Riparian cottonwood trees and adjacent river sediments have different microbial communities and produce methane with contrasting carbon isotope compositions

Rivers and their adjacent riparian forests are intimately linked by the exchange of water, nutrients, and organic matter. Both riparian cottonwood trees and adjacent river sediments host microbial communities including archeal methanogens, supporting methane production and emission to the atmosphere. Here we combine microbial community and in vitro stable isotope analyses to characterize the drivers of methane cycling in distinct anoxic habitats (river sediments vs. riparian cottonwood stems) associated with the Oldman River, southern Alberta (Canada). We demonstrate that, differences in the chemical characteristics of organic matter support divergent microbial communities that generate methane from distinct metabolic pathways. Organic matter in river sediments had C/N ratios approximately 50-fold lower than in tree stems and had more diverse dissolved organic components. Contrasting substrate availability between river sediment and tree stems was likely the primary mechanism for the greater microbial diversity in river sediments than in tree stems, the significantly different bacterial communities, and the trend toward differing abundance of methanogen orders. The methane carbon isotope composition (delta C-13 values) differed for the tree stem (-103.6 parts per thousand to -70.6 parts per thousand) and river sediment (-55.1 parts per thousand to -48.4 parts per thousand) environments, suggesting that methane was primarily produced via CO2-reduction in tree stems by Methanobacteriales, while river sediments produced more methane through acetate fermentation primarily by Methanosarcinales. This study demonstrates the importance of organic matter quality and microbial community composition in driving metabolic processes contributing to methane production and emission in rivers and adjacent riparian forests. Plain Language Summary In semi-arid habitats, riparian trees are restricted to areas adjacent to flowing rivers. Some riparian tree stems and adjacent river sediments harbor microorganisms that produce methane that is released to the atmosphere. In this study we compared the microbial communities that exist in cottonwood riparian trees stems and the adjacent river sediment. Our results indicated that the bacterial communities and the methane-producing archeal communities strongly differed between the tree stems and river sediment, likely because the organic matter in the two environments had contrasting chemical characteristics. As a consequence of the differences in the microbial communities and organic matter, the archeal microbes produce methane via different biochemical pathways that result in the methane released by the tree stems and river sediments having contrasting amounts of two stable isotopes of carbon (C-13 and C-12). This establishes the opportunity to identify and separate, based on its stable carbon isotope ratio, the methane that is released from tree stems and river sediment in these adjacent and linked terrestrial and aquatic ecosystems. Our study also provides greater understanding of factors controlling methane production in tree stems and river sediments, processes that are currently not included in global methane budgets.