Diverse gene functions in a soil mobilome

TY - JOUR

T1 - Diverse gene functions in a soil mobilome

AU - Luo, Wenting

AU - Xu, Zhuofei

AU - Riber, Leise

AU - Hansen, Lars H.

AU - Sørensen, Søren Johannes

PY - 2016

Y1 - 2016

N2 - Accessing bacterial mobilomes of any given environment enables the investigation of genetic traits encoded by circular genetic elements, and how their transfer drives the adaptation of microbial communities. Here we take advantage of Illumina HiSeq sequencing and report, for the first time, the soil mobilome sampled from a well-characterized field in Hygum, Denmark. Soil bacterial cells were obtained by Nycodenz extraction, total DNA was purified by removing sheared chromosomal DNA using exonuclease digestion, and the remaining circular DNA was amplified with the phi29 polymerase and finally sequenced. The soil mobilome represented a wide range of known bacterial gene functions and highlighted the enrichment of plasmids, transposable elements and phages when compared to a well-characterized soil metagenome that, on the other hand, was dominated by basic biosynthesis and metabolism functions. Approximately one eighth of the gene set was of plasmid-intrinsic traits, including replication, conjugation, mobilization and stability based on Pfam database analysis. Resistance determinants toward aminoglycosides, beta-lactams and glycopeptides as well as multi-drug functions indicated that a substantial fraction of the soil resistome is plasmid-encoded and potentially mobilizable. Additionally, we recovered more than half of all Pfam-listed plasmid replication protein families, of which the composition of both common and rare replication families was significantly different from a previously reported wastewater and rat cecum mobilome. This comprehensive analysis reveals a distinct plasmid gene pool in the soil environment and suggests the prevalence of specific plasmid groups and plasmid-encoded genetic traits in distinct ecological environments.

AB - Accessing bacterial mobilomes of any given environment enables the investigation of genetic traits encoded by circular genetic elements, and how their transfer drives the adaptation of microbial communities. Here we take advantage of Illumina HiSeq sequencing and report, for the first time, the soil mobilome sampled from a well-characterized field in Hygum, Denmark. Soil bacterial cells were obtained by Nycodenz extraction, total DNA was purified by removing sheared chromosomal DNA using exonuclease digestion, and the remaining circular DNA was amplified with the phi29 polymerase and finally sequenced. The soil mobilome represented a wide range of known bacterial gene functions and highlighted the enrichment of plasmids, transposable elements and phages when compared to a well-characterized soil metagenome that, on the other hand, was dominated by basic biosynthesis and metabolism functions. Approximately one eighth of the gene set was of plasmid-intrinsic traits, including replication, conjugation, mobilization and stability based on Pfam database analysis. Resistance determinants toward aminoglycosides, beta-lactams and glycopeptides as well as multi-drug functions indicated that a substantial fraction of the soil resistome is plasmid-encoded and potentially mobilizable. Additionally, we recovered more than half of all Pfam-listed plasmid replication protein families, of which the composition of both common and rare replication families was significantly different from a previously reported wastewater and rat cecum mobilome. This comprehensive analysis reveals a distinct plasmid gene pool in the soil environment and suggests the prevalence of specific plasmid groups and plasmid-encoded genetic traits in distinct ecological environments.

KW - Mobile genetic elements

KW - Mobilome

KW - Plasmid metagenome

KW - Soil microbiology

U2 - 10.1016/j.soilbio.2016.07.018

DO - 10.1016/j.soilbio.2016.07.018

M3 - Journal article

AN - SCOPUS:84979529954

SN - 0038-0717

VL - 101

SP - 175

EP - 183

JO - Soil Biology & Biochemistry

JF - Soil Biology & Biochemistry

ER -