Metagenomic Analysis of a Biphenyl-Degrading Soil Bacterial Consortium Reveals the Metabolic Roles of Specific Populations

Frontiers in Microbiology
Daniel Garrido-SanzRafael Rivilla

Abstract

Polychlorinated biphenyls (PCBs) are widespread persistent pollutants that cause several adverse health effects. Aerobic bioremediation of PCBs involves the activity of either one bacterial species or a microbial consortium. Using multiple species will enhance the range of PCB congeners co-metabolized since different PCB-degrading microorganisms exhibit different substrate specificity. We have isolated a bacterial consortium by successive enrichment culture using biphenyl (analog of PCBs) as the sole carbon and energy source. This consortium is able to grow on biphenyl, benzoate, and protocatechuate. Whole-community DNA extracted from the consortium was used to analyze biodiversity by Illumina sequencing of a 16S rRNA gene amplicon library and to determine the metagenome by whole-genome shotgun Illumina sequencing. Biodiversity analysis shows that the consortium consists of 24 operational taxonomic units (≥97% identity). The consortium is dominated by strains belonging to the genusPseudomonas, but also contains betaproteobacteria andRhodococcusstrains. whole-genome shotgun (WGS) analysis resulted in contigs containing 78.3 Mbp of sequenced DNA, representing around 65% of the expected DNA in the consortium. Bioinformatic analysi...Continue Reading

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Citations

Sep 11, 2018·Critical Reviews in Biotechnology·Arun Kumar DangiPratyoosh Shukla
Mar 29, 2019·Current Opinion in Infectious Diseases·Bodo LinzEric T Harvill
May 22, 2019·Functional & Integrative Genomics·Niti B JadejaAtya Kapley
Aug 23, 2019·Microbial Ecology·Yihua SunMeng Li
Oct 5, 2019·Microbiology Resource Announcements·Elaine L OliveiraStephan C Schuster
May 28, 2020·Microorganisms·Daniel Garrido-SanzRafael Rivilla
Nov 12, 2020·Journal, Genetic Engineering & Biotechnology·Lateef Babatunde Salam, Oluwafemi Sunday Obayori
Nov 13, 2020·Frontiers in Microbiology·Israel RiveraEric T Harvill
Mar 2, 2021·Frontiers in Bioengineering and Biotechnology·Sandhya MishraShaohua Chen
Jun 11, 2021·Chemosphere·Petrić InesUdiković-Kolić Nikolina
May 8, 2018·Environmental Science & Technology·Longfei JiangGan Zhang

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Datasets Mentioned

BETA
SRR6076973
MF996860

Methods Mentioned

BETA
PCR
whole-genome shotgun sequencing

Software Mentioned

RAST
samtools
QUAST
MEGA
bowtie2
SIP
R package iNEXT
Perl scripts
QIIME
UPARSE

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