Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms

[1]  Huan Wang,et al.  TCA cycle enhancement and uptake of monomeric substrates support growth of marine Roseobacter at low temperature , 2022, Communications Biology.

[2]  J. Pachón,et al.  iTRAQ-Based Quantitative Proteomic Analysis of Acinetobacter baumannii under Hypoxia and Normoxia Reveals the Role of OmpW as a Virulence Factor , 2022, Microbiology spectrum.

[3]  M. H. Wong,et al.  Active maintenance of proton motive force mediates starvation-induced bacterial antibiotic tolerance in Escherichia coli , 2021, Communications Biology.

[4]  Y. Boucher,et al.  Roseobacters in a Sea of Poly- and Paraphyly: Whole Genome-Based Taxonomy of the Family Rhodobacteraceae and the Proposal for the Split of the “Roseobacter Clade” Into a Novel Family, Roseobacteraceae fam. nov. , 2021, Frontiers in Microbiology.

[5]  A. Frolova,et al.  Niche partitioning of bacterial communities along the stratified water column in the Black Sea , 2021, MicrobiologyOpen.

[6]  D. Canfield,et al.  Sulfur cycling in oceanic oxygen minimum zones , 2021, Limnology and Oceanography.

[7]  P. Qian,et al.  Expanding our understanding of marine viral diversity through metagenomic analyses of biofilms , 2021, Marine Life Science & Technology.

[8]  Qian Wang,et al.  Selection of antibiotic resistance genes on biodegradable and non-biodegradable microplastics. , 2020, Journal of hazardous materials.

[9]  M. Cannat,et al.  Microbial ecology of the newly discovered serpentinite-hosted Old City hydrothermal field (southwest Indian ridge) , 2020, The ISME Journal.

[10]  A. Stams,et al.  The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters , 2020, Environmental microbiology.

[11]  Samir R. Damare,et al.  Diversity of culturable Sulphur-oxidising bacteria in the oxygen minimum zones of the northern Indian Ocean , 2020 .

[12]  T. Ferdelman,et al.  Kelp deposition changes mineralization pathways and microbial communities in a sandy beach , 2020, Limnology and Oceanography.

[13]  Jing Zhang,et al.  A novel bacterial thiosulfate oxidation pathway provides a new clue about the formation of zero-valent sulfur in deep sea , 2020, The ISME Journal.

[14]  N. Nomura,et al.  Biofilms: hot spots of horizontal gene transfer (HGT) in aquatic environments, with a focus on a new HGT mechanism , 2020, FEMS microbiology ecology.

[15]  Binbin Zhang,et al.  Metagenomic Resolution of Functional Diversity in Copper Surface-Associated Marine Biofilms , 2019, Front. Microbiol..

[16]  Donovan H Parks,et al.  GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database , 2019, Bioinform..

[17]  E. Torrents,et al.  Optimal environmental and culture conditions allow the in vitro coexistence of Pseudomonas aeruginosa and Staphylococcus aureus in stable biofilms , 2019, Scientific Reports.

[18]  Luis Pedro Coelho,et al.  Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome , 2019, Cell.

[19]  L. Procópio The role of biofilms in the corrosion of steel in marine environments , 2019, World Journal of Microbiology and Biotechnology.

[20]  S. Wuertz,et al.  Bacteria and archaea on Earth and their abundance in biofilms , 2019, Nature Reviews Microbiology.

[21]  S. Bougouffa,et al.  Marine biofilms constitute a bank of hidden microbial diversity and functional potential , 2019, Nature Communications.

[22]  A. Phillippy,et al.  High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries , 2018, Nature Communications.

[23]  Jin Sun,et al.  Gut Microbial Divergence between Two Populations of the Hadal Amphipod Hirondellea gigas , 2018, Applied and Environmental Microbiology.

[24]  W. Brazelton,et al.  Deeply-sourced formate fuels sulfate reducers but not methanogens at Lost City hydrothermal field , 2018, Scientific Reports.

[25]  M. Simon,et al.  Composition of Total and Cell-Proliferating Bacterioplankton Community in Early Summer in the North Sea – Roseobacters Are the Most Active Component , 2017, Front. Microbiol..

[26]  J. Banfield,et al.  dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication , 2017, The ISME Journal.

[27]  J. Imlay,et al.  Escherichia coli cytochrome c peroxidase is a respiratory oxidase that enables the use of hydrogen peroxide as a terminal electron acceptor , 2017, Proceedings of the National Academy of Sciences.

[28]  S. Golden,et al.  Type 4 pili are dispensable for biofilm development in the cyanobacterium Synechococcus elongatus , 2017, Environmental microbiology.

[29]  Jan P. Meier-Kolthoff,et al.  Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats , 2017, The ISME Journal.

[30]  E. Hada,et al.  Thiomicrospira hydrogeniphila sp. nov., an aerobic, hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a seawater tank containing a block of beef tallow. , 2016, International journal of systematic and evolutionary microbiology.

[31]  J. Heilmann,et al.  Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis , 2016, The ISME Journal.

[32]  Hing-Fung Ting,et al.  MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. , 2016, Methods.

[33]  Anders Krogh,et al.  Fast and sensitive taxonomic classification for metagenomics with Kaiju , 2016, Nature Communications.

[34]  M. Göker,et al.  Biofilm plasmids with a rhamnose operon are widely distributed determinants of the ‘swim-or-stick' lifestyle in roseobacters , 2016, The ISME Journal.

[35]  D. Nelson,et al.  Contributions of tropodithietic acid and biofilm formation to the probiotic activity of Phaeobacter inhibens , 2016, BMC Microbiology.

[36]  H. Cao,et al.  Synchronized dynamics of bacterial niche-specific functions during biofilm development in a cold seep brine pool. , 2015, Environmental microbiology.

[37]  Natàlia Hurtós,et al.  The Kallisti Limnes, carbon dioxide-accumulating subsea pools , 2015, Scientific Reports.

[38]  L. Polerecky,et al.  Assessment of the stoichiometry and efficiency of CO2 fixation coupled to reduced sulfur oxidation , 2015, Front. Microbiol..

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

[40]  F. Yildiz,et al.  The Type II Secretion System Delivers Matrix Proteins for Biofilm Formation by Vibrio cholerae , 2014, Journal of bacteriology.

[41]  C. Arnosti,et al.  Composition and enzymatic function of particle-associated and free-living bacteria: a coastal/offshore comparison , 2014, The ISME Journal.

[42]  K. Siddiqui,et al.  Influence of Calcium in Extracellular DNA Mediated Bacterial Aggregation and Biofilm Formation , 2014, PloS one.

[43]  Brian Bushnell,et al.  BBMap: A Fast, Accurate, Splice-Aware Aligner , 2014 .

[44]  J. Huber,et al.  Phylogenetic diversity and functional gene patterns of sulfur-oxidizing subseafloor Epsilonproteobacteria in diffuse hydrothermal vent fluids , 2013, Front. Microbiol..

[45]  B. Hall,et al.  Building phylogenetic trees from molecular data with MEGA. , 2013, Molecular biology and evolution.

[46]  Xiao Zhang,et al.  PotD protein stimulates biofilm formation by Escherichia coli , 2013, Biotechnology Letters.

[47]  T. Schmidt,et al.  Shallow breathing: bacterial life at low O2 , 2013, Nature Reviews Microbiology.

[48]  R. Morris,et al.  Isolation of an aerobic sulfur oxidizer from the SUP05/Arctic96BD-19 clade , 2012, The ISME Journal.

[49]  R. Amann,et al.  Roseobacter clade bacteria are abundant in coastal sediments and encode a novel combination of sulfur oxidation genes , 2012, The ISME Journal.

[50]  Alexandra J. Scott,et al.  Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2 , 2012, Bioinform..

[51]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[52]  Xiaolin Tian,et al.  Quorum Sensing and Bacterial Social Interactions in Biofilms , 2012, Sensors.

[53]  Mukesh Jain,et al.  NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data , 2012, PloS one.

[54]  C. Fuqua,et al.  Agrobacterium tumefaciens ExoR represses succinoglycan biosynthesis and is required for biofilm formation and motility , 2010, Microbiology.

[55]  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 .

[56]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[57]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[58]  S. Okabe,et al.  Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli , 2008, Journal of bacteriology.

[59]  C. Cavanaugh,et al.  CO2 Uptake and Fixation by Endosymbiotic Chemoautotrophs from the Bivalve Solemya velum , 2006, Applied and Environmental Microbiology.

[60]  H. Biebl,et al.  Environmental biology of the marine Roseobacter lineage. , 2006, Annual review of microbiology.

[61]  C. Friedrich,et al.  Prokaryotic sulfur oxidation. , 2005, Current opinion in microbiology.

[62]  B. Tebo,et al.  Diverse Mn(II)-Oxidizing Bacteria Isolated from Submarine Basalts at Loihi Seamount , 2005 .

[63]  Ian T. Paulsen,et al.  Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment , 2004, Nature.

[64]  Alok J. Saldanha,et al.  Java Treeview - extensible visualization of microarray data , 2004, Bioinform..

[65]  S Miyano,et al.  Open source clustering software. , 2004, Bioinformatics.

[66]  Dean Laslett,et al.  ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. , 2004, Nucleic acids research.

[67]  D. Sorokin Oxidation of Inorganic Sulfur Compounds by Obligately Organotrophic Bacteria , 2003, Microbiology.

[68]  J. Imhoff,et al.  Phylogeny and distribution of the soxB gene among thiosulfate-oxidizing bacteria. , 2001, FEMS microbiology letters.

[69]  R. Kraft,et al.  Novel Genes Coding for Lithotrophic Sulfur Oxidation of Paracoccus pantotrophus GB17 , 2000, Journal of bacteriology.

[70]  C. Prigent-Combaret,et al.  Developmental pathway for biofilm formation in curli-producing Escherichia coli strains: role of flagella, curli and colanic acid. , 2000, Environmental microbiology.

[71]  G. Muyzer,et al.  Diversity of Thiosulfate-Oxidizing Bacteria from Marine Sediments and Hydrothermal Vents , 2000, Applied and Environmental Microbiology.

[72]  N. Sauvonnet,et al.  Pilus formation and protein secretion by the same machinery in Escherichia coli , 2000, The EMBO journal.

[73]  M. Moran,et al.  Transformation of Sulfur Compounds by an Abundant Lineage of Marine Bacteria in the α-Subclass of the ClassProteobacteria , 1999, Applied and Environmental Microbiology.

[74]  J. Imhoff,et al.  Tetrathionate production by sulfur oxidizing bacteria and the role of tetrathionate in the sulfur cycle of Baltic Sea sediments , 1999 .

[75]  B. Jørgensen,et al.  A Thiosulfate Shunt in the Sulfur Cycle of Marine Sediments , 1990, Science.

[76]  C. Cavanaugh Symbiotic chemoautotrophic bacteria in marine invertebrates from sulphide-rich habitats , 1983, Nature.

[77]  J. H. Tuttle,et al.  Thiosulfate stimulation of microbial dark assimilation of carbon dioxide in shallow marine waters , 1977, Microbial Ecology.

[78]  W. Whitman Bergey's Manual of Systematics of Archaea and Bacteria , 2016 .

[79]  J. Sólyom,et al.  Structure and dynamics , 2010 .

[80]  C. Dahl,et al.  Microbial sulfur metabolism , 2008 .

[81]  P. Vandamme,et al.  DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. , 2007, International journal of systematic and evolutionary microbiology.

[82]  F. Ceriotti,et al.  IFCC primary reference procedures for the measurement of catalytic activity concentrations of enzymes at 37°C: International Federation of Clinical Chemistry and Laboratory Medicine (IFCC): Scientific Division, Committee on Reference Systems for Enzymes (C-RSE): Part 8. Reference procedure for the m , 2006 .