Metabolic potential of microbial communities from ferruginous sediments

Abstract

Ferruginous (Fe-rich, SO -poor) conditions are generally restricted to freshwater sediments on Earth today, but were likely widespread during the Archean and Proterozoic Eons. Lake Towuti, Indonesia, is a large ferruginous lake that likely hosts geochemical processes analogous to those that operated in the ferruginous Archean ocean. The metabolic potential of microbial communities and related biogeochemical cycling under such conditions remain largely unknown. We combined geochemical measurements (pore water chemistry, sulfate reduction rates) with metagenomics to link metabolic potential with geochemical processes in the upper 50 cm of sediment. Microbial diversity and quantities of genes for dissimilatory sulfate reduction (dsrAB) and methanogenesis (mcrA) decrease with increasing depth, as do rates of potential sulfate reduction. The presence of taxa affiliated with known iron- and sulfate-reducers implies potential use of ferric iron and sulfate as electron acceptors. Pore-water concentrations of acetate imply active production through fermentation. Fermentation likely provides substrates for respiration with iron and sulfate as electron donors and for methanogens that were detected throughout the core. The presence of ANME-1 16S and mcrA genes suggests potential for anaerobic methane oxidation. Overall our data suggest that microbial community metabolism in anoxic ferruginous sediments support coupled Fe, S and C biogeochemical cycling.

Vivianite formation in ferruginous sediments from Lake Towuti, Indonesia

“…Concentrations of DIC, which is produced during OM degradation, gradually increase with depth ( Fig. 2a), suggesting that OM remineralization in shallow sediment is mainly driven by fermentation and methanogenesis rather than microbial Fe reduction (Vuillemin et al, 2018). In the vivianitebearing intervals, DIC concentrations remain rather constant (4 mM).…”

“…2a), potential rates of sulfide production remain very low compared to the Fe delivery flux and HS − production has a negligible effect on P release from the sediment. Such low SO 2− 4 concentrations further result in the loss of most sulfate and increased methanogenesis within the first upper meter of sediment (Vuillemin et al, 2018). As a result, processes of OM remineralization are predominantly driven by fermentation and methanogenesis (Friese et al, 2018) and DIC steadily increases with depth ( Fig.…”

“…The onset of autotrophic methanogenesis is expected to reduce DIC activity in pore water. Moreover, Ca 2+ and Mg 2+ concentrations in pore water, which are predicted to control the solubility of PO 3− 4 in ferruginous systems (Jones et al, 2015), drop around these depths as divalent cations can precipitate during siderite formation (Vuillemin et al, 2019a), suggesting that PO 3− 4 can then outcompete CO 2− 3 for available Fe 2+ and thereby saturate pore water with respect to vivianite (Table 1) Vivianite formation is indeed reported to occur under methanogenic conditions, often initiating below the sulfate-methane transition zone (Reed et al, 2011;Dijkstra et al, 2016), presently located within the upper meter of sediment (Vuillemin et al, 2018). Since pore waters are sat-A.…”

Carbon release and transformation from coastal peat deposits controlled by submarine groundwater discharge: a column experiment study

“…The molecular data are mostly dependent on the choice of primers. Although the primers used in this study are well evaluated and have been applied for estimating the abundance of methanogens (Wen et al 2018) and sulfate reducers (Vuillemin et al 2018), the primers used are covering only a small diversity of microorganisms involved in the complex biogeochemical processes. However, the total abundance of microorganisms across the sediment columns has identified the peat as the favorable habitat.…”

“…DNA concentrations were quantified with a Nanophotometer P360 (Implen GmbH) and Qubit 2.0 Fluorometer (Thermo Fisher Scientific). Quantitative polymerase chain reaction (qPCR) for the determination of functional gene copy numbers of methanogenic archaea and SRB was performed via SybrGreen assays on a Bio‐Rad CFX instrument (Bio‐Rad) as described elsewhere (Vuillemin et al 2018; Wen et al 2018) with slight modifications. In detail, the methyl coenzyme M reductase alpha subunit ( mcrA ) as the functional methanogenic gene was amplified with the primer combination mlas‐F/mcra‐R ( ggT gTM ggD TTC ACM CAR TA / CgT TCA TBg CgT AgT TVg gRT AgT ) with primer annealing at 60°C.…”