The effects of earthworms Eisenia spp. on microbial community are habitat dependent

• Eisenia spp. shifted microbial biomass and community structure in substrates passing through the gut.
• Gut transit increased anaerobes and reduced cultivable bacterial species richness.
• Eisenia spp. accelerated bacterial growth rate with gut passage in soil but not in compost.
• Worms from soil affected archaeal community structure more than worms from compost.
• The richer the earthworm habitat, the lower their influence on microbiota with gut transit.

The effects of earthworms Eisenia spp. on microorganisms of three different habitat soil, compost, and vermiculture were studied. Microbial communities of gut and fresh faeces of earthworms and substrates, the worms were collected from, were analysed. Microbial biomass and composition of the total microbial community were examined using phospholipid fatty acid (PLFA) biomarkers. Archaeal and bacterial communities were studied by polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE). The culturing methods were used for assessment of counts, species richness and growth strategy of bacteria.In comparison with the substrates, the viable microbial biomass and the group of non-ester-linked PLFAs indicative of anaerobes were higher in both the gut and faeces of all earthworm populations. The prokaryotic community evaluated using DGGE revealed that archaeal community structure in the gut and faeces of earthworms from populations differed from that in substrates, whereas the passage through the gut had less influence on the bacterial community structure, particularly in compost and vermiculture.The counts of culturable bacteria increased due to gut passage only in forest and vermiculture populations. The fast-growing bacteria increased due to gut passage only in forest soil population. Actinobacteria (Arthrobacter, Microbacterium, Lechevalieria and Nesterenkonia) and Firmicutes (Bacillus and Paenibacillus) were generally favoured in substrates and their species richness decreased with gut passage, whereas Gammaproteobacteria (Aeromonas, Enterobacter, Pseudomonas and Salmonella) dominated in gut contents. The impact of earthworm activity on the microbial community was higher in nutrient-poor forest soil than in nutrient-rich compost and vermiculture substrates.