The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics
Identifieur interne : 000244 ( Istex/Checkpoint ); précédent : 000243; suivant : 000245The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics
Auteurs : Timothy J. Williams [Australie] ; David Wilkins [Australie] ; Emilie Long [Australie, France] ; Flavia Evans [Australie] ; Mathew Z. Demaere [Australie] ; Mark J. Raftery [Australie] ; Ricardo Cavicchioli [Australie]Source :
- Environmental Microbiology [ 1462-2912 ] ; 2013-05.
Descripteurs français
- Wicri :
- topic : Antarctique, Base de données.
English descriptors
- KwdEn :
- Abell, Acid metabolism, Algal, Alphaproteobacteria, Alteromonadales, Amino, Amino acids, Antarctic, Antarctic peninsula, Antarctic surface waters, Antarctica, Antcomb, Appl, Appl environ microbiol, Archaea, Archaeal, Arctic ocean, Austral summer, Bacterioplankton, Bacteroidetes, Biosynthesis, Blackwell publishing, Bowman, Burtonii, Carbohydrate, Chlorophyll, Clade, Class alphaproteobacteria, Class flavobacteria, Community composition, Database, Dehydrogenase, Delong, Diatom, East antarctica, Ecol, Environ, Environ microbiol, Environmental microbiology, Eukaryotic phytoplankton, Fems, Fems microbiol ecol, Flavobacteria, Fosmid libraries, Gaas, Gaas analysis, Gammaproteobacteria, Genome, Giovannoni, Grzymski, Heterotroph, Highest sequence identity, Isme, Kirchman, Labile, Labile solutes, Limnol oceanogr, Marine antarctic flavobacteria, Metabolism, Metagenome, Metagenome data, Metagenomic, Metaproteome, Metaproteomic, Metaproteomics, Microbial, Microbiol, Microbiology, Newcomb, Nutrient, Ocean surface, Oceanospirillales, Oceanospirillales alteromonadales, Organic matter, Otus, Outer membrane proteins, Pathway, Pelagibacter ubique, Phylogenetic, Phylogenetic assignment, Phytoplankton, Phytoplankton blooms, Pinhassi, Polaribacter, Primary production, Proc natl acad, Relative abundance, Relative abundances, Rhodobacterales, Roseobacter, Roseobacter clade, Seawater, Solute, Southern ocean, Southern ocean metagenome data, Southern ocean metagenomes, Sowell, Subunit, Surface waters, Synthetase, Teeling, Transport system, Transporter, Trna biosynthesis, Unique peptides, Uorescence, Water column depth.
- Teeft :
- Abell, Acid metabolism, Algal, Alphaproteobacteria, Alteromonadales, Amino, Amino acids, Antarctic, Antarctic peninsula, Antarctic surface waters, Antarctica, Antcomb, Appl, Appl environ microbiol, Archaea, Archaeal, Arctic ocean, Austral summer, Bacterioplankton, Bacteroidetes, Biosynthesis, Blackwell publishing, Bowman, Burtonii, Carbohydrate, Chlorophyll, Clade, Class alphaproteobacteria, Class flavobacteria, Community composition, Database, Dehydrogenase, Delong, Diatom, East antarctica, Ecol, Environ, Environ microbiol, Environmental microbiology, Eukaryotic phytoplankton, Fems, Fems microbiol ecol, Flavobacteria, Fosmid libraries, Gaas, Gaas analysis, Gammaproteobacteria, Genome, Giovannoni, Grzymski, Heterotroph, Highest sequence identity, Isme, Kirchman, Labile, Labile solutes, Limnol oceanogr, Marine antarctic flavobacteria, Metabolism, Metagenome, Metagenome data, Metagenomic, Metaproteome, Metaproteomic, Metaproteomics, Microbial, Microbiol, Microbiology, Newcomb, Nutrient, Ocean surface, Oceanospirillales, Oceanospirillales alteromonadales, Organic matter, Otus, Outer membrane proteins, Pathway, Pelagibacter ubique, Phylogenetic, Phylogenetic assignment, Phytoplankton, Phytoplankton blooms, Pinhassi, Polaribacter, Primary production, Proc natl acad, Relative abundance, Relative abundances, Rhodobacterales, Roseobacter, Roseobacter clade, Seawater, Solute, Southern ocean, Southern ocean metagenome data, Southern ocean metagenomes, Sowell, Subunit, Surface waters, Synthetase, Teeling, Transport system, Transporter, Trna biosynthesis, Unique peptides, Uorescence, Water column depth.
Abstract
Heterotrophic marine bacteria play key roles in remineralizing organic matter generated from primary production. However, far more is known about which groups are dominant than about the cellular processes they perform in order to become dominant. In the Southern Ocean, eukaryotic phytoplankton are the dominant primary producers. In this study we used metagenomics and metaproteomics to determine how the dominant bacterial and archaeal plankton processed bloom material. We examined the microbial community composition in 14 metagenomes and found that the relative abundance of Flavobacteria (dominated by Polaribacter) was positively correlated with chlorophyll a fluorescence, and the relative abundance of SAR11 was inversely correlated with both fluorescence and Flavobacteria abundance. By performing metaproteomics on the sample with the highest relative abundance of Flavobacteria (Newcomb Bay, East Antarctica) we defined how Flavobacteria attach to and degrade diverse complex organic material, how they make labile compounds available to Alphaproteobacteria (especially SAR11) and Gammaproteobacteria, and how these heterotrophic Proteobacteria target and utilize these nutrients. The presence of methylotrophic proteins for archaea and bacteria also indicated the importance of metabolic specialists. Overall, the study provides functional data for the microbial mechanisms of nutrient cycling at the surface of the coastal Southern Ocean.
Url:
DOI: 10.1111/1462-2920.12017
Affiliations:
- Australie, France
- Nouvelle-Galles du Sud, Île-de-France
- Paris, Sydney
- Université Pierre-et-Marie-Curie
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ISTEX:EAE38D4D3AF96C645B4652BE6941D6A4E1EFF53ELe document en format XML
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Demaere</name><affiliation wicri:level="3"><country xml:lang="fr">Australie</country><wicri:regionArea>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales, 2052, Sydney</wicri:regionArea><placeName><settlement type="city">Sydney</settlement><region type="état">Nouvelle-Galles du Sud</region></placeName></affiliation></author><author><name sortKey="Raftery, Mark J" sort="Raftery, Mark J" uniqKey="Raftery M" first="Mark J." last="Raftery">Mark J. Raftery</name><affiliation wicri:level="3"><country xml:lang="fr">Australie</country><wicri:regionArea>Bioanalytical Mass Spectrometry Facility, The University of New South Wales, New South Wales, 2052, Sydney</wicri:regionArea><placeName><settlement type="city">Sydney</settlement><region type="état">Nouvelle-Galles du Sud</region></placeName></affiliation></author><author><name sortKey="Cavicchioli, Ricardo" sort="Cavicchioli, Ricardo" uniqKey="Cavicchioli R" first="Ricardo" last="Cavicchioli">Ricardo Cavicchioli</name><affiliation wicri:level="3"><country xml:lang="fr">Australie</country><wicri:regionArea>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales, 2052, Sydney</wicri:regionArea><placeName><settlement type="city">Sydney</settlement><region type="état">Nouvelle-Galles du Sud</region></placeName></affiliation><affiliation wicri:level="1"><country wicri:rule="url">Australie</country></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Environmental Microbiology</title><title level="j" type="sub">Marine Microbial Ecophysiology and Metagenomics</title><title level="j" type="alt">ENVIRONMENTAL MICROBIOLOGY</title><idno type="ISSN">1462-2912</idno><idno type="eISSN">1462-2920</idno><imprint><biblScope unit="vol">15</biblScope><biblScope unit="issue">5</biblScope><biblScope unit="page" from="1302">1302</biblScope><biblScope unit="page" to="1317">1317</biblScope><biblScope unit="page-count">16</biblScope><date type="published" when="2013-05">2013-05</date></imprint><idno type="ISSN">1462-2912</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1462-2912</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Abell</term><term>Acid metabolism</term><term>Algal</term><term>Alphaproteobacteria</term><term>Alteromonadales</term><term>Amino</term><term>Amino acids</term><term>Antarctic</term><term>Antarctic peninsula</term><term>Antarctic surface waters</term><term>Antarctica</term><term>Antcomb</term><term>Appl</term><term>Appl environ microbiol</term><term>Archaea</term><term>Archaeal</term><term>Arctic ocean</term><term>Austral summer</term><term>Bacterioplankton</term><term>Bacteroidetes</term><term>Biosynthesis</term><term>Blackwell publishing</term><term>Bowman</term><term>Burtonii</term><term>Carbohydrate</term><term>Chlorophyll</term><term>Clade</term><term>Class alphaproteobacteria</term><term>Class flavobacteria</term><term>Community composition</term><term>Database</term><term>Dehydrogenase</term><term>Delong</term><term>Diatom</term><term>East antarctica</term><term>Ecol</term><term>Environ</term><term>Environ microbiol</term><term>Environmental microbiology</term><term>Eukaryotic phytoplankton</term><term>Fems</term><term>Fems microbiol ecol</term><term>Flavobacteria</term><term>Fosmid libraries</term><term>Gaas</term><term>Gaas analysis</term><term>Gammaproteobacteria</term><term>Genome</term><term>Giovannoni</term><term>Grzymski</term><term>Heterotroph</term><term>Highest sequence identity</term><term>Isme</term><term>Kirchman</term><term>Labile</term><term>Labile solutes</term><term>Limnol oceanogr</term><term>Marine antarctic flavobacteria</term><term>Metabolism</term><term>Metagenome</term><term>Metagenome data</term><term>Metagenomic</term><term>Metaproteome</term><term>Metaproteomic</term><term>Metaproteomics</term><term>Microbial</term><term>Microbiol</term><term>Microbiology</term><term>Newcomb</term><term>Nutrient</term><term>Ocean surface</term><term>Oceanospirillales</term><term>Oceanospirillales alteromonadales</term><term>Organic matter</term><term>Otus</term><term>Outer membrane proteins</term><term>Pathway</term><term>Pelagibacter ubique</term><term>Phylogenetic</term><term>Phylogenetic assignment</term><term>Phytoplankton</term><term>Phytoplankton blooms</term><term>Pinhassi</term><term>Polaribacter</term><term>Primary production</term><term>Proc natl acad</term><term>Relative abundance</term><term>Relative abundances</term><term>Rhodobacterales</term><term>Roseobacter</term><term>Roseobacter clade</term><term>Seawater</term><term>Solute</term><term>Southern ocean</term><term>Southern ocean metagenome data</term><term>Southern ocean metagenomes</term><term>Sowell</term><term>Subunit</term><term>Surface waters</term><term>Synthetase</term><term>Teeling</term><term>Transport system</term><term>Transporter</term><term>Trna biosynthesis</term><term>Unique peptides</term><term>Uorescence</term><term>Water column depth</term></keywords><keywords scheme="Teeft" xml:lang="en"><term>Abell</term><term>Acid metabolism</term><term>Algal</term><term>Alphaproteobacteria</term><term>Alteromonadales</term><term>Amino</term><term>Amino acids</term><term>Antarctic</term><term>Antarctic peninsula</term><term>Antarctic surface waters</term><term>Antarctica</term><term>Antcomb</term><term>Appl</term><term>Appl environ microbiol</term><term>Archaea</term><term>Archaeal</term><term>Arctic ocean</term><term>Austral summer</term><term>Bacterioplankton</term><term>Bacteroidetes</term><term>Biosynthesis</term><term>Blackwell publishing</term><term>Bowman</term><term>Burtonii</term><term>Carbohydrate</term><term>Chlorophyll</term><term>Clade</term><term>Class alphaproteobacteria</term><term>Class flavobacteria</term><term>Community composition</term><term>Database</term><term>Dehydrogenase</term><term>Delong</term><term>Diatom</term><term>East antarctica</term><term>Ecol</term><term>Environ</term><term>Environ microbiol</term><term>Environmental microbiology</term><term>Eukaryotic phytoplankton</term><term>Fems</term><term>Fems microbiol ecol</term><term>Flavobacteria</term><term>Fosmid libraries</term><term>Gaas</term><term>Gaas analysis</term><term>Gammaproteobacteria</term><term>Genome</term><term>Giovannoni</term><term>Grzymski</term><term>Heterotroph</term><term>Highest sequence identity</term><term>Isme</term><term>Kirchman</term><term>Labile</term><term>Labile solutes</term><term>Limnol oceanogr</term><term>Marine antarctic flavobacteria</term><term>Metabolism</term><term>Metagenome</term><term>Metagenome data</term><term>Metagenomic</term><term>Metaproteome</term><term>Metaproteomic</term><term>Metaproteomics</term><term>Microbial</term><term>Microbiol</term><term>Microbiology</term><term>Newcomb</term><term>Nutrient</term><term>Ocean surface</term><term>Oceanospirillales</term><term>Oceanospirillales alteromonadales</term><term>Organic matter</term><term>Otus</term><term>Outer membrane proteins</term><term>Pathway</term><term>Pelagibacter ubique</term><term>Phylogenetic</term><term>Phylogenetic assignment</term><term>Phytoplankton</term><term>Phytoplankton blooms</term><term>Pinhassi</term><term>Polaribacter</term><term>Primary production</term><term>Proc natl acad</term><term>Relative abundance</term><term>Relative abundances</term><term>Rhodobacterales</term><term>Roseobacter</term><term>Roseobacter clade</term><term>Seawater</term><term>Solute</term><term>Southern ocean</term><term>Southern ocean metagenome data</term><term>Southern ocean metagenomes</term><term>Sowell</term><term>Subunit</term><term>Surface waters</term><term>Synthetase</term><term>Teeling</term><term>Transport system</term><term>Transporter</term><term>Trna biosynthesis</term><term>Unique peptides</term><term>Uorescence</term><term>Water column depth</term></keywords><keywords scheme="Wicri" type="topic" xml:lang="fr"><term>Antarctique</term><term>Base de données</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract">Heterotrophic marine bacteria play key roles in remineralizing organic matter generated from primary production. However, far more is known about which groups are dominant than about the cellular processes they perform in order to become dominant. In the Southern Ocean, eukaryotic phytoplankton are the dominant primary producers. In this study we used metagenomics and metaproteomics to determine how the dominant bacterial and archaeal plankton processed bloom material. We examined the microbial community composition in 14 metagenomes and found that the relative abundance of Flavobacteria (dominated by Polaribacter) was positively correlated with chlorophyll a fluorescence, and the relative abundance of SAR11 was inversely correlated with both fluorescence and Flavobacteria abundance. By performing metaproteomics on the sample with the highest relative abundance of Flavobacteria (Newcomb Bay, East Antarctica) we defined how Flavobacteria attach to and degrade diverse complex organic material, how they make labile compounds available to Alphaproteobacteria (especially SAR11) and Gammaproteobacteria, and how these heterotrophic Proteobacteria target and utilize these nutrients. The presence of methylotrophic proteins for archaea and bacteria also indicated the importance of metabolic specialists. Overall, the study provides functional data for the microbial mechanisms of nutrient cycling at the surface of the coastal Southern Ocean.</div></front></TEI><affiliations><list><country><li>Australie</li><li>France</li></country><region><li>Nouvelle-Galles du Sud</li><li>Île-de-France</li></region><settlement><li>Paris</li><li>Sydney</li></settlement><orgName><li>Université Pierre-et-Marie-Curie</li></orgName></list><tree><country name="Australie"><region name="Nouvelle-Galles du Sud"><name sortKey="Williams, Timothy J" sort="Williams, Timothy J" uniqKey="Williams T" first="Timothy J." last="Williams">Timothy J. Williams</name></region><name sortKey="Cavicchioli, Ricardo" sort="Cavicchioli, Ricardo" uniqKey="Cavicchioli R" first="Ricardo" last="Cavicchioli">Ricardo Cavicchioli</name><name sortKey="Cavicchioli, Ricardo" sort="Cavicchioli, Ricardo" uniqKey="Cavicchioli R" first="Ricardo" last="Cavicchioli">Ricardo Cavicchioli</name><name sortKey="Demaere, Mathew Z" sort="Demaere, Mathew Z" uniqKey="Demaere M" first="Mathew Z." last="Demaere">Mathew Z. Demaere</name><name sortKey="Evans, Flavia" sort="Evans, Flavia" uniqKey="Evans F" first="Flavia" last="Evans">Flavia Evans</name><name sortKey="Long, Emilie" sort="Long, Emilie" uniqKey="Long E" first="Emilie" last="Long">Emilie Long</name><name sortKey="Raftery, Mark J" sort="Raftery, Mark J" uniqKey="Raftery M" first="Mark J." last="Raftery">Mark J. Raftery</name><name sortKey="Wilkins, David" sort="Wilkins, David" uniqKey="Wilkins D" first="David" last="Wilkins">David Wilkins</name></country><country name="France"><region name="Île-de-France"><name sortKey="Long, Emilie" sort="Long, Emilie" uniqKey="Long E" first="Emilie" last="Long">Emilie Long</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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