Distribution, activities, and interactions of methanogens and sulfate-reducing prokaryotes in the Florida Everglades

• Published in: Applied and Environmental Microbiology 2015-11, Vol.81 (21), p.7431-7442
• Main Authors: Bae, Hee-Sung, Holmes, M Elizabeth, Chanton, Jeffrey P, Reddy, K Ramesh, Ogram, Andrew
• Format: Article
• Language: English
• Subjects: Biota; DNA Primers - genetics; Florida; Fractionation; Methane - metabolism; Methanomicrobiales; Methanosaetaceae; Methanosarcinales; Microbial Ecology; Microbiology; Molecular Sequence Data; Oxidation-Reduction; Oxidoreductases - genetics; Oxidoreductases Acting on Sulfur Group Donors - genetics; Polymerase chain reaction; Prokaryotes; Prokaryotic Cells - classification; Prokaryotic Cells - metabolism; Real-Time Polymerase Chain Reaction; Sequence Analysis, DNA; Soil Microbiology; Sulfates - metabolism; Water conservation; Wetlands
• ISSN: 0099-2240; 1098-5336; 1098-6596
• DOI: 10.1128/AEM.01583-15

To gain insight into the mechanisms controlling methanogenic pathways in the Florida Everglades, the distribution and functional activities of methanogens and sulfate-reducing prokaryotes (SRPs) were investigated in soils (0 to 2 or 0 to 4 cm depth) across the well-documented nutrient gradient in the water conservation areas (WCAs) caused by runoff from the adjacent Everglades Agricultural Area. The methyl coenzyme M reductase gene (mcrA) sequences that were retrieved from WCA-2A, an area with relatively high concentrations of SO4 (2-) (≥39 μM), indicated that methanogens inhabiting this area were broadly distributed within the orders Methanomicrobiales, Methanosarcinales, Methanocellales, Methanobacteriales, and Methanomassiliicoccales. In more than 3 years of monitoring, quantitative PCR (qPCR) using newly designed group-specific primers revealed that the hydrogenotrophic Methanomicrobiales were more numerous than the Methanosaetaceae obligatory acetotrophs in SO4 (2-)-rich areas of WCA-2A, while the Methanosaetaceae were dominant over the Methanomicrobiales in WCA-3A (with relatively low SO4 (2-) concentrations; ≤4 μM). qPCR of dsrB sequences also indicated that SRPs are present at greater numbers than methanogens in the WCAs. In an incubation study with WCA-2A soils, addition of MoO4 (2-) (a specific inhibitor of SRP activity) resulted in increased methane production rates, lower apparent fractionation factors [αapp; defined as (amount of δ(13)CO2 + 1,000)/(amount of δ(13)CH4 + 1,000)], and higher Methanosaetaceae mcrA transcript levels compared to those for the controls without MoO4 (2-). These results indicate that SRPs play crucial roles in controlling methanogenic pathways and in shaping the structures of methanogen assemblages as a function of position along the nutrient gradient.