TY - JOUR

T1 - Insights into the earthworm gut multi-kingdom microbial communities

AU - Sapkota, Rumakanta

AU - Santos, Susana

AU - Farias, Pedro Daniel Geadas

AU - Krogh, Paul Henning

AU - Winding, Anne

PY - 2020/7

Y1 - 2020/7

N2 - Earthworms are widely known to impact soil health, having a keyrole in nutrient cycling and are often referred to as soil engineers.They are vital for soil microbial assemblages particularly through theirfeeding and burrowing activity in soil. Earthworms feed on soil organicmatter and litter, and the resulting casts alter the soil microbialcommunity. However, the gut microbiome of earthworms remains less known.In this study, we used amplicon sequencing of the 16S rRNA gene forbacteria and 18S rRNA gene for eukaryotes to assess the gut communityassemblages of earthworm species within three genera Aporrectodea,Allolobophora and Lumbricus that represent different life forms sharingthe same habitat. The objective was to compare the gut microbiomeprofiles of eukaryotic and prokaryotic organisms to assess significanceof earthworm life forms, and to explore the cross kingdom networks in anattempt to identify keystone species. We found a high eukaryoticdiversity with a dominance of the SAR supergroup along with fungi andmetazoan in the earthworm gut. The bacterial community were dominated bymembers of Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, andVerrucomicrobia. The eukaryotic and prokaryotic communities showedsimilar differences in alpha diversity, being lowest in Lumbricusherculeus. The beta diversity showed earthworm species as a key factor inshaping gut microbiomes with L. herculeus harboring distinct microbiomescompared to species of Aporrectodea caliginosa, A. longa, A. tuberculataand Allolobophora chlorotica. Cross kingdom networks showed highinteractions between several protist and bacterial OTUs. In conclusion,this study suggested that the community assemblages of gut microbiomeswas shaped by earthworm species and life form, and such assemblageconsist of cross kingdom interactions among eukaryotes and prokaryotes.

AB - Earthworms are widely known to impact soil health, having a keyrole in nutrient cycling and are often referred to as soil engineers.They are vital for soil microbial assemblages particularly through theirfeeding and burrowing activity in soil. Earthworms feed on soil organicmatter and litter, and the resulting casts alter the soil microbialcommunity. However, the gut microbiome of earthworms remains less known.In this study, we used amplicon sequencing of the 16S rRNA gene forbacteria and 18S rRNA gene for eukaryotes to assess the gut communityassemblages of earthworm species within three genera Aporrectodea,Allolobophora and Lumbricus that represent different life forms sharingthe same habitat. The objective was to compare the gut microbiomeprofiles of eukaryotic and prokaryotic organisms to assess significanceof earthworm life forms, and to explore the cross kingdom networks in anattempt to identify keystone species. We found a high eukaryoticdiversity with a dominance of the SAR supergroup along with fungi andmetazoan in the earthworm gut. The bacterial community were dominated bymembers of Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, andVerrucomicrobia. The eukaryotic and prokaryotic communities showedsimilar differences in alpha diversity, being lowest in Lumbricusherculeus. The beta diversity showed earthworm species as a key factor inshaping gut microbiomes with L. herculeus harboring distinct microbiomescompared to species of Aporrectodea caliginosa, A. longa, A. tuberculataand Allolobophora chlorotica. Cross kingdom networks showed highinteractions between several protist and bacterial OTUs. In conclusion,this study suggested that the community assemblages of gut microbiomeswas shaped by earthworm species and life form, and such assemblageconsist of cross kingdom interactions among eukaryotes and prokaryotes.

KW - Microbiomes

KW - Protists

KW - Eukaryotic microbes

KW - eDNA

KW - metabarcoding

KW - amplicon sequencing

U2 - 10.1016/j.scitotenv.2020.138301

DO - 10.1016/j.scitotenv.2020.138301

M3 - Journal article

VL - 727

JO - Science of the Total Environment

JF - Science of the Total Environment

SN - 0048-9697

M1 - 138301

ER -