High‐resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils

Abstract

Despite being key contributors to biogeochemical processes, archaea are frequently outnumbered by bacteria, and consequently are underrepresented in combined molecular surveys. Here, we demonstrate an approach to concurrently survey the archaea alongside the bacteria with high-resolution 16S rRNA gene sequencing, linking these community data to geochemical parameters. We applied this integrated analysis to hydric soils sampled across a model methane-emitting freshwater wetland. Geochemical profiles, archaeal communities, and bacterial communities were independently correlated with soil depth and water cover. Centimeters of soil depth and corresponding geochemical shifts consistently affected microbial community structure more than hundreds of meters of lateral distance. Methanogens with diverse metabolisms were detected across the wetland, but displayed surprising OTU-level partitioning by depth. Candidatus Methanoperedens spp. archaea thought to perform anaerobic oxidation of methane linked to iron reduction were abundant. Domain-specific sequencing also revealed unexpectedly diverse non-methane-cycling archaeal members. OTUs within the underexplored Woesearchaeota and Bathyarchaeota were prevalent across the wetland, with subgroups and individual OTUs exhibiting distinct occupancy and abundance distributions aligned with environmental gradients. This study adds to our understanding of ecological range for key archaeal taxa in a model freshwater wetland, and links these taxa and individual OTUs to hypotheses about processes governing biogeochemical cycling.

Microbial subnetworks related to short-term diel O2fluxes within geochemically distinct freshwater wetlands

“…These results show that spatial differences exist within the tested 3-meter scale and underscore the importance of analyzing spatially distinct zones within wetland systems, as microbial communities can be distinct in community structure throughout a wetland, and therefore, may respond to diel fluxes differentially. Similar types of spatial variability in bacterial communities has also been found in other studies which explored wetland microbial communities (Song et al, 2012; Narrowe et al, 2017). While microbial community structure can also be impacted by dominant vegetative type (Tang et al, 2011), the samples collected in this study were taken within the same vegetation type (defined as at least 75% of one morphotype).…”

Rice paddyNitrospiraeencode and express genes related to sulfate respiration: proposal of the new genusCandidatusSulfobium

“…and magnetotactic Nitrospirae , are regularly observed in 16S rRNA gene- and dsrAB -based surveys of anoxic freshwater and marine environments of moderate temperature. These environments include marine (37) and estuarine (48) sediments, groundwater (42, 49), lake sediment (50), wetland soil (51), and rice paddy fields (10, 52, 53). Also in rice paddy soil analyzed in this study, eight species-level operational taxonomic units (OTUs) of such Nitrospirae were observed previously by 16S rRNA gene-based amplicon sequencing (Fig.…”

Relationships Between Methane and Carbon Dioxide Fluxes in a Temperate Cattail‐Dominated Freshwater Wetland

“…In the case of CH 4 emissions, accounting for hot moments and hot spots is vital for designing management practices to mitigate the negative climate feedbacks (McClain et al, 2003;Wilson et al, 2009). Hot spots and moments can also account for the contrasting activity of methanogenic and methanotrophic consortia (e.g., (Narrowe et al, 2017)), which have important implications when connecting plant and microbial interactions modeling efforts (Bridgham et al, 2013).…”