Genomes and Genes
Summary: The variety of all native living organisms and their various forms and interrelationships.
Publications310 found, 100 shown here
- Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communitiesPatrick 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...
- MEGAN analysis of metagenomic dataDaniel 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...
- 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...
- The human microbiome projectPeter 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...
- Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimatesVictor 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...
- Ironing out the wrinkles in the rare biosphere through improved OTU clusteringSusan 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...
- Diversity of the human intestinal microbial floraPaul 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...
- Impacts of biodiversity on the emergence and transmission of infectious diseasesFelicia Keesing
Department of Biology, Bard College, Annandale, New York 12504, USA
Nature 468:647-52. 2010Current unprecedented declines in biodiversity reduce the ability of ecological communities to provide many fundamental ecosystem services...
- A core gut microbiome in obese and lean twinsPeter J Turnbaugh
Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
Nature 457:480-4. 2009....
- Ecological and evolutionary forces shaping microbial diversity in the human intestineRuth 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...
- Extinction risk from climate changeChris 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...
- The biodiversity of the Mediterranean Sea: estimates, patterns, and threatsMarta Coll
Institut de Ciencies del Mar, Scientific Spanish Council ICM CSIC, Barcelona, Spain
PLoS ONE 5:e11842. 2010The Mediterranean Sea is a marine biodiversity hot spot...
- Topographical and temporal diversity of the human skin microbiomeElizabeth 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...
- Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencingSusan 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...
- Global biodiversity: indicators of recent declinesStuart 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...
- Accelerated species inventory on Madagascar using coalescent-based models of species delineationMichael 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 ..
- Pyrosequencing enumerates and contrasts soil microbial diversityLuiz 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...
- Quantifying the evidence for biodiversity effects on ecosystem functioning and servicesPatricia Balvanera
Centro de Investigaciones en Ecosistemas, UNAM, Morelia, Mexico
Ecol Lett 9:1146-56. 2006Concern is growing about the consequences of biodiversity loss for ecosystem functioning, for the provision of ecosystem services, and for human well being...
- The diversity and biogeography of soil bacterial communitiesNoah 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 ..
- Picante: R tools for integrating phylogenies and ecologySteven W Kembel
Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR, USA
Bioinformatics 26:1463-4. 2010....
- Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scaleChristian L Lauber
Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, 80309, USA
Appl Environ Microbiol 75:5111-20. 2009....
- Cryptic species as a window on diversity and conservationDavid 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...
- DNA barcoding for ecologistsAlice 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...
- Computational improvements reveal great bacterial diversity and high metal toxicity in soilJason 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...
- DNA barcoding Australia's fish speciesRobert 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...
- Microbial biogeography: putting microorganisms on the mapJennifer 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...
- ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequencesYijun 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...
- Genetic diversity and connectivity of deep-sea hydrothermal vent metapopulationsRobert 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...
- The role of DNA barcodes in understanding and conservation of mammal diversity in southeast AsiaCharles M Francis
Canadian Wildlife Service, Environment Canada, Ottawa, Ontario, Canada
PLoS ONE 5:e12575. 2010Southeast Asia is recognized as a region of very high biodiversity, much of which is currently at risk due to habitat loss and other threats...
- Parallel declines in pollinators and insect-pollinated plants in Britain and the NetherlandsJ 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...
- The status of the world's land and marine mammals: diversity, threat, and knowledgeJan 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...
- Biodiversity in a complex world: consolidation and progress in functional biodiversity researchHelmut 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. 2009The global decline of biodiversity caused by human domination of ecosystems worldwide is supposed to alter important process rates and state variables in these ecosystems...
- Global patterns in bacterial diversityCatherine 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...
- Ecological linkages between aboveground and belowground biotaDavid 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.
- Effects of biodiversity on the functioning of trophic groups and ecosystemsBradley 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....
- The contribution of species richness and composition to bacterial servicesThomas 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 ..
- Emerging infectious disease and the loss of biodiversity in a Neotropical amphibian communityKaren 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...
- Environmental genome shotgun sequencing of the Sargasso SeaJ 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...
- DNA barcoding the floras of biodiversity hotspotsRenaud 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...
- Scenarios for global biodiversity in the 21st centuryHenrique 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...
- Microbial seed banks: the ecological and evolutionary implications of dormancyJay 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.
- Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversityC 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.
- Global patterns and predictions of seafloor biomass using random forestsChih 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...
- Beyond predictions: biodiversity conservation in a changing climateTerence P Dawson
School of the Environment, University of Dundee, Dundee DD1 4HN, Scotland, UK
Science 332:53-8. 2011Climate 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...
- Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of MarmaraAchim 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...
- Projecting coral reef futures under global warming and ocean acidificationJohn M Pandolfi
Australian Research Council ARC Centre of Excellence for Coral Reef Studies, St Lucia, Queensland 4072, Australia
Science 333:418-22. 2011....
- The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystemsMarcel 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...
- Global threats to human water security and river biodiversityC 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 ..
- Spatial distribution and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in mangrove sedimentsMeng 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...
- Inferring the dynamics of diversification: a coalescent approachHelene Morlon
Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
PLoS Biol 8:. 2010Recent 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...
- Quantifying the biodiversity value of tropical primary, secondary, and plantation forestsJ 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. 2007b>Biodiversity loss from deforestation may be partly offset by the expansion of secondary forests and plantation forestry in the tropics...
- A serpentinite-hosted ecosystem: the Lost City hydrothermal fieldDeborah S Kelley
School of Oceanography, University of Washington, Seattle, WA 98195, USA
Science 307:1428-34. 2005....
- Multiple functions increase the importance of biodiversity for overall ecosystem functioningLars Gamfeldt
Department of Marine Ecology, Goteborg University, Tjärnö Marine Biological Laboratory, SE 452 96 Strömstad, Sweden
Ecology 89:1223-31. 2008b>Biodiversity is proposed to be important for the rate of ecosystem functions...
- Protracted speciation revitalizes the neutral theory of biodiversityJames Rosindell
Institute of Integrative and Comparative Biology, University of Leeds, UK
Ecol Lett 13:716-27. 2010Understanding 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 ..
- Diversity dynamics: molecular phylogenies need the fossil recordTiago 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...
- Niche conservatism as an emerging principle in ecology and conservation biologyJohn 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?)...
- The merging of community ecology and phylogenetic biologyJeannine 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...
- Global diversity in the human salivary microbiomeIvan Nasidze
Max Planck Institute for Evolutionary Anthropology, D 04103 Leipzig, Germany
Genome Res 19:636-43. 2009....
- Generalized models reveal stabilizing factors in food websThilo 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...
- Influence of phylogeny on fungal community assembly and ecosystem functioningHafiz Maherali
Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
Science 316:1746-8. 2007....
- Current state and perspectives of fungal DNA barcoding and rapid identification proceduresDominik 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...
- Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promisesS Creer
Environment Centre Wales, Bangor University, Gwynedd, UK
Mol Ecol 19:4-20. 2010b>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...
- Immigration history controls diversification in experimental adaptive radiationTadashi 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...
- Emerging horizons in biodiversity and ecosystem functioning researchJulia Reiss
School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
Trends Ecol Evol 24:505-14. 2009Two decades of intensive research have provided compelling evidence for a link between biodiversity and ecosystem functioning (B-EF)...
- Host-bacterial mutualism in the human intestineFredrik 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...
- Estimating diversification rates from phylogenetic informationRobert 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...
- The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leavesAmanda J Redford
Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
Environ Microbiol 12:2885-93. 2010..ponderosa needles...
- Stochastic community assembly causes higher biodiversity in more productive environmentsJonathan M Chase
Department of Biology and Tyson Research Center, Washington University, St Louis, MO 63130, USA
Science 328:1388-91. 2010Net primary productivity is a principal driver of biodiversity; large-scale regions with higher productivity generally have more species...
- Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime AntarcticaLia 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....
- Global patterns and predictors of marine biodiversity across taxaDerek 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 ..
- Factors controlling community structure in heterogeneous metacommunitiesKendi F Davies
Department of Environmental Science and Policy, University of California, Davis, CA 95616, USA
J Anim Ecol 78:937-44. 2009..4. Our study illustrates that heterogeneity is not always the strongest driver of diversity, while experimentally demonstrating mechanisms by which heterogeneity alters community structure...
- Prokaryotic genomes and diversity in surface ocean waters: interrogating the global ocean sampling metagenomeErin 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)...
- Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)Scot E Dowd
USDA ARS Livestock Issues Research Unit, Lubbock, TX 79403, USA
BMC Microbiol 8:125. 2008..We have evaluated the microbiome from the feces of 20 commercial, lactating dairy cows...
- Loss of plant species after chronic low-level nitrogen deposition to prairie grasslandsChristopher M Clark
Department of Ecology, Evolution and Behavior, 100 Ecology, 1987 Upper Buford Circle, University of Minnesota, St Paul, Minnesota 55108, USA
Nature 451:712-5. 2008..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...
- The velocity of climate changeScott R Loarie
Carnegie Institution for Science, Department of Global Ecology, Stanford, California 94305, USA
Nature 462:1052-5. 2009..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: importance, threats, status and conservation challengesDavid Dudgeon
Department of Ecology and Biodiversity, The University of Hong Kong, Hong Kong SAR, China
Biol Rev Camb Philos Soc 81:163-82. 2006Freshwater 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...
- Climate change threats to plant diversity in EuropeWilfried Thuiller
Centre d Ecologie Fonctionnelle et Evolutive, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5175, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
Proc Natl Acad Sci U S A 102:8245-50. 2005..We found that risks of extinction for European plants may be large, even in moderate scenarios of climate change and despite inter-model variability...
- 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversityM Buee
INRA, UMR 1136 INRA Nancy Université Interactions Arbres Microorganismes, INRA Nancy, 54280 Champenoux, France
New Phytol 184:449-56. 2009..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...
- Biofilms in chronic infections - a matter of opportunity - monospecies biofilms in multispecies infectionsMette Burmølle
Department of Biology, University of Copenhagen, Denmark
FEMS Immunol Med Microbiol 59:324-36. 2010..We discuss these differences from both the diagnostic and the scientific point of view...
- The impact of conservation on the status of the world's vertebratesMichael 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.
- Seabird bycatch in pelagic longline fisheries is grossly underestimated when using only haul dataNigel Brothers
Marine Ecology and Technology Consultant, Wonga Beach, Queensland, Australia
PLoS ONE 5:e12491. 2010..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...
- A constant flux of diverse thermophilic bacteria into the cold Arctic seabedCasey Hubert
Biogeochemistry Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359 Bremen, Germany
Science 325:1541-4. 2009..These transport pathways may broadly influence microbial community composition in the marine environment...
- Phylogenetic structure in tropical hummingbird communitiesCatherine H Graham
Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY 11784 5245, USA
Proc Natl Acad Sci U S A 106:19673-8. 2009....
- Soil bacterial and fungal communities across a pH gradient in an arable soilJohannes Rousk
Department of Microbial Ecology, Lund University, Ecology Building, Lund, Sweden
ISME J 4:1340-51. 2010..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...
- Seed arrival, ecological filters, and plant species richness: a meta-analysisJonathan A Myers
Department of Biological Sciences, Division of Systematics, Louisiana State University, Baton Rouge, LA 70803, USA
Ecol Lett 12:1250-60. 2009Theoretical 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...
- Water quality as a regional driver of coral biodiversity and macroalgae on the Great Barrier ReefGlenn De'ath
Australian Institute of Marine Science, PMB 3, Townsville, Queensland 4810, Australia
Ecol Appl 20:840-50. 2010..were consistent with the trophic requirements of the biota, suggesting that both macroalgal cover and coral biodiversity are partially controlled by energy supply limitation...
- Longitudinal investigation of the faecal microbiota of healthy full-term infants using fluorescence in situ hybridization and denaturing gradient gel electrophoresisLaure C Roger
Microbial Ecology and Health Group, Food Microbial Sciences Unit, Department of Food and Nutritional Sciences, University of Reading, Whiteknights Campus, PO Box 226, Reading RG6 6AP, UK
Microbiology 156:3317-28. 2010..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...
- Effectiveness of the global protected area network in representing species diversityAna S L Rodrigues
Center for Applied Biodiversity Science, Conservation International, Washington, DC 20036, USA
Nature 428:640-3. 2004..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 ..
- Biodiversity and evolution of primary carbon metabolism in Aspergillus nidulans and other Aspergillus sppMichel Flipphi
Instituto de Agroquímica y Technologia de Alimentos, Consejo Superior de Investigaciones Cientificas, Apartado de Correos 73, Burjassot, 46100 Valencia, Spain
Fungal Genet Biol 46:S19-S44. 2009....
- Survey of Pseudomonas aeruginosa and its phages: de novo peptide sequencing as a novel tool to assess the diversity of worldwide collected virusesPieter Jan Ceyssens
Division of Gene Technology, Katholieke Universiteit Leuven, Leuven, Belgium
Environ Microbiol 11:1303-13. 2009..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...
- Community niche predicts the functioning of denitrifying bacterial assemblagesJoana F Salles
Universite de Lyon, INRA, CNRS, Universite Lyon 1, Ecologie Microbienne UMR 5557, USC 1193, bat G Mendel, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France
Ecology 90:3324-32. 2009Predicting biodiversity effects on ecosystem functioning requires adequate evaluation of the mechanisms explaining why more diverse systems could perform better than less diverse ones...
- Confounding factors in the detection of species responses to habitat fragmentationRobert M Ewers
School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
Biol Rev Camb Philos Soc 81:117-42. 2006Habitat 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...
- Microbiology: metagenomicsPhilip Hugenholtz
Nature 455:481-3. 2008
- Contaminants reduce the richness and evenness of marine communities: a review and meta-analysisEmma L Johnston
Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
Environ Pollut 157:1745-52. 2009b>Biodiversity of marine ecosystems is integral to their stability and function and is threatened by anthropogenic processes...
- Marine biodiversity in the Australian regionAlan J Butler
CSIRO Wealth from Oceans National Research Flagship, Hobart, Tasmania, Australia
PLoS ONE 5:e11831. 2010..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.
- Effect of lake trophic status and rooted macrophytes on community composition and abundance of ammonia-oxidizing prokaryotes in freshwater sedimentsMartina Herrmann
Department of Biological Sciences, Microbiology, Aarhus University, Ny Munkegade, Building 1540, DK 8000 Aarhus C, Denmark
Appl Environ Microbiol 75:3127-36. 2009..uniflora and J. bulbosus, increase AOA abundance; and (iii) AOA community composition is generally determined by lake trophy, not by plant species-specific interactions...
- Undersampling bias: the null hypothesis for singleton species in tropical arthropod surveysJonathan A Coddington
Department of Entomology, National Museum of Natural History, NHB 105, Smithsonian Institution, PO Box 37012, Washington, DC 20013 7012, USA
J Anim Ecol 78:573-84. 2009..7. The lognormal distribution deserves greater consideration as a richness estimator when undersampling bias is severe...
- Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuaryAnnika C Mosier
Department of Environmental Earth System Science, Stanford University, Stanford, CA 94305, USA
Environ Microbiol 10:3002-16. 2008..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...
- Likelihood methods for detecting temporal shifts in diversification ratesDaniel L Rabosky
Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853 2701, USA
Evolution 60:1152-64. 2006..I illustrate use of the method by analyzing a published phylogeny for Australian agamid lizards...
- Habitat utilization by coral reef fish: implications for specialists vs. generalists in a changing environmentShaun K Wilson
School of Marine Science and Technology, University of Newcastle, Newcastle upon Tyne, NE1 7RU, UK
J Anim Ecol 77:220-8. 2008....
- Assessing the risk of invasive spread in fragmented landscapesKimberly A With
Division of Biology, Kansas State University, Manhattan, KS 66506, USA
Risk Anal 24:803-15. 2004..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 ..
- EID - Effects of avian migration & anthropogenic change on the distribution & traThomas Smith; Fiscal Year: 2007..young scientists with the cross-disciplinary, integrative training necessary to address complex issues in biodiversity analysis and conservation...
- EID - Effects of avian migration & anthropogenic change on the distribution & traThomas Smith; Fiscal Year: 2009..young scientists with the cross-disciplinary, integrative training necessary to address complex issues in biodiversity analysis and conservation...
- Biodiversity, Habitat Fragmentation, & Lyme Disease RiskRICHARD OSTFELD; Fiscal Year: 2003..Our research comprises a rigorous, multidisciplinary approach to understanding the linkages between ecology and risk of infectious disease. ..
- Biodiversity, Habitat Fragmentation, & Lyme Disease RiskRICHARD OSTFELD; Fiscal Year: 2006..Our research comprises a rigorous, multidisciplinary approach to understanding the linkages between ecology and risk of infectious disease. ..
- Riparian nutrients and food webs on a regulated riverTERESA 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 ..
- CHRONOBIOLOGIC MARKERS FOR LAB MEDICINE AND THERAPYFranz 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. ..