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Updated: Feb 16, 2026

Compost Microcosms as Microbially Diverse, Natural-like Environments for Microbiome Research in Caenorhabditis elegans
Published on: September 13, 2022
Exploring microbial diversity using cell-size fractionated enrichment incubations from subsurface aquifers at Äspö,
George Westmeijer1,2, Stephanie Turner1, Patrik Hevele1
1Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, Kalmar, Sweden.
Abstract:
The continental subsurface hosts energy-constrained groundwaters with a high diversity of ecologically elusive microorganisms adapted to the prevailing low-energy conditions. This study explored potential interactions among microbes using anaerobic enrichment incubations with three types of groundwater of contrasting hydrochemistry from the Äspö Hard Rock Laboratory, Sweden. Removing cells larger than 0.45 µm from the inoculum resulted in incubations enriched in populations characterized by very small genomes, including Patescibacteria, Nanobdellota, and Omnitrophota. These incubations had a higher diversity than non-fractionated incubations. However, cell numbers and community structure of the fractionated incubations did not change over an incubation period up to four months, despite high microbial diversity and experimental amendments with either simple (acetate) or more complex (cell lysate) carbon sources. In addition, network analysis on the groundwaters revealed multiple co-occurrences between populations affiliated with the Patescibacteria and the Desulfobacterota. Overall, these findings support that a considerable part of microbial diversity has a small cell size in these low energy groundwaters and strong co-occurrences among populations as an important survival strategy.
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