and Euryarchaeota. Bacterial sequences were dominated by relatives of Hydrogenobaculum spp. above 65–70°C, but increased in diversity below 60°C. Cultivation of relevant iron-oxidizing and iron-reducing microbial isolates included Sulfolobus str. MK3, Sulfobacillus str. MK2, Acidicaldus str. MK6, and a new candidate genus in the Sulfolobales referred to as Sulfolobales str. MK5. Strains MK3 and MK5 are capable of oxidizing ferrous iron autotrophically, while strain MK2 oxidizes iron mixotrophically. Similar rates of iron oxidation were measured for M. yellowstonensis str. MK1 and Sulfolobales str. MK5. Biomineralized phases of ferric iron varied among cultures and field sites, and included ferric oxyhydroxides, K-jarosite, goethite, hematite, and scorodite depending on geochemical conditions. Strains MK5 and MK6 are capable of reducing ferric iron under anaerobic conditions with complex carbon sources. The combination of geochemical and molecular data as well as physiological observations of isolates suggests that the community structure of acidic Fe mats is linked with Fe cycling across temperatures ranging from 53 to 88°C. PMID:22470372

  16. Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data.

    Directory of Open Access Journals (Sweden)

    Pedro M Meirelles

    Full Text Available Seamounts are considered important sources of biodiversity and minerals. However, their biodiversity and health status are not well understood; therefore, potential conservation problems are unknown. The mesophotic reefs of the Vitória-Trindade Seamount Chain (VTC were investigated via benthic community and fish surveys, metagenomic and water chemistry analyses, and water microbial abundance estimations. The VTC is a mosaic of reef systems and includes fleshy algae dominated rhodolith beds, crustose coralline algae (CCA reefs, and turf algae dominated rocky reefs of varying health levels. Macro-carnivores and larger fish presented higher biomass at the CCA reefs (4.4 kg per frame than in the rhodolith beds and rocky reefs (0.0 to 0.1 kg per frame. A larger number of metagenomic sequences identified as primary producers (e.g., Chlorophyta and Streptophyta were found at the CCA reefs. However, the rocky reefs contained more diseased corals (>90% than the CCA reefs (~40% and rhodolith beds (~10%. Metagenomic analyses indicated a heterotrophic and fast-growing microbiome in rocky reef corals that may possibly lead to unhealthy conditions possibly enhanced by environmental features (e.g. light stress and high loads of labile dissolved organic carbon. VTC mounts represent important hotspots of biodiversity that deserve further conservation actions.

  17. Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data.

    Science.gov (United States)

    Meirelles, Pedro M; Amado-Filho, Gilberto M; Pereira-Filho, Guilherme H; Pinheiro, Hudson T; de Moura, Rodrigo L; Joyeux, Jean-Christophe; Mazzei, Eric F; Bastos, Alex C; Edwards, Robert A; Dinsdale, Elizabeth; Paranhos, Rodolfo; Santos, Eidy O; Iida, Tetsuya; Gotoh, Kazuyoshi; Nakamura, Shota; Sawabe, Tomoo; Rezende, Carlos E; Gadelha, Luiz M R; Francini-Filho, Ronaldo B; Thompson, Cristiane; Thompson, Fabiano L

    2015-01-01

    Seamounts are considered important sources of biodiversity and minerals. However, their biodiversity and health status are not well understood; therefore, potential conservation problems are unknown. The mesophotic reefs of the Vitória-Trindade Seamount Chain (VTC) were investigated via benthic community and fish surveys, metagenomic and water chemistry analyses, and water microbial abundance estimations. The VTC is a mosaic of reef systems and includes fleshy algae dominated rhodolith beds, crustose coralline algae (CCA) reefs, and turf algae dominated rocky reefs of varying health levels. Macro-carnivores and larger fish presented higher biomass at the CCA reefs (4.4 kg per frame) than in the rhodolith beds and rocky reefs (0.0 to 0.1 kg per frame). A larger number of metagenomic sequences identified as primary producers (e.g., Chlorophyta and Streptophyta) were found at the CCA reefs. However, the rocky reefs contained more diseased corals (>90%) than the CCA reefs (~40%) and rhodolith beds (~10%). Metagenomic analyses indicated a heterotrophic and fast-growing microbiome in rocky reef corals that may possibly lead to unhealthy conditions possibly enhanced by environmental features (e.g. light stress and high loads of labile dissolved organic carbon). VTC mounts represent important hotspots of biodiversity that deserve further conservation actions.

  18. Riparian landscapes: Linking geodiversity with habitat and biodiversity

    Science.gov (United States)

    Chmieleski, Jana; Danzeisen, Laura

    2017-04-01

    Keywords: Oder valley, biodiversity, geodiversity River landscapes of all scales originally showed a high diversity of structures and habitats at a small spatial entity, such as the stream beds, terrasses, sand and gravel banks. This variety, with a lot of different elements, patches and patterns, represents not only a variety of geoelements or geomorhological features but also a large biodiversity, both of habitats and species. Riparian landscapes are both, a natural as well as a geoheritage, often even a cultural heritage (sustainabe land use practices). Embankments, utilization for agriculture, constructions for navigation, management measures lead to a strong loss of these structures. This impacts the value of the landscape as well ecosystem functions, not only the biodiversity and the geodiversity but also the recreation function or the aesthetic values. A case study from the National Park Lower Oder Valley in the Northeastern part of Germany, wich is also part of a Geopark („Eiszeitland am Oderrand") presents the connections of the diversity of geomorphological features with biodiversity and shows the loss of features (loss of values) due to intensive utilisation by using GIS-analysis and landscape-metrics. The Northern part of the Oder valley (National Park, transnational protection area of Germany and Poland) have been modified by man since centuries but even so remained in near-natural state that allows semi-(natural) stream dynamics. While the Oder's reparian zone is marked by the stream itself, by its bayous, reed beds, periodically flooded wet meadows and by its natural riparian forest the mineral morainic plateaus are marked by semi-natural forests and dry grasslands. Two areas of different degradation states, a) near-natural and wilderness area and b) grassland area will be compared in order to identify: quantity and extent of features, relation of measure and coverage, connectivity with other features, quantity and types of habitats (with

  19. Minimizing the biodiversity impact of Neotropical oil palm development.

    Science.gov (United States)

    Gilroy, James J; Prescott, Graham W; Cardenas, Johann S; Castañeda, Pamela González del Pliego; Sánchez, Andrés; Rojas-Murcia, Luis E; Medina Uribe, Claudia A; Haugaasen, Torbjørn; Edwards, David P

    2015-04-01

    Oil palm agriculture is rapidly expanding in the Neotropics, at the expense of a range of natural and seminatural habitats. A key question is how this expansion should be managed to reduce negative impacts on biodiversity. Focusing on the Llanos of Colombia, a mixed grassland-forest system identified as a priority zone for future oil palm development, we survey communities of ants, dung beetles, birds and herpetofauna occurring in oil palm plantations and the other principal form of agriculture in the region--improved cattle pasture--together with those of surrounding natural forests. We show that oil palm plantations have similar or higher species richness across all four taxonomic groups than improved pasture. For dung beetles, species richness in oil palm was equal to that of forest, whereas the other three taxa had highest species richness in forests. Hierarchical modelling of species occupancy probabilities indicated that oil palm plantations supported a higher proportion of species characteristic of forests than did cattle pastures. Across the bird community, occupancy probabilities within oil palm were positively influenced by increasing forest cover in a surrounding 250 m radius, whereas surrounding forest cover did not strongly influence the occurrence of other taxonomic groups in oil palm. Overall, our results suggest that the conversion of existing improved pastures to oil palm has limited negative impacts on biodiversity. As such, existing cattle pastures of the Colombian Llanos could offer a key opportunity to meet governmental targets for oil palm development without incurring significant biodiversity costs. Our results also highlight the value of preserving remnant forests within these agricultural landscapes, protecting high biodiversity and exporting avian 'spill-over' effects into oil palm plantations. © 2014 John Wiley & Sons Ltd.

  20. Identifying Centres of Plant Biodiversity in South Australia.

    Directory of Open Access Journals (Sweden)

    Greg R Guerin

    Full Text Available We aimed to identify regional centres of plant biodiversity in South Australia, a sub-continental land area of 983,482 km2, by mapping a suite of metrics. Broad-brush conservation issues associated with the centres were mapped, specifically climate sensitivity, exposure to habitat fragmentation, introduced species and altered fire regimes. We compiled 727,417 plant species records from plot-based field surveys and herbarium records and mapped the following: species richness (all species; South Australian endemics; conservation-dependent species; introduced species; georeferenced weighted endemism, phylogenetic diversity, georeferenced phylogenetic endemism; and measures of beta diversity at local and state-wide scales. Associated conservation issues mapped were: climate sensitivity measured via ordination and non-linear modelling; habitat fragmentation represented by the proportion of remnant vegetation within a moving window; fire prone landscapes assessed using fire history records; invasive species assessed through diversity metrics, species distribution and literature. Compared to plots, herbarium data had higher spatial and taxonomic coverage but records were more biased towards major transport corridors. Beta diversity was influenced by sampling intensity and scale of comparison. We identified six centres of high plant biodiversity for South Australia: Western Kangaroo Island; Southern Mount Lofty Ranges; Anangu Pitjantjatjara Yankunytjatjara lands; Southern Flinders Ranges; Southern Eyre Peninsula; Lower South East. Species composition in the arid-mediterranean ecotone was the most climate sensitive. Fragmentation mapping highlighted the dichotomy between extensive land-use and high remnancy in the north and intensive land-use and low remnancy in the south. Invasive species were most species rich in agricultural areas close to population centres. Fire mapping revealed large variation in frequency across the state. Biodiversity scores were

  1. Identifying Centres of Plant Biodiversity in South Australia.

    Science.gov (United States)

    Guerin, Greg R; Biffin, Ed; Baruch, Zdravko; Lowe, Andrew J

    2016-01-01

    We aimed to identify regional centres of plant biodiversity in South Australia, a sub-continental land area of 983,482 km2, by mapping a suite of metrics. Broad-brush conservation issues associated with the centres were mapped, specifically climate sensitivity, exposure to habitat fragmentation, introduced species and altered fire regimes. We compiled 727,417 plant species records from plot-based field surveys and herbarium records and mapped the following: species richness (all species; South Australian endemics; conservation-dependent species; introduced species); georeferenced weighted endemism, phylogenetic diversity, georeferenced phylogenetic endemism; and measures of beta diversity at local and state-wide scales. Associated conservation issues mapped were: climate sensitivity measured via ordination and non-linear modelling; habitat fragmentation represented by the proportion of remnant vegetation within a moving window; fire prone landscapes assessed using fire history records; invasive species assessed through diversity metrics, species distribution and literature. Compared to plots, herbarium data had higher spatial and taxonomic coverage but records were more biased towards major transport corridors. Beta diversity was influenced by sampling intensity and scale of comparison. We identified six centres of high plant biodiversity for South Australia: Western Kangaroo Island; Southern Mount Lofty Ranges; Anangu Pitjantjatjara Yankunytjatjara lands; Southern Flinders Ranges; Southern Eyre Peninsula; Lower South East. Species composition in the arid-mediterranean ecotone was the most climate sensitive. Fragmentation mapping highlighted the dichotomy between extensive land-use and high remnancy in the north and intensive land-use and low remnancy in the south. Invasive species were most species rich in agricultural areas close to population centres. Fire mapping revealed large variation in frequency across the state. Biodiversity scores were not always

  2. Biodiversity as a solution to mitigate climate change impacts on the functioning of forest ecosystems.

    Science.gov (United States)

    Hisano, Masumi; Searle, Eric B; Chen, Han Y H

    2018-02-01

    Forest ecosystems are critical to mitigating greenhouse gas emissions through carbon sequestration. However, climate change has affected forest ecosystem functioning in both negative and positive ways, and has led to shifts in species/functional diversity and losses in plant species diversity which may impair the positive effects of diversity on ecosystem functioning. Biodiversity may mitigate climate change impacts on (I) biodiversity itself, as more-diverse systems could be more resilient to climate change impacts, and (II) ecosystem functioning through the positive relationship between diversity and ecosystem functioning. By surveying the literature, we examined how climate change has affected forest ecosystem functioning and plant diversity. Based on the biodiversity effects on ecosystem functioning (B→EF), we specifically address the potential for biodiversity to mitigate climate change impacts on forest ecosystem functioning. For this purpose, we formulate a concept whereby biodiversity may reduce the negative impacts or enhance the positive impacts of climate change on ecosystem functioning. Further B→EF studies on climate change in natural forests are encouraged to elucidate how biodiversity might influence ecosystem functioning. This may be achieved through the detailed scrutiny of large spatial/long temporal scale data sets, such as long-term forest inventories. Forest management strategies based on B→EF have strong potential for augmenting the effectiveness of the roles of forests in the mitigation of climate change impacts on ecosystem functioning. © 2017 Cambridge Philosophical Society.

  3. Floristic characteristics and biodiversity patterns in the Baishuijiang River basin, China.

    Science.gov (United States)

    Liu, Bing; Zhao, Wenzhi; Wen, Zijuan; Teng, Jirong; Li, Xiaohong

    2009-07-01

    A case study was conducted on the forest ecosystem in the Baishuijiang River basin of China to reveal the influences of environmental factors and human disturbance on the floristic characteristics and biodiversity patterns. Field surveys of the floristic composition, environmental factors, and disturbance factors were conducted along an elevation gradient, and the relationships between biodiversity pattern and environmental factors were analyzed using CCA (canonical correspondence analysis). The results showed that the floristic composition of higher plants consisted of 197 families, 796 genera, 2165 species, 19 subspecies, 239 varietas, and 12 forma, and it was characterized by the multi-geographic composition and by the transition from tropical to temperate zones. Along an elevation gradient, the variations in alpha and beta diversity were best described by a bimodal curve, and the peak values occurred at middle elevations. The CCA indicated that the elevation had the greatest influence on the biodiversity pattern, followed by the topographic index, slope direction, slope, slope position, slope shape, and vegetation coverage. In addition, human disturbance has greatly impacted the floristic composition and biodiversity patterns, and the biodiversity indices were higher with intermediate disturbance at middle elevations compared to higher and lower disturbances at low and high elevations, respectively. This reflected a disturbance-diversity pattern and thus revealed the obvious importance to maintain the intermediate disturbance for biodiversity conservation.

  4. The effects of energy grass plantations on biodiversity

    Energy Technology Data Exchange (ETDEWEB)

    Semere, T.; Slater, F.

    2005-07-01

    The ecological impact on local wildlife of biomass plantations of three different species of grasses has been monitored in the years 2002 to 2004 inclusive at farms in Herefordshire UK. Two of the grasses were not native to Britain. Wildlife monitored included ground flora, beetles, insects, birds, small mammals, butterflies, bees and hoverflies. The results provide a baseline of biodiversity data from biomass farms in England, although due to poor crop growth, the data from the switch-grass plantation was incomplete. The surveys were carried out by Cardiff University supported financially by the DTI.

  5. Effects of biodiversity strengthen over time as ecosystem functioning declines at low and increases at high biodiversity

    National Research Council Canada - National Science Library

    Meyer, S; Ebeling, A; Eisenhauer, Nico; Mommer, L; Ravenek, Janneke M; Weigelt, Alexana

    2016-01-01

    Human-caused declines in biodiversity have stimulated intensive research on the consequences of biodiversity loss for ecosystem services and policy initiatives to preserve the functioning of ecosystem...

  6. How Essential Biodiversity Variables and remote sensing can help national biodiversity monitoring

    Directory of Open Access Journals (Sweden)

    Petteri Vihervaara

    2017-04-01

    Full Text Available Essential Biodiversity Variables (EBVs have been suggested to harmonize biodiversity monitoring worldwide. Their aim is to provide a small but comprehensive set of monitoring variables that would give a balanced picture of the development of biodiversity and the reaching of international and national biodiversity targets. Globally, GEO BON (Group on Earth Observations Biodiversity Observation Network has suggested 22 candidate EBVs to be monitored. In this article we regard EBVs as a conceptual tool that may help in making national scale biodiversity monitoring more robust by pointing out where to focus further development resources. We look at one country –Finland –with a relatively advanced biodiversity monitoring scheme and study how well Finland’s current biodiversity state indicators correspond with EBVs. In particular, we look at how national biodiversity monitoring could be improved by using available remote sensing (RS applications. Rapidly emerging new technologies from drones to airborne laser scanning and new satellite sensors providing imagery with very high resolution (VHR open a whole new world of opportunities for monitoring the state of biodiversity and ecosystems at low cost. In Finland, several RS applications already exist that could be expanded into national indicators. These include the monitoring of shore habitats and water quality parameters, among others. We hope that our analysis and examples help other countries with similar challenges. Along with RS opportunities, our analysis revealed also some needs to develop the EBV framework itself.

  7. Biofilm Thickness Influences Biodiversity in Nitrifying MBBRs-Implications on Micropollutant Removal

    DEFF Research Database (Denmark)

    Torresi, Elena; Fowler, Jane; Polesel, Fabio

    2016-01-01

    In biofilm systems for wastewater treatment (e.g., moving bed biofilms reactors-MBBRs) biofilm thickness is typically not under direct control. Nevertheless, biofilm thickness is likely to have a profound effect on the microbial diversity and activity, as a result of diffusion limitation and thus...... at 50, 200, 300, 400, and 500 μm. The impact of biofilm thickness on microbial community was assessed via 16S rRNA gene amplicon sequencing and ammonia monooxygenase (amoA) abundance quantification through quantitative PCR (qPCR). Results from batch experiments and microbial analysis showed that (i......) the thickest biofilm (500 μm) presented the highest specific biotransformation rate constants (kbio, L g(-1) d(-1)) for 14 out of 22 micropollutants; (ii) biofilm thickness positively associated with biodiversity, which was suggested as the main factor for the observed enhancement of kbio; (iii) the thinnest...

  8. Late Quaternary climate change shapes island biodiversity

    DEFF Research Database (Denmark)

    Weigelt, Patrick; Steinbauer, Manuel; Cabral, Juliano

    2016-01-01

    Island biogeographical models consider islands either as geologically static with biodiversity resulting from ecologically neutral immigration–extinction dynamics1, or as geologically dynamic with biodiversity resulting from immigration–speciation–extinction dynamics influenced by changes in island...... sea levels3, 4 and caused massive changes in island area, isolation and connectivity5, orders of magnitude faster than the geological processes of island formation, subsidence and erosion considered in island theory2, 6. Consequences of these oscillations for present biodiversity remain unassessed5, 7...

  9. Both Direct and Vicarious Experiences of Nature Affect Children’s Willingness to Conserve Biodiversity

    Directory of Open Access Journals (Sweden)

    Masashi Soga

    2016-05-01

    Full Text Available Children are becoming less likely to have direct contact with nature. This ongoing loss of human interactions with nature, the extinction of experience, is viewed as one of the most fundamental obstacles to addressing global environmental challenges. However, the consequences for biodiversity conservation have been examined very little. Here, we conducted a questionnaire survey of elementary schoolchildren and investigated effects of the frequency of direct (participating in nature-based activities and vicarious experiences of nature (reading books or watching TV programs about nature and talking about nature with parents or friends on their affective attitudes (individuals’ emotional feelings toward and willingness to conserve biodiversity. A total of 397 children participated in the surveys in Tokyo. Children’s affective attitudes and willingness to conserve biodiversity were positively associated with the frequency of both direct and vicarious experiences of nature. Path analysis showed that effects of direct and vicarious experiences on children’s willingness to conserve biodiversity were mediated by their affective attitudes. This study demonstrates that children who frequently experience nature are likely to develop greater emotional affinity to and support for protecting biodiversity. We suggest that children should be encouraged to experience nature and be provided with various types of these experiences.

  10. Can wide consultation help with setting priorities for large-scale biodiversity monitoring programs?

    Directory of Open Access Journals (Sweden)

    Frédéric Boivin

    Full Text Available Climate and other global change phenomena affecting biodiversity require monitoring to track ecosystem changes and guide policy and management actions. Designing a biodiversity monitoring program is a difficult task that requires making decisions that often lack consensus due to budgetary constrains. As monitoring programs require long-term investment, they also require strong and continuing support from all interested parties. As such, stakeholder consultation is key to identify priorities and make sound design decisions that have as much support as possible. Here, we present the results of a consultation conducted to serve as an aid for designing a large-scale biodiversity monitoring program for the province of Québec (Canada. The consultation took the form of a survey with 13 discrete choices involving tradeoffs in respect to design priorities and 10 demographic questions (e.g., age, profession. The survey was sent to thousands of individuals having expected interests and knowledge about biodiversity and was completed by 621 participants. Overall, consensuses were few and it appeared difficult to create a design fulfilling the priorities of the majority. Most participants wanted 1 a monitoring design covering the entire territory and focusing on natural habitats; 2 a focus on species related to ecosystem services, on threatened and on invasive species. The only demographic characteristic that was related to the type of prioritization was the declared level of knowledge in biodiversity (null to high, but even then the influence was quite small.

  11. Both Direct and Vicarious Experiences of Nature Affect Children's Willingness to Conserve Biodiversity.

    Science.gov (United States)

    Soga, Masashi; Gaston, Kevin J; Yamaura, Yuichi; Kurisu, Kiyo; Hanaki, Keisuke

    2016-05-25

    Children are becoming less likely to have direct contact with nature. This ongoing loss of human interactions with nature, the extinction of experience, is viewed as one of the most fundamental obstacles to addressing global environmental challenges. However, the consequences for biodiversity conservation have been examined very little. Here, we conducted a questionnaire survey of elementary schoolchildren and investigated effects of the frequency of direct (participating in nature-based activities) and vicarious experiences of nature (reading books or watching TV programs about nature and talking about nature with parents or friends) on their affective attitudes (individuals' emotional feelings) toward and willingness to conserve biodiversity. A total of 397 children participated in the surveys in Tokyo. Children's affective attitudes and willingness to conserve biodiversity were positively associated with the frequency of both direct and vicarious experiences of nature. Path analysis showed that effects of direct and vicarious experiences on children's willingness to conserve biodiversity were mediated by their affective attitudes. This study demonstrates that children who frequently experience nature are likely to develop greater emotional affinity to and support for protecting biodiversity. We suggest that children should be encouraged to experience nature and be provided with various types of these experiences.

  12. Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

    DEFF Research Database (Denmark)

    Frøslev, Tobias Guldberg; Kjøller, Rasmus; Bruun, Hans Henrik

    2017-01-01

    soil from 130 sites in Denmark spanning major environmental gradients. OTU tables are produced with several different OTU definition algorithms and subsequently curated with LULU, and validated against field survey data. LULU curation consistently improves α-diversity estimates and other biodiversity...

  13. Contribution of large-scale forest inventories to biodiversity assessment and monitoring

    Science.gov (United States)

    Piermaria Corona; Gherardo Chirici; Ronald E. McRoberts; Susanne Winter; Anna. Barbati

    2011-01-01

    Statistically-designed inventories and biodiversity monitoring programs are gaining relevance for biological conservation and natural resources management. Mandated periodic surveys provide unique opportunities to identify and satisfy natural resources management information needs. However, this is not an end in itself but rather is the beginning of a process that...

  14. The Lives and Times of the Narragansett Bay Benthos: Biodiversity Trends over 182 Years

    Science.gov (United States)

    Narragansett Bay has high benthic invertebrate biodiversity that supports many ecosystem functions and services. A master list was compiled of all benthic species collected from the Bay beginning in 1862, including a U.S. Bureau of Commercial Fisheries survey in 1871 and studies ...

  15. Actiniaria from Ria de Arosa, Galicia, northwestern Spain, in the Netherlands Centre for Biodiversity Naturalis, Leiden

    NARCIS (Netherlands)

    Hartog, den J.C.; Ates, R.M.L.

    2011-01-01

    Twentysix species of sea anemones (Actiniaria) collected in Galicia, northwestern Spain are present in the collection of the Netherlands Centre for Biodiversity Naturalis. They are listed and discussed. The cnidom of seventeen species is surveyed. Diadumene cincta is not a recent immigrant in

  16. Some aspects of socio-economic activities that affect biodiversity of ...

    African Journals Online (AJOL)

    This paper examines the socio-economic activities of man along the coastal wetlands of Lagos State with a view of assessing the resultant effect on the Biodiversity of the area. For the benefit of this study, the area was divided into three zones. The procedures adopted were preliminary interview, market survey and structural ...

  17. Spatial variation in the biodiversity of Bedouin gardens in the St ...

    African Journals Online (AJOL)

    Three wadi systems in the St. Katherine Protectorate (south Sinai, Egypt) were surveyed for spatial variation in the biodiversity of plants, flying and ground insects during August- September, 2000. Plant diversity and species richness were significantly different among the systems (the St. Katherine and Gebal systems were ...

  18. Evaluation of Filtration and DNA Extraction Methods for Environmental DNA Biodiversity Assessments across Multiple Trophic Levels

    Directory of Open Access Journals (Sweden)

    Anni Djurhuus

    2017-10-01

    Full Text Available Metabarcoding of marine environmental DNA (eDNA, originating from tissue, cells, or extracellular DNA, offers the opportunity to survey the biological composition of communities across multiple trophic levels from a non-invasive seawater sample. Here we compare results of eDNA metabarcoding of multiple trophic levels from individual seawater samples collected from a kelp forest in Monterey Bay, California in order to establish methods for future cross-trophic level eDNA analysis. Triplicate 1 L water samples were filtered using five different 47 mm diameter membrane filters (PVDF, PES, GFF, PCTE, and NC and DNA was extracted from triplicates of each filter-type using three widely-used extraction methods (the DNeasy Blood and Tissue kit, the MoBio PowerWater DNA Isolation kit, and standard phenol/chloroform methods resulting in 45 individual eDNA samples prepared with 15 workflow combinations. Each DNA extract was amplified using PCR primers for the 16S rRNA gene (microorganisms; Bacteria and Archaea, 18S rRNA gene (phytoplankton, and the 12S rRNA gene (vertebrates, and PCR products were sequenced on an Illumina MiSeq platform. The richness and community composition of microbial, phytoplankton, and vertebrate OTUs were not significantly different between any of the 0.2 μm pore-size filter types extracted with the DNeasy or MoBio kits. However, phenol/chloroform extraction resulted in significantly different community structures. This study provides insight into multiple choices for extraction and filtration methods to use eDNA metabarcoding for biodiversity assessment of multiple trophic levels from a single sample. We recommend any combination of either DNeasy or MoBio with PES, PCTE, PVDF, or NC filters for a cross trophic level comparison.

  19. Making the case for biodiversity in South Africa: Re-framing biodiversity communications

    OpenAIRE

    Kristal Maze; Mandy Barnett; Emily A. Botts; Anthea Stephens; Mike Freedman; Lars Guenther

    2016-01-01

    Background: Biodiversity education and public awareness do not always contain the motivational messages that inspire action amongst decision-makers. Traditional messages from the biodiversity sector are often framed around threat, with a generally pessimistic tone. Aspects of social marketing can be used to support positive messaging that is more likely to inspire action amongst the target audience.Objectives: The South African biodiversity sector embarked on a market research process to bett...

  20. Microbial Ecosystems, Protection of

    NARCIS (Netherlands)

    Bodelier, P.L.E.; Nelson, K.E.

    2014-01-01

    Synonyms Conservation of microbial diversity and ecosystem functions provided by microbes; Preservation of microbial diversity and ecosystem functions provided by microbes Definition The use, management, and conservation of ecosystems in order to preserve microbial diversity and functioning.

  1. Biodiversity promotes tree growth during succession in subtropical forest.

    Directory of Open Access Journals (Sweden)

    Martin Barrufol

    Full Text Available Losses of plant species diversity can affect ecosystem functioning, with decreased primary productivity being the most frequently reported effect in experimental plant assemblages, including tree plantations. Less is known about the role of biodiversity in natural ecosystems, including forests, despite their importance for global biogeochemical cycling and climate. In general, experimental manipulations of tree diversity will take decades to yield final results. To date, biodiversity effects in natural forests therefore have only been reported from sample surveys or meta-analyses with plots not initially selected for diversity. We studied biomass and growth of subtropical forests stands in southeastern China. Taking advantage of variation in species recruitment during secondary succession, we adopted a comparative study design selecting forest plots to span a gradient in species richness. We repeatedly censored the stem diameter of two tree size cohorts, comprising 93 species belonging to 57 genera and 33 families. Tree size and growth were analyzed in dependence of species richness, the functional diversity of growth-related traits, and phylogenetic diversity, using both general linear and structural equation modeling. Successional age covaried with diversity, but differently so in the two size cohorts. Plot-level stem basal area and growth were positively related with species richness, while growth was negatively related to successional age. The productivity increase in species-rich, functionally and phylogenetically diverse plots was driven by both larger mean sizes and larger numbers of trees. The biodiversity effects we report exceed those from experimental studies, sample surveys and meta-analyses, suggesting that subtropical tree diversity is an important driver of forest productivity and re-growth after disturbance that supports the provision of ecological services by these ecosystems.

  2. Biodiversity promotes tree growth during succession in subtropical forest.

    Science.gov (United States)

    Barrufol, Martin; Schmid, Bernhard; Bruelheide, Helge; Chi, Xiulian; Hector, Andrew; Ma, Keping; Michalski, Stefan; Tang, Zhiyao; Niklaus, Pascal A

    2013-01-01

    Losses of plant species diversity can affect ecosystem functioning, with decreased primary productivity being the most frequently reported effect in experimental plant assemblages, including tree plantations. Less is known about the role of biodiversity in natural ecosystems, including forests, despite their importance for global biogeochemical cycling and climate. In general, experimental manipulations of tree diversity will take decades to yield final results. To date, biodiversity effects in natural forests therefore have only been reported from sample surveys or meta-analyses with plots not initially selected for diversity. We studied biomass and growth of subtropical forests stands in southeastern China. Taking advantage of variation in species recruitment during secondary succession, we adopted a comparative study design selecting forest plots to span a gradient in species richness. We repeatedly censored the stem diameter of two tree size cohorts, comprising 93 species belonging to 57 genera and 33 families. Tree size and growth were analyzed in dependence of species richness, the functional diversity of growth-related traits, and phylogenetic diversity, using both general linear and structural equation modeling. Successional age covaried with diversity, but differently so in the two size cohorts. Plot-level stem basal area and growth were positively related with species richness, while growth was negatively related to successional age. The productivity increase in species-rich, functionally and phylogenetically diverse plots was driven by both larger mean sizes and larger numbers of trees. The biodiversity effects we report exceed those from experimental studies, sample surveys and meta-analyses, suggesting that subtropical tree diversity is an important driver of forest productivity and re-growth after disturbance that supports the provision of ecological services by these ecosystems.

  3. Marine biodiversity, ecosystem functioning, and carbon cycles

    National Research Council Canada - National Science Library

    Grégory Beaugrand; Martin Edwards; Louis Legendre; David Karl

    2010-01-01

    .... We also show that this rise in biodiversity paralleled a decrease in the mean size of zooplanktonic copepods and that the reorganization of the planktonic ecosystem toward dominance by smaller...

  4. The Circumpolar Biodiversity Monitoring Program Terrestrial Plan

    DEFF Research Database (Denmark)

    Christensen, Tom; Payne, J.; Doyle, M.

    The Conservation of Arctic Flora and Fauna (CAFF), the biodiversity working group of the Arctic Council, established the Circumpolar Biodiversity Monitoring Program (CBMP) to address the need for coordinated and standardized monitoring of Arctic environments in terrestrial, marine, freshwater...... and coastal environments. The CBMP Terrestrial Plan is a framework to focus and coordinate monitoring of terrestrial biodiversity across the Arctic. The goal of the plan is to improve the collective ability of Arctic traditional knowledge (TK) holders, northern communities, and scientists to detect......, understand and report on long-term change in Arctic terrestrial ecosystems and biodiversity, and to identify knowledge gaps and priorities. This poster will outline the key management questions the plan aims to address and the proposed nested, multi-scaled approach linking targeted, research based monitoring...

  5. Coastal and marine biodiversity of India

    Digital Repository Service at National Institute of Oceanography (India)

    Venkataraman, K.; Wafar, M.V.M.

    This paper summarizes what is known of the coastal and marine biodiversity of the Indian seas and their various ecosystems, from past literature, museum records and other lesser-known sources of information. The synthesis suggests that the number...

  6. Antarctica and the strategic plan for biodiversity

    Science.gov (United States)

    Chown, Steven L.; Brooks, Cassandra M.; Terauds, Aleks; Le Bohec, Céline; van Klaveren-Impagliazzo, Céline; Whittington, Jason D.; Butchart, Stuart H. M.; Coetzee, Bernard W. T.; Collen, Ben; Convey, Peter; Gaston, Kevin J.; Gilbert, Neil; Gill, Mike; Höft, Robert; Johnston, Sam; Kennicutt, Mahlon C.; Kriesell, Hannah J.; Le Maho, Yvon; Lynch, Heather J.; Palomares, Maria; Puig-Marcó, Roser; Stoett, Peter; McGeoch, Melodie A.

    2017-01-01

    The Strategic Plan for Biodiversity, adopted under the auspices of the Convention on Biological Diversity, provides the basis for taking effective action to curb biodiversity loss across the planet by 2020—an urgent imperative. Yet, Antarctica and the Southern Ocean, which encompass 10% of the planet’s surface, are excluded from assessments of progress against the Strategic Plan. The situation is a lost opportunity for biodiversity conservation globally. We provide such an assessment. Our evidence suggests, surprisingly, that for a region so remote and apparently pristine as the Antarctic, the biodiversity outlook is similar to that for the rest of the planet. Promisingly, however, much scope for remedial action exists. PMID:28350825

  7. Assessing the suitability of diversity metrics to detect biodiversity change

    NARCIS (Netherlands)

    Santini, L.; Belmaker, J.; Costello, M.J.; Pereira, H.M.; Rossberg, A.G.; Schipper, A.M.; Ceaușu, S.; Dornelas, M.; Hilbers, J.P.; Hortal, J.; Huijbregts, M.A.J.; Navarro, L.M.; Schiffers, K.H.; Visconti, P.; Rondinini, C.

    2016-01-01

    A large number of diversity metrics are available to study and monitor biodiversity, and their responses to biodiversity changes are not necessarily coherent with each other. The choice of biodiversity metrics may thus strongly affect our interpretation of biodiversity change and, hence,

  8. Forest Biodiversity, Climate Change and Governance

    OpenAIRE

    Tacconi, Luca

    2010-01-01

    The main drivers of tropical forest biodiversity loss are land clearing for agriculture, pasture and timber plantation development, followed by logging activities that degrade forests. Deforestation and forest degradation also significantly contribute to climate change, given that they contribute about 12–15% of total greenhouse gas emissions. Climate change in turn negatively affects biodiversity and agricultural activities in tropical countries. Therefore the governance of forest biodiversi...

  9. Delivering Biodiversity Knowledge in the Information Age

    OpenAIRE

    Hobern, Donald; Apostolico, Alberto; Bello, Juan Carlos; CANHOS Dora; Dubois, Gregoire; ELIZABETH Arnaud; Field, Dawn; Hardisty, Alex; HARRISON Jerry; HEYDORN Bryan; Mata, Erick; Page, Roderic; Parr, Cynthia; Price, Jeff; WILLOUGHBY Selwyn

    2013-01-01

    The Global Biodiversity Informatics Outlook helps to focus effort and investment towards better understanding of life on Earth and our impacts upon it. It proposes a framework that will help harness the immense power of information technology and an open data culture, to gather unprecedented evidence about biodiversity and to inform better decisions. This document is accompanied by a website, www.biodiversityinformatics.org, that will report progress towards each part of the framework and...

  10. The biodiversity-dependent ecosystem service debt.

    Science.gov (United States)

    Isbell, Forest; Tilman, David; Polasky, Stephen; Loreau, Michel

    2015-02-01

    Habitat destruction is driving biodiversity loss in remaining ecosystems, and ecosystem functioning and services often directly depend on biodiversity. Thus, biodiversity loss is likely creating an ecosystem service debt: a gradual loss of biodiversity-dependent benefits that people obtain from remaining fragments of natural ecosystems. Here, we develop an approach for quantifying ecosystem service debts, and illustrate its use to estimate how one anthropogenic driver, habitat destruction, could indirectly diminish one ecosystem service, carbon storage, by creating an extinction debt. We estimate that c. 2-21 Pg C could be gradually emitted globally in remaining ecosystem fragments because of plant species loss caused by nearby habitat destruction. The wide range for this estimate reflects substantial uncertainties in how many plant species will be lost, how much species loss will impact ecosystem functioning and whether plant species loss will decrease soil carbon. Our exploratory analysis suggests that biodiversity-dependent ecosystem service debts can be globally substantial, even when locally small, if they occur diffusely across vast areas of remaining ecosystems. There is substantial value in conserving not only the quantity (area), but also the quality (biodiversity) of natural ecosystems for the sustainable provision of ecosystem services. © 2014 John Wiley & Sons Ltd/CNRS.

  11. The integration of biodiversity into One Health.

    Science.gov (United States)

    Romanelli, C; Cooper, H D; de Souza Dias, B F

    2014-08-01

    A better understanding of the links between biodiversity, health and disease presents major opportunities for policy development, and can enhance our understanding of how health-focused measures affect biodiversity, and conservation measures affect health. The breadth and complexity of these relationships, and the socio-economic drivers by which they are influenced, in the context of rapidly shifting global trends, reaffirm the need for an integrative, multidisciplinary and systemic approach to the health of people, livestock and wildlife within the ecosystem context. Loss of biodiversity, habitat fragmentation and the loss of natural environments threaten the full range of life-supporting services provided by ecosystems at all levels of biodiversity, including species, genetic and ecosystem diversity. The disruption of ecosystem services has direct and indirect implications for public health, which are likely to exacerbate existing health inequities, whether through exposure to environmental hazards or through the loss of livelihoods. One Health provides a valuable framework for the development of mutually beneficial policies and interventions at the nexus between health and biodiversity, and it is critical that One Health integrates biodiversity into its strategic agenda.

  12. Towards a Duty of Care for Biodiversity

    Science.gov (United States)

    Earl, G.; Curtis, A.; Allan, C.

    2010-04-01

    The decline in biodiversity is a worldwide phenomenon, with current rates of species extinction more dramatic than any previously recorded. Habitat loss has been identified as the major cause of biodiversity decline. In this article we suggest that a statutory duty of care would complement the current mix of policy options for biodiversity conservation. Obstacles hindering the introduction of a statutory duty of care include linguistic ambiguity about the terms ‘duty of care’ and ‘stewardship’ and how they are applied in a natural resource management context, and the absence of a mechanism to guide its implementation. Drawing on international literature and key informant interviews we have articulated characteristics of duty of care to reduce linguistic ambiguity, and developed a framework for implementing a duty of care for biodiversity at the regional scale. The framework draws on key elements of the common law ‘duty of care’, the concepts of ‘taking reasonable care’ and ‘avoiding foreseeable harm’, in its logic. Core elements of the framework include desired outcomes for biodiversity, supported by current recommended practices. The focus on outcomes provides opportunities for the development of innovative management practices. The framework incorporates multiple pathways for the redress of non-compliance including tiered negative sanctions, and positive measures to encourage compliance. Importantly, the framework addresses the need for change and adaptation that is a necessary part of biodiversity management.

  13. [Mechanism on biodiversity managing crop diseases].

    Science.gov (United States)

    Yang, Jing; Shi, Zhu-Feng; Gao, Dong; Liu, Lin; Zhu, You-Yong; Li, Cheng-Yun

    2012-11-01

    Reasonable utilization of natural resource and protection of ecological environment is the foundation for implementing agricultural sustainable development. Biodiversity research and protection are becoming an important issue concerned commonly in the world. Crop disease is one of the important natural disasters for food production and safety, and is also one of the main reasons that confine sustainable development of agricultural production. Large-scale deployment of single highly resistant variety results in reduction of agro-biodiversity level. In this case, excessive loss of agro-biodiversity has become the main challenge in sustainable agriculture. Biodiversity can not only effectively alleviate disease incidence and loss of crop production, but also reduce pollution of agricultural ecological environment caused by excessive application of pesticides and fertilizers to the agricultural ecological environment. Discovery of the mechanism of biodiversity to control crop diseases can reasonably guide the rational deployment and rotation of different crops and establish optimization combinations of different crops. This review summarizes recent advances of research on molecular, physiological, and ecological mechanisms of biodiversity managing crop diseases, and proposes some research that needs to be strengthened in the future.

  14. Efficient Evaluation of Biodiversity Concerns in Protected Areas

    Directory of Open Access Journals (Sweden)

    Sam Ferreira

    2013-01-01

    Full Text Available Monitoring is a vital component of keeping protected areas in desired states. Lack of robust designs, however, impedes efficient monitoring. We ask two questions—how does effort at a specific site as well as number of sites in a plant community influence richness, abundance, and diversity indicators. Large mammal herbivory biodiversity influences are a key concern for managers of Mokala National Park. We anticipated that changes in biodiversity indicators (vegetation, ants, and birds associate with herbivore intensity of use of landscapes. We identified flat deep sandy plains and undulating shallow rocky hills as focal landscapes. Our focus was on finding optimized effort at survey sites as well as the number of sites. Monitoring to evaluate change in diversity and abundance needs far less effort than evaluating change in richness. Furthermore, given the variance at the landscape level, monitoring of species abundance and diversity allows easier detection with less effort and at shorter intervals between surveys than that required for richness. Even though a mechanisms-based approach directs monitoring, conservationists need to evaluate feasibility. In our case, measurement of richness is unlikely to detect herbivore effects. In general though, we have illustrated that focused monitoring designs can robustly evaluate conservation objectives.

  15. Protistan diversity in the Arctic: a case of paleoclimate shaping modern biodiversity?

    Directory of Open Access Journals (Sweden)

    Thorsten Stoeck

    Full Text Available BACKGROUND: The impact of climate on biodiversity is indisputable. Climate changes over geological time must have significantly influenced the evolution of biodiversity, ultimately leading to its present pattern. Here we consider the paleoclimate data record, inferring that present-day hot and cold environments should contain, respectively, the largest and the smallest diversity of ancestral lineages of microbial eukaryotes. METHODOLOGY/PRINCIPAL FINDINGS: We investigate this hypothesis by analyzing an original dataset of 18S rRNA gene sequences from Western Greenland in the Arctic, and data from the existing literature on 18S rRNA gene diversity in hydrothermal vent, temperate sediments, and anoxic water column communities. Unexpectedly, the community from the cold environment emerged as one of the richest observed to date in protistan species, and most diverse in ancestral lineages. CONCLUSIONS/SIGNIFICANCE: This pattern is consistent with natural selection sweeps on aerobic non-psychrophilic microbial eukaryotes repeatedly caused by low temperatures and global anoxia of snowball Earth conditions. It implies that cold refuges persisted through the periods of greenhouse conditions, which agrees with some, although not all, current views on the extent of the past global cooling and warming events. We therefore identify cold environments as promising targets for microbial discovery.

  16. The Sweet and the Bitter: Intertwined Positive and Negative Social Impacts of a Biodiversity Offset

    Directory of Open Access Journals (Sweden)

    Cécile Bidaud

    2017-01-01

    Full Text Available Major developments, such as mines, will often have unavoidable environmental impacts. In such cases, investors, governments, or even a company's own standards increasingly require implementation of biodiversity offsets (investment in conservation with a measurable outcome with the aim of achieving 'no net loss' or even a 'net gain' of biodiversity. Where conservation is achieved by changing the behaviour of people directly using natural resources, the offset might be expected to have social impacts but such impacts have received very little attention. Using the case study of Ambatovy, a major nickel mine in the eastern rainforests of Madagascar and a company at the vanguard of developing biodiversity offsets, we explore local perceptions of the magnitude and distribution of impacts of the biodiversity offset project on local wellbeing. We used both qualitative (key informant interviews and focus group discussions and quantitative (household survey methods. We found that the biodiversity offsets, which comprise both conservation restrictions and development activities, influenced wellbeing in a mixture of positive and negative ways. However, overall, respondents felt that they had suffered a net cost from the biodiversity offset. It is a matter of concern that benefits from development activities do not compensate for the costs of the conservation restrictions, that those who bear the costs are not the same people as those who benefit, and that there is a mismatch in timing between the immediate restrictions and the associated development activities which take some time to deliver benefits. These issues matter both from the perspective of environmental justice, and for the long-term sustainability of the biodiversity benefits the offset is supposed to deliver.

  17. Contribution of citizen science to improve knowledge on marine biodiversity in the Gulf Region

    Directory of Open Access Journals (Sweden)

    Aurora M. Castilla

    2017-10-01

    Of the ten species of sea snakes listed in the literature to be present in the Gulf Region, most of them have been reported for Qatar, Bahrain, United Arab Emirates and Saudi Arabia. However, the number of species present is often assumed based on their occurrence within the Arabian Gulf rather than on actual captures and appropriate identification. The creation of marine reference biological scientific collections to properly identify the species and make accurate biodiversity inventories is an urgent priority for the countries in the Gulf region. To this end, contributions by stakeholders and the general public for this study have proven to be very useful. However a larger networking with local and international scientists and stakeholders is still needed to adequately survey the country’s current biodiversity, identify research priorities and eventually provide the scientific input needed to assist biodiversity management related to renewable resource management and marine conservation in the Arabian Gulf Region.

  18. Climate-smart management of biodiversity

    Science.gov (United States)

    Nadeau, Christopher P.; Fuller, Angela K.; Rosenblatt, Daniel L.

    2015-01-01

    Determining where biodiversity is likely to be most vulnerable to climate change and methods to reduce that vulnerability are necessary first steps to incorporate climate change into biodiversity management plans. Here, we use a spatial climate change vulnerability assessment to (1) map the potential vulnerability of terrestrial biodiversity to climate change in the northeastern United States and (2) provide guidance on how and where management actions for biodiversity could provide long-term benefits under climate change (i.e., climate-smart management considerations). Our model suggests that biodiversity will be most vulnerable in Delaware, Maryland, and the District of Columbia due to the combination of high climate change velocity, high landscape resistance, and high topoclimate homogeneity. Biodiversity is predicted to be least vulnerable in Vermont, Maine, and New Hampshire because large portions of these states have low landscape resistance, low climate change velocity, and low topoclimate homogeneity. Our spatial climate-smart management considerations suggest that: (1) high topoclimate diversity could moderate the effects of climate change across 50% of the region; (2) decreasing local landscape resistance in conjunction with other management actions could increase the benefit of those actions across 17% of the region; and (3) management actions across 24% of the region could provide long-term benefits by promoting short-term population persistence that provides a source population capable of moving in the future. The guidance and framework we provide here should allow conservation organizations to incorporate our climate-smart management considerations into management plans without drastically changing their approach to biodiversity conservation.

  19. Data hosting infrastructure for primary biodiversity data

    Science.gov (United States)

    2011-01-01

    Background Today, an unprecedented volume of primary biodiversity data are being generated worldwide, yet significant amounts of these data have been and will continue to be lost after the conclusion of the projects tasked with collecting them. To get the most value out of these data it is imperative to seek a solution whereby these data are rescued, archived and made available to the biodiversity community. To this end, the biodiversity informatics community requires investment in processes and infrastructure to mitigate data loss and provide solutions for long-term hosting and sharing of biodiversity data. Discussion We review the current state of biodiversity data hosting and investigate the technological and sociological barriers to proper data management. We further explore the rescuing and re-hosting of legacy data, the state of existing toolsets and propose a future direction for the development of new discovery tools. We also explore the role of data standards and licensing in the context of data hosting and preservation. We provide five recommendations for the biodiversity community that will foster better data preservation and access: (1) encourage the community's use of data standards, (2) promote the public domain licensing of data, (3) establish a community of those involved in data hosting and archival, (4) establish hosting centers for biodiversity data, and (5) develop tools for data discovery. Conclusion The community's adoption of standards and development of tools to enable data discovery is essential to sustainable data preservation. Furthermore, the increased adoption of open content licensing, the establishment of data hosting infrastructure and the creation of a data hosting and archiving community are all necessary steps towards the community ensuring that data archival policies become standardized. PMID:22373257

  20. Biodiversity information platforms: From standards to interoperability

    Directory of Open Access Journals (Sweden)

    Walter Berendsohn

    2011-11-01

    Full Text Available One of the most serious bottlenecks in the scientific workflows of biodiversity sciences is the need to integrate data from different sources, software applications, and services for analysis, visualisation and publication. For more than a quarter of a century the TDWG Biodiversity Information Standards organisation has a central role in defining and promoting data standards and protocols supporting interoperability between disparate and locally distributed systems. Although often not sufficiently recognized, TDWG standards are the foundation of many popular Biodiversity Informatics applications and infrastructures ranging from small desktop software solutions to large scale international data networks. However, individual scientists and groups of collaborating scientist have difficulties in fully exploiting the potential of standards that are often notoriously complex, lack non-technical documentations, and use different representations and underlying technologies. In the last few years, a series of initiatives such as Scratchpads, the EDIT Platform for Cybertaxonomy, and biowikifarm have started to implement and set up virtual work platforms for biodiversity sciences which shield their users from the complexity of the underlying standards. Apart from being practical work-horses for numerous working processes related to biodiversity sciences, they can be seen as information brokers mediating information between multiple data standards and protocols. The ViBRANT project will further strengthen the flexibility and power of virtual biodiversity working platforms by building software interfaces between them, thus facilitating essential information flows needed for comprehensive data exchange, data indexing, web-publication, and versioning. This work will make an important contribution to the shaping of an international, interoperable, and user-oriented biodiversity information infrastructure.

  1. International Center for Himalayan Biodiversity (ICHB): Conserving Himalayan Biodiversity--A Global Responsibility

    Science.gov (United States)

    Ram Bhandari

    2006-01-01

    Biodiversity is a global endowment of nature. Conservation of biodiversity includes all species of plants, animals and other organisms, the range of genetic stocks within each species, and ecosystem diversity. Food, many types of medicine and industrial products are provided by the biological resources that are the basis of life on Earth. The value of the Earth’s...

  2. Biodiversity Scenarios: Projections of 21st century change in biodiversity and associated ecosystem services

    CSIR Research Space (South Africa)

    Scholes, B

    2010-01-01

    Full Text Available Diversity Citation Leadley, P., Pereira, H.M., Alkemade, R., Fernandez-Manjarrés, J.F., Proença, V., Scharlemann, J.P.W., Walpole, M.J. (2010) Biodiversity Scenarios: Projections of 21st century change in biodiversity and associated ecosystem services...

  3. Compensation for biodiversity loss – Advice to the Netherlands' Taskforce on Biodiversity and Natural Resources

    NARCIS (Netherlands)

    Bie, de S.; Dessel, van B.

    2011-01-01

    Compensation of damage to biodiversity is one of the mechanisms to settle environmental costs. It concerns creating new opportunities for biodiversity, which as a minimum equals the residual impact after a company or organization has attempted to avoid, prevent and mitigate that impact. In the

  4. Breaking boundaries for biodiversity : expanding the policy agenda to halt biodiversity loss

    NARCIS (Netherlands)

    Veen, M.P.; Sanders, M.E.; Tekelenburg, A.; Gerritsen, A.L.; Lörzing, J.A.; Brink, Th.

    2010-01-01

    Our assessment from the perspective of the Netherlands, a country in the temperate zone, showed a slightly positive picture, in line with the overall results for this zone. The loss of biodiversity in the Netherlands has been slowed down, but the European target – halting the loss of biodiversity

  5. Challenges of Biodiversity Education: A Review of Education Strategies for Biodiversity Education

    Science.gov (United States)

    Navarro-Perez, Moramay; Tidball, Keith G.

    2012-01-01

    Biodiversity conservation has increasingly gained recognition in national and international agendas. The Convention on Biological Diversity (CBD) has positioned biodiversity as a key asset to be protected to ensure our well-being and that of future generations. Nearly 20 years after its inception, results are not as expected, as shown in the…

  6. Making the case for biodiversity in South Africa: Re-framing biodiversity communications

    Directory of Open Access Journals (Sweden)

    Kristal Maze

    2016-12-01

    Conclusion: Based on the findings, a communications strategy known as ‘Making the case for biodiversity’ was developed that re-framed the economic, emotional and practical value propositions for biodiversity. The communications strategy has already resulted in greater political and economic attention towards biodiversity in South Africa.

  7. Biodiversity and Activity of the Gut Microbiota across the Life History of the Insect Herbivore Spodoptera littoralis

    OpenAIRE

    Bosheng Chen; Beng-Soon Teh; Chao Sun; Sirui Hu; Xingmeng Lu; Wilhelm Boland; Yongqi Shao

    2016-01-01

    Microbes that live inside insects play critical roles in host nutrition, physiology, and behavior. Although Lepidoptera (butterflies and moths) are one of the most diverse insect taxa, their microbial symbionts are little-studied, particularly during metamorphosis. Here, using ribosomal tag pyrosequencing of DNA and RNA, we investigated biodiversity and activity of gut microbiotas across the holometabolous life cycle of Spodoptera littoralis, a notorious agricultural pest worldwide. Proteobac...

  8. Root Zone Microbial Communities and Restoration of Plant Communities in Owens Valley, California - Phase 1

    National Research Council Canada - National Science Library

    Fredrickson, Herbert; Furey, John; Price, David; Foote, Chris; Richmond, Margaret

    2007-01-01

    .... These interrelationships depend on soil characteristics affecting the microbial communities. This study was designed to provide survey information on microbial communities in soils from native and disturbed areas at ten locations spanning Owens Valley...

  9. Monitoring Hawaiian biodiversity: Pilot study to assess changes to forest birds and their habitat

    Science.gov (United States)

    Gorresen, P. Marcos; Camp, Richard J.; Gaudioso, Jacqueline; Brinck, Kevin W.; Berkowitz, Paul; Jacobi, James D.

    2017-01-01

    Biological diversity, or biodiversity, is the variety and abundance of species in a defined area, and is one of the oldest and most basic descriptions of biological communities. Understanding how populations and communities are structured and change over space and time in response to internal and external forces is a management priority. Effective management practices and conservation strategies depend on our understanding of the relationship between changes in biodiversity and ecological drivers such as invasive species, land use and climate change. To demonstrate how changes in biodiversity may be monitored over a large (400 km2) tract of native forest habitat, we compared bird and plant community composition and structure in an upper montane region of Hawai‘i Island originally surveyed in 1977 as part of the Hawai‘i Forest Bird Survey (Scott et al. 1986) with a comprehensive sample of the same region in 2015.Our findings suggest that across a region spanning an elevation range of 600 to 2,000 m considerable changes occurred in the plant and bird communities between 1977 and 2015. Endemic and indigenous plants species richness (i.e., total number of species) decreased dramatically in the low and middle elevations below an invasive weed front, whereas naturalized plant species richness did not change between the two periods at any elevation. Endemic bird abundance decreased and two species were lost in the lower elevations (species increased in the same area. In addition to changes in community composition, the structure of the forest showed evidence of changes in dominant and sub-dominant tree canopy cover, shrub and herbaceous cover, dominant tree canopy height, and matted fern cover. Biodiversity monitoring helps to define specific conservation targets and to measure progress towards reaching those targets. It is difficult to ascribe causative factors to a change in biodiversity without directly manipulating the environment. Forest habitat in a variety of

  10. Regime Shift in Sandy Beach Microbial Communities following Deepwater Horizon Oil Spill Remediation Efforts

    OpenAIRE

    Annette Summers Engel; Gupta, Axita A.

    2014-01-01

    Sandy beaches support a wide variety of underappreciated biodiversity that is critical to coastal ecosystems. Prior to the 2010 Deepwater Horizon oil spill, the diversity and function of supratidal beach sediment microbial communities along Gulf of Mexico coastlines were not well understood. As such, it was unclear if microbial community compositional changes would occur following exposure to beached oil, if indigenous communities could biodegrade oil, or how cleanup efforts, such as sand was...

  11. Exploring the under-investigated ?microbial dark matter? of drinking water treatment plants

    OpenAIRE

    Bruno, Antonia; Sandionigi, Anna; Rizzi, Ermanno; Bernasconi, Marzia; Vicario, Saverio; Galimberti, Andrea; Cocuzza, Clementina; Labra, Massimo; Casiraghi, Maurizio

    2017-01-01

    Scientists recently reported the unexpected detection of unknown or poorly studied bacterial diversity in groundwater. The ability to uncover this neglected biodiversity mainly derives from technical improvements, and the term ?microbial dark matter? was used to group taxa poorly investigated and not necessarily monophyletic. We focused on such under-investigated microbial dark matter of drinking water treatment plant from groundwater, across carbon filters, to post-chlorination. We tackled t...

  12. Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity

    OpenAIRE

    Marc Troussellier; Arthur Escalas; Thierry Bouvier; David Mouillot; David Mouillot

    2017-01-01

    Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism–microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be ne...

  13. EnviroAtlas - Biodiversity Metrics by 12-digit HUC for the Southwestern United States

    Science.gov (United States)

    This EnviroAtlas dataset was produced by a joint effort of New Mexico State University, US EPA, and the US Geological Survey (USGS) to support research and online mapping activities related to EnviroAtlas. Ecosystem services, i.e., services provided to humans from ecological systems, have become a key issue of this century in resource management, conservation planning, and environmental decision analysis. Mapping and quantifying ecosystem services have become strategic national interests for integrating ecology with economics to help understand the effects of human policies and actions and their subsequent impacts on both ecosystem function and human well-being. Some aspects of biodiversity are valued by humans in varied ways, and thus are important to include in any assessment that seeks to identify and quantify the benefits of ecosystems to humans. Some biodiversity metrics clearly reflect ecosystem services (e.g., abundance and diversity of harvestable species), whereas others may reflect indirect and difficult to quantify relationships to services (e.g., relevance of species diversity to ecosystem resilience, or cultural and aesthetic values). Wildlife habitat has been modeled at broad spatial scales and can be used to map a number of biodiversity metrics. We map 15 biodiversity metrics reflecting ecosystem services or other aspects of biodiversity for all vertebrate species except fish. Metrics include species richness for all vertebrates, specific taxon gr

  14. The changing biodiversity of Alabama Drosophila: important impacts of seasonal variation, urbanization, and invasive species.

    Science.gov (United States)

    Bombin, Andrei; Reed, Laura K

    2016-10-01

    Global warming and anthropogenic disturbances significantly influence the biosphere, tremendously increasing species extinction rates. In Central Alabama, we analyzed Drosophilidae species composition change nearly 100 years after the previous survey. We found ten Drosophilid species that were not reported during the last major biodiversity studies, two of which are invasive pests. In addition, we analyzed the influence of seasonal environmental variables characteristic of the subtropical climate zone on Drosophila abundance and biodiversity. We found a significant correlation between temperature and abundance of total Drosophila as well as for six of the seven most represented species individually, with a maximum abundance at intermediate temperatures (18-26°C). In addition, temperature was positively correlated with biodiversity of Drosophila. Precipitation produced a significant effect on the abundance of five species of Drosophila, with different optima for each species, but did not affect overall biodiversity. We concluded that in the subtropical climate zone of Central Alabama, seasonal temperature and precipitation changes produce a significant effect on Drosophila abundance and biodiversity, while local land use also impacts fly abundance, contributing to an apparent shift in species composition over the last century. We expect global climate change and other anthropogenic factors to further impact Drosophila species composition in the subtropical climate zone into the future.

  15. Making the case for biodiversity in South Africa: Re-framing biodiversity communications

    Directory of Open Access Journals (Sweden)

    Kristal Maze

    2016-05-01

    Full Text Available Background: Biodiversity education and public awareness do not always contain the motivational messages that inspire action amongst decision-makers. Traditional messages from the biodiversity sector are often framed around threat, with a generally pessimistic tone. Aspects of social marketing can be used to support positive messaging that is more likely to inspire action amongst the target audience.Objectives: The South African biodiversity sector embarked on a market research process to better understand the target audiences for its messages and develop a communications strategy that would reposition biodiversity as integral to the development trajectory of South Africa.Method: The market research process combined stakeholder analysis, market research, engagement and facilitated dialogue. Eight concept messages were developed that framed biodiversity communications in different ways. These messages were tested with the target audience to assess which were most relevant in a developing-world context.Results: The communications message that received the highest ranking in the market research process was the concept of biodiversity as a ‘national asset’. This frame places biodiversity as an equivalent national priority to other economic and social imperatives. Other messages that ranked highly were the emotional message of biodiversity as ‘our children’s legacy’ and the action-based ‘practical solutions’.Conclusion: Based on the findings, a communications strategy known as ‘Making the case for biodiversity’ was developed that re-framed the economic, emotional and practical value propositions for biodiversity. The communications strategy has already resulted in greater political and economic attention towards biodiversity in South Africa.

  16. Please mind the gap – Visual census and cryptic biodiversity assessment at central Red Sea coral reefs

    KAUST Repository

    Pearman, John K.

    2016-04-26

    Coral reefs harbor the most diverse assemblages in the ocean, however, a large proportion of the diversity is cryptic and, therefore, undetected by standard visual census techniques. Cryptic and exposed communities differ considerably in species composition and ecological function. This study compares three different coral reef assessment protocols: i) visual benthic reef surveys: ii) visual census of Autonomous Reef Monitoring Structures (ARMS) plates; and iii) metabarcoding techniques of the ARMS (including sessile, 106–500 μm and 500–2000 μm size fractions), that target the cryptic and exposed communities of three reefs in the central Red Sea. Visual census showed a dominance of Cnidaria (Anthozoa) and Rhodophyta on the reef substrate, while Porifera, Bryozoa and Rhodophyta were the most abundant groups on the ARMS plates. Metabarcoding, targeting the 18S rRNA gene, significantly increased estimates of the species diversity (p < 0.001); revealing that Annelida were generally the dominant phyla (in terms of reads) of all fractions and reefs. Furthermore, metabarcoding detected microbial eukaryotic groups such as Syndiniophyceae, Mamiellophyceae and Bacillariophyceae as relevant components of the sessile fraction. ANOSIM analysis showed that the three reef sites showed no differences based on the visual census data. Metabarcoding showed a higher sensitivity for identifying differences between reef communities at smaller geographic scales than standard visual census techniques as significant differences in the assemblages were observed amongst the reefs. Comparison of the techniques showed no similar patterns for the visual techniques while the metabarcoding of the ARMS showed similar patterns amongst fractions. Establishing ARMS as a standard tool in reef monitoring will not only advance our understanding of local processes and ecological community response to environmental changes, as different faunal components will provide complementary information but

  17. Geography of conservation spending, biodiversity, and culture.

    Science.gov (United States)

    McClanahan, T R; Rankin, P S

    2016-10-01

    We used linear and multivariate models to examine the associations between geography, biodiversity, per capita economic output, national spending on conservation, governance, and cultural traits in 55 countries. Cultural traits and social metrics of modernization correlated positively with national spending on conservation. The global distribution of this spending culture was poorly aligned with the distribution of biodiversity. Specifically, biodiversity was greater in the tropics where cultures tended to spend relatively less on conservation and tended to have higher collectivism, formalized and hierarchical leadership, and weaker governance. Consequently, nations lacking social traits frequently associated with modernization, environmentalism, and conservation spending have the largest component of Earth's biodiversity. This has significant implications for setting policies and priorities for resource management given that biological diversity is rapidly disappearing and cultural traits change slowly. Therefore, we suggest natural resource management adapt to and use characteristics of existing social organization rather than wait for or promote social values associated with conservation spending. Supporting biocultural traditions, engaging leaders to increase conservation commitments, cross-national efforts that complement attributes of cultures, and avoiding interference with nature may work best to conserve nature in collective and hierarchical societies. Spending in modernized nations may be a symbolic response to a symptom of economic development and environmental degradation, and here conservation actions need to ensure that biodiversity is not being lost. © 2016 Society for Conservation Biology.

  18. Mapping and Quantifying Terrestrial Vertebrate Biodiversity at ...

    Science.gov (United States)

    The ability to assess, report, map, and forecast functions of ecosystems is critical to our capacity to make informed decisions to maintain the sustainable nature of our environment. Because of the variability among living organisms and levels of organization (e.g. genetic, species, ecosystem), biodiversity has always been difficult to measure precisely, especially within a systematic manner and over multiple scales. In answer to this challenge, the U.S. Environmental Protection Agency has created a partnership with other Federal agencies, academic institutions, and Non-Governmental Organizations to develop the EnviroAtlas (https://www.epa.gov/enviroatlas), an online national Decision Support Tool that allows users to view and analyze the geographical description of the supply and demand for ecosystem services, as well as the drivers of change. As part of the EnviroAtlas, an approach has been developed that uses deductive habitat models for all terrestrial vertebrates of the conterminous United States and clusters them into biodiversity metrics that relate to ecosystem service-relevant categories. Metrics, such as species and taxon richness, have been developed and integrated with other measures of biodiversity. Collectively, these metrics provide a consistent scalable process from which to make geographic comparisons, provide thematic assessments, and to monitor status and trends in biodiversity. The national biodiversity component operates across approximatel

  19. Effects of plant diversity, functional group composition, and fertilization on soil microbial properties in experimental grassland.

    Directory of Open Access Journals (Sweden)

    Tanja Strecker

    Full Text Available Loss of biodiversity and increased nutrient inputs are two of the most crucial anthropogenic factors driving ecosystem change. Although both received considerable attention in previous studies, information on their interactive effects on ecosystem functioning is scarce. In particular, little is known on how soil biota and their functions are affected by combined changes in plant diversity and fertilization.We investigated the effects of plant diversity, functional community composition, and fertilization on the biomass and respiration of soil microbial communities in a long-term biodiversity experiment in semi-natural grassland (Jena Experiment. Plant species richness enhanced microbial basal respiration and microbial biomass, but did not significantly affect microbial specific respiration. In contrast, the presence of legumes and fertilization significantly decreased microbial specific respiration, without altering microbial biomass. The effect of legumes was superimposed by fertilization as indicated by a significant interaction between the presence of legumes and fertilization. Further, changes in microbial stoichiometry (C-to-N ratio and specific respiration suggest the presence of legumes to reduce N limitation of soil microorganisms and to modify microbial C use efficiency.Our study highlights the role of plant species and functional group diversity as well as interactions between plant community composition and fertilizer application for soil microbial functions. Our results suggest soil microbial stoichiometry to be a powerful indicator of microbial functioning under N limited conditions. Although our results support the notion that plant diversity and fertilizer application independently affect microbial functioning, legume effects on microbial N limitation were superimposed by fertilization, indicating significant interactions between the functional composition of plant communities and nutrient inputs for soil processes.

  20. Effects of plant diversity, functional group composition, and fertilization on soil microbial properties in experimental grassland.

    Science.gov (United States)

    Strecker, Tanja; Barnard, Romain L; Niklaus, Pascal A; Scherer-Lorenzen, Michael; Weigelt, Alexandra; Scheu, Stefan; Eisenhauer, Nico

    2015-01-01

    Loss of biodiversity and increased nutrient inputs are two of the most crucial anthropogenic factors driving ecosystem change. Although both received considerable attention in previous studies, information on their interactive effects on ecosystem functioning is scarce. In particular, little is known on how soil biota and their functions are affected by combined changes in plant diversity and fertilization. We investigated the effects of plant diversity, functional community composition, and fertilization on the biomass and respiration of soil microbial communities in a long-term biodiversity experiment in semi-natural grassland (Jena Experiment). Plant species richness enhanced microbial basal respiration and microbial biomass, but did not significantly affect microbial specific respiration. In contrast, the presence of legumes and fertilization significantly decreased microbial specific respiration, without altering microbial biomass. The effect of legumes was superimposed by fertilization as indicated by a significant interaction between the presence of legumes and fertilization. Further, changes in microbial stoichiometry (C-to-N ratio) and specific respiration suggest the presence of legumes to reduce N limitation of soil microorganisms and to modify microbial C use efficiency. Our study highlights the role of plant species and functional group diversity as well as interactions between plant community composition and fertilizer application for soil microbial functions. Our results suggest soil microbial stoichiometry to be a powerful indicator of microbial functioning under N limited conditions. Although our results support the notion that plant diversity and fertilizer application independently affect microbial functioning, legume effects on microbial N limitation were superimposed by fertilization, indicating significant interactions between the functional composition of plant communities and nutrient inputs for soil processes.

  1. Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

    Energy Technology Data Exchange (ETDEWEB)

    Walters, William; Hyde, Embriette R.; Berg-Lyons, Donna; Ackermann, Gail; Humphrey, Greg; Parada, Alma; Gilbert, Jack A.; Jansson, Janet K.; Caporaso, J. Gregory; Fuhrman, Jed A.; Apprill, Amy; Knight, Rob; Bik, Holly

    2015-12-22

    ABSTRACT

    Designing primers for PCR-based taxonomic surveys that amplify a broad range of phylotypes in varied community samples is a difficult challenge, and the comparability of data sets amplified with varied primers requires attention. Here, we examined the performance of modified 16S rRNA gene and internal transcribed spacer (ITS) primers for archaea/bacteria and fungi, respectively, with nonaquatic samples. We moved primer bar codes to the 5′ end, allowing for a range of different 3′ primer pairings, such as the 515f/926r primer pair, which amplifies variable regions 4 and 5 of the 16S rRNA gene. We additionally demonstrated that modifications to the 515f/806r (variable region 4) 16S primer pair, which improves detection ofThaumarchaeotaand clade SAR11 in marine samples, do not degrade performance on taxa already amplified effectively by the original primer set. Alterations to the fungal ITS primers did result in differential but overall improved performance compared to the original primers. In both cases, the improved primers should be widely adopted for amplicon studies.

    ImportanceWe continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections between microbes and the ecosystems they populate, from ice caps to the human body. It is important to confirm that modifications to these tools do not cause new, detrimental biases that would inhibit the field rather than continue to move it forward. We therefore demonstrated that two recently modified primer pairs that target taxonomically discriminatory regions of bacterial and fungal genomic DNA do not introduce new biases when used on a variety of sample types, from soil to

  2. Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.

    Directory of Open Access Journals (Sweden)

    Ramona L Walls

    Full Text Available The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques, as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1 individual organisms, including voucher specimens from ecological studies and museum specimens, 2 bulk or environmental samples (e.g., gut contents, soil, water that include DNA, other molecules, and potentially many organisms, especially microbes, and 3 survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and

  3. Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.

    Science.gov (United States)

    Walls, Ramona L; Deck, John; Guralnick, Robert; Baskauf, Steve; Beaman, Reed; Blum, Stanley; Bowers, Shawn; Buttigieg, Pier Luigi; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, Andréa; Midford, Peter; Morrison, Norman; Ó Tuama, Éamonn; Schildhauer, Mark; Smith, Barry; Stucky, Brian J; Thomer, Andrea; Wieczorek, John; Whitacre, Jamie; Wooley, John

    2014-01-01

    The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.

  4. Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies

    Science.gov (United States)

    Baskauf, Steve; Blum, Stanley; Bowers, Shawn; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, Andréa; Midford, Peter; Tuama, Éamonn Ó.; Schildhauer, Mark; Smith, Barry; Stucky, Brian J.; Thomer, Andrea; Wieczorek, John; Whitacre, Jamie; Wooley, John

    2014-01-01

    The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers

  5. Two-stage microbial community experimental design.

    Science.gov (United States)

    Tickle, Timothy L; Segata, Nicola; Waldron, Levi; Weingart, Uri; Huttenhower, Curtis

    2013-12-01

    Microbial community samples can be efficiently surveyed in high throughput by sequencing markers such as the 16S ribosomal RNA gene. Often, a collection of samples is then selected for subsequent metagenomic, metabolomic or other follow-up. Two-stage study design has long been used in ecology but has not yet been studied in-depth for high-throughput microbial community investigations. To avoid ad hoc sample selection, we developed and validated several purposive sample selection methods for two-stage studies (that is, biological criteria) targeting differing types of microbial communities. These methods select follow-up samples from large community surveys, with criteria including samples typical of the initially surveyed population, targeting specific microbial clades or rare species, maximizing diversity, representing extreme or deviant communities, or identifying communities distinct or discriminating among environment or host phenotypes. The accuracies of each sampling technique and their influences on the characteristics of the resulting selected microbial community were evaluated using both simulated and experimental data. Specifically, all criteria were able to identify samples whose properties were accurately retained in 318 paired 16S amplicon and whole-community metagenomic (follow-up) samples from the Human Microbiome Project. Some selection criteria resulted in follow-up samples that were strongly non-representative of the original survey population; diversity maximization particularly undersampled community configurations. Only selection of intentionally representative samples minimized differences in the selected sample set from the original microbial survey. An implementation is provided as the microPITA (Microbiomes: Picking Interesting Taxa for Analysis) software for two-stage study design of microbial communities.

  6. Biodiversity at the Ecosystem Level - Patterns and Processes

    DEFF Research Database (Denmark)

    This publication contains the presentations and discussions from the second DanBIF conference, entitled Biodiversity at the Ecosystem Level – Patterns and Processes. The questions asked at this conference were: What is biodiversity at the ecosystem level? How is it related to biodiversity at other...... levels of organization? How may GBIF (Global Biodiversity Information Facility) deal with ecosystem level data and informatics? The conference had two important goals. The first was to present an overview of contemporary research related to ecosystem level biodiversity and the second was to help GBIF...... formulate a strategy for dealing with biodiversity above the species and molecular levels and make data available for the end-users....

  7. Molecular biodiversity of Red Sea demosponges

    KAUST Repository

    Erpenbeck, Dirk

    2016-01-07

    Sponges are important constituents of coral reef ecosystems, including those around the Arabian Peninsula. Despite their importance, our knowledge on demosponge diversity in this area is insufficient to recognize, for example, faunal changes caused by anthropogenic disturbances. We here report the first assessment of demosponge molecular biodiversity from Arabia, with focus on the Saudi Arabian Red Sea, based on mitochondrial and nuclear ribosomal molecular markers gathered in the framework of the Sponge Barcoding Project. We use a rapid molecular screening approach on Arabian demosponge collections and analyze results in comparison against published material in terms of biodiversity. We use a variable region of 28S rDNA, applied for the first time in the assessment of demosponge molecular diversity. Our data constitutes a solid foundation for a future more comprehensive understanding of sponge biodiversity of the Red Sea and adjacent waters.

  8. Biodiversity analysis in the digital era

    Science.gov (United States)

    2016-01-01

    This paper explores what the virtual biodiversity e-infrastructure will look like as it takes advantage of advances in ‘Big Data’ biodiversity informatics and e-research infrastructure, which allow integration of various taxon-level data types (genome, morphology, distribution and species interactions) within a phylogenetic and environmental framework. By overcoming the data scaling problem in ecology, this integrative framework will provide richer information and fast learning to enable a deeper understanding of biodiversity evolution and dynamics in a rapidly changing world. The Atlas of Living Australia is used as one example of the advantages of progressing towards this future. Living in this future will require the adoption of new ways of integrating scientific knowledge into societal decision making. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481789

  9. Plate tectonics drive tropical reef biodiversity dynamics.

    Science.gov (United States)

    Leprieur, Fabien; Descombes, Patrice; Gaboriau, Théo; Cowman, Peter F; Parravicini, Valeriano; Kulbicki, Michel; Melián, Carlos J; de Santana, Charles N; Heine, Christian; Mouillot, David; Bellwood, David R; Pellissier, Loïc

    2016-05-06

    The Cretaceous breakup of Gondwana strongly modified the global distribution of shallow tropical seas reshaping the geographic configuration of marine basins. However, the links between tropical reef availability, plate tectonic processes and marine biodiversity distribution patterns are still unknown. Here, we show that a spatial diversification model constrained by absolute plate motions for the past 140 million years predicts the emergence and movement of diversity hotspots on tropical reefs. The spatial dynamics of tropical reefs explains marine fauna diversification in the Tethyan Ocean during the Cretaceous and early Cenozoic, and identifies an eastward movement of ancestral marine lineages towards the Indo-Australian Archipelago in the Miocene. A mechanistic model based only on habitat-driven diversification and dispersal yields realistic predictions of current biodiversity patterns for both corals and fishes. As in terrestrial systems, we demonstrate that plate tectonics played a major role in driving tropical marine shallow reef biodiversity dynamics.

  10. A conservation agenda for the Pantanal's biodiversity

    Directory of Open Access Journals (Sweden)

    CJR Alho

    Full Text Available The Pantanal's biodiversity constitutes a valuable natural resource, in economic, cultural, recreational, aesthetic, scientific and educational terms. The vegetation plus the seasonal productivity support a diverse and abundant fauna. Many endangered species occur in the region, and waterfowl are exceptionally abundant during the dry season. Losses of biodiversity and its associated natural habitats within the Pantanal occur as a result of unsustainable land use. Implementation of protected areas is only a part of the conservation strategy needed. We analyse biodiversity threats to the biome under seven major categories: 1 conversion of natural vegetation into pasture and agricultural crops, 2 destruction or degradation of habitat mainly due to wild fire, 3 overexploitation of species mainly by unsustainable fishing, 4 water pollution, 5 river flow modification with implantation of small hydroelectric plants, 6 unsustainable tourism, and 7 introduction of invasive exotic species.

  11. Novel urban ecosystems, biodiversity, and conservation.

    Science.gov (United States)

    Kowarik, Ingo

    2011-01-01

    With increasing urbanization the importance of cities for biodiversity conservation grows. This paper reviews the ways in which biodiversity is affected by urbanization and discusses the consequences of different conservation approaches. Cities can be richer in plant species, including in native species, than rural areas. Alien species can lead to both homogenization and differentiation among urban regions. Urban habitats can harbor self-sustaining populations of rare and endangered native species, but cannot replace the complete functionality of (semi-)natural remnants. While many conservation approaches tend to focus on such relict habitats and native species in urban settings, this paper argues for a paradigm shift towards considering the whole range of urban ecosystems. Although conservation attitudes may be challenged by the novelty of some urban ecosystems, which are often linked to high numbers of nonnative species, it is promising to consider their associated ecosystem services, social benefits, and possible contribution to biodiversity conservation. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. Plate tectonics drive tropical reef biodiversity dynamics

    Science.gov (United States)

    Leprieur, Fabien; Descombes, Patrice; Gaboriau, Théo; Cowman, Peter F.; Parravicini, Valeriano; Kulbicki, Michel; Melián, Carlos J.; de Santana, Charles N.; Heine, Christian; Mouillot, David; Bellwood, David R.; Pellissier, Loïc

    2016-01-01

    The Cretaceous breakup of Gondwana strongly modified the global distribution of shallow tropical seas reshaping the geographic configuration of marine basins. However, the links between tropical reef availability, plate tectonic processes and marine biodiversity distribution patterns are still unknown. Here, we show that a spatial diversification model constrained by absolute plate motions for the past 140 million years predicts the emergence and movement of diversity hotspots on tropical reefs. The spatial dynamics of tropical reefs explains marine fauna diversification in the Tethyan Ocean during the Cretaceous and early Cenozoic, and identifies an eastward movement of ancestral marine lineages towards the Indo-Australian Archipelago in the Miocene. A mechanistic model based only on habitat-driven diversification and dispersal yields realistic predictions of current biodiversity patterns for both corals and fishes. As in terrestrial systems, we demonstrate that plate tectonics played a major role in driving tropical marine shallow reef biodiversity dynamics. PMID:27151103

  13. Biodiversity analysis in the digital era.

    Science.gov (United States)

    La Salle, John; Williams, Kristen J; Moritz, Craig

    2016-09-05

    This paper explores what the virtual biodiversity e-infrastructure will look like as it takes advantage of advances in 'Big Data' biodiversity informatics and e-research infrastructure, which allow integration of various taxon-level data types (genome, morphology, distribution and species interactions) within a phylogenetic and environmental framework. By overcoming the data scaling problem in ecology, this integrative framework will provide richer information and fast learning to enable a deeper understanding of biodiversity evolution and dynamics in a rapidly changing world. The Atlas of Living Australia is used as one example of the advantages of progressing towards this future. Living in this future will require the adoption of new ways of integrating scientific knowledge into societal decision making.This article is part of the themed issue 'From DNA barcodes to biomes'. © 2016 The Authors.

  14. The circumpolar biodiversity monitoring program - Terrestrial plan

    DEFF Research Database (Denmark)

    Christensen, Tom; Payne, J.; Doyle, M.

    and attributes to monitor in the plan related to soil invertebrates. Focal Ecosystem Components (FECs) of the soil decomposer system include the soil living invertebrates such as microarthropods, enchytraeids and earthworms and the functions performed by microorganisms such as nitrification, decomposition......The Circumpolar Biodiversity Monitoring Program, CBMP, Terrestrial Plan, www.caff.is/terrestrial, is a framework to focus and coordinate monitoring of terrestrial biodiversity across the Arctic. The goal of the plan is to improve the collective ability of Arctic traditional knowledge (TK) holders......, northern communities, and scientists to detect, understand and report on long-term change in Arctic terrestrial ecosystems and biodiversity. This presentation will outline the key management questions the plan aims to address and the proposed nested, multi-scaled approach linking targeted, research based...

  15. A conservation agenda for the Pantanal's biodiversity.

    Science.gov (United States)

    Alho, C J R; Sabino, J

    2011-04-01

    The Pantanal's biodiversity constitutes a valuable natural resource, in economic, cultural, recreational, aesthetic, scientific and educational terms. The vegetation plus the seasonal productivity support a diverse and abundant fauna. Many endangered species occur in the region, and waterfowl are exceptionally abundant during the dry season. Losses of biodiversity and its associated natural habitats within the Pantanal occur as a result of unsustainable land use. Implementation of protected areas is only a part of the conservation strategy needed. We analyse biodiversity threats to the biome under seven major categories: 1) conversion of natural vegetation into pasture and agricultural crops, 2) destruction or degradation of habitat mainly due to wild fire, 3) overexploitation of species mainly by unsustainable fishing, 4) water pollution, 5) river flow modification with implantation of small hydroelectric plants, 6) unsustainable tourism, and 7) introduction of invasive exotic species.

  16. Insights into biodiversity sampling strategies for freshwater microinvertebrate faunas through bioblitz campaigns and DNA barcoding

    Science.gov (United States)

    2013-01-01

    Background Biodiversity surveys have long depended on traditional methods of taxonomy to inform sampling protocols and to determine when a representative sample of a given species pool of interest has been obtained. Questions remain as to how to design appropriate sampling efforts to accurately estimate total biodiversity. Here we consider the biodiversity of freshwater ostracods (crustacean class Ostracoda) from the region of Churchill, Manitoba, Canada. Through an analysis of observed species richness and complementarity, accumulation curves, and richness estimators, we conduct an a posteriori analysis of five bioblitz-style collection strategies that differed in terms of total duration, number of sites, protocol flexibility to heterogeneous habitats, sorting of specimens for analysis, and primary purpose of collection. We used DNA barcoding to group specimens into molecular operational taxonomic units for comparison. Results Forty-eight provisional species were identified through genetic divergences, up from the 30 species previously known and documented in literature from the Churchill region. We found differential sampling efficiency among the five strategies, with liberal sorting of specimens for molecular analysis, protocol flexibility (and particularly a focus on covering diverse microhabitats), and a taxon-specific focus to collection having strong influences on garnering more accurate species richness estimates. Conclusions Our findings have implications for the successful design of future biodiversity surveys and citizen-science collection projects, which are becoming increasingly popular and have been shown to produce reliable results for a variety of taxa despite relying on largely untrained collectors. We propose that efficiency of biodiversity surveys can be increased by non-experts deliberately selecting diverse microhabitats; by conducting two rounds of molecular analysis, with the numbers of samples processed during round two informed by the

  17. Impact of GM crops on biodiversity.

    Science.gov (United States)

    Carpenter, Janet E

    2011-01-01

    The potential impact of GM crops on biodiversity has been a topic of interest both in general as well as specifically in the context of the Convention on Biological Diversity. Agricultural biodiversity has been defined at levels from genes to ecosystems that are involved or impacted by agricultural production (www.cbd.int/agro/whatis.shtml). After fifteen years of commercial cultivation, a substantial body of literature now exists addressing the potential impacts of GM crops on the environment. This review takes a biodiversity lens to this literature, considering the impacts at three levels: the crop, farm and landscape scales. Within that framework, this review covers potential impacts of the introduction of genetically engineered crops on: crop diversity, biodiversity of wild relatives, non-target soil organisms, weeds, land use, non-target above-ground organisms, and area-wide pest suppression. The emphasis of the review is peer-reviewed literature that presents direct measures of impacts on biodiversity. In addition, possible impacts of changes in management practises such as tillage and pesticide use are also discussed to complement the literature on direct measures. The focus of the review is on technologies that have been commercialized somewhere in the world, while results may emanate from non-adopting countries and regions. Overall, the review finds that currently commercialized GM crops have reduced the impacts of agriculture on biodiversity, through enhanced adoption of conservation tillage practices, reduction of insecticide use and use of more environmentally benign herbicides and increasing yields to alleviate pressure to convert additional land into agricultural use.

  18. The impact of wastewater treatment effluent on microbial biomasses and diversities in coastal sediment microcosms of Hangzhou Bay.

    Science.gov (United States)

    Tao, Yile; Dai, Tianjiao; Huang, Bei; Wen, Donghui

    2017-01-15

    Disposal of wastewater treatment plant (WWTP) effluent into sea, a typical anthropogenic disturbance, may influence many environmental factors and change the coastal microbial community structure. In this study, by setting up coastal sediment microcosms perturbed by WWTP effluent, the changes of microbial community structure under different degree of disturbances were investigated. Quantitative PCR (qPCR) and terminal restriction fragment length polymorphism (T-RFLP) were used to analyzed the biomass and biodiversity. High throughput sequencing analysis was used to identify the classification of the microorganisms. Our study suggested that low ratio of WWTP effluent may stimulate dominant species, which increase the biomass but decrease the biodiversity; while high ratio of WWTP effluent may depress all species, which decrease the biomass but increase the biodiversity. In other words, the impact was dose-dependent. The changes of microbial community structure may provide a metric for water environmental assessment and pollution control. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Biodiversity in a Florida Sandhill Ecosystem

    Directory of Open Access Journals (Sweden)

    Samantha Robertson

    2009-01-01

    Full Text Available This project compares two transects of land in the University of South Florida's Botanical Gardens for their biodiversity. The transects were chosen to represent a Florida sandhill ecosystem and the individual Longleaf Pine, Saw Palmetto, Turkey Oak, Laurel Oak and Live Oak specimens were counted. All other species above waist height were counted as "other"?. Once the individuals were counted, the Simpson's and Shannon-Wiener indices were calculated. Since the Shannon-Wiener index incorporates several diversity characteristics, it is typically more reliable than Simpson's. However, both biodiversity indices agreed that transect B was more diverse than transect A.

  20. Bats, Blood-Feeders and Biodiversity

    DEFF Research Database (Denmark)

    Bohmann, Kristine

    DNA metabarcoding of environmental samples has rapidly become a valuable tool for ecological studies such as biodiversity and diet studies. To reveal the diversity in environmental samples such as soil, water, and faeces, this approach principally employs PCR amplification of environmental DNA...... minimising the occurrence of errors. Centered around metabarcoding dietary studies of bat droppings and leech gut contents, this continuous exploration and refinement is reflected in both the work and structure of this thesis. After a thesis introduction and two chapters on environmental DNA and biodiversity...

  1. Insect biodiversity and conservation in Australasia.

    Science.gov (United States)

    Cranston, Peter S

    2010-01-01

    Australasia, which consists of Australia and the adjacent islands of the southwestern Pacific Ocean, has an insect diversity approximately proportional to the land mass. This diversity is distinctive, with some major groups missing and others having radiated. Iconic species are familiar to most people living in Australia and New Zealand, and a range of insects once contributed to Aboriginal Australian culture and diet. Conservation of Australasian entomological biodiversity is an increasing challenge for contemporary scientists. Examples are provided of insect conservation schemes from New Guinea, New Zealand, and Australia. Funding for insect biodiversity studies beyond flagship species is needed.

  2. Mosquitoes of eastern Amazonian Ecuador: biodiversity, bionomics and barcodes

    Directory of Open Access Journals (Sweden)

    Yvonne-Marie Linton

    2013-01-01

    Full Text Available Two snapshot surveys to establish the diversity and ecological preferences of mosquitoes (Diptera: Culicidae in the terra firme primary rain forest surrounding the Tiputini Biodiversity Station in the UNESCO Yasuní Biosphere Reserve of eastern Amazonian Ecuador were carried out in November 1998 and May 1999. The mosquito fauna of this region is poorly known; the focus of this study was to obtain high quality link-reared specimens that could be used to unequivocally confirm species level diversity through integrated systematic study of all life stages and DNA sequences. A total of 2,284 specimens were preserved; 1,671 specimens were link-reared with associated immature exuviae, all but 108 of which are slide mounted. This study identified 68 unique taxa belonging to 17 genera and 27 subgenera. Of these, 12 are new to science and 37 comprise new country records. DNA barcodes [658-bp of the mtDNA cytochrome c oxidase ( COI I gene] are presented for 58 individuals representing 20 species and nine genera. DNA barcoding proved useful in uncovering and confirming new species and we advocate an integrated systematics approach to biodiversity studies in future. Associated bionomics of all species collected are discussed. An updated systematic checklist of the mosquitoes of Ecuador (n = 179 is presented for the first time in 60 years.

  3. Mosquitoes of eastern Amazonian Ecuador: biodiversity, bionomics and barcodes.

    Science.gov (United States)

    Linton, Yvonne-Marie; Pecor, James E; Porter, Charles H; Mitchell, Luke Brett; Garzón-Moreno, Andrés; Foley, Desmond H; Pecor, David Brooks; Wilkerson, Richard C

    2013-01-01

    Two snapshot surveys to establish the diversity and ecological preferences of mosquitoes (Diptera: Culicidae) in the terra firme primary rain forest surrounding the Tiputini Biodiversity Station in the UNESCO Yasuní Biosphere Reserve of eastern Amazonian Ecuador were carried out in November 1998 and May 1999. The mosquito fauna of this region is poorly known; the focus of this study was to obtain high quality link-reared specimens that could be used to unequivocally confirm species level diversity through integrated systematic study of all life stages and DNA sequences. A total of 2,284 specimens were preserved; 1,671 specimens were link-reared with associated immature exuviae, all but 108 of which are slide mounted. This study identified 68 unique taxa belonging to 17 genera and 27 subgenera. Of these, 12 are new to science and 37 comprise new country records. DNA barcodes [658-bp of the mtDNA cytochrome c oxidase (COI) I gene] are presented for 58 individuals representing 20 species and nine genera. DNA barcoding proved useful in uncovering and confirming new species and we advocate an integrated systematics approach to biodiversity studies in future. Associated bionomics of all species collected are discussed. An updated systematic checklist of the mosquitoes of Ecuador (n=179) is presented for the first time in 60 years.

  4. Mosquitoes of eastern Amazonian Ecuador: biodiversity, bionomics and barcodes

    Science.gov (United States)

    Linton, Yvonne-Marie; Pecor, James E; Porter, Charles H; Mitchell, Luke Brett; Garzón-Moreno, Andrés; Foley, Desmond H; Pecor, David Brooks; Wilkerson, Richard C

    2013-01-01

    Two snapshot surveys to establish the diversity and ecological preferences of mosquitoes (Diptera: Culicidae) in the terra firme primary rain forest surrounding the Tiputini Biodiversity Station in the UNESCO Yasuní Biosphere Reserve of eastern Amazonian Ecuador were carried out in November 1998 and May 1999. The mosquito fauna of this region is poorly known; the focus of this study was to obtain high quality link-reared specimens that could be used to unequivocally confirm species level diversity through integrated systematic study of all life stages and DNA sequences. A total of 2,284 specimens were preserved; 1,671 specimens were link-reared with associated immature exuviae, all but 108 of which are slide mounted. This study identified 68 unique taxa belonging to 17 genera and 27 subgenera. Of these, 12 are new to science and 37 comprise new country records. DNA barcodes [658-bp of the mtDNA cytochrome c oxidase ( COI ) I gene] are presented for 58 individuals representing 20 species and nine genera. DNA barcoding proved useful in uncovering and confirming new species and we advocate an integrated systematics approach to biodiversity studies in future. Associated bionomics of all species collected are discussed. An updated systematic checklist of the mosquitoes of Ecuador (n = 179) is presented for the first time in 60 years. PMID:24473809

  5. Modelling avian biodiversity using raw, unclassified satellite imagery.

    Science.gov (United States)

    St-Louis, Véronique; Pidgeon, Anna M; Kuemmerle, Tobias; Sonnenschein, Ruth; Radeloff, Volker C; Clayton, Murray K; Locke, Brian A; Bash, Dallas; Hostert, Patrick

    2014-01-01

    Applications of remote sensing for biodiversity conservation typically rely on image classifications that do not capture variability within coarse land cover classes. Here, we compare two measures derived from unclassified remotely sensed data, a measure of habitat heterogeneity and a measure of habitat composition, for explaining bird species richness and the spatial distribution of 10 species in a semi-arid landscape of New Mexico. We surveyed bird abundance from 1996 to 1998 at 42 plots located in the McGregor Range of Fort Bliss Army Reserve. Normalized Difference Vegetation Index values of two May 1997 Landsat scenes were the basis for among-pixel habitat heterogeneity (image texture), and we used the raw imagery to decompose each pixel into different habitat components (spectral mixture analysis). We used model averaging to relate measures of avian biodiversity to measures of image texture and spectral mixture analysis fractions. Measures of habitat heterogeneity, particularly angular second moment and standard deviation, provide higher explanatory power for bird species richness and the abundance of most species than measures of habitat composition. Using image texture, alone or in combination with other classified imagery-based approaches, for monitoring statuses and trends in biological diversity can greatly improve conservation efforts and habitat management.

  6. Functional Ecological Gene Networks to Reveal the Changes Among Microbial Interactions Under Elevated Carbon Dioxide Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Ye; Zhou, Jizhong; Luo, Feng; He, Zhili; Tu, Qichao; Zhi, Xiaoyang

    2010-05-17

    Biodiversity and its responses to environmental changes is a central issue in ecology, and for society. Almost all microbial biodiversity researches focus on species richness and abundance but ignore the interactions among different microbial species/populations. However, determining the interactions and their relationships to environmental changes in microbial communities is a grand challenge, primarily due to the lack of information on the network structure among different microbial species/populations. Here, a novel random matrix theory (RMT)-based conceptual framework for identifying functional ecological gene networks (fEGNs) is developed with the high throughput functional gene array hybridization data from the grassland microbial communities in a long-term FACE (Free Air CO2 Enrichment) experiment. Both fEGNs under elevated CO2 (eCO2) and ambient CO2 (aCO2) possessed general characteristics of many complex systems such as scale-free, small-world, modular and hierarchical. However, the topological structure of the fEGNs is distinctly different between eCO2 and aCO2, suggesting that eCO2 dramatically altered the interactions among different microbial functional groups/populations. In addition, the changes in network structure were significantly correlated with soil carbon and nitrogen dynamics, and plant productivity, indicating the potential importance of network interactions in ecosystem functioning. Elucidating network interactions in microbial communities and their responses to environmental changes are fundamentally important for research in microbial ecology, systems microbiology, and global change.

  7. Bioerosion by microbial euendoliths in benthic foraminifera from heavy metal-polluted coastal environments of Portovesme (south-western Sardinia, Italy

    Directory of Open Access Journals (Sweden)

    A. Cherchi

    2012-11-01

    Full Text Available A monitoring survey of the coastal area facing the industrial area of Portoscuso-Portovesme (south-western Sardinia, Italy revealed intense bioerosional processes. Benthic foraminifera collected at the same depth (about 2 m but at different distances from the pollution source show extensive microbial infestation, anomalous Mg/Ca molar ratios and high levels of heavy metals in the shell associated with a decrease in foraminifera richness, population density and biodiversity with the presence of morphologically abnormal specimens. We found that carbonate dissolution induced by euendoliths is selective, depending on the Mg content and morpho-structural types of foraminiferal taxa. This study provides evidences for a connection between heavy metal dispersion, decrease in pH of the sea-water and bioerosional processes on foraminifera.

  8. Analysis of the functional diversity of the microbial communities in a ...

    African Journals Online (AJOL)

    No clear trends concerning the influence of maintenance shut-downs and cleaning of machines could be observed in the sessile phase, while a shift in the microbial community could be observed in the planktonic phase. Biodiversity indices indicated that a high functional diversity existed in both the planktonic and sessile ...

  9. Contributions of understory and/or overstory vegetations to soil microbial PLFA and nematode diversities in Eucalyptus monocultures.

    Science.gov (United States)

    Zhao, Jie; Wan, Songze; Zhang, Chenlu; Liu, Zhanfeng; Zhou, Lixia; Fu, Shenglei

    2014-01-01

    Ecological interactions between aboveground and belowground biodiversity have received many attentions in the recent decades. Although soil biodiversity declined with the decrease of plant diversity, many previous studies found plant species identities were more important than plant diversity in controlling soil biodiversity. This study focused on the responses of soil biodiversity to the altering of plant functional groups, namely overstory and understory vegetations, rather than plant diversity gradient. We conducted an experiment by removing overstory and/or understory vegetation to compare their effects on soil microbial phospholipid fatty acid (PLFA) and nematode diversities in eucalyptus monocultures. Our results indicated that both overstory and understory vegetations could affect soil microbial PLFA and nematode diversities, which manifested as the decrease in Shannon-Wiener diversity index (H') and Pielou evenness index (J) and the increase in Simpson dominance index (λ) after vegetation removal. Soil microclimate change explained part of variance of soil biodiversity indices. Both overstory and understory vegetations positively correlated with soil microbial PLFA and nematode diversities. In addition, the alteration of soil biodiversity might be due to a mixing effect of bottom-up control and soil microclimate change after vegetation removal in the studied plantations. Given the studied ecosystem is common in humid subtropical and tropical region of the world, our findings might have great potential to extrapolate to large scales and could be conducive to ecosystem management and service.

  10. Biodiversity enhances ecosystem multifunctionality across trophic levels and habitats.

    Science.gov (United States)

    Lefcheck, Jonathan S; Byrnes, Jarrett E K; Isbell, Forest; Gamfeldt, Lars; Griffin, John N; Eisenhauer, Nico; Hensel, Marc J S; Hector, Andy; Cardinale, Bradley J; Duffy, J Emmett

    2015-04-24

    The importance of biodiversity for the integrated functioning of ecosystems remains unclear because most evidence comes from analyses of biodiversity's effect on individual functions. Here we show that the effects of biodiversity on ecosystem function become more important as more functions are considered. We present the first systematic investigation of biodiversity's effect on ecosystem multifunctionality across multiple taxa, trophic levels and habitats using a comprehensive database of 94 manipulations of species richness. We show that species-rich communities maintained multiple functions at higher levels than depauperate ones. These effects were stronger for herbivore biodiversity than for plant biodiversity, and were remarkably consistent across aquatic and terrestrial habitats. Despite observed tradeoffs, the overall effect of biodiversity on multifunctionality grew stronger as more functions were considered. These results indicate that prior research has underestimated the importance of biodiversity for ecosystem functioning by focusing on individual functions and taxonomic groups.

  11. Status and strategies for marine biodiversity of Goa

    Digital Repository Service at National Institute of Oceanography (India)

    Untawale, A.G.

    The status of marine biodiversity and factors responsible for the degradation and loss of marine biodiversity are discussed. Goa has abundant marine wealth. Phytoplankton, marine algae, manglicolous fungi, seagrasses, mangrove flora and other...

  12. Biodiversity enhances ecosystem multifunctionality across trophic levels and habitats

    Science.gov (United States)

    Lefcheck, Jonathan S.; Byrnes, Jarrett E. K.; Isbell, Forest; Gamfeldt, Lars; Griffin, John N.; Eisenhauer, Nico; Hensel, Marc J. S.; Hector, Andy; Cardinale, Bradley J.; Duffy, J. Emmett

    2015-01-01

    The importance of biodiversity for the integrated functioning of ecosystems remains unclear because most evidence comes from analyses of biodiversity's effect on individual functions. Here we show that the effects of biodiversity on ecosystem function become more important as more functions are considered. We present the first systematic investigation of biodiversity's effect on ecosystem multifunctionality across multiple taxa, trophic levels and habitats using a comprehensive database of 94 manipulations of species richness. We show that species-rich communities maintained multiple functions at higher levels than depauperate ones. These effects were stronger for herbivore biodiversity than for plant biodiversity, and were remarkably consistent across aquatic and terrestrial habitats. Despite observed tradeoffs, the overall effect of biodiversity on multifunctionality grew stronger as more functions were considered. These results indicate that prior research has underestimated the importance of biodiversity for ecosystem functioning by focusing on individual functions and taxonomic groups. PMID:25907115

  13. International cooperation on biodiversity conservation when spatial structures matter

    NARCIS (Netherlands)

    Alvarado-Quesada, Irene; Weikard, Hans Peter

    2017-01-01

    International cooperation on biodiversity conservation when spatial structures matter. Spatial Economic Analysis. This paper considers the stability of international environmental agreements (IEAs) for biodiversity conservation with an explicit spatial structure. It studies the impact of distance

  14. Why financial incentives can destroy economically valuable biodiversity in Ethiopia

    NARCIS (Netherlands)

    Gatzweiler, F.; Reichhuber, A.; Hein, L.G.

    2007-01-01

    Ethiopian montane rainforests are economically valuable repositories of biodiversity, especially of wild Coffea arabica populations, and they are vanishing at accelerating rates. Our research results confirm theory which explains biodiversity loss by diverging private and social net benefits from

  15. Finding common ground for biodiversity and ecosystem services

    CSIR Research Space (South Africa)

    Reyers, B

    2012-05-01

    Full Text Available Recently, some members of the conservation community have used ecosystem services as a strategy to conserve biodiversity. Others in the community have criticized this strategy as a distraction from the mission of biodiversity conservation...

  16. Functionally Stable and Phylogenetically Diverse Microbial Enrichments from Microbial Fuel Cells during Wastewater Treatment

    Science.gov (United States)

    Ishii, Shun'ichi; Suzuki, Shino; Norden-Krichmar, Trina M.; Nealson, Kenneth H.; Sekiguchi, Yuji; Gorby, Yuri A.; Bretschger, Orianna

    2012-01-01

    Microbial fuel cells (MFCs) are devices that exploit microorganisms as biocatalysts to recover energy from organic matter in the form of electricity. One of the goals of MFC research is to develop the technology for cost-effective wastewater treatment. However, before practical MFC applications are implemented it is important to gain fundamental knowledge about long-term system performance, reproducibility, and the formation and maintenance of functionally-stable microbial communities. Here we report findings from a MFC operated for over 300 days using only primary clarifier effluent collected from a municipal wastewater treatment plant as the microbial resource and substrate. The system was operated in a repeat-batch mode, where the reactor solution was replaced once every two weeks with new primary effluent that consisted of different microbial and chemical compositions with every batch exchange. The turbidity of the primary clarifier effluent solution notably decreased, and 97% of biological oxygen demand (BOD) was removed after an 8–13 day residence time for each batch cycle. On average, the limiting current density was 1000 mA/m2, the maximum power density was 13 mW/m2, and coulombic efficiency was 25%. Interestingly, the electrochemical performance and BOD removal rates were very reproducible throughout MFC operation regardless of the sample variability associated with each wastewater exchange. While MFC performance was very reproducible, the phylogenetic analyses of anode-associated electricity-generating biofilms showed that the microbial populations temporally fluctuated and maintained a high biodiversity throughout the year-long experiment. These results suggest that MFC communities are both self-selecting and self-optimizing, thereby able to develop and maintain functional stability regardless of fluctuations in carbon source(s) and regular introduction of microbial competitors. These results contribute significantly toward the practical application of

  17. Functionally stable and phylogenetically diverse microbial enrichments from microbial fuel cells during wastewater treatment.

    Directory of Open Access Journals (Sweden)

    Shun'ichi Ishii

    Full Text Available Microbial fuel cells (MFCs are devices that exploit microorganisms as biocatalysts to recover energy from organic matter in the form of electricity. One of the goals of MFC research is to develop the technology for cost-effective wastewater treatment. However, before practical MFC applications are implemented it is important to gain fundamental knowledge about long-term system performance, reproducibility, and the formation and maintenance of functionally-stable microbial communities. Here we report findings from a MFC operated for over 300 days using only primary clarifier effluent collected from a municipal wastewater treatment plant as the microbial resource and substrate. The system was operated in a repeat-batch mode, where the reactor solution was replaced once every two weeks with new primary effluent that consisted of different microbial and chemical compositions with every batch exchange. The turbidity of the primary clarifier effluent solution notably decreased, and 97% of biological oxygen demand (BOD was removed after an 8-13 day residence time for each batch cycle. On average, the limiting current density was 1000 mA/m(2, the maximum power density was 13 mW/m(2, and coulombic efficiency was 25%. Interestingly, the electrochemical performance and BOD removal rates were very reproducible throughout MFC operation regardless of the sample variability associated with each wastewater exchange. While MFC performance was very reproducible, the phylogenetic analyses of anode-associated electricity-generating biofilms showed that the microbial populations temporally fluctuated and maintained a high biodiversity throughout the year-long experiment. These results suggest that MFC communities are both self-selecting and self-optimizing, thereby able to develop and maintain functional stability regardless of fluctuations in carbon source(s and regular introduction of microbial competitors. These results contribute significantly toward the

  18. Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene

    DEFF Research Database (Denmark)

    Bowman, Jeff S.; Rasmussen, Simon; Blom, Nikolaj

    2011-01-01

    Dramatic decreases in the extent of Arctic multiyear ice (MYI) suggest this environment may disappear as early as 2100, replaced by ecologically different first-year ice. To better understand the implications of this loss on microbial biodiversity, we undertook a detailed census of the microbial...... community in MYI at two sites near the geographic North Pole using parallel tag sequencing of the 16S rRNA gene. Although the composition of the MYI microbial community has been characterized by previous studies, microbial community structure has not been. Although richness was lower in MYI than...

  19. Is biofuel policy harming biodiversity in Europe?

    NARCIS (Netherlands)

    Eggers, J.; Tröltzsch, K.; Falcucci, A.; Verburg, P.H.; Ozinga, W.A.

    2009-01-01

    We assessed the potential impacts of land-use changes resulting from a change in the current biofuel policy on biodiversity in Europe. We evaluated the possible impact of both arable and woody biofuel crops on changes in distribution of 313 species pertaining to different taxonomic groups. Using

  20. Biodiversity, conservation biology, and rational choice.

    Science.gov (United States)

    Frank, David

    2014-03-01

    This paper critically discusses two areas of Sahotra Sarkar's recent work in environmental philosophy: biodiversity and conservation biology and roles for decision theory in incorporating values explicitly in the environmental policy process. I argue that Sarkar's emphasis on the practices of conservation biologists, and especially the role of social and cultural values in the choice of biodiversity constituents, restricts his conception of biodiversity to particular practical conservation contexts. I argue that life scientists have many reasons to measure many types of diversity, and that biodiversity metrics could be value-free. I argue that Sarkar's emphasis on the limitations of normative decision theory is in tension with his statement that decision theory can "put science and ethics together." I also challenge his claim that multi-criteria decision tools lacking axiomatic foundations in preference and utility theory are "without a rational basis," by presenting a case of a simple "outranking" multi-criteria decision rule that can violate a basic normative requirement of preferences (transitivity) and ask whether there may nevertheless be contexts in which such a procedure might assist decision makers. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Plant biodiversity changes in Carboniferous tropical wetlands

    DEFF Research Database (Denmark)

    Cleal, C. J.; Uhl, D.; Cascales-Miñana, B.

    2012-01-01

    Using a combination of species richness, polycohort and constrained cluster analyses, the plant biodiversity of Pennsylvanian (late Carboniferous) tropical wetlands (“coal swamps”) has been investigated in five areas in Western Europe and eastern North America: South Wales, Pennines, Ruhr, Saarland...

  2. Enhancing Life Sciences Teachers' Biodiversity Knowledge

    African Journals Online (AJOL)

    In terms of biodiversity, the Eastern Cape has a higher biome diversity than any other province in South Africa, including all South African biomes except the desert (Hamann. & Tuinder, 2012), as well as a number of .... Focusing on assessment, an excursion to the mangrove forest was conducted. As part of the excursion, ...

  3. Biodiversity in the anthropocene : Prospects and policy

    NARCIS (Netherlands)

    Seddon, Nathalie; Mace, Georgina M.; Naeem, Shahid; Tobias, Joseph A.; Pigot, Alex L.; Cavanagh, Rachel; Mouillot, David; Vause, James; Walpole, Matt

    2016-01-01

    Meeting the ever-increasing needs of the Earth’s human population without excessively reducing biological diversity is one of the greatest challenges facing humanity, suggesting that newapproaches to biodiversity conservation are required. One idea rapidly gaining momentum-as well as opposition-is

  4. Novel urban ecosystems, biodiversity, and conservation

    Energy Technology Data Exchange (ETDEWEB)

    Kowarik, Ingo, E-mail: kowarik@tu-berlin.de [Department of Ecology, Technische Universitaet Berlin, Rothenburgstr. 12, D 12165 Berlin (Germany)

    2011-08-15

    With increasing urbanization the importance of cities for biodiversity conservation grows. This paper reviews the ways in which biodiversity is affected by urbanization and discusses the consequences of different conservation approaches. Cities can be richer in plant species, including in native species, than rural areas. Alien species can lead to both homogenization and differentiation among urban regions. Urban habitats can harbor self-sustaining populations of rare and endangered native species, but cannot replace the complete functionality of (semi-)natural remnants. While many conservation approaches tend to focus on such relict habitats and native species in urban settings, this paper argues for a paradigm shift towards considering the whole range of urban ecosystems. Although conservation attitudes may be challenged by the novelty of some urban ecosystems, which are often linked to high numbers of nonnative species, it is promising to consider their associated ecosystem services, social benefits, and possible contribution to biodiversity conservation. - Highlights: > This paper reviews biotic responses to urbanization and urban conservation approaches. > Cities may be rich in both native and nonnative species. > Urban habitats cannot replace the functionality of natural remnants. > However, even novel urban habitats may harbour rare and endangered species. > Conservation approaches should consider the perspective of novel urban ecosystems. - This paper reviews the ways in which biodiversity is affected by urbanization and argues for expanding urban conservation approaches.

  5. Problems of Biodiversity Management in Indonesia

    Directory of Open Access Journals (Sweden)

    OKID PARAMA ASTIRIN

    2000-01-01

    Full Text Available Indonesia is an archipelago of 17.508 islands with land width of 1.9 millions km2 and sea of 3.1 millions km2, having many types of habitat and become one of biodiversity center in the world. There are about 28.000 plants species, 350.000 animals species and about 10.000 microbes predicted lived endemically in Indonesia. The country that represents only 1.32% of the world having 10% of total flowering plants, 12% of mammals, 16% reptiles and amphibian, 17% birds, 25% fishes and 15% of insects in the world. Most of the biodiversity were not investigated and utilized yet. The direct use of the biodiversity is not any risk, and in addition, between government, society and industries sometime does not have the same view and attitude. Habitat destruction and over-exploitation have caused Indonesia having long list of endangered species including 126 birds, 63 mammals and 21 reptiles. The extinction of some species occurred just few years ago like trulek jawa (Vanellus macropterus, insectivore bird (Eutrichomyias rowleyi in North Sulawesi, and tiger sub species (Panthera tigris in Java and Bali. It seems that now is time for all Indonesians to introspect and look for the way that can be used for preserving biodiversity.

  6. Insect Biodiversity in the Palearctic Region

    Science.gov (United States)

    Overview of insect biological diversity in the Palearctic is provided. Among World greatest biogeographic Regions, Palearctic is the largest with the longest history of faunistic and biodiversity studies, it is the best known with respect to its overall insect diversity. The following subdivision of...

  7. Traditional African Knowledge In Biodiversity Conservation ...

    African Journals Online (AJOL)

    ... practically by parents, family and society. The loss of certain aspects of our cultures has reduced the possibility of imaginative new approaches. To achieve the objective of applying traditional Afrrcan knowledge in biodiversity conservation the interest of local communities must be properly addressed in policy formulation.

  8. Banning Trophy Hunting Will Exacerbate Biodiversity Loss.

    Science.gov (United States)

    Di Minin, Enrico; Leader-Williams, Nigel; Bradshaw, Corey J A

    2016-02-01

    International pressure to ban trophy hunting is increasing. However, we argue that trophy hunting can be an important conservation tool, provided it can be done in a controlled manner to benefit biodiversity conservation and local people. Where political and governance structures are adequate, trophy hunting can help address the ongoing loss of species. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. 'Conservationists' and the 'Local People' in Biodiversity ...

    African Journals Online (AJOL)

    Studies on biodiversity in Africa show its rapid loss and degradation. This is commonly explained with non-sustainable use by local people. Across Africa, extensive systems of protected areas (PAs) have been established to mitigate this trend. Creation of PAs, however, resulted in manifold conflicts with people who depend ...

  10. PROSPECTS AND CHALLENGES OF BIODIVERSITY IN

    African Journals Online (AJOL)

    losses due to pest and disease attack or unfavourable environmental conditions can be reduced. ... Prospects and challenges biodiversity in small—holder systems 53. It is thought that the subsequent dispersal of .... When measuring genetic diversity on-farm three important aspects should be considered. These.

  11. Mainstreaming biodiversity where it matters most

    NARCIS (Netherlands)

    Karlsson-Vinkhuyzen, S.I.S.E.; Boelee, E.; Cools, J.; Visseren-Hamakers, I.J.; Hoof, van L.J.W.; Hospes, O.; Kok, M.; Peerlings, J.H.M.; Podvin, K.J.; Tatenhove, van J.P.M.; Termeer, C.J.A.M.

    2014-01-01

    This report presents the result of applying the framework in five cases in or on the cross roads between agriculture, forestry and fisheries where considerable pressure on biodiversity is exerted. The cases were selected based on several criteria with the aim that they together cover as broad span

  12. Indicators for livestock and crop biodiversity

    NARCIS (Netherlands)

    Eaton, D.J.F.; Windig, J.J.; Hiemstra, S.J.; Veller, van M.G.P.; Trach, N.X.; Hao, P.X.; Doan, D.H.; Hu, R.

    2006-01-01

    The focus of this study is on indicators for genetic resources, relevant for food and agriculture, for future food security and other functions of genetic resources or agro-biodiversity. The is one small area in the range of levels and sectors. It is recognized that there are many interrelationships

  13. Temporal degradation of data limits biodiversity research.

    Science.gov (United States)

    Tessarolo, Geiziane; Ladle, Richard; Rangel, Thiago; Hortal, Joaquin

    2017-09-01

    Spatial and/or temporal biases in biodiversity data can directly influence the utility, comparability, and reliability of ecological and evolutionary studies. While the effects of biased spatial coverage of biodiversity data are relatively well known, temporal variation in data quality (i.e., the congruence between recorded and actual information) has received much less attention. Here, we develop a conceptual framework for understanding the influence of time on biodiversity data quality based on three main processes: (1) the natural dynamics of ecological systems-such as species turnover or local extinction; (2) periodic taxonomic revisions, and; (3) the loss of physical and metadata due to inefficient curation, accidents, or funding shortfalls. Temporal decay in data quality driven by these three processes has fundamental consequences for the usage and comparability of data collected in different time periods. Data decay can be partly ameliorated by adopting standard protocols for generation, storage, and sharing data and metadata. However, some data degradation is unavoidable due to natural variations in ecological systems. Consequently, changes in biodiversity data quality over time need be carefully assessed and, if possible, taken into account when analyzing aging datasets.

  14. Biodiversity and systematics in cephalopods: Unresolved problems ...

    African Journals Online (AJOL)

    Some problems of cephalopod biodiversity are discussed. Many squid species are represented by 2–4 intraspecies groupings that may be wholly or partly sympatric, but differ in spawning season and size at maturity. They may be genetically distinct stock units, but their taxonomic status remains unresolved. Discovery of a ...

  15. Managing Agricultural Biodiversity for Nutrition, Health, Livelihoods ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Managing Agricultural Biodiversity for Nutrition, Health, Livelihoods and Sustainable Production Systems (Sub-Saharan Africa). The quality of diets within Africa food ... Diversification des moyens de subsistance des petits producteurs de tabac du sud de la province de Nyanza, au Kenya - Phase I. La majeure partie de la ...

  16. Managing Agricultural Biodiversity for Nutrition, Health, Livelihoods ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Managing Agricultural Biodiversity for Nutrition, Health, Livelihoods and Sustainable Production Systems (Sub-Saharan Africa). The quality of diets within Africa food systems appears to be getting worse as evidenced by the increase in micronutrient deficiencies, chronic diseases and low resistance to infectious diseases.

  17. A biosystematic basis for pelagic biodiversity

    NARCIS (Netherlands)

    Spoel, van der S.

    1994-01-01

    Biodiversity can be considered to be a human appreciation of the biological entity diversity. Diversity can be expressed numerically on the basis of taxa found, but it can also be expressed as the contribution of a specimen to the diversity, for which a formula is proposed. Diversity is the sum of

  18. Plantation forests, climate change and biodiversity

    Science.gov (United States)

    S.M. Pawson; A. Brin; E.G. Brockerhoff; D. Lamb; T.W. Payn; A. Paquette; J.A. Parrotta

    2013-01-01

    Nearly 4 % of the world’s forests are plantations, established to provide a variety of ecosystem services, principally timber and other wood products. In addition to such services, plantation forests provide direct and indirect benefits to biodiversity via the provision of forest habitat for a wide range of species, and by reducing negative impacts on natural forests...

  19. Diseases threatening banana biodiversity in Uganda ...

    African Journals Online (AJOL)

    Recent on station and on-farm studies suggest the major diseases threatening banana biodiversity in Uganda include: 1)Black sigatoka which severely affects all East African Highland (EA-AAA) banana cultivars and a range of introduced genotypes; 2) Fusarium wilt which affects several introduced genotypes though all EA ...

  20. Biodiversity-A Manual for College Teachers

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 2; Issue 10. Biodiversity – A Manual for College Teachers. N S Leela. Book Review Volume 2 Issue 10 October 1997 pp 80-81. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/002/10/0080-0081 ...

  1. Calculating Biodiversity in the Real World

    Science.gov (United States)

    Schen, Melissa; Berger, Leslie

    2014-01-01

    One of the standards for life science addressed in the "Next Generation Science Standards" (NGSS Lead States 2013) is "Ecosystems: Interactions, Energy, and Dynamics" (HS-LS2). A critical concept included in this core idea is biodiversity. To show competency, students are expected to design investigations, collect data, and…

  2. Endangered Species & Biodiversity: A Classroom Project & Theme

    Science.gov (United States)

    Lauro, Brook

    2012-01-01

    Students discover the factors contributing to species losses worldwide by conducting a project about endangered species as a component of a larger classroom theme of biodiversity. Groups conduct research using online endangered- species databases and present results to the class using PowerPoint. Students will improve computer research abilities…

  3. Norms and the Conservation of Biodiversity

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 13; Issue 7. Norms and the Conservation of Biodiversity. Sahotra Sarkar. General Article Volume 13 Issue 7 July 2008 pp 627-637. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/013/07/0627-0637 ...

  4. Frontiers in research on biodiversity and disease.

    Science.gov (United States)

    Johnson, Pieter T J; Ostfeld, Richard S; Keesing, Felicia

    2015-10-01

    Global losses of biodiversity have galvanised efforts to understand how changes to communities affect ecological processes, including transmission of infectious pathogens. Here, we review recent research on diversity-disease relationships and identify future priorities. Growing evidence from experimental, observational and modelling studies indicates that biodiversity changes alter infection for a range of pathogens and through diverse mechanisms. Drawing upon lessons from the community ecology of free-living organisms, we illustrate how recent advances from biodiversity research generally can provide necessary theoretical foundations, inform experimental designs, and guide future research at the interface between infectious disease risk and changing ecological communities. Dilution effects are expected when ecological communities are nested and interactions between the pathogen and the most competent host group(s) persist or increase as biodiversity declines. To move beyond polarising debates about the generality of diversity effects and develop a predictive framework, we emphasise the need to identify how the effects of diversity vary with temporal and spatial scale, to explore how realistic patterns of community assembly affect transmission, and to use experimental studies to consider mechanisms beyond simple changes in host richness, including shifts in trophic structure, functional diversity and symbiont composition. © 2015 John Wiley & Sons Ltd/CNRS.

  5. Intensive agriculture reduces soil biodiversity across Europe

    NARCIS (Netherlands)

    Tsiafouli, M.A.; Thébault, E.; Sgardelis, S.; Ruiter, de P.C.; Putten, van der W.H.; Birkhofer, K.; Hemerik, L.; Vries, de F.T.; Bardgett, R.D.; Brady, M.; Bjornlund, L.; Bracht Jörgensen, H.; Christensen, S.; Herfelt, D' T.; Hotes, S.; Hol, W.H.G.; Frouz, J.; Liiri, M.; Mortimer, S.R.; Setälä, H.; Stary, J.; Tzanopoulos, J.; Uteseny, C.; Wolters, V.; Hedlund, K.

    2015-01-01

    Soil biodiversity plays a key role in regulating the processes that underpin the delivery of ecosystem goods and services in terrestrial ecosystems. Agricultural intensification is known to change the diversity of individual groups of soil biota, but less is known about how intensification affects

  6. Soil phosphorus constrains biodiversity across European grasslands.

    Science.gov (United States)

    Ceulemans, Tobias; Stevens, Carly J; Duchateau, Luc; Jacquemyn, Hans; Gowing, David J G; Merckx, Roel; Wallace, Hilary; van Rooijen, Nils; Goethem, Thomas; Bobbink, Roland; Dorland, Edu; Gaudnik, Cassandre; Alard, Didier; Corcket, Emmanuel; Muller, Serge; Dise, Nancy B; Dupré, Cecilia; Diekmann, Martin; Honnay, Olivier

    2014-12-01

    Nutrient pollution presents a serious threat to biodiversity conservation. In terrestrial ecosystems, the deleterious effects of nitrogen pollution are increasingly understood and several mitigating environmental policies have been developed. Compared to nitrogen, the effects of increased phosphorus have received far less attention, although some studies have indicated that phosphorus pollution may be detrimental for biodiversity as well. On the basis of a dataset covering 501 grassland plots throughout Europe, we demonstrate that, independent of the level of atmospheric nitrogen deposition and soil acidity, plant species richness was consistently negatively related to soil phosphorus. We also identified thresholds in soil phosphorus above which biodiversity appears to remain at a constant low level. Our results indicate that nutrient management policies biased toward reducing nitrogen pollution will fail to preserve biodiversity. As soil phosphorus is known to be extremely persistent and we found no evidence for a critical threshold below which no environmental harm is expected, we suggest that agro-environmental schemes should include grasslands that are permanently free from phosphorus fertilization. © 2014 John Wiley & Sons Ltd.

  7. Biodiversity footprint of companies - Summary report

    NARCIS (Netherlands)

    Rooij, van W.; Arets, E.J.M.M.

    2017-01-01

    Companies are becoming increasingly aware of their impact on biodiversity and natural capital. This may result from their implicit dependence on natural capital, from increasingly more critical consumers, or from the genuine concern of company managers and owners. Consequently, companies have an

  8. Linking Biotechnology and Agricultural Biodiversity Resources in ...

    African Journals Online (AJOL)

    komla

    biodiversity resources which, with the appropriate application of biotechnological tools for conservation and use, can ... The paper explores some of the key applications of biotechnology for conservation of agricultural ..... International Technical Workshop jointly organized by the Food and Agriculture Organization of the.

  9. Biodiversity intactness score for South Africa

    CSIR Research Space (South Africa)

    Biggs, R

    2006-07-01

    Full Text Available under grazing management. This suggests that the policy action with the greatest potential to limit further loss of biodiversity is to prevent the degradation of these areas, which could potentially halve the abundance of the remaining wild organisms....

  10. Enhancing Life Sciences Teachers' Biodiversity Knowledge : A ...

    African Journals Online (AJOL)

    This paper provides insights into how Life Sciences teachers in the Eastern Cape can be supported through professional learning communities (PLCs) as a potential approach to enhancing their biodiversity knowledge. PLCs are communities that provide the setting and necessary support for groups of classroom teachers to ...

  11. VBioindex: A Visual Tool to Estimate Biodiversity

    Directory of Open Access Journals (Sweden)

    Dong Su Yu

    2015-09-01

    Full Text Available Biological diversity, also known as biodiversity, is an important criterion for measuring the value of an ecosystem. As biodiversity is closely related to human welfare and quality of life, many efforts to restore and maintain the biodiversity of species have been made by government agencies and non-governmental organizations, thereby drawing a substantial amount of international attention. In the fields of biological research, biodiversity is widely measured using traditional statistical indices such as the Shannon-Wiener index, species richness, evenness, and relative dominance of species. However, some biologists and ecologists have difficulty using these indices because they require advanced mathematical knowledge and computational techniques. Therefore, we developed VBioindex, a user-friendly program that is capable of measuring the Shannon-Wiener index, species richness, evenness, and relative dominance. VBioindex serves as an easy to use interface and visually represents the results in the form of a simple chart and in addition, VBioindex offers functions for long-term investigations of datasets using time-series analyses.

  12. Linking Biotechnology and Agricultural Biodiversity Resources in ...

    African Journals Online (AJOL)

    Proper harnessing of the linkages between biotechnology and the diversity of biological resources is required to meet challenges of food security, health, poverty and wealth creation in West African countries. The paper explores some of the key applications of biotechnology for conservation of agricultural biodiversity ...

  13. Connecting Earth observation to high-throughput biodiversity data

    DEFF Research Database (Denmark)

    Bush, Alex; Sollmann, Rahel; Wilting, Andreas

    2017-01-01

    Understandably, given the fast pace of biodiversity loss, there is much interest in using Earth observation technology to track biodiversity, ecosystem functions and ecosystem services. However, because most biodiversity is invisible to Earth observation, indicators based on Earth observation cou...... observation data. This approach is achievable now, offering efficient and near-real-time monitoring of management impacts on biodiversity and its functions and services....

  14. THE IMPACT OF GROWTH ON BIODIVERSITY: AN EMPIRICAL ASSESSMENT

    OpenAIRE

    de santis, roberta

    2012-01-01

    Several studies investigating environmental Kuznets curve (EKC) relationship for biodiversity, suffer from limitations and the empirical evidence is inconclusive. More specifically, with few exceptions, the previous EKC studies for biodiversity looked into the diversity of a particular species or a number of species rather than a broader measure of biodiversity. In addition, these studies do not control for some economic factors that could directly or indirectly affect the biodiversity stock ...

  15. Biodiversity conservation status in the Republic of Kosovo with focus on biodiversity centres.

    Science.gov (United States)

    Zeqir, Veselaj; Behxhet, Mustafa; Avni, Hajdari; Zenel, Krasniqi

    2012-04-01

    This paper presents the most recent results on Kosovo biodiversity conservation efforts with focus on two main biodiversity centers of Kosovo: Sharri mountain (already declared as National Park) and Bjeshket e Nemuna mountains in process of designation as a National park. The study presents collection of up to date publications on biodiversity of Kosovo. Of course, there is still to be investigated particularly in the field of lower plants as well invertebrate fauna species. Beside the small territory of 10,887 km2, Kosovo is quite rich in both plant and animal biodiversity. Up to date 1800 vascular plant species have been recorded, while expected number is about 2500 species. Number of higher vertebrates is 210, while the invertebrates are not studied with exception of Lepidoptera with about 150 species. There is no Red List of species for Kosovo developed yet, while some short term conservation measures have already taken place.

  16. Standardized Assessment of Biodiversity Trends in Tropical Forest Protected Areas: The End Is Not in Sight.

    Science.gov (United States)

    Beaudrot, Lydia; Ahumada, Jorge A; O'Brien, Timothy; Alvarez-Loayza, Patricia; Boekee, Kelly; Campos-Arceiz, Ahimsa; Eichberg, David; Espinosa, Santiago; Fegraus, Eric; Fletcher, Christine; Gajapersad, Krisna; Hallam, Chris; Hurtado, Johanna; Jansen, Patrick A; Kumar, Amit; Larney, Eileen; Lima, Marcela Guimarães Moreira; Mahony, Colin; Martin, Emanuel H; McWilliam, Alex; Mugerwa, Badru; Ndoundou-Hockemba, Mireille; Razafimahaimodison, Jean Claude; Romero-Saltos, Hugo; Rovero, Francesco; Salvador, Julia; Santos, Fernanda; Sheil, Douglas; Spironello, Wilson R; Willig, Michael R; Winarni, Nurul L; Zvoleff, Alex; Andelman, Sandy J

    2016-01-01

    Extinction rates in the Anthropocene are three orders of magnitude higher than background and disproportionately occur in the tropics, home of half the world's species. Despite global efforts to combat tropical species extinctions, lack of high-quality, objective information on tropical biodiversity has hampered quantitative evaluation of conservation strategies. In particular, the scarcity of population-level monitoring in tropical forests has stymied assessment of biodiversity outcomes, such as the status and trends of animal populations in protected areas. Here, we evaluate occupancy trends for 511 populations of terrestrial mammals and birds, representing 244 species from 15 tropical forest protected areas on three continents. For the first time to our knowledge, we use annual surveys from tropical forests worldwide that employ a standardized camera trapping protocol, and we compute data analytics that correct for imperfect detection. We found that occupancy declined in 22%, increased in 17%, and exhibited no change in 22% of populations during the last 3-8 years, while 39% of populations were detected too infrequently to assess occupancy changes. Despite extensive variability in occupancy trends, these 15 tropical protected areas have not exhibited systematic declines in biodiversity (i.e., occupancy, richness, or evenness) at the community level. Our results differ from reports of widespread biodiversity declines based on aggregated secondary data and expert opinion and suggest less extreme deterioration in tropical forest protected areas. We simultaneously fill an important conservation data gap and demonstrate the value of large-scale monitoring infrastructure and powerful analytics, which can be scaled to incorporate additional sites, ecosystems, and monitoring methods. In an era of catastrophic biodiversity loss, robust indicators produced from standardized monitoring infrastructure are critical to accurately assess population outcomes and identify

  17. Biodiversity and global health—hubris, humility and the unknown

    Science.gov (United States)

    Stephens, Carolyn

    2012-03-01

    In November 2011, botanists on a remote island off Papua New Guinea discovered a new species of orchid—uniquely and mysteriously night-flowering [1]. New to science, and with so much more to understand, this flower is threatened by deforestation [2]. Also in November 2011, a survey of 583 conservation scientists reported a unanimous (99.5%) view that 'it is likely a serious loss of biological diversity is underway at a global extent' and that, for scientists, 'protection of biological diversity for its cultural and spiritual values and because of its usefulness to humans were low priorities, which suggests that many scientists do not fully support the utilitarian concept of ecosystem services' [3]. In terms of management, some scientists now advocate controversial conservation strategies such as triage (prioritization of species that provide unique or necessary functions to ecosystems) [4, 5]. Meanwhile, there are many scientists who contend that there is an urgent need to improve our understanding of the importance of biodiversity for human health and well-being, arguing that only an anthropocentric view of biodiversity within a paradigm 'ecosystem service' will enable decision-makers to prioritize the theme [6-9]. A 2011 UN report argues that this need for understanding is especially urgent in fragile and vulnerable ecosystems where communities depend directly on the resources of their environment [10]. Here we have a paradox: international conservation scientists think that we cannot protect biodiversity on the basis of its cultural and spiritual value, nor its usefulness to humans. Other scientists argue that using a utilitarian ecosystem services framework is the only way to get humans to protect biodiversity. Meanwhile, communities directly dependent on biodiverse ecosystems are often those who best understand and protect biodiversity, for exactly these reasons of use and spiritual connection, but they do not hold only a utilitarian view of their

  18. Precambrian Skeletonized Microbial Eukaryotes

    Science.gov (United States)

    Lipps, Jere H.

    2017-04-01

    . Tintinnids first appear in the mid-Mesozoic, like other modern planktic groups, including planktic foraminifera, new types of radiolarians, and a host of skeletal micro-algae. Microbial eukaryotes track algal eukaryote and metazoan evolution—none or very few in the Precambrian, some in the early Paleozoic with radiations in the later Paleozoic, Mesozoic and Cenozoic, with extinctions ( 30) reducing their biodiversity at particular times in the fossil record—thus indicating strong environmental selection on all marine groups.

  19. The effect of buffer zone width on biodiversity

    DEFF Research Database (Denmark)

    Navntoft, Søren; Sigsgaard, Lene; Kristensen, Kristian

    2012-01-01

    Field margin management for conservation purposes is a way to protect both functional biodiversity and biodiversity per se without considerable economical loss as field margins are less productive. However, the effect of width of the buffer zone on achievable biodiversity gains has received little...

  20. Soil biodiversity and soil community composition determine ecosystem multifunctionality

    NARCIS (Netherlands)

    Wagg, C.; Bender, S.F.; Widmer, D.; van der Heijden, Marcellus|info:eu-repo/dai/nl/240923901

    2014-01-01

    Biodiversity loss has become a global concern as evidence accumulates that it will negatively affect ecosystem services on which society depends. So far, most studies have focused on the ecological consequences of above-ground biodiversity loss; yet a large part of Earth’s biodiversity is literally