Marine microbial community dynamics and their ecological interpretation
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[1] E. Mauceli,et al. Viral Glycosphingolipids Induce Lytic Infection and Cell Death in Marine Phytoplankton , 2009 .
[2] Dennis Swanger,et al. Advances in microbial ecology , 1979, Economic Botany.
[3] Stephanie Dutkiewicz,et al. Modeling diverse communities of marine microbes. , 2011, Annual review of marine science.
[4] Michael W Lomas,et al. Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea , 2011, The ISME Journal.
[5] D. Karl,et al. Microbial oceanography and the Hawaii Ocean Time-series programme , 2014, Nature Reviews Microbiology.
[6] P. Falkowski,et al. Climatically driven macroevolutionary patterns in the size of marine diatoms over the Cenozoic. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[7] J. Raes,et al. Microbial interactions: from networks to models , 2012, Nature Reviews Microbiology.
[8] Susan M. Huse,et al. Microbial diversity in the deep sea and the underexplored “rare biosphere” , 2006, Proceedings of the National Academy of Sciences.
[9] A. Wichels,et al. Bacterial community dynamics during the winter-spring transition in the North Sea. , 2007, FEMS microbiology ecology.
[10] Rotem Sorek,et al. Genomic island variability facilitates Prochlorococcus–virus coexistence , 2011, Nature.
[11] D. Ediger,et al. Short-term variability in primary productivity during a wind driven diatom bloom in the Gulf of Eilat (Aqaba). , 2009 .
[12] E. Casamayor,et al. Inter‐annual recurrence of archaeal assemblages in the coastal NW Mediterranean Sea (Blanes Bay Microbial Observatory) , 2010 .
[13] D. Caron,et al. Marine bacterial, archaeal and protistan association networks reveal ecological linkages , 2011, The ISME Journal.
[14] B. Hickey. Circulation over the Santa Monica-San Pedro Basin and Shelf , 1992 .
[15] Dongmei Ai,et al. Efficient statistical significance approximation for local similarity analysis of high-throughput time series data , 2013, Bioinform..
[16] H. Teeling,et al. Diversity and activity of marine bacterioplankton during a diatom bloom in the North Sea assessed by total RNA and pyrotag sequencing. , 2014, Marine genomics.
[17] C. Weihe,et al. Diversity and temporal dynamics of Southern California coastal marine cyanophage isolates , 2013 .
[18] Sarah L. Westcott,et al. Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform , 2013, Applied and Environmental Microbiology.
[19] C. Carlson,et al. Basin-scale patterns in the abundance of SAR11 subclades, marine Actinobacteria (OM1), members of the Roseobacter clade and OCS116 in the South Atlantic. , 2012, Environmental microbiology.
[20] C. Pedrós-Alió,et al. Seasonality in bacterial diversity in north-west Mediterranean coastal waters: assessment through clone libraries, fingerprinting and FISH. , 2007, FEMS microbiology ecology.
[21] D. Vaulot,et al. DIEL PATTERNS OF GROWTH AND DIVISION IN MARINE PICOPLANKTON IN CULTURE , 2001 .
[22] J. J. Morris,et al. COEXISTENCE OF EVOLVING BACTERIA STABILIZED BY A SHARED BLACK QUEEN FUNCTION , 2014, Evolution; international journal of organic evolution.
[23] Annika C. Mosier,et al. Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation , 2011, The ISME Journal.
[24] Nicholas R. Bates,et al. Overview of the US JGOFS Bermuda Atlantic Time-series Study (BATS): a decade-scale look at ocean biology and biogeochemistry , 2001 .
[25] I. Salter,et al. Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters , 2013, Proceedings of the National Academy of Sciences.
[26] R. Kudela,et al. Nitrogen cycle of the open ocean: from genes to ecosystems. , 2011, Annual review of marine science.
[27] J. Fuhrman,et al. Community structure of marine bacterioplankton: patterns, networks, and relationships to function , 2008 .
[28] J. Fuhrman,et al. Short-term observations of marine bacterial and viral communities: patterns, connections and resilience , 2013, The ISME Journal.
[29] Michael W. Lomas,et al. Sea Change: Charting the Course for Biogeochemical Ocean Time-Series Research in a New Millennium , 2013 .
[30] Debojyoti Dutta,et al. Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors , 2006, Bioinform..
[31] Scott A Givan,et al. Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data , 2007, Biology Direct.
[32] Jang-Cheon Cho,et al. Temporal and spatial response of bacterioplankton lineages to annual convective overturn at the Bermuda Atlantic Time‐series Study site , 2005 .
[33] Susan M. Huse,et al. Long Term Seasonal Dynamics of Synechococcus Population Structure in the Gulf of Aqaba, Northern Red Sea , 2011, Front. Microbio..
[34] Feng Chen,et al. Abundance and Distribution of Synechococcus spp. and Cyanophages in the Chesapeake Bay , 2011, Applied and Environmental Microbiology.
[35] R. Beinart,et al. Seasonal change in the abundance of Synechococcus and multiple distinct phylotypes in Monterey Bay determined by rbcL and narB quantitative PCR. , 2012, Environmental microbiology.
[36] D. Sims,et al. Long-term oceanographic and ecological research in the Western English Channel. , 2005, Advances in marine biology.
[37] Noah Fierer,et al. Using network analysis to explore co-occurrence patterns in soil microbial communities , 2011, The ISME Journal.
[38] Sallie W. Chisholm,et al. Marine phytoplankton distributions measured using shipboard flow cytometry , 1985 .
[39] J. Fuhrman,et al. Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight , 2013, The ISME Journal.
[40] W. Doolittle,et al. Population Genomics: How Bacterial Species Form and Why They Don't Exist , 2012, Current Biology.
[41] B. Palenik,et al. Temporal variation of Synechococcus clades at a coastal Pacific Ocean monitoring site , 2009, The ISME Journal.
[42] E. Delong,et al. The Microbial Engines That Drive Earth's Biogeochemical Cycles , 2008, Science.
[43] J. Waterbury,et al. Iron Stress in Open-Ocean Cyanobacteria (Synechococcus, Trichodesmium, andCrocosphaera spp.): Identification of the IdiA Protein , 2001, Applied and Environmental Microbiology.
[44] Sharon L. Grim,et al. Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data , 2013, Methods in ecology and evolution.
[45] J. Fuhrman,et al. Diel variations in bacterioplankton, phytoplankton, and related parameters in the Southern California Bight. , 1985 .
[46] N. Pace,et al. The Analysis of Natural Microbial Populations by Ribosomal RNA Sequences , 1986 .
[47] M. Marston,et al. Genetic Diversity and Temporal Variation in the Cyanophage Community Infecting Marine Synechococcus Species in Rhode Island's Coastal Waters , 2003, Applied and Environmental Microbiology.
[48] C. A. Scholin,et al. What are "ecogenomic sensors?" A review and thoughts for the future , 2009 .
[49] Philip Hugenholtz,et al. Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging , 2012, mBio.
[50] C. Suttle. Marine viruses — major players in the global ecosystem , 2007, Nature Reviews Microbiology.
[51] A. Eiler,et al. Non-Random Assembly of Bacterioplankton Communities in the Subtropical North Pacific Ocean , 2011, Front. Microbio..
[52] N. Kashtan,et al. Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus , 2014, Science.
[53] S. Giovannoni,et al. Seasonality in Ocean Microbial Communities , 2012, Science.
[54] J. Fuhrman,et al. Population ecology of nitrifying archaea and bacteria in the Southern California Bight. , 2010, Environmental microbiology.
[55] Kishori M. Konwar,et al. Expanding the boundaries of local similarity analysis , 2013, BMC Genomics.
[56] Sallie W. Chisholm,et al. Phytoplankton population dynamics at the Bermuda Atlantic Time-series station in the Sargasso Sea , 2001 .
[57] R. Burton,et al. Seasonality and vertical structure of microbial communities in an ocean gyre , 2009, The ISME Journal.
[58] Roman Marin,et al. Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages , 2014, Science.
[59] R. Lenski,et al. The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss , 2012, mBio.
[60] Jed A Fuhrman,et al. Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California , 2011, The ISME Journal.
[61] D. Lindell,et al. Host-dependent differences in abundance, composition and host range of cyanophages from the Red Sea. , 2015, Environmental microbiology.
[62] William A. Walters,et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms , 2012, The ISME Journal.
[63] Dawn Field,et al. The seasonal structure of microbial communities in the Western English Channel. , 2009, Environmental microbiology.
[64] Robert R. Bidigare,et al. Seasonal patterns of ocean biogeochemistry at the U.S. JGOFS Bermuda Atlantic time-series study site , 1994 .
[65] John D. Storey,et al. Statistical significance for genomewide studies , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[66] E. Delong,et al. Time-series analyses of Monterey Bay coastal microbial picoplankton using a 'genome proxy' microarray. , 2011, Environmental microbiology.
[67] Mikhail Tikhonov,et al. Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution , 2013, The ISME Journal.
[68] I. Hewson,et al. Annually reoccurring bacterial communities are predictable from ocean conditions , 2006, Proceedings of the National Academy of Sciences.
[69] D. Caron,et al. Small-scale temporal and spatial variations in protistan community composition at the San Pedro Ocean Time-series station off the coast of southern California , 2013 .
[70] C. Carlson,et al. Microbial dynamics in cyclonic and anticyclonic mode-water eddies in the northwestern Sargasso Sea , 2008 .
[71] Philip Hugenholtz,et al. Viral tagging reveals discrete populations in Synechococcus viral genome sequence space , 2014, Nature.
[72] D. Scanlan,et al. Genetic diversity of marine Synechococcus and co-occurring cyanophage communities: evidence for viral control of phytoplankton. , 2005, Environmental microbiology.
[73] I. Hewson,et al. Remarkable heterogeneity in meso‐ and bathypelagic bacterioplankton assemblage composition , 2006 .
[74] Rosalia Santoleri,et al. Seasonal variability of the mixed layer depth in the Mediterranean Sea as derived from in situ profiles , 2005 .
[75] Daniel Patrick Smith,et al. The presence of the glycolysis operon in SAR11 genomes is positively correlated with ocean productivity. , 2010, Environmental microbiology.
[76] S. Giovannoni,et al. Spatiotemporal distributions of rare bacterioplankton populations indicate adaptive strategies in the oligotrophic ocean , 2013 .
[77] R. Amann,et al. Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom , 2012, Science.
[78] A. Ramette. Multivariate analyses in microbial ecology , 2007, FEMS microbiology ecology.
[79] J. Kennett,et al. LATE QUATERNARY CLIMATICALLY RELATED PLANKTONIC FORAMINIFERAL ASSEMBLAGE CHANGES : HOLE 893 A , SANTA BARBARA BASIN , CALIFORNIA 1 , 2006 .
[80] C. Duarte,et al. The Mediterranean climate as a template for Mediterranean marine ecosystems: the example of the northeast Spanish littoral , 1999 .
[81] Sallie W. Chisholm,et al. Niche Partitioning Among Prochlorococcus Ecotypes Along Ocean-Scale Environmental Gradients , 2006, Science.
[82] John B. Waterbury,et al. Resistance to Co-Occurring Phages Enables Marine Synechococcus Communities To Coexist with Cyanophages Abundant in Seawater , 1993, Applied and environmental microbiology.
[83] R. Rosenberg,et al. Spreading Dead Zones and Consequences for Marine Ecosystems , 2008, Science.
[84] J. Fuhrman,et al. Bacterial and Archaeal Community Structure and its Patterns , 2008 .
[85] James T Staley,et al. The bacterial species dilemma and the genomic–phylogenetic species concept , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.
[86] J. Fuhrman,et al. Seasonality and monthly dynamics of marine myovirus communities. , 2012, Environmental microbiology.
[87] Charles R. Brown,et al. Ecology and Evolution of Darwin’s Finches , 2001, Heredity.
[88] Alicia J. Shepard,et al. Rapid diversification of coevolving marine Synechococcus and a virus , 2012, Proceedings of the National Academy of Sciences.
[89] Sallie W. Chisholm,et al. A novel free-living prochlorophyte abundant in the oceanic euphotic zone , 1988, Nature.
[90] R. Stepanauskas,et al. Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists , 2011, Science.
[91] J. Kennett,et al. Dansgaard-Oeschger Cycles and the California Current System: Planktonic foraminiferal response to rapid climate change in Santa Barbara Basin, Ocean Drilling Program Hole 893A , 2000 .
[92] H. Sverdrup,et al. On Conditions for the Vernal Blooming of Phytoplankton , 1953 .
[93] Andrea K. Bartram,et al. Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads , 2011, Applied and Environmental Microbiology.
[94] D. Kirchman. Microbial ecology of the oceans , 2008 .
[95] B. Shapiro,et al. Ordering microbial diversity into ecologically and genetically cohesive units. , 2014, Trends in microbiology.
[96] Fengzhu Sun,et al. Marine Bacterial, Archaeal, and Protistan Association Networks , 2014 .
[97] Sallie W. Chisholm,et al. Cyanophages infecting the oceanic cyanobacterium Prochlorococcus , 2003, Nature.
[98] Fengzhu Sun,et al. Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates , 2011, BMC Systems Biology.
[99] L. Roesch,et al. Network topology reveals high connectance levels and few key microbial genera within soils , 2014, Front. Environ. Sci..
[100] P. Hugenholtz,et al. Contrasting Life Strategies of Viruses That Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging , 2013, mBio.
[101] A. Buchan,et al. Master recyclers: features and functions of bacteria associated with phytoplankton blooms , 2014, Nature Reviews Microbiology.
[102] P. Toscas,et al. Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters. , 2015, Environmental microbiology.
[103] E. Delong,et al. Pattern and synchrony of gene expression among sympatric marine microbial populations , 2013, Proceedings of the National Academy of Sciences.
[104] J. Fuhrman,et al. Beta diversity of marine bacteria depends on temporal scale. , 2013, Ecology.
[105] F. Cohan,et al. A Systematics for Discovering the Fundamental Units of Bacterial Diversity , 2007, Current Biology.
[106] Yu Hen Hu,et al. A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota, WI, USA , 2012, The ISME Journal.
[107] D. Lindell,et al. Ultraphytoplankton succession is triggered by deep winter mixing in the Gulf of Aqaba (Eilat), Red Sea , 1995 .
[108] R. Stepanauskas,et al. Targeted Sorting of Single Virus-Infected Cells of the Coccolithophore Emiliania huxleyi , 2011, PloS one.
[109] P. Hugenholtz,et al. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes , 2013, Nature Biotechnology.
[110] M. Wagner,et al. Microbial diversity and the genetic nature of microbial species , 2008, Nature Reviews Microbiology.
[111] Craig E. Nelson,et al. Community differentiation and population enrichment of Sargasso Sea bacterioplankton in the euphotic zone of a mesoscale mode-water eddy. , 2014, Environmental microbiology.
[112] J. Fuhrman,et al. Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years , 2014, The ISME Journal.
[113] I. Hewson,et al. Temporal and spatial scales of variation in bacterioplankton assemblages of oligotrophic surface waters , 2006 .
[114] Joseph Tzanopoulos,et al. Long-term observation of a pollination network: fluctuation in species and interactions, relative invariance of network structure and implications for estimates of specialization. , 2008, Ecology letters.
[115] Fei-xue Fu,et al. Nutrient Cycles and Marine Microbes in a CO2-Enriched Ocean , 2009 .
[116] U. Sommer,et al. Seasonal dynamics of phytoplankton in the Gulf of Aqaba, Red Sea , 2007, Hydrobiologia.
[117] K. Arrigo,et al. The interplay between upwelling and deep convective mixing in determining the seasonal phytoplankton dynamics in the Gulf of Aqaba: Evidence from SeaWiFS and MODIS , 2003 .
[118] C. Suttle,et al. Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[119] D. Caron,et al. Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists , 2013, The ISME Journal.
[120] C. Pedrós-Alió,et al. Seasonal changes in the taxonomic composition of bacterioplankton in a coastal oligotrophic system , 2003 .
[121] S. Giovannoni,et al. High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences , 2013, The ISME Journal.
[122] F. Chen,et al. Diverse and dynamic populations of cyanobacterial podoviruses in the Chesapeake Bay unveiled through DNA polymerase gene sequences. , 2009, Environmental microbiology.
[123] D. Cayan,et al. Climate and Chlorophyll a: Long-Term Trends in the Central North Pacific Ocean , 1987, Science.
[124] C. Pedrós-Alió,et al. Diel variations in bacterial heterotrophic activity and growth in the northwestern Mediterranean Sea , 1998 .
[125] M. Keller,et al. Dependence of the Cyanobacterium Prochlorococcus on Hydrogen Peroxide Scavenging Microbes for Growth at the Ocean's Surface , 2011, PloS one.
[126] J. Ryther,et al. Annual variations in primary production of the Sargasso sea off Bermuda , 1961 .
[127] H. Huber,et al. Microbial syntrophy: interaction for the common good. , 2013, FEMS microbiology reviews.
[128] R. Pingree,et al. Tidal fronts on the shelf seas around the British Isles , 1978 .
[129] S. Tringe,et al. Tackling soil diversity with the assembly of large, complex metagenomes , 2014, Proceedings of the National Academy of Sciences.
[130] David M. Karl,et al. The Hawaii Ocean Time-series (HOT) program: Background, rationale and field implementation , 1996 .
[131] Lawrence A. David,et al. Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton , 2008, Science.
[132] J. Kennett,et al. 21. LATE QUATERNARY CLIMATICALLY RELATED PLANKTONIC FORAMINIFERAL ASSEMBLAGE CHANGES: HOLE 893A, SANTA BARBARA BASIN, CALIFORNIA1 , 1995 .
[133] S. Chisholm,et al. Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans , 2010, The ISME Journal.
[134] P. Falkowski,et al. A universal driver of macroevolutionary change in the size of marine phytoplankton over the Cenozoic , 2007, Proceedings of the National Academy of Sciences.
[135] Ken O. Buesseler,et al. Biogeochemical impacts due to mesoscale eddy activity in the Sargasso Sea as measured at the Bermuda Atlantic Time-series Study (BATS) , 2003 .
[136] J. G. Field,et al. The Ecological Role of Water-Column Microbes in the Sea* , 1983 .
[137] C. Fraser,et al. The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity , 2009, Science.
[138] G. Herndl,et al. Diel periodicity of bacterioplankton in the euphotic zone of the subtropical Atlantic Ocean , 2000 .
[139] J. Fuhrman. General Distributions and the 'rare Biosphere' Microbial Community Structure and Its Functional Implications Review Insight , 2022 .
[140] G. Rocap,et al. Diversity and Distribution of Marine Synechococcus: Multiple Gene Phylogenies for Consensus Classification and Development of qPCR Assays for Sensitive Measurement of Clades in the Ocean , 2012, Front. Microbio..