Characterizing an Anoxic Habitat: Sulfur Bacteria in a Meromictic Alpine Lake

Tracing long-distance electron transfer and cable bacteria in freshwater sediments by agar pillar gradient columns

Cable bacteria (CB) perform electrogenic sulphur oxidation (e-SOX) by spatially separating redox-half-reactions over cm-distances. For freshwater systems, the ecology of CB is not yet well understood, partly because they proved difficult to cultivate. This study introduces a new "agar pillar" approach to selectively enrich and investigate CB-populations. Within sediment columns, a central agar pillar is embedded, providing a sediment-free gradient-system in equilibrium with the surrounding sediment. We incubated freshwater sediments from a streambed, a sulfidic lake, and a hydrocarbon polluted aquifer in such agar pillar columns. Microprofiling revealed typical patterns of e-SOx, such as the development of a suboxic zone and the establishment of electric potentials. The bacterial communities in the sediments and agar pillars were analysed over depth by PacBio near-full-length 16S rRNA gene amplicon sequencing, allowing for a precise phylogenetic placement of taxa detected. The selective niche of the agar pillar was preferentially colonized by CB related to Candidatus Electronema for surface-water sediments, including several potentially novel species, but not for putative groundwater CB affiliated with Desulfurivibrio spp. The presence of CB was seemingly linked to co-enriched fermenters, hinting at a possible role of e-SOx-populations as an electron sink for heterotrophic microbes. These findings add to our current understanding of the diversity and ecology of CB in freshwater systems, and to a discrimination of CB from surface and groundwater sediments. The agar pillar approach provides a new strategy that may facilitate the cultivation of redox gradient-dependent microorganisms, including previously unrecognized CB populations.

Protistan diversity in a permanently stratified meromictic lake (Lake Alatsee, SW Germany)

Protists play a crucial role for ecosystem function(ing) and oxygen is one of the strongest barriers against their local dispersal. However, protistan diversity in freshwater habitats with oxygen gradients received very little attention. We applied high-throughput sequencing of the V9 region (18S rRNA gene) to provide a hitherto unique spatiotemporal analysis of protistan diversity along the oxygen gradient of a freshwater meromictic lake (Lake Alatsee, SW Germany). In the mixolimnion, the communities experienced most seasonal structural changes, with Stramenopiles dominating in autumn and Dinoflagellata in summer. The suboxic interface supported the highest diversity, but only 23 OTUs95% (mainly Euglenozoa, after quality check and removal of operational taxonomic units (OTUs) with less than three sequences) were exclusively associated with this habitat. Eukaryotic communities in the anoxic monimolimnion showed the most stable seasonal pattern, with Chrysophyta and Bicosoecida being the dominant taxa. Our data pinpoint to the ecological role of the interface as a short-term 'meeting point' for protists, contributing to the coupling of the mixolimnion and the monimolimnion. Our analyses of divergent genetic diversity suggest a high degree of previously undescribed OTUs. Future research will have to reveal if this result actually points to a high number of undescribed species in such freshwater habitats.