Environmental filtering: A case of bacterial community assembly in soil

TY - JOUR

T1 - Environmental filtering: A case of bacterial community assembly in soil

AU - Yan, Yan

AU - Klinkhamer, Peter G.L.

AU - van Veen, Johannes A.

AU - Kuramae, Eiko E.

N1 - 6757, ME; Data Archiving: Data archived at ENA: All MiSeq data were uploaded to the ENA and are publicly accessible under study accession number PRJEB31454.

PY - 2019

Y1 - 2019

N2 - Soil has a strong effect on the assembly of bacterial communities, as revealed by studies in which sterilized soil is inoculated with dilution series of bacterial suspensions from the same soil. However, the impact of soil on the assembly of bacterial communities after inoculation with suspensions from different soils is not clear. Here, we explored environmental filtering of bacterial community assembly. Diluted suspensions from different soils harboring different bacterial diversities were used to cross-inoculate three pre-sterilized soils. The main differences in the abiotic factors of the soils were organic matter, ammonium, nitrate, and phosphorus content, pH and the C:N ratio. We used 16S rRNA gene amplicon sequencing to determine the bacterial community structure of the suspensions and the soils. When the different diluted suspensions were used to inoculate their native soils, the regrown soil bacterial communities clustered together; by contrast, the communities were separated when the same suspensions were used to inoculate soils other than their native soils. The diversity indices of the suspensions decreased significantly upon dilution. The strength of selection of bacterial communities by soil was stronger for the 10−1 diluted soil samples than for the 10−9 diluted soil samples. Thus, differences in abiotic factors shape and explain the variation in bacterial community assemblage among these soils.

AB - Soil has a strong effect on the assembly of bacterial communities, as revealed by studies in which sterilized soil is inoculated with dilution series of bacterial suspensions from the same soil. However, the impact of soil on the assembly of bacterial communities after inoculation with suspensions from different soils is not clear. Here, we explored environmental filtering of bacterial community assembly. Diluted suspensions from different soils harboring different bacterial diversities were used to cross-inoculate three pre-sterilized soils. The main differences in the abiotic factors of the soils were organic matter, ammonium, nitrate, and phosphorus content, pH and the C:N ratio. We used 16S rRNA gene amplicon sequencing to determine the bacterial community structure of the suspensions and the soils. When the different diluted suspensions were used to inoculate their native soils, the regrown soil bacterial communities clustered together; by contrast, the communities were separated when the same suspensions were used to inoculate soils other than their native soils. The diversity indices of the suspensions decreased significantly upon dilution. The strength of selection of bacterial communities by soil was stronger for the 10−1 diluted soil samples than for the 10−9 diluted soil samples. Thus, differences in abiotic factors shape and explain the variation in bacterial community assemblage among these soils.

KW - national

UR - https://www.ebi.ac.uk/ena/browser/view/PRJEB31454

U2 - 10.1016/j.soilbio.2019.107531

DO - 10.1016/j.soilbio.2019.107531

M3 - Article

SN - 0038-0717

VL - 136

JO - Soil Biology & Biochemistry

JF - Soil Biology & Biochemistry

M1 - 107531

ER -