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ABSTRACT Hydrologic shifts due to climate change will affect the cycling of carbon (C) stored in boreal peatlands. Carbon cycling in these systems is carried out by microorganisms and plants in close association. This study investigated the effects of experimentally manipulated water tables (lowered and raised) and plant functional groups on the peat and root microbiomes in a boreal rich fen. All samples were sequenced and processed for bacterial, archaeal (16S DNA genes; V4), and fungal (internal transcribed spacer 2 [ITS2]) DNA. Depth had a strong effect on microbial and fungal communities across all water table treatments. Bacterial and archaeal communities were most sensitive to the water table treatments, particularly at the 10- to 20-cm depth; this area coincides with the rhizosphere or rooting zone. Iron cyclers, particularly members of the family Geobacteraceae , were enriched around the roots of sedges, horsetails, and grasses. The fungal community was affected largely by plant functional group, especially cinquefoils. Fungal endophytes (particularly Acephala spp.) were enriched in sedge and grass roots, which may have underappreciated implications for organic matter breakdown and cycling. Fungal lignocellulose degraders were enriched in the lowered water table treatment. Our results were indicative of two main methanogen communities, a rooting zone community dominated by the archaeal family Methanobacteriaceae and a deep peat community dominated by the family Methanomicrobiaceae . IMPORTANCE This study demonstrated that roots and the rooting zone in boreal fens support organisms likely capable of methanogenesis, iron cycling, and fungal endophytic association and are directly or indirectly affecting carbon cycling in these ecosystems. These taxa, which react to changes in the water table and associate with roots and, particularly, graminoids, may gain greater biogeochemical influence, as projected higher precipitation rates could lead to an increased abundance of sedges and grasses in boreal fens. 

Aims Climate warming in northern ecosystems is triggering widespread permafrost thaw, during which deep soil nutrients, such as nitrogen, could become available for biological uptake. Permafrost thaw shift frozen organic matter to a saturated state, which could impede nutrient uptake. We assessed whether soil nitrogen can be accessed by the deep roots of vascular plants in thermokarst bogs, potentially allowing for increases in primary productivity. Methods We conducted an ammonium uptake experiment on Carex aquatilis Wahlenb. roots excavated from thermokarst bogs in interior Alaska. Ammonium uptake capacity was compared between deep and shallow roots. We also quantified differences in root ammonium uptake capacity and plant size characteristics (plant aboveground and belowground biomass, maximum shoot height, and maximum root length) between the actively-thawing margin and the centre of each thermokarst bog as a proxy for time-following-thaw. Results Deep roots had greater ammonium uptake capacity than shallow roots, while rooting depth, but not belowground biomass, was positively correlated with aboveground biomass. Although there were no differences in aboveground biomass between the margin and centre, our findings suggest that plants can benefit from investing in the acquisition of resources near the vertical thaw front. Conclusions Our results suggest that deep roots of C. aquatilis can contribute to plant nitrogen uptake and are therefore able to tolerate anoxic conditions in saturated thermokarst bogs. This work furthers our understanding of how subarctic and wetland plants respond to warming and how enhanced plant biomass production might help offset ecosystem carbon release with future permafrost thaw.