Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities

The ISME Journal
Tyler P BarnumJohn D Coates

Abstract

Dissimilatory perchlorate reduction is an anaerobic respiratory pathway that in communities might be influenced by metabolic interactions. Because the genes for perchlorate reduction are horizontally transferred, previous studies have been unable to identify uncultivated perchlorate-reducing populations. Here we recovered metagenome-assembled genomes from perchlorate-reducing sediment enrichments and employed a manual scaffolding approach to reconstruct gene clusters for perchlorate reduction found within mobile genetic elements. De novo assembly and binning of four enriched communities yielded 48 total draft genomes. In addition to canonical perchlorate reduction gene clusters and taxa, a new type of gene cluster with an alternative perchlorate reductase was identified. Phylogenetic analysis indicated past exchange between these gene clusters, and the presence of plasmids with either gene cluster shows that the potential for gene transfer via plasmid persisted throughout enrichment. However, a majority of genomes in each community lacked perchlorate reduction genes. Putative chlorate-reducing or sulfur-reducing populations were dominant in most communities, supporting the hypothesis that metabolic interactions might result fro...Continue Reading

References

Dec 10, 1996·Proceedings of the National Academy of Sciences of the United States of America·L BanciP Turano
Jan 10, 2003·Nucleic Acids Research·Daniel H HaftOwen White
Jan 6, 2004·Nucleic Acids Research·Dean Laslett, Bjorn Canback
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Apr 12, 2005·Environmental Science & Technology·Purnendu K DasguptaSrinath Rajagopalan
Mar 30, 2007·International Journal of Systematic and Evolutionary Microbiology·Yumiko KodamaKazuya Watanabe
Feb 28, 2009·Environmental Science & Technology·Srinath RajagopalanW Andrew Jackson
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Mar 10, 2010·BMC Bioinformatics·Doug HyattLoren J Hauser
Apr 28, 2010·Proceedings of the National Academy of Sciences of the United States of America·Brett J BakerJillian F Banfield
Aug 17, 2010·Bioinformatics·Robert C Edgar
Dec 15, 2010·Bioinformatics·Marten BoetzerWalter Pirovano
Feb 22, 2011·Bioinformatics·Diego DarribaDavid Posada
Aug 23, 2011·Applied and Environmental Microbiology·Ryan A MelnykJohn D Coates
Oct 1, 2011·Nature Methods·Thomas Nordahl PetersenHenrik Nielsen
Nov 1, 2011·PLoS Computational Biology·Sean R Eddy
Nov 22, 2011·Nucleic Acids Research·UNKNOWN UniProt Consortium
Jul 27, 2012·The ISME Journal·J Kirk HarrisNorman R Pace
Nov 30, 2012·Nucleic Acids Research·Christian QuastFrank Oliver Glöckner
Aug 15, 2013·Nature Communications·Nicola SegataCurtis Huttenhower
Oct 5, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Gordon GremmeStefan Kurtz
Oct 24, 2013·Extremophiles : Life Under Extreme Conditions·Aharon OrenLily Mana
Mar 20, 2014·Bioinformatics·Torsten Seemann
Jul 30, 2014·Frontiers in Microbiology·Anna EngelbrektsonJohn D Coates
Sep 15, 2014·Nature Methods·Johannes AlnebergChristopher Quince
Dec 17, 2014·Biochimica Et Biophysica Acta·Rosa María Martínez-EspinosaMaría José Bonete
Feb 28, 2015·Nature Communications·Birgit LuefJillian F Banfield
Mar 11, 2015·Environmental Microbiology Reports·Patrick GregoireJohn D Coates
May 7, 2015·Nucleic Acids Research·Robert D FinnSean R Eddy
Jun 18, 2015·Nature·Christopher T BrownJillian F Banfield
Jun 24, 2015·Bioinformatics·Ryan R WickKathryn E Holt
Sep 4, 2015·Environmental Microbiology Reports·Martin G LiebensteinerBart P Lomans

❮ Previous
Next ❯

Citations

Mar 14, 2020·Bioinformatics·Vijini MallawaarachchiYu Lin
Jul 1, 2020·International Journal of Systematic and Evolutionary Microbiology·Aharon OrenMartha E Trujillo
Jan 9, 2019·Frontiers in Microbiology·Siavash AtashgahiDetmer Sipkema
Sep 12, 2019·Frontiers in Microbiology·Evgenii I OlekhnovichElena N Ilina
Aug 25, 2018·Frontiers in Microbiology·Anna L EngelbrektsonJohn D Coates
Jul 25, 2020·BMC Bioinformatics·Tatiana DvorkinaSergey Nurk
May 6, 2021·Algorithms for Molecular Biology : AMB·Vijini G MallawaarachchiYu Lin
Feb 14, 2021·Bioinformatics·Bennett J Kapili, Anne E Dekas

❮ Previous
Next ❯

Datasets Mentioned

BETA
PRJNA387015

Software Mentioned

SSPACE
Picard Tools
FigTree
BLAST
Annotation Sketch
MEM
PSOX
CONCOCT
CheckM
AliView

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.