Genomic evidence for the degradation of terrestrial organic matter by pelagic Arctic Ocean Chloroflexi bacteria

Colatriano, David; Tran, Patricia Q.; Guéguen, Celine; Williams, William J.; Lovejoy, Connie; Walsh, David A.

doi:10.1038/s42003-018-0086-7

Title: Genomic evidence for the degradation of terrestrial organic matter by pelagic Arctic Ocean Chloroflexi bacteria

Abstract

Abstract The Arctic Ocean currently receives a large supply of global river discharge and terrestrial dissolved organic matter. Moreover, an increase in freshwater runoff and riverine transport of organic matter to the Arctic Ocean is a predicted consequence of thawing permafrost and increased precipitation. The fate of the terrestrial humic-rich organic material and its impact on the marine carbon cycle are largely unknown. Here, a metagenomic survey of the Canada Basin in the Western Arctic Ocean showed that pelagic Chloroflexi from the Arctic Ocean are replete with aromatic compound degradation genes, acquired in part by lateral transfer from terrestrial bacteria. Our results imply marine Chloroflexi have the capacity to use terrestrial organic matter and that their role in the carbon cycle may increase with the changing hydrological cycle.

Authors:

Colatriano, David; Tran, Patricia Q.; Guéguen, Celine; Williams, William J.;

; Walsh, David A.

Publication Date:: Thu Jul 05 00:00:00 EDT 2018

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC)

OSTI Identifier:: 1457807

Alternate Identifier(s):: OSTI ID: 1624528

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Published Article

Journal Name:: Communications Biology

Additional Journal Information:: Journal Name: Communications Biology Journal Volume: 1 Journal Issue: 1; Journal ID: ISSN 2399-3642

Publisher:: Nature Publishing Group

Country of Publication:: United Kingdom

Language:: English

Subject:: Life Sciences & Biomedicine - Other Topics; Science & Technology - Other Topics

Citation Formats


                    Colatriano, David, Tran, Patricia Q., Guéguen, Celine, Williams, William J., Lovejoy, Connie, and Walsh, David A. Genomic evidence for the degradation of terrestrial organic matter by pelagic Arctic Ocean Chloroflexi bacteria.  United Kingdom: N. p., 2018. 
Web.  doi:10.1038/s42003-018-0086-7.

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                    Colatriano, David, Tran, Patricia Q., Guéguen, Celine, Williams, William J., Lovejoy, Connie, & Walsh, David A. Genomic evidence for the degradation of terrestrial organic matter by pelagic Arctic Ocean Chloroflexi bacteria.  United Kingdom.  https://doi.org/10.1038/s42003-018-0086-7

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                    Colatriano, David, Tran, Patricia Q., Guéguen, Celine, Williams, William J., Lovejoy, Connie, and Walsh, David A. Thu .  
"Genomic evidence for the degradation of terrestrial organic matter by pelagic Arctic Ocean Chloroflexi bacteria".  United Kingdom.  https://doi.org/10.1038/s42003-018-0086-7.

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@article{osti_1457807,

  title        = {Genomic evidence for the degradation of terrestrial organic matter by pelagic Arctic Ocean Chloroflexi bacteria},

  author       = {Colatriano, David and Tran, Patricia Q. and Guéguen, Celine and Williams, William J. and Lovejoy, Connie and Walsh, David A.},

  abstractNote = {Abstract The Arctic Ocean currently receives a large supply of global river discharge and terrestrial dissolved organic matter. Moreover, an increase in freshwater runoff and riverine transport of organic matter to the Arctic Ocean is a predicted consequence of thawing permafrost and increased precipitation. The fate of the terrestrial humic-rich organic material and its impact on the marine carbon cycle are largely unknown. Here, a metagenomic survey of the Canada Basin in the Western Arctic Ocean showed that pelagic Chloroflexi from the Arctic Ocean are replete with aromatic compound degradation genes, acquired in part by lateral transfer from terrestrial bacteria. Our results imply marine Chloroflexi have the capacity to use terrestrial organic matter and that their role in the carbon cycle may increase with the changing hydrological cycle.},

  doi          = {10.1038/s42003-018-0086-7},

  journal      = {Communications Biology},

  number       = 1,

  volume       = 1,

  place        = {United Kingdom},

  year         = {Thu Jul 05 00:00:00 EDT 2018},

  month        = {Thu Jul 05 00:00:00 EDT 2018}

}

Copy to clipboard

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Title: Genomic evidence for the degradation of terrestrial organic matter by pelagic Arctic Ocean Chloroflexi bacteria

Abstract

Citation Formats

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees journal, April 2016

Photobleaching of fluorescent dissolved organic matter in Beaufort Sea and North Atlantic Subtropical Gyre journal, December 2015

Prevalence of the Chloroflexi-Related SAR202 Bacterioplankton Cluster throughout the Mesopelagic Zone and Deep Ocean journal, May 2004

Characterization of the Gallate Dioxygenase Gene: Three Distinct Ring Cleavage Dioxygenases Are Involved in Syringate Degradation by Sphingomonas paucimobilis SYK-6 journal, July 2005

Microbial degradation of aromatic compounds — from one strategy to four journal, October 2011

Distribution of PARAFAC modeled CDOM components in the North Pacific Ocean, Bering, Chukchi and Beaufort Seas journal, December 2013

Biochemical and Genetic Characterization of a Gentisate 1,2-Dioxygenase from Sphingomonas sp. Strain RW5 journal, August 1998

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures journal, January 2012

Export of young terrigenous dissolved organic carbon from rivers to the Arctic Ocean: AGE OF ARCTIC DISSOLVED ORGANIC CARBON journal, March 2004

Accounting For Alignment Uncertainty in Phylogenomics journal, January 2012

Activation of old carbon by erosion of coastal and subsea permafrost in Arctic Siberia journal, August 2012

Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior journal, January 2006

Abundance and activity of Chloroflexi-type SAR202 bacterioplankton in the meso- and bathypelagic waters of the (sub)tropical Atlantic journal, July 2008

The nature of colored dissolved organic matter in the southern Canada Basin and East Siberian Sea journal, December 2012

Bacterioplankton communities of Crater Lake, OR: dynamic changes with euphotic zone food web structure and stable deep water populations journal, January 2007

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities journal, October 2009

16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the Green Non-Sulfur bacteria. journal, July 1996

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MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph journal, January 2015

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Ring-Cleaving Dioxygenases with a Cupin Fold journal, January 2012

Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy journal, June 2007

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Cultivation of Uncultured Chloroflexi Subphyla: Significance and Ecophysiology of Formerly Uncultured Chloroflexi 'Subphylum I' with Natural and Biotechnological Relevance journal, January 2009

Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean journal, July 2010

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Freshwater and its role in the Arctic Marine System: Sources, disposition, storage, export, and physical and biogeochemical consequences in the Arctic and global oceans: FRESHWATER AND THE ARCTIC MARINE SYSTEM journal, March 2016

Towards a rain-dominated Arctic journal, March 2017

MUSCLE: multiple sequence alignment with high accuracy and high throughput journal, March 2004

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Proteinortho: Detection of (Co-)orthologs in large-scale analysis journal, April 2011

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans journal, January 2018

Unusual bacterioplankton community structure in ultra‐oligotrophic Crater Lake journal, April 2001

The fate of terrigenous dissolved organic carbon on the Eurasian shelves and export to the North Atlantic: ARCTIC TERRIGENOUS DOC REMOVAL journal, January 2017

The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081) journal, January 2016

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 journal, October 2013

Impacts of permafrost degradation on arctic river biogeochemistry journal, January 2009

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter journal, April 2017

Major flux of terrigenous dissolved organic matter through the Arctic Ocean journal, December 1999

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
journal, April 2016

Photobleaching of fluorescent dissolved organic matter in Beaufort Sea and North Atlantic Subtropical Gyre
journal, December 2015

Prevalence of the Chloroflexi-Related SAR202 Bacterioplankton Cluster throughout the Mesopelagic Zone and Deep Ocean
journal, May 2004

Characterization of the Gallate Dioxygenase Gene: Three Distinct Ring Cleavage Dioxygenases Are Involved in Syringate Degradation by Sphingomonas paucimobilis SYK-6
journal, July 2005

Microbial degradation of aromatic compounds — from one strategy to four
journal, October 2011

Distribution of PARAFAC modeled CDOM components in the North Pacific Ocean, Bering, Chukchi and Beaufort Seas
journal, December 2013

Biochemical and Genetic Characterization of a Gentisate 1,2-Dioxygenase from Sphingomonas sp. Strain RW5
journal, August 1998

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures
journal, January 2012

Export of young terrigenous dissolved organic carbon from rivers to the Arctic Ocean: AGE OF ARCTIC DISSOLVED ORGANIC CARBON
journal, March 2004

Accounting For Alignment Uncertainty in Phylogenomics
journal, January 2012

Activation of old carbon by erosion of coastal and subsea permafrost in Arctic Siberia
journal, August 2012

Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior
journal, January 2006

Abundance and activity of Chloroflexi-type SAR202 bacterioplankton in the meso- and bathypelagic waters of the (sub)tropical Atlantic
journal, July 2008

The nature of colored dissolved organic matter in the southern Canada Basin and East Siberian Sea
journal, December 2012

Bacterioplankton communities of Crater Lake, OR: dynamic changes with euphotic zone food web structure and stable deep water populations
journal, January 2007

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
journal, October 2009

16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the Green Non-Sulfur bacteria.
journal, July 1996

Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean
journal, August 2009

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
journal, January 2015

The Pathway Tools Pathway Prediction Algorithm
journal, December 2011

Ring-Cleaving Dioxygenases with a Cupin Fold
journal, January 2012

Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
journal, June 2007

Characterizing the Promiscuity of LigAB, a Lignin Catabolite Degrading Extradiol Dioxygenase from Sphingomonas paucimobilis SYK-6
journal, September 2013

Cultivation of Uncultured Chloroflexi Subphyla: Significance and Ecophysiology of Formerly Uncultured Chloroflexi 'Subphylum I' with Natural and Biotechnological Relevance
journal, January 2009

Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean
journal, July 2010

Phylogenetic Composition of Bacterioplankton Assemblages from the Arctic Ocean
journal, February 2002

Freshwater and its role in the Arctic Marine System: Sources, disposition, storage, export, and physical and biogeochemical consequences in the Arctic and global oceans: FRESHWATER AND THE ARCTIC MARINE SYSTEM
journal, March 2016

Towards a rain-dominated Arctic
journal, March 2017

MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015

Proteinortho: Detection of (Co-)orthologs in large-scale analysis
journal, April 2011

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans
journal, January 2018

Unusual bacterioplankton community structure in ultra‐oligotrophic Crater Lake
journal, April 2001

The fate of terrigenous dissolved organic carbon on the Eurasian shelves and export to the North Atlantic: ARCTIC TERRIGENOUS DOC REMOVAL
journal, January 2017

The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081)
journal, January 2016

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
journal, October 2013

Impacts of permafrost degradation on arctic river biogeochemistry
journal, January 2009

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter
journal, April 2017

Major flux of terrigenous dissolved organic matter through the Arctic Ocean
journal, December 1999