biodiversity

..This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer...

..Also, simulations that evaluate the performance of the approach for different read lengths are presented...

..Members of the rare biosphere are highly divergent from each other and, at different times in earth's history, may have had a profound impact on shaping planetary processes...

..A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease...

..We suggest that stringent quality-based trimming of 16S pyrotags and clustering thresholds no greater than 97% identity should be used to avoid overestimates of the rare biosphere...

..This new clustering method can reduce the OTU richness in environmental samples by as much as 30-60% but does not reduce the fraction of OTUs in long-tailed rank abundance curves that defines the rare biosphere...

..We discovered significant intersubject variability and differences between stool and mucosa community composition. Characterization of this immensely diverse ecosystem is the first step in elucidating its role in health and disease...

Current unprecedented declines in biodiversity reduce the ability of ecological communities to provide many fundamental ecosystem services...

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..The ecological rules that govern the shape of microbial diversity in the gut apply to mutualists and pathogens alike...

..These estimates show the importance of rapid implementation of technologies to decrease greenhouse gas emissions and strategies for carbon sequestration...

The Mediterranean Sea is a marine biodiversity hot spot...

..This topographical and temporal survey provides a baseline for studies that examine the role of bacterial communities in disease states and the microbial interdependencies required to maintain healthy skin...

..This technique allows the cost-effective exploration of changes in microbial community structure, including the rare biosphere, over space and time and can be applied immediately to initiatives, such as the Human Microbiome Project...

..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...

..This provides a method of species discovery and biodiversity assessment using single-locus data from mixed or environmental samples while building a globally available ..

..This work is the most comprehensive examination to date of bacterial diversity in soil and suggests that agricultural management of soil may significantly influence the diversity of bacteria and archaea...

Concern is growing about the consequences of biodiversity loss for ecosystem functioning, for the provision of ecosystem services, and for human well being...

..a continental-scale description of soil bacterial communities and the environmental factors influencing their biodiversity. We collected 98 soil samples from across North and South America and used a ribosomal DNA-fingerprinting ..

..r-forge.r-project.org) and from CRAN (http://cran.r-project.org)...

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..The discovery of cryptic species is likely to be non-random with regard to taxon and biome and, hence, could have profound implications for evolutionary theory, biogeography and conservation planning...

..Short DNA fragments persist in the environment and might allow an assessment of local biodiversity from soil or water. Even DNA-based diet composition can be estimated using fecal samples...

..Metal pollution reduced diversity more than 99.9%, revealing the highly toxic effect of metal contamination, especially for rare taxa...

..We conclude that cox1 sequencing, or 'barcoding', can be used to identify fish species...

..However, recent studies also dispute the idea that 'everything is everywhere'. We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world...

..Large-scale experiments are presented that clearly demonstrate the effectiveness of the newly proposed algorithm. The source code and user guide are freely available at http://www.biotech.ufl.edu/people/sun/esprit.html...

..Understanding the diversity and connectivity of vent metapopulations provides essential information for designing deep-sea preserves in regions that are under consideration for submarine mining of precious metals...

Southeast Asia is recognized as a region of very high biodiversity, much of which is currently at risk due to habitat loss and other threats...

..Taken together, these findings strongly suggest a causal connection between local extinctions of functionally linked plant and pollinator species...

..Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action...

The global decline of biodiversity caused by human domination of ecosystems worldwide is supposed to alter important process rates and state variables in these ecosystems...

..This work provides a framework for understanding the impact of environmental factors on bacterial evolution and for the direction of future sequencing efforts to discover new lineages...

..aboveground-belowground approach to community and ecosystem ecology is enhancing our understanding of the regulation and functional significance of biodiversity and of the environmental impacts of human-induced global change phenomena.

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..b>Biodiversity influences the way in which ecosystems function, but the form of the relationship between bacterial ..

..in an amphibian community at El Copé, Panama, and subsequent mass mortality and loss of amphibian biodiversity across eight families of frogs and salamanders...

..2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity...

..Here, we undertook intensive field collections in two biodiversity hotspots (Mesoamerica and southern Africa). Using >1,600 samples, we compared eight potential barcodes...

..scenarios are coming of age as a tool for evaluating the impact of future socioeconomic development pathways on biodiversity and ecosystem services...

..to allow them to successfully enter and exit a dormant state, and discuss the implications of microbial seed banks for evolutionary dynamics, population persistence, maintenance of biodiversity, and the stability of ecosystem processes.

..We show that Andean uplift was crucial for the evolution of Amazonian landscapes and ecosystems, and that current biodiversity patterns are rooted deep in the pre-Quaternary.

..This biomass census and associated maps are vital components of mechanistic deep-sea food web models and global carbon cycling, and as such provide fundamental information that can be incorporated into evidence-based management...

Climate change is predicted to become a major threat to biodiversity in the 21st century, but accurate predictions and effective solutions have proved difficult to formulate...

..The Marmara sediment clustered with the soil metagenome, highlighting the common ecological role of both types of microbial communities in the degradation of organic matter and the completion of biogeochemical cycles...

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..Overall, this review shows that soil microbes must be considered as important drivers of plant diversity and productivity in terrestrial ecosystems...

..Here we present the first worldwide synthesis to jointly consider human and biodiversity perspectives on water security using a spatial framework that quantifies multiple stressors and accounts for ..

..The results provide a better understanding on using mangrove wetlands as biological treatment systems for removal of nutrients...

Recent analyses of the fossil record and molecular phylogenies suggest that there are fundamental limits to biodiversity, possibly arising from constraints in the availability of space, resources, or ecological niches...

b>Biodiversity loss from deforestation may be partly offset by the expansion of secondary forests and plantation forestry in the tropics...

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b>Biodiversity is proposed to be important for the rate of ecosystem functions...

Understanding the maintenance and origin of biodiversity is a formidable task, yet many ubiquitous ecological patterns are predicted by a surprisingly simple and widely studied neutral model that ignores functional differences between ..

..We need to embrace the fossil record if we want to fully understand the diversity dynamics of the living biota...

..g. invasives, global warming, tropical richness), and (3) suggests new areas for research (e.g. why are some clades largely nocturnal? why do related species share diseases?)...

..Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earth's biota in a time of rapid global change...

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..Third, we report two universal rules: Food-web stability is enhanced when (i) species at a high trophic level feed on multiple prey species and (ii) species at an intermediate trophic level are fed upon by multiple predator species...

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..Especially the next generation sequencing technologies can be expected to have a tremendous effect on fungal biodiversity and ecology research...

b>Biodiversity assessment is the key to understanding the relationship between biodiversity and ecosystem functioning, but there is a well-acknowledged biodiversity identification gap related to eukaryotic meiofaunal organisms...

..These results demonstrate that immigration and diversification are tightly linked processes, with small differences in immigration history greatly affecting the evolutionary emergence of diversity...

Two decades of intensive research have provided compelling evidence for a link between biodiversity and ecosystem functioning (B-EF)...

..We are also starting to understand how certain keystone members of the microbiota operate to maintain the stability and functional adaptability of this microbial organ...

..Recognizing these biases will encourage the development of more realistic models of diversification and the regulation of species richness...

..ponderosa needles...

Net primary productivity is a principal driver of biodiversity; large-scale regions with higher productivity generally have more species...

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..Our findings indicate a fundamental role of temperature or kinetic energy in structuring cross-taxon marine biodiversity, and indicate that changes in ocean temperature, in conjunction with other human impacts, may ultimately ..

..4. Our study illustrates that heterogeneity is not always the strongest driver of diversity, while experimentally demonstrating mechanisms by which heterogeneity alters community structure...

..8 copies of the 16S rRNA gene, suggesting that these bacteria have relatively streamlined genomes in comparison to those of cultured bacteria and bacteria from other habitats (e.g., soil or acid mine drainage)...

..We have evaluated the microbiome from the feces of 20 commercial, lactating dairy cows...

..A second experiment showed that a decade after cessation of nitrogen addition, relative plant species number, although not species abundances, had recovered, demonstrating that some effects of nitrogen addition are reversible...

..These results indicate management strategies for minimizing biodiversity loss from climate change. Montane landscapes may effectively shelter many species into the next century...

Freshwater biodiversity is the over-riding conservation priority during the International Decade for Action - 'Water for Life' - 2005 to 2015. Fresh water makes up only 0.01% of the World's water and approximately 0...

..We found that risks of extinction for European plants may be large, even in moderate scenarios of climate change and despite inter-model variability...

..The large proportion of unidentified sequences, however, calls for curated sequence databases. The use of pyrosequencing on soil samples will accelerate the study of the spatiotemporal dynamics of fungal communities in forest ecosystems...

..We discuss these differences from both the diagnostic and the scientific point of view...

..Nonetheless, current conservation efforts remain insufficient to offset the main drivers of biodiversity loss in these groups: agricultural expansion, logging, overexploitation, and invasive alien species.

..Using only haul data to calculate seabird bycatch grossly underestimates actual bycatch levels, with the level of seabird bycatch from pelagic longline fishing possibly double what was previously thought...

..These transport pathways may broadly influence microbial community composition in the marine environment...

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..Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth...

Theoretical models predict that effects of dispersal on local biodiversity are influenced by the size and composition of the species pool, as well as ecological filters that limit local species membership...

..were consistent with the trophic requirements of the biota, suggesting that both macroalgal cover and coral biodiversity are partially controlled by energy supply limitation...

..These data can be of help to future clinical trials (e.g. targeted weaning products) to organize protocols and obtain a more accurate outline of the changes and dynamics of the infant GI microbiota...

..targets, or of the extent to which the current global protected area network fulfils its goal of protecting biodiversity. Here, we combine five global data sets on the distribution of species and protected areas to provide the first ..

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..aeruginosa and the global spread of P. aeruginosa phage species, and points at the resistance of two clinically predominant, widespread P. aeruginosa strains against phage attack...

Predicting biodiversity effects on ecosystem functioning requires adequate evaluation of the mechanisms explaining why more diverse systems could perform better than less diverse ones...

Habitat loss has pervasive and disruptive impacts on biodiversity in habitat remnants. The magnitude of the ecological impacts of habitat loss can be exacerbated by the spatial arrangement -- or fragmentation -- of remaining habitat...

b>Biodiversity of marine ecosystems is integral to their stability and function and is threatened by anthropogenic processes...

..Taxonomic expertise in Australia is unevenly distributed across taxa, and declining. Comments are given briefly on biodiversity management measures in Australia, including but not limited to marine protected areas.

..uniflora and J. bulbosus, increase AOA abundance; and (iii) AOA community composition is generally determined by lake trophy, not by plant species-specific interactions...

..7. The lognormal distribution deserves greater consideration as a richness estimator when undersampling bias is severe...

..Overall, this study significantly enhances our understanding of estuarine ammonia-oxidizing microbial communities and highlights the environmental conditions and niches under which different AOA and beta-AOB phylotypes may thrive...

..I illustrate use of the method by analyzing a published phylogeny for Australian agamid lizards...

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..greatest in landscapes with a concentrated pattern of disturbance, especially below some critical threshold of biodiversity. Below the critical biodiversity threshold, the introduction of a single species can trigger a cascade of ..

..young scientists with the cross-disciplinary, integrative training necessary to address complex issues in biodiversity analysis and conservation...

..young scientists with the cross-disciplinary, integrative training necessary to address complex issues in biodiversity analysis and conservation...

..Our research comprises a rigorous, multidisciplinary approach to understanding the linkages between ecology and risk of infectious disease. ..

..Our research comprises a rigorous, multidisciplinary approach to understanding the linkages between ecology and risk of infectious disease. ..

..Rivers are not only vital sources of water for agriculture and human consumption, but key areas of biodiversity. The middle Rio Grande river (MRG), which flows through central New Mexico, contains one of the most extensive ..

..the mapping of chronomes in selected species, with focus on the relative importance of the biological day vs. the biological week and of the transyear vs. the calendar year. ..