Characterization of the Archaeal Community in a Minerotrophic Fen and Terminal Restriction Fragment Length Polymorphism-Directed Isolation of a Novel Hydrogenotrophic Methanogen

Abstract

Minerotrophic fen peatlands are widely distributed in northern latitudes and, because of their rapid turnover of organic matter, are potentially larger sources of atmospheric methane than bog peatlands per unit area. However, studies of the archaeal community composition in fens are scarce particularly in minerotrophic sites. Several 16S rRNA-based primer sets were used to obtain a broad characterization of the archaeal community in a minerotrophic fen in central New York State. A wide archaeal diversity was observed in the site: 11 euryarchaeal and 2 crenarchaeal groups, most of which were uncultured. The E1 group, a novel cluster in the order Methanomicrobiales, and Methanosaetaceae were the codominant groups in all libraries and results of terminal restriction fragment length polymorphism (T-RFLP) analysis. Given its abundance and potential hydrogenotrophic methane contribution, the E1 group was targeted for culture attempts with a low-ionic-strength medium (PM1). Initial attempts yielded Methanospirillumdominated cultures. However, by incorporating a T-RFLP analysis as a quick selection tool for treatments and replicates, we were able to select an enrichment dominated by E1. Further dilutions to 10 ؊9 and tracking with T-RFLP yielded a strain named E1-9c. E1-9c is a novel coccoid hydrogenotrophic, mesophilic, slightly acidophilic methanogen and is highly sensitive to Na 2 S concentrations (requires <0.12 mM for growth). We propose E1-9c as the first representative of a novel genus in the Methanomicrobiales order.Peatlands are wetlands where the rate of accumulation of organic matter exceeds its rate of decomposition (26), producing organic peat soil. On a global basis, these ecosystems are estimated to store more than 30% of all terrestrial soil carbon (28), and their anoxic and reducing conditions are suitable for CH 4 production by methanogenic Archaea (67). It is important to gain a better understanding of the processes and microorganisms involved in CH 4 production in peatlands because these ecosystems represent the largest natural sources of CH 4 for the atmosphere, levels of which have more than doubled in the past 200 years (17). Moreover, peatlands are not homogeneous ecosystems but include a wide range of sites that can substantially differ in vegetation, hydrology, and chemistry (9, 62). The distinctions between bogs and fens include many of these differences.Bogs (ombrotrophic or rain-fed sites) are dominated by Sphagnum mosses (27); receive only atmospheric inputs of water, cations, and nutrients; and are nutrient-poor, low-pH (Յ4) ecosystems (26). In contrast, fens have a greater plant diversity, are commonly dominated by sedges and woody plants, receive the inputs of groundwater and runoff from surrounding uplands, and exhibit higher alkalinity and pH levels (5.5 to 7 in moderate minerotrophic fens; Ͼ7 in calcareous fens) (26, 64).Bogs are abundant in boreal regions and have been the focus of many studies of methanogenic processes, environmental controls, and methanogenic Archaea (2, 3, 9, 11, ...

Competing Formate- and Carbon Dioxide-Utilizing Prokaryotes in an Anoxic Methane-Emitting Fen Soil

“…Several studies have demonstrated that wetland soils contain complex prokaryotic communities (10,15,40,43), a finding consistent with the aforementioned network of trophically linked processes that yield methane. The methanogenic community of the fen Schlöppnerbrunnen in southeast Germany is composed of Methanobacteriaceae, Methanomicrobiaceae, Methanosaetaceae, and Methanosarcinaceae (32,90).…”

Linking Sequence to Function in Soil Bacteria: Sequence-Directed Isolation of Novel Bacteria Contributing to Soilborne Plant Disease Suppression

“…Methods used to classify microbes that generate specific TRFs include the analysis of isolates or clone collections for matching TRF sizes, as well as sequencing of selected TRF clones (e.g., see references 38 and 55). T-RFLP has been used to guide the isolation of methanogenic archaea (12) and biodegraders (25), but those investigations monitored solely for TRF size and did not consider sequence. Ribosomal-sequence-directed isolation of microorganisms involved in plant disease suppression was performed previously for fungal species, using data generated from oligonucleotide fingerprinting of rRNA (43,57).…”

Anaerobic oxidation of methane: an underappreciated aspect of methane cycling in peatland ecosystems?

“…For instance, Scholten et al (2005) reported AOM in an alkaline, SO 2− 4 -rich lake mediated by a SRB, whereas known ANMEs were not involved; they suggested the SRB acts alone, meaning that yet undiscovered mechanisms might exist. For peatlands, most contain a high diversity of methanogens (Cadillo-Quiroz et al, 2008); however, ANME relatives appear to be restricted to nutrient-rich, grass dominated fen peatlands, at very low numbers, and they do not appear to occur in the extensive acidic peatlands dominated by mosses and shrubs (Dettling et al, 2007).…”