Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes

MBio
Ankita KothariAindrila Mukhopadhyay

Abstract

Naturally occurring plasmids constitute a major category of mobile genetic elements responsible for harboring and transferring genes important in survival and fitness. A targeted evaluation of plasmidomes can reveal unique adaptations required by microbial communities. We developed a model system to optimize plasmid DNA isolation procedures targeted to groundwater samples which are typically characterized by low cell density (and likely variations in the plasmid size and copy numbers). The optimized method resulted in successful identification of several hundred circular plasmids, including some large plasmids (11 plasmids more than 50 kb in size, with the largest being 1.7 Mb in size). Several interesting observations were made from the analysis of plasmid DNA isolated in this study. The plasmid pool (plasmidome) was more conserved than the corresponding microbiome distribution (16S rRNA based). The circular plasmids were diverse as represented by the presence of seven plasmid incompatibility groups. The genes carried on these groundwater plasmids were highly enriched in metal resistance. Results from this study confirmed that traits such as metal, antibiotic, and phage resistance along with toxin-antitoxin systems are encoded...Continue Reading

References

Nov 24, 1979·Nucleic Acids Research·H C Birnboim, J Doly
May 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·K GerdesS Molin
Sep 1, 1985·Journal of Bacteriology·A JafféS Hiraga
Sep 1, 1983·Applied and Environmental Microbiology·D G Anderson, L L McKay
Nov 1, 1982·Applied and Environmental Microbiology·N F BurtonA T Bull
Dec 19, 2003·Nucleic Acids Research·Raphaël LeplaeAriane Toussaint
Oct 11, 2005·Nucleic Acids Research·Ross OverbeekVeronika Vonstein
Jan 1, 1981·Applied and Environmental Microbiology·H S Hada, R K Sizemore
Sep 1, 1984·Applied and Environmental Microbiology·H KoboriH Shizuya
Jun 26, 2007·Applied and Environmental Microbiology·Qiong WangJames R Cole
Oct 4, 2008·Nucleic Acids Research·Bo Liu, Mihai Pop
Jun 23, 2009·Genome Research·Martin KrzywinskiMarco A Marra
Nov 26, 2009·Nucleic Acids Research·Raphaël LeplaeAriane Toussaint
Jan 19, 2010·Trends in Microbiology·Peter W HarrisonJ Peter W Young
Feb 23, 2010·BMC Microbiology·Wilfried RozhonBrigitte Poppenberger
May 22, 2010·FEMS Microbiology Letters·Sonia R VartoukianWilliam G Wade
Aug 17, 2010·Bioinformatics·Robert C Edgar
Aug 26, 2010·Bioinformatics·Nikos Darzentas
Sep 2, 2010·Microbiology and Molecular Biology Reviews : MMBR·Chris SmillieFernando de la Cruz
Oct 12, 2010·Nucleic Acids Research·Yucheng ShaoZixin Deng
Jun 28, 2011·Bioinformatics·Robert C EdgarRob Knight
Jun 30, 2011·FEMS Microbiology Reviews·Maria Pilar Garcillán-BarciaFernando de la Cruz
Aug 17, 2011·Frontiers in Microbiology·Rustam I Aminov
Mar 21, 2012·Proceedings of the National Academy of Sciences of the United States of America·Aya Brown KavItzhak Mizrahi
Oct 13, 2012·Mobile Genetic Elements·Itzhak Mizrahi
Nov 30, 2012·Nucleic Acids Research·Christian QuastFrank Oliver Glöckner
May 8, 2013·Antimicrobial Agents and Chemotherapy·Andrew G McArthurGerard D Wright
Aug 27, 2013·Applied and Environmental Microbiology·Sarah P PreheimEric J Alm
Sep 24, 2013·Journal of Microbiological Methods·Aya Brown KavItzhak Mizrahi
Dec 7, 2013·Nucleic Acids Research·Chandan PalD G Joakim Larsson
Feb 8, 2014·PloS One·Tue Sparholt JørgensenLars Hestbjerg Hansen
Mar 19, 2014·Frontiers in Microbiology·Jayashree RayAindrila Mukhopadhyay
Mar 29, 2014·Nature Communications·Thomas L RueggMichael P Thelen
Apr 30, 2014·Antimicrobial Agents and Chemotherapy·Alessandra CarattoliHenrik Hasman
Aug 15, 2014·PloS One·Anders NormanSøren Johannes Sørensen

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Citations

Sep 25, 2019·Proceedings of the National Academy of Sciences of the United States of America·Jörn PetersenAnne-Kristin Kaster
Jul 14, 2020·Frontiers in Microbiology·María Florencia PerezJulián Rafael Dib
Jun 2, 2021·MSystems·Philipp KirstahlerSünje Johanna Pamp
Aug 25, 2021·Journal of Environmental Management·Rongxuan WangRyo Honda
Nov 4, 2021·Scientific Reports·María Florencia PerezJulián Rafael Dib

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Methods Mentioned

BETA
environmental stress
atomic fluorescence spectrometry
PCR

Software Mentioned

py
UCLUST
rgi
pm
Perl scripts
BLAST
CARD
UD
MG
mothur

Related Concepts

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Antimicrobial Resistance (ASM)

Antimicrobial resistance poses a significant threat to the continued successful use of antimicrobial agents for the treatment of bacterial infections.

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Antimicrobial resistance poses a significant threat to the continued successful use of antimicrobial agents for the treatment of bacterial infections.