biodiversity

Summary

Summary: The variety of all native living organisms and their various forms and interrelationships.

Top Publications

  1. pmc Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
    Patrick D Schloss
    Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
    Appl Environ Microbiol 75:7537-41. 2009
  2. pmc A core gut microbiome in obese and lean twins
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 457:480-4. 2009
  3. pmc MEGAN analysis of metagenomic data
    Daniel H Huson
    Center for Bioinformatics, Tubingen University, Sand 14, 72076 Tubingen, Germany
    Genome Res 17:377-86. 2007
  4. pmc Bacterial community variation in human body habitats across space and time
    Elizabeth K Costello
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Science 326:1694-7. 2009
  5. pmc Microbial diversity in the deep sea and the underexplored "rare biosphere"
    Mitchell L Sogin
    Josephine Bay Paul Center, Marine Biological Laboratory at Woods Hole, 7 MBL Street, Woods Hole, MA 02543, USA
    Proc Natl Acad Sci U S A 103:12115-20. 2006
  6. pmc Diversity of the human intestinal microbial flora
    Paul B Eckburg
    Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Room S 169, 300 Pasteur Drive, Stanford CA 94305 5107, USA
    Science 308:1635-8. 2005
  7. pmc Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies
    Patrick D Schloss
    Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS ONE 6:e27310. 2011
  8. doi Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
    Victor Kunin
    Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
    Environ Microbiol 12:118-23. 2010
  9. pmc Ironing out the wrinkles in the rare biosphere through improved OTU clustering
    Susan M Huse
    Josephine Bay Paul Center, Marine Biological Laboratory at Woods Hole, 7 MBL Street, Woods Hole, MA 02543, USA
    Environ Microbiol 12:1889-98. 2010
  10. pmc The human microbiome project
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 449:804-10. 2007

Detail Information

Publications338 found, 100 shown here

  1. pmc Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
    Patrick D Schloss
    Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
    Appl Environ Microbiol 75:7537-41. 2009
    ..This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer...
  2. pmc A core gut microbiome in obese and lean twins
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 457:480-4. 2009
    ....
  3. pmc MEGAN analysis of metagenomic data
    Daniel H Huson
    Center for Bioinformatics, Tubingen University, Sand 14, 72076 Tubingen, Germany
    Genome Res 17:377-86. 2007
    ..Also, simulations that evaluate the performance of the approach for different read lengths are presented...
  4. pmc Bacterial community variation in human body habitats across space and time
    Elizabeth K Costello
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Science 326:1694-7. 2009
    ..These results indicate that our microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease...
  5. pmc Microbial diversity in the deep sea and the underexplored "rare biosphere"
    Mitchell L Sogin
    Josephine Bay Paul Center, Marine Biological Laboratory at Woods Hole, 7 MBL Street, Woods Hole, MA 02543, USA
    Proc Natl Acad Sci U S A 103:12115-20. 2006
    ..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...
  6. pmc Diversity of the human intestinal microbial flora
    Paul B Eckburg
    Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Room S 169, 300 Pasteur Drive, Stanford CA 94305 5107, USA
    Science 308:1635-8. 2005
    ..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...
  7. pmc Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies
    Patrick D Schloss
    Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS ONE 6:e27310. 2011
    ....
  8. doi Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
    Victor Kunin
    Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
    Environ Microbiol 12:118-23. 2010
    ..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...
  9. pmc Ironing out the wrinkles in the rare biosphere through improved OTU clustering
    Susan M Huse
    Josephine Bay Paul Center, Marine Biological Laboratory at Woods Hole, 7 MBL Street, Woods Hole, MA 02543, USA
    Environ Microbiol 12:1889-98. 2010
    ..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...
  10. pmc The human microbiome project
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 449:804-10. 2007
    ..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...
  11. pmc Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa
    Carlotta De Filippo
    Department of Preclinical and Clinical Pharmacology, University of Florence, 50139 Firenze, Italy
    Proc Natl Acad Sci U S A 107:14691-6. 2010
    ....
  12. doi Impacts of biodiversity on the emergence and transmission of infectious diseases
    Felicia Keesing
    Department of Biology, Bard College, Annandale, New York 12504, USA
    Nature 468:647-52. 2010
    Current unprecedented declines in biodiversity reduce the ability of ecological communities to provide many fundamental ecosystem services...
  13. ncbi Extinction risk from climate change
    Chris D Thomas
    Centre for Biodiversity and Conservation, School of Biology, University of Leeds, Leeds LS2 9JT, UK
    Nature 427:145-8. 2004
    ..These estimates show the importance of rapid implementation of technologies to decrease greenhouse gas emissions and strategies for carbon sequestration...
  14. ncbi Ecological and evolutionary forces shaping microbial diversity in the human intestine
    Ruth E Ley
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Cell 124:837-48. 2006
    ..The ecological rules that govern the shape of microbial diversity in the gut apply to mutualists and pathogens alike...
  15. pmc Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing
    Susan M Huse
    Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
    PLoS Genet 4:e1000255. 2008
    ..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...
  16. pmc Topographical and temporal diversity of the human skin microbiome
    Elizabeth A Grice
    Genetics and Molecular Biology Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
    Science 324:1190-2. 2009
    ..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...
  17. pmc Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale
    Christian L Lauber
    Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, 80309, USA
    Appl Environ Microbiol 75:5111-20. 2009
    ....
  18. ncbi Status and trends of amphibian declines and extinctions worldwide
    Simon N Stuart
    IUCN Species Survival Commission Conservation International Center for Applied Biodiversity Science Biodiversity Assessment Unit, 1919 M Street N W, Washington, DC 20036, USA
    Science 306:1783-6. 2004
    ..The lack of conservation remedies for these poorly understood declines means that hundreds of amphibian species now face extinction...
  19. doi Picante: R tools for integrating phylogenies and ecology
    Steven W Kembel
    Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR, USA
    Bioinformatics 26:1463-4. 2010
    ....
  20. ncbi Multivariate dispersion as a measure of beta diversity
    Marti J Anderson
    Ecol Lett 9:683-93. 2006
    ..We propose a new dissimilarity measure which allows the relative weight placed on changes in composition vs. abundance to be specified explicitly...
  21. pmc The diversity and biogeography of soil bacterial communities
    Noah Fierer
    Department of Biology and Nicholas School of the Environment and Earth Sciences, Duke University, Durham, NC 27708, USA
    Proc Natl Acad Sci U S A 103:626-31. 2006
    ..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 ..
  22. ncbi Species concepts and species delimitation
    Kevin de Queiroz
    Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560 0162, USA
    Syst Biol 56:879-86. 2007
    ..Fourth, and perhaps most significantly, a unified species concept shifts emphasis away from the traditional species criteria, encouraging biologists to develop new methods of species delimitation that are not tied to those properties...
  23. pmc Pyrosequencing enumerates and contrasts soil microbial diversity
    Luiz F W Roesch
    Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611 0700, USA
    ISME J 1:283-90. 2007
    ..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...
  24. ncbi Microbial biogeography: putting microorganisms on the map
    Jennifer B Hughes Martiny
    Department of Ecology and Evolutionary Biology, 80 Waterman Street, Box G W, Brown University, Providence, Rhode Island 02912, USA
    Nat Rev Microbiol 4:102-12. 2006
    ..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...
  25. doi Accelerated species inventory on Madagascar using coalescent-based models of species delineation
    Michael T Monaghan
    Entomology Department, Natural History Museum, London, UK
    Syst Biol 58:298-311. 2009
    ..This provides a method of species discovery and biodiversity assessment using single-locus data from mixed or environmental samples while building a globally available ..
  26. doi Global biodiversity: indicators of recent declines
    Stuart H M Butchart
    United Nations Environment Programme World Conservation Monitoring Centre, 219 Huntingdon Road, Cambridge CB3 0DL, UK
    Science 328:1164-8. 2010
    ..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...
  27. ncbi Impacts of biodiversity loss on ocean ecosystem services
    Boris Worm
    Department of Biology, Dalhousie University, Halifax, NS, Canada B3H 4J1
    Science 314:787-90. 2006
    ..We analyzed local experiments, long-term regional time series, and global fisheries data to test how biodiversity loss affects marine ecosystem services across temporal and spatial scales...
  28. ncbi Toward an ecological classification of soil bacteria
    Noah Fierer
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
    Ecology 88:1354-64. 2007
    ....
  29. ncbi Host-bacterial mutualism in the human intestine
    Fredrik Backhed
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Science 307:1915-20. 2005
    ..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...
  30. doi Has the Earth's sixth mass extinction already arrived?
    Anthony D Barnosky
    Department of Integrative Biology, University of California, Berkeley, California 94720, USA
    Nature 471:51-7. 2011
    ..Our results confirm that current extinction rates are higher than would be expected from the fossil record, highlighting the need for effective conservation measures...
  31. pmc Global patterns in bacterial diversity
    Catherine A Lozupone
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 104:11436-40. 2007
    ..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...
  32. doi Towards the human intestinal microbiota phylogenetic core
    Julien Tap
    INRA, UEPSD, UR910, 78350 Jouy en Josas, France
    Environ Microbiol 11:2574-84. 2009
    ..Its role in human health deserves further study...
  33. pmc Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos
    Mehrdad Hajibabaei
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
    PLoS ONE 6:e17497. 2011
    Timely and accurate biodiversity analysis poses an ongoing challenge for the success of biomonitoring programs...
  34. ncbi Quantifying the evidence for biodiversity effects on ecosystem functioning and services
    Patricia Balvanera
    Centro de Investigaciones en Ecosistemas, UNAM, Morelia, Mexico
    Ecol Lett 9:1146-56. 2006
    Concern is growing about the consequences of biodiversity loss for ecosystem functioning, for the provision of ecosystem services, and for human well being...
  35. pmc How many species are there on Earth and in the ocean?
    Camilo Mora
    Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    PLoS Biol 9:e1001127. 2011
    ..Yet the answer to this question remains enigmatic, as efforts to sample the world's biodiversity to date have been limited and thus have precluded direct quantification of global species richness, and because ..
  36. doi Biodiversity loss and its impact on humanity
    Bradley J Cardinale
    School of Natural Resources and Environment, University of Michigan, Ann Arbor, Michigan 48109, USA
    Nature 486:59-67. 2012
    ..This observation led to the question of how such loss of biological diversity will alter the functioning of ecosystems and their ability to provide society with the goods and services needed to prosper...
  37. ncbi Cryptic species as a window on diversity and conservation
    David Bickford
    Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Republic of Singapore
    Trends Ecol Evol 22:148-55. 2007
    ..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...
  38. pmc The biodiversity of the Mediterranean Sea: estimates, patterns, and threats
    Marta Coll
    Institut de Ciencies del Mar, Scientific Spanish Council ICM CSIC, Barcelona, Spain
    PLoS ONE 5:e11842. 2010
    The Mediterranean Sea is a marine biodiversity hot spot...
  39. doi Scenarios for global biodiversity in the 21st century
    Henrique M Pereira
    Centro de Biologia Ambiental, Faculdade de Ciencias da Universidade de Lisboa, 1749 016 Lisboa, Portugal
    Science 330:1496-501. 2010
    ..scenarios are coming of age as a tool for evaluating the impact of future socioeconomic development pathways on biodiversity and ecosystem services...
  40. ncbi Effects of biodiversity on the functioning of trophic groups and ecosystems
    Bradley J Cardinale
    Department of Ecology, Evolution and Marine Biology, University of California at Santa Barbara, Santa Barbara, California 93106, USA
    Nature 443:989-92. 2006
    ....
  41. doi Beyond predictions: biodiversity conservation in a changing climate
    Terence P Dawson
    School of the Environment, University of Dundee, Dundee DD1 4HN, Scotland, UK
    Science 332:53-8. 2011
    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...
  42. doi A global synthesis reveals biodiversity loss as a major driver of ecosystem change
    David U Hooper
    Department of Biology, Western Washington University, Bellingham, Washington 98225 9160, USA
    Nature 486:105-8. 2012
    ....
  43. pmc Intestinal microbiota in healthy adults: temporal analysis reveals individual and common core and relation to intestinal symptoms
    Jonna Jalanka-Tuovinen
    Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
    PLoS ONE 6:e23035. 2011
    ..The health perception and occurrence of intestinal symptoms was recorded by questionnaire at each sampling point...
  44. doi Biodiversity improves water quality through niche partitioning
    Bradley J Cardinale
    University of Michigan, School of Natural Resources and Environment, Ann Arbor, Michigan 48109 1041, USA
    Nature 472:86-9. 2011
    ..This has led some to suggest that conservation of biodiversity might be a useful tool for managing nutrient uptake and storage, but this suggestion has been controversial, in ..
  45. pmc DNA barcoding Australia's fish species
    Robert D Ward
    CSIRO Marine and Atmospheric Research, GPO Box 1538, Hobart, Tasmania 7001, Australia
    Philos Trans R Soc Lond B Biol Sci 360:1847-57. 2005
    ..We conclude that cox1 sequencing, or 'barcoding', can be used to identify fish species...
  46. pmc DNA barcoding the floras of biodiversity hotspots
    Renaud Lahaye
    Department of Botany and Plant Biotechnology, APK Campus, University of Johannesburg, P O Box 524, Auckland Park 2006, Johannesburg, South Africa
    Proc Natl Acad Sci U S A 105:2923-8. 2008
    ..Here, we undertook intensive field collections in two biodiversity hotspots (Mesoamerica and southern Africa). Using >1,600 samples, we compared eight potential barcodes...
  47. doi Navigating the multiple meanings of β diversity: a roadmap for the practicing ecologist
    Marti J Anderson
    Institute of Information and Mathematical Sciences, Massey University, Albany Campus, Auckland, New Zealand
    Ecol Lett 14:19-28. 2011
    ..We advocate careful consideration of relevant questions, matched by appropriate analyses. The rigorous application of null models will also help to reveal potential processes driving observed patterns in β diversity...
  48. doi Rebuilding global fisheries
    Boris Worm
    Biology Department, Dalhousie University, Halifax, NS B3H 4J1, Canada
    Science 325:578-85. 2009
    ..Impacts of international fleets and the lack of alternatives to fishing complicate prospects for rebuilding fisheries in many poorer regions, highlighting the need for a global perspective on rebuilding marine resources...
  49. doi Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes
    Thomas M Gihring
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 6038, USA
    Environ Microbiol 14:285-90. 2012
    ..The need to equalize the number of reads being compared across libraries is reiterated, and investigators are directed towards available tools for making unbiased diversity comparisons...
  50. doi A renaissance for the pioneering 16S rRNA gene
    Susannah G Tringe
    DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
    Curr Opin Microbiol 11:442-6. 2008
    ..The standard conclusion that microbial ecosystems are remarkably complex and diverse is now being replaced by detailed insights into microbial ecology and evolution based only on this one historically important marker gene...
  51. ncbi Marine microbial diversity: can it be determined?
    Carlos Pedrós-Alió
    Institut de Ciencies del Mar, CMIMA CSIC, P Marítim de la Barceloneta 37 42, 08003 Barcelona, Spain
    Trends Microbiol 14:257-63. 2006
    ..Despite global dispersal of microorganisms, this number is probably rather large. The total biodiversity of an ecosystem is composed of two elements: first, a set of abundant taxa that carry out most ecosystem ..
  52. doi The impact of conservation on the status of the world's vertebrates
    Michael Hoffmann
    IUCN SSC Species Survival Commission, c o United Nations Environment Programme World Conservation Monitoring Centre, 219 Huntingdon Road, Cambridge CB3 0DL, UK
    Science 330:1503-9. 2010
    ..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.
  53. doi The bacterial species challenge: making sense of genetic and ecological diversity
    Christophe Fraser
    Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
    Science 323:741-6. 2009
    ..The resulting data may help to discriminate among the many theories of prokaryotic species that have been produced to date...
  54. ncbi Depletion, degradation, and recovery potential of estuaries and coastal seas
    Heike K Lotze
    Biology Department, Dalhousie University, 1355 Oxford Street, Halifax, NS, Canada B3H 4J1
    Science 312:1806-9. 2006
    ..Our results provide detailed historical baselines and quantitative targets for ecosystem-based management and marine conservation...
  55. pmc ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences
    Yijun Sun
    Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610 3622, USA
    Nucleic Acids Res 37:e76. 2009
    ..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...
  56. doi Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis
    Anne Salonen
    Department of Basic Veterinary Sciences, Division of Microbiology and Epidemiology, University of Helsinki, P O Box 66, FI 00014, Helsinki, Finland
    J Microbiol Methods 81:127-34. 2010
    ..The assessment of performance differences between different methodologies serves as a concrete step towards the comparison and reliable meta-analysis of the results obtained in different laboratories...
  57. doi Genomic and functional adaptation in surface ocean planktonic prokaryotes
    Shibu Yooseph
    J Craig Venter Institute, Rockville, Maryland 20850, USA
    Nature 468:60-6. 2010
    ..Their genomic features also lead us to propose that one method used to avoid predation by viruses and/or bacterivores is by means of slow growth and the maintenance of low biomass...
  58. doi The rational exploration of microbial diversity
    Christopher Quince
    Department of Civil Engineering, University of Glasgow, Glasgow, UK
    ISME J 2:997-1006. 2008
    ..This would initiate a new phase in the exploration of the microbial world...
  59. pmc Microbial ecology of the dark ocean above, at, and below the seafloor
    Beth N Orcutt
    Department of Biological Sciences, University of Southern California, 3616 Trousdale Blvd, Los Angeles, CA 90089, USA
    Microbiol Mol Biol Rev 75:361-422. 2011
    ..We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats...
  60. doi GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity
    Zhili He
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, 101 David L Boren Boulevard, Norman, OK 73019, USA
    ISME J 4:1167-79. 2010
    ..As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning...
  61. doi DNA barcoding for ecologists
    Alice Valentini
    Laboratoire d Ecologie Alpine, Universite Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
    Trends Ecol Evol 24:110-7. 2009
    ..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...
  62. ncbi Ecological linkages between aboveground and belowground biota
    David A Wardle
    Landcare Research, Post Office Box 69, Lincoln, New Zealand
    Science 304:1629-33. 2004
    ..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.
  63. ncbi From plant traits to plant communities: a statistical mechanistic approach to biodiversity
    Bill Shipley
    Departement de Biologie, Universite de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
    Science 314:812-4. 2006
    We developed a quantitative method, analogous to those used in statistical mechanics, to predict how biodiversity will vary across environments, which plant species from a species pool will be found in which relative abundances in a given ..
  64. doi Genetic diversity and connectivity of deep-sea hydrothermal vent metapopulations
    Robert C Vrijenhoek
    Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
    Mol Ecol 19:4391-411. 2010
    ..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...
  65. ncbi Computational improvements reveal great bacterial diversity and high metal toxicity in soil
    Jason Gans
    Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87501, USA
    Science 309:1387-90. 2005
    ..Metal pollution reduced diversity more than 99.9%, revealing the highly toxic effect of metal contamination, especially for rare taxa...
  66. pmc The role of DNA barcodes in understanding and conservation of mammal diversity in southeast Asia
    Charles M Francis
    Canadian Wildlife Service, Environment Canada, Ottawa, Ontario, Canada
    PLoS ONE 5:e12575. 2010
    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...
  67. ncbi Parallel declines in pollinators and insect-pollinated plants in Britain and the Netherlands
    J C Biesmeijer
    Institute of Integrative and Comparative Biology and Earth and Biosphere Institute, University of Leeds, Leeds, LS2 9JT, UK
    Science 313:351-4. 2006
    ..Taken together, these findings strongly suggest a causal connection between local extinctions of functionally linked plant and pollinator species...
  68. doi The status of the world's land and marine mammals: diversity, threat, and knowledge
    Jan Schipper
    International Union for Conservation of Nature IUCN Species Programme, IUCN, 28 Rue Mauverney, 1196 Gland, Switzerland
    Science 322:225-30. 2008
    ..Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action...
  69. doi Biodiversity in a complex world: consolidation and progress in functional biodiversity research
    Helmut Hillebrand
    Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg, Schleusenstrasse 1, 26382 Wilhelmshaven, Germany
    Ecol Lett 12:1405-19. 2009
    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...
  70. ncbi The contribution of species richness and composition to bacterial services
    Thomas Bell
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
    Nature 436:1157-60. 2005
    ..b>Biodiversity influences the way in which ecosystems function, but the form of the relationship between bacterial ..
  71. ncbi Environmental genome shotgun sequencing of the Sargasso Sea
    J Craig Venter
    Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA
    Science 304:66-74. 2004
    ..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...
  72. pmc Emerging infectious disease and the loss of biodiversity in a Neotropical amphibian community
    Karen R Lips
    Department of Zoology, Southern Illinois University, Carbondale, 62901 6501, USA
    Proc Natl Acad Sci U S A 103:3165-70. 2006
    ..in an amphibian community at El Copé, Panama, and subsequent mass mortality and loss of amphibian biodiversity across eight families of frogs and salamanders...
  73. pmc Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara
    Achim Quaiser
    Unité d Ecologie, Systematique et Evolution, CNRS UMR8079, Universite Paris Sud 11, Orsay, France
    ISME J 5:285-304. 2011
    ..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...
  74. pmc Global patterns and predictions of seafloor biomass using random forests
    Chih Lin Wei
    Department of Oceanography, Texas A and M University, College Station, Texas, United States of America
    PLoS ONE 5:e15323. 2010
    ..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...
  75. ncbi A serpentinite-hosted ecosystem: the Lost City hydrothermal field
    Deborah S Kelley
    School of Oceanography, University of Washington, Seattle, WA 98195, USA
    Science 307:1428-34. 2005
    ....
  76. doi Projecting coral reef futures under global warming and ocean acidification
    John M Pandolfi
    Australian Research Council ARC Centre of Excellence for Coral Reef Studies, St Lucia, Queensland 4072, Australia
    Science 333:418-22. 2011
    ....
  77. doi Microbial seed banks: the ecological and evolutionary implications of dormancy
    Jay T Lennon
    W K Kellogg Biological Station, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, Michigan 49060, USA
    Nat Rev Microbiol 9:119-30. 2011
    ..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.
  78. doi Global threats to human water security and river biodiversity
    C J Vörösmarty
    The Environmental CrossRoads Initiative, City University of New York, The City College of New York, New York, New York 10035, USA
    Nature 467:555-61. 2010
    ..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 ..
  79. pmc Inferring the dynamics of diversification: a coalescent approach
    Helene Morlon
    Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
    PLoS Biol 8:. 2010
    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...
  80. doi Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity
    C Hoorn
    Paleoecology and Landscape Ecology, Institute for Biodiversity and Ecosystem Dynamics IBED, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
    Science 330:927-31. 2010
    ..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.
  81. pmc Spatial distribution and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in mangrove sediments
    Meng Li
    School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People s Republic of China
    Appl Microbiol Biotechnol 89:1243-54. 2011
    ..The results provide a better understanding on using mangrove wetlands as biological treatment systems for removal of nutrients...
  82. ncbi The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems
    Marcel G A van der Heijden
    Department of Animal Ecology, Faculty of Earth and Life Sciences, Institute of Ecological Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
    Ecol Lett 11:296-310. 2008
    ..Overall, this review shows that soil microbes must be considered as important drivers of plant diversity and productivity in terrestrial ecosystems...
  83. pmc Quantifying the biodiversity value of tropical primary, secondary, and plantation forests
    J Barlow
    Centre for Ecology, Evolution and Conservation, School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
    Proc Natl Acad Sci U S A 104:18555-60. 2007
    b>Biodiversity loss from deforestation may be partly offset by the expansion of secondary forests and plantation forestry in the tropics...
  84. ncbi Multiple functions increase the importance of biodiversity for overall ecosystem functioning
    Lars Gamfeldt
    Department of Marine Ecology, Goteborg University, Tjärnö Marine Biological Laboratory, SE 452 96 Strömstad, Sweden
    Ecology 89:1223-31. 2008
    b>Biodiversity is proposed to be important for the rate of ecosystem functions...
  85. doi Diversity dynamics: molecular phylogenies need the fossil record
    Tiago B Quental
    Museum of Paleontology and Department of Integrative Biology, University of California at Berkeley, Berkeley, CA 94720, USA
    Trends Ecol Evol 25:434-41. 2010
    ..We need to embrace the fossil record if we want to fully understand the diversity dynamics of the living biota...
  86. doi Niche conservatism as an emerging principle in ecology and conservation biology
    John J Wiens
    Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
    Ecol Lett 13:1310-24. 2010
    ..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?)...
  87. doi Protracted speciation revitalizes the neutral theory of biodiversity
    James Rosindell
    Institute of Integrative and Comparative Biology, University of Leeds, UK
    Ecol Lett 13:716-27. 2010
    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 ..
  88. ncbi Influence of phylogeny on fungal community assembly and ecosystem functioning
    Hafiz Maherali
    Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
    Science 316:1746-8. 2007
    ....
  89. doi Current state and perspectives of fungal DNA barcoding and rapid identification procedures
    Dominik Begerow
    Ruhr Universitat Bochum, Geobotanik ND03 174, Universitatsstr 150, 44801 Bochum, Germany
    Appl Microbiol Biotechnol 87:99-108. 2010
    ..Especially the next generation sequencing technologies can be expected to have a tremendous effect on fungal biodiversity and ecology research...
  90. doi Generalized models reveal stabilizing factors in food webs
    Thilo Gross
    Max Planck Institute for Physics of Complex Systems, Nothnitzer Strasse 38, 01187 Dresden, Germany
    Science 325:747-50. 2009
    ..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...
  91. doi The merging of community ecology and phylogenetic biology
    Jeannine Cavender-Bares
    Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN 55108, USA
    Ecol Lett 12:693-715. 2009
    ..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...
  92. pmc Global diversity in the human salivary microbiome
    Ivan Nasidze
    Max Planck Institute for Evolutionary Anthropology, D 04103 Leipzig, Germany
    Genome Res 19:636-43. 2009
    ....
  93. ncbi Immigration history controls diversification in experimental adaptive radiation
    Tadashi Fukami
    Department of Zoology, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
    Nature 446:436-9. 2007
    ..These results demonstrate that immigration and diversification are tightly linked processes, with small differences in immigration history greatly affecting the evolutionary emergence of diversity...
  94. doi Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises
    S Creer
    Environment Centre Wales, Bangor University, Gwynedd, UK
    Mol Ecol 19:4-20. 2010
    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...
  95. doi Emerging horizons in biodiversity and ecosystem functioning research
    Julia Reiss
    School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
    Trends Ecol Evol 24:505-14. 2009
    Two decades of intensive research have provided compelling evidence for a link between biodiversity and ecosystem functioning (B-EF)...
  96. ncbi Estimating diversification rates from phylogenetic information
    Robert E Ricklefs
    Department of Biology, University of Missouri St Louis, MO 63121 4499, USA
    Trends Ecol Evol 22:601-10. 2007
    ..Recognizing these biases will encourage the development of more realistic models of diversification and the regulation of species richness...
  97. doi Stochastic community assembly causes higher biodiversity in more productive environments
    Jonathan M Chase
    Department of Biology and Tyson Research Center, Washington University, St Louis, MO 63130, USA
    Science 328:1388-91. 2010
    Net primary productivity is a principal driver of biodiversity; large-scale regions with higher productivity generally have more species...
  98. pmc The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves
    Amanda J Redford
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
    Environ Microbiol 12:2885-93. 2010
    ..ponderosa needles...
  99. doi Global patterns and predictors of marine biodiversity across taxa
    Derek P Tittensor
    Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax B3H 4J1, Canada
    Nature 466:1098-101. 2010
    ..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 ..
  100. doi Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica
    Lia C R S Teixeira
    Laboratório de Ecologia Microbiana Molecular, Departamento de Microbiologia Geral, Instituto de Microbiologia Professor Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
    ISME J 4:989-1001. 2010
    ....
  101. pmc Prokaryotic genomes and diversity in surface ocean waters: interrogating the global ocean sampling metagenome
    Erin J Biers
    Department of Marine Sciences, University of Georgia, Athens, Georgia 30602, USA
    Appl Environ Microbiol 75:2221-9. 2009
    ..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)...

Research Grants74

  1. EID - Effects of avian migration & anthropogenic change on the distribution & tra
    Thomas Smith; Fiscal Year: 2007
    ..young scientists with the cross-disciplinary, integrative training necessary to address complex issues in biodiversity analysis and conservation...
  2. EID - Effects of avian migration & anthropogenic change on the distribution & tra
    Thomas Smith; Fiscal Year: 2009
    ..young scientists with the cross-disciplinary, integrative training necessary to address complex issues in biodiversity analysis and conservation...
  3. Biodiversity, Habitat Fragmentation, & Lyme Disease Risk
    RICHARD OSTFELD; Fiscal Year: 2003
    ..Our research comprises a rigorous, multidisciplinary approach to understanding the linkages between ecology and risk of infectious disease. ..
  4. Biodiversity, Habitat Fragmentation, & Lyme Disease Risk
    RICHARD OSTFELD; Fiscal Year: 2006
    ..Our research comprises a rigorous, multidisciplinary approach to understanding the linkages between ecology and risk of infectious disease. ..
  5. Riparian nutrients and food webs on a regulated river
    TERESA TIBBETS; Fiscal Year: 2005
    ..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 ..
  6. CHRONOBIOLOGIC MARKERS FOR LAB MEDICINE AND THERAPY
    Franz Halberg; Fiscal Year: 2007
    ..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. ..