Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient

Abstract

SummaryBiogenic production and release of methane (CH4) from thawing permafrost has the potential to be a strong source of radiative forcing. We investigated changes in the active layer microbial community of three sites representative of distinct permafrost thaw stages at a palsa mire in northern Sweden. The palsa sites with intact permafrost, and low radiative forcing signature had a phylogenetically clustered community dominated by Acidobacteria and Proteobacteria. The bog with thawing permafrost and low radiative forcing signature was dominated by hydrogenotrophic methanogens and Acidobacteria, had lower alpha diversity, and midrange phylogenetic clustering, characteristic of ecosystem disturbance affecting habitat filtering, shifting from palsa-like to fen-like at the waterline. The fen had no underlying permafrost, and the highest alpha, beta and phylogenetic diversity, was dominated by Proteobacteria and Euryarchaeota, and was significantly enriched in methanogens. The mire microbial network was modular with module cores consisting of clusters of Acidobacteria, Euryarchaeota, or Xanthomonodales. Loss of underlying permafrost with associated hydrological shifts correlated to changes in microbial composition, alpha, beta, and phylogenetic diversity associated with a higher radiative forcing signature. These results support the complex role of microbial interactions in mediating carbon budget changes and climate feedback in response to climate forcing.

Soil viruses are underexplored players in ecosystem carbon processing

“…Intriguingly, while our virome-derived vOTU richness was lowest in the palsa, Emerson et al’s (46) much greater sampling recovered the most vOTUs in the palsa, more than double that in the fen (42% vs. 18.9% of total vOTUs). This major difference could potentially be due to the known increase in microbial alpha diversity along the thaw gradient (15, 16), causing increased difficulty of viral genome reconstruction in the bulk-soil metagenomes; specifically, this could be due to poorer assembly of temperate phages within an increasingly diverse microbiota, or of lytic or free viruses due to concomitantly increasing viral diversity (which is consistent with the increased vOTU richness with thaw in our virome dataset). Notably, neither this dataset nor that of Emerson et al (46) captured ssDNA or RNA viruses, which potentially represent up to half of viral particles (122–124).…”

“…Eight viruses were linked to more than one host, but always within the same species. The four predicted microbial hosts are among the most abundant in the microbial communities, and have notable roles in C cycling (15; 16). Three are acidophilic, obligately aerobic chemoorganoheterotrophs and include the Mire’s dominant polysaccharide-degrading lineage ( Acidobacteria ), and the fourth is an obligate anaerobe shown to be syntrophic with methanogens ( Smithella).…”

“…In addition, at Stordalen Mire (and at other similar sites; 110), microbiota are strongly differentiated by thaw-stage habitat, with some limited overlap among ‘dry’ communities (i.e. those above the water table, the palsa and shallow bog), and among ‘wet’ ones (those below the water table, the deeper bog and fen) (14, 15, 16). These shifting microbial hosts likely impact viral community structure.…”

Increases in temperature and nutrient availability positively affect methane‐cycling microorganisms in Arctic thermokarst lake sediments

“…(2017) who used the same extraction method and 16S rRNA gene amplification as our study. The most abundant Archaea belonged to Rice Cluster II, Methanosaetaceae, and Bathyarchaeota, which are commonly found in permafrost sediments and soils (Mondav et al, 2017;Winkel et al, 2018).…”

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“…Habitats broadly span three stages of permafrost thaw: palsa (drained soil, dominated by small shrubs, and underlain by intact permafrost), bog (partially inundated peat, dominated by Sphagnum moss, and underlain by partially thawed permafrost), and fen (fully inundated peat, dominated by sedges, and with no detectable permafrost at <1 m) (further described in Hodgkins et al 2014). These soils vary chemically (Hodgkins et al, 2014;Normand et al 2017;Wilson et al 2017), hydraulically (Christensen et al 2004Malmer et al 2005;Olefeldt et al 2012;Jonasson et al 2012), and biologically (Mondav et al 2014;McCalley et al 2014;Mondav et al 2017;Woodcroft et al 2018), creating three distinct habitats. Soil was collected with an 11 cm-diameter custom circular push corer at palsa sites, and with a 10 cm × 10 cm square Wardenaar corer (Eijkelkamp, The Netherlands) at the bog and fen sites.…”