Rapid bacterioplankton transcription cascades regulate organic matter utilization during phytoplankton bloom progression in a coastal upwelling system

[1]  Ryan S. Mueller,et al.  Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits , 2021, Proceedings of the National Academy of Sciences.

[2]  R. Amann,et al.  Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom , 2021, The ISME Journal.

[3]  R. Amann,et al.  Diatom fucan polysaccharide precipitates carbon during algal blooms , 2021, Nature Communications.

[4]  M. Moran,et al.  Niche dimensions of a marine bacterium are identified using invasion studies in coastal seawater , 2021, Nature Microbiology.

[5]  B. Reguera,et al.  Thin layers of phytoplankton and harmful algae events in a coastal upwelling system , 2020 .

[6]  S. Nahnsen,et al.  Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline , 2020, Frontiers in Microbiology.

[7]  M. Moran,et al.  Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy , 2020, The ISME Journal.

[8]  Benjamin Pontiller,et al.  Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription , 2020, Frontiers in Microbiology.

[9]  R. Amann,et al.  The Biogeochemistry of Marine Polysaccharides: Sources, Inventories, and Bacterial Drivers of the Carbohydrate Cycle. , 2020, Annual review of marine science.

[10]  E. Teira,et al.  Spatial and temporal variability in the response of phytoplankton and prokaryotes to B-vitamin amendments in an upwelling system , 2020, Biogeosciences.

[11]  Manuel Liebeke,et al.  Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan , 2020, Nature Microbiology.

[12]  D. Hernández-Becerril,et al.  Spatial Distribution Patterns of Bacterioplankton in the Oxygen Minimum Zone of the Tropical Mexican Pacific , 2020, Microbial Ecology.

[13]  F. Lauro,et al.  Temporal and spatial dynamics of Bacteria, Archaea and protists in equatorial coastal waters , 2019, Scientific Reports.

[14]  R. Amann,et al.  In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes , 2019, The ISME Journal.

[15]  S. Giovannoni,et al.  SAR11 bacteria have a high affinity and multifunctional glycine betaine transporter. , 2019, Environmental microbiology.

[16]  R. Amann,et al.  Selfish, sharing and scavenging bacteria in the Atlantic Ocean: a biogeographical study of bacterial substrate utilisation , 2018, The ISME Journal.

[17]  T. Schweder,et al.  Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides , 2018, The ISME Journal.

[18]  F. Ballantyne,et al.  Identifying labile DOM components in a coastal ocean through depleted bacterial transcripts and chemical signals , 2018, Environmental microbiology.

[19]  Zhenglu Yang,et al.  dbCAN2: a meta server for automated carbohydrate-active enzyme annotation , 2018, Nucleic Acids Res..

[20]  J. Fuhrman,et al.  Vertical and Seasonal Patterns Control Bacterioplankton Communities at Two Horizontally Coherent Coastal Upwelling Sites off Galicia (NW Spain) , 2018, Microbial Ecology.

[21]  R. Reinhardt,et al.  Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise , 2018, The ISME Journal.

[22]  Ramunas Stepanauskas,et al.  Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics , 2017, Proceedings of the National Academy of Sciences.

[23]  A. Enrich-Prast,et al.  Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula , 2017 .

[24]  Guanjun Chen,et al.  Agarilytica rhodophyticola gen. nov., sp. nov., isolated from Gracilaria blodgettii. , 2017, International journal of systematic and evolutionary microbiology.

[25]  Stephen P. Dearth,et al.  Recognition cascade and metabolite transfer in a marine bacteria‐phytoplankton model system , 2017, Environmental microbiology.

[26]  W. Helbert,et al.  New structural insights into the cell-wall polysaccharide of the diatom Phaeodactylum tricornutum , 2017 .

[27]  Ryan S. Mueller,et al.  Phylogenetically conserved resource partitioning in the coastal microbial loop , 2017, The ISME Journal.

[28]  M. Moran,et al.  Bacterial transcriptome remodeling during sequential co-culture with a marine dinoflagellate and diatom , 2017, The ISME Journal.

[29]  R. Stocker,et al.  Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships , 2017, Nature Microbiology.

[30]  W. Liesack,et al.  Comparative Genomics of Four Isosphaeraceae Planctomycetes: A Common Pool of Plasmids and Glycoside Hydrolase Genes Shared by Paludisphaera borealis PX4T, Isosphaera pallida IS1BT, Singulisphaera acidiphila DSM 18658T, and Strain SH-PL62 , 2017, Front. Microbiol..

[31]  S. Spring,et al.  Characterization of the first cultured representative of a Bacteroidetes clade specialized on the scavenging of cyanobacteria , 2017, Environmental microbiology.

[32]  S. Giovannoni.  SAR11 Bacteria: The Most Abundant Plankton in the Oceans. , 2017, Annual review of marine science.

[33]  Ben Nichols,et al.  Distributed under Creative Commons Cc-by 4.0 Vsearch: a Versatile Open Source Tool for Metagenomics , 2022 .

[34]  M. Cottrell,et al.  Transcriptional Control in Marine Copiotrophic and Oligotrophic Bacteria with Streamlined Genomes , 2016, Applied and Environmental Microbiology.

[35]  Daniel H. Huson,et al.  MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data , 2016, PLoS Comput. Biol..

[36]  J. Fuhrman,et al.  Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. , 2016, Environmental microbiology.

[37]  Vera Pawlowsky-Glahn,et al.  It's all relative: analyzing microbiome data as compositions. , 2016, Annals of epidemiology.

[38]  A. Godhe,et al.  Spatio-Temporal Interdependence of Bacteria and Phytoplankton during a Baltic Sea Spring Bloom , 2016, Front. Microbiol..

[39]  P. Keeling,et al.  Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean , 2016, The ISME Journal.

[40]  P. Dorrestein,et al.  Deciphering ocean carbon in a changing world , 2016, Proceedings of the National Academy of Sciences.

[41]  J. Fuhrman,et al.  Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom , 2016, Nature Microbiology.

[42]  D. Kirchman.  Growth Rates of Microbes in the Oceans. , 2016, Annual review of marine science.

[43]  M. Moran,et al.  The transcriptional response of prokaryotes to phytoplankton-derived dissolved organic matter in seawater. , 2015, Environmental microbiology.

[44]  J. A. Vilar,et al.  Annual trend patterns of phytoplankton species abundance belie homogeneous taxonomical group responses to climate in the NE Atlantic upwelling. , 2015, Marine environmental research.

[45]  E. Delong,et al.  High molecular weight dissolved organic matter enrichment selects for methylotrophs in dilution to extinction cultures , 2015, The ISME Journal.

[46]  Ying-yi Huo,et al.  Gilvimarinus polysaccharolyticus sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Gilvimarinus. , 2015, International journal of systematic and evolutionary microbiology.

[47]  R. Amann,et al.  Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom , 2014, The ISME Journal.

[48]  Chao Xie,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[49]  Kunihiko Sadakane,et al.  MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph , 2014, Bioinform..

[50]  J. Fuhrman,et al.  Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years , 2014, The ISME Journal.

[51]  Francisco M. Cornejo-Castillo,et al.  Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. , 2014, Environmental microbiology.

[52]  Otto X. Cordero,et al.  Distinct dissolved organic matter sources induce rapid transcriptional responses in coexisting populations of Prochlorococcus, Pelagibacter and the OM60 clade. , 2014, Environmental microbiology.

[53]  A. Buchan,et al.  Master recyclers: features and functions of bacteria associated with phytoplankton blooms , 2014, Nature Reviews Microbiology.

[54]  Roman Marin,et al.  Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages , 2014, Science.

[55]  F. Azam,et al.  Single bacterial strain capable of significant contribution to carbon cycling in the surface ocean , 2014, Proceedings of the National Academy of Sciences.

[56]  M. Morgante,et al.  An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis , 2013, PloS one.

[57]  M. Cunliffe,et al.  Seasonal microbial community dynamics correlate with phytoplankton-derived polysaccharides in surface coastal waters , 2013, The ISME Journal.

[58]  F. Nazzi,et al.  Correction: From Chemistry to Behavior. Molecular Structure and Bioactivity of Repellents against Ixodes ricinus Ticks , 2013, PLoS ONE.

[59]  T. Williams,et al.  The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics. , 2013, Environmental microbiology.

[60]  F. Fraga,et al.  Upwelling off the Galician Coast, Northwest Spain , 2013 .

[61]  E. Delong,et al.  Pattern and synchrony of gene expression among sympatric marine microbial populations , 2013, Proceedings of the National Academy of Sciences.

[62]  C. Pedrós-Alió,et al.  Ecology of marine Bacteroidetes: a comparative genomics approach , 2013, The ISME Journal.

[63]  Pelin Yilmaz,et al.  The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..

[64]  F. Rodríguez-Valera,et al.  Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph , 2012, Scientific Reports.

[65]  P. Weber,et al.  Taxon-specific C/N relative use efficiency for amino acids in an estuarine community. , 2012, FEMS microbiology ecology.

[66]  H. Sarmento,et al.  Use of phytoplankton-derived dissolved organic carbon by different types of bacterioplankton. , 2012, Environmental microbiology.

[67]  R. Amann,et al.  Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom , 2012, Science.

[68]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[69]  A. Tsuda,et al.  Differing Growth Responses of Major Phylogenetic Groups of Marine Bacteria to Natural Phytoplankton Blooms in the Western North Pacific Ocean , 2011, Applied and Environmental Microbiology.

[70]  E. Delong,et al.  Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea , 2010, Proceedings of the National Academy of Sciences.

[71]  Vera L. Trainer,et al.  Dinoflagellate blooms in upwelling systems: Seeding, variability, and contrasts with diatom bloom behaviour , 2010 .

[72]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[73]  Mary Ann Moran,et al.  Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon , 2010, Environmental microbiology.

[74]  Mary Ann Moran,et al.  Genome characteristics of a generalist marine bacterial lineage , 2010, The ISME Journal.

[75]  Mary Ann Moran,et al.  Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics , 2009, Journal of visualized experiments : JoVE.

[76]  J. Pernthaler,et al.  Response of Alteromonadaceae and Rhodobacteriaceae to glucose and phosphorus manipulation in marine mesocosms. , 2007, Environmental microbiology.

[77]  Luke E. Ulrich,et al.  Ecological Genomics of Marine Roseobacters , 2007, Applied and Environmental Microbiology.

[78]  F. Wilkerson,et al.  The phytoplankton bloom response to wind events and upwelled nutrients during the CoOP WEST study , 2006 .

[79]  J. Pernthaler,et al.  Roseobacter and SAR11 dominate microbial glucose uptake in coastal North Sea waters. , 2006, Environmental microbiology.

[80]  E. Marañón,et al.  Phytoplankton size structure and primary production in a highly dynamic coastal ecosystem (Ria de Vigo, NW-Spain): Seasonal and short-time scale variability , 2006 .

[81]  X. Morán,et al.  Seasonal dynamics of picoplankton in shelf waters of the southern Bay of Biscay , 2006 .

[82]  F. G. Figueiras,et al.  The microplankton succession in the Ría de Vigo revisited: species assemblages and the role of weather-induced, hydrodynamic variability , 2005 .

[83]  Francesc Peters,et al.  Changes in Bacterioplankton Composition under Different Phytoplankton Regimens , 2004, Applied and Environmental Microbiology.

[84]  R. Malmstrom,et al.  Contribution of SAR11 Bacteria to Dissolved Dimethylsulfoniopropionate and Amino Acid Uptake in the North Atlantic Ocean , 2004, Applied and Environmental Microbiology.

[85]  F. Azam,et al.  Dynamics of Bacterial Community Composition and Activity during a Mesocosm Diatom Bloom , 2000, Applied and Environmental Microbiology.

[86]  M. Cottrell,et al.  Natural Assemblages of Marine Proteobacteria and Members of the Cytophaga-Flavobacter Cluster Consuming Low- and High-Molecular-Weight Dissolved Organic Matter , 2000, Applied and Environmental Microbiology.

[87]  J. Gattuso,et al.  CARBON AND CARBONATE METABOLISM IN COASTAL AQUATIC ECOSYSTEMS , 1998 .

[88]  X. Álvarez‐Salgado,et al.  Simultaneous determination of dissolved organic carbon and total dissolved nitrogen in seawater by high temperature catalytic oxidation: conditions for precise shipboard measurements , 1998 .

[89]  Farooq Azam,et al.  Microbial Control of Oceanic Carbon Flux: The Plot Thickens , 1998, Science.

[90]  F. F. Pérèz,et al.  Modelling Thermohaline Properties in an Estuarine Upwelling Ecosystem (Rı́a de Vigo: NW Spain) Using Box-Jenkins Transfer Function Models , 1997 .

[91]  N. Welschmeyer.  Fluorometric analysis of chlorophyll a in the presence of chlorophyll b and pheopigments , 1994 .

[92]  E. I. Hamilton,et al.  A manual of chemical & biological methods for seawater analysis , 1984 .

[93]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[94]  M. Moran,et al.  Bacterial community transcription patterns during a marine phytoplankton bloom. , 2012, Environmental microbiology.

[95]  E. Delong,et al.  Transcriptional responses of surface water marine microbial assemblages to deep-sea water amendment. , 2012, Environmental microbiology.

[96]  X. Álvarez‐Salgado,et al.  Differential responses of phytoplankton and heterotrophic bacteria to organic and inorganic nutrient additions in coastal waters off the NW Iberian Peninsula , 2010 .

[97]  Richard D. Smith,et al.  Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea , 2009, The ISME Journal.

[98]  David C. Smith,et al.  A simple, economical method for measuring bacterial protein synthesis rates in seawater using 3H-leucine , 1992 .

[99]  C. Moloney,et al.  Short-term variability during an anchor station study in the southern Benguela upwelling system: Phytoplankton dynamics , 1991 .