Methanomethylovorans are the dominant dimethylsulfide-degrading methanogens in gravel and sandy river sediment microcosms.

BACKGROUND: Rivers and streams are important components of the global carbon cycle and methane budget. However, our understanding of the microbial diversity and the metabolic pathways underpinning methylotrophic methane production in river sediments is limited. Dimethylsulfide is an important methylated compound, found in freshwater sediments. Yet, the magnitude of DMS-dependent methanogenesis nor the methanogens carrying out this process in river sediments have been explored before. This study addressed this knowledge gap in DMS-dependent methanogenesis in gravel and sandy river sediments. RESULTS: Significant methane production via DMS degradation was found in all sediment  microcosms. Sandy, less permeable river sediments had higher methane yields (83 and 92%) than gravel, permeable sediments (40 and 48%). There was no significant difference between the methanogen diversity in DMS-amended gravel and sandy sediment microcosms, which Methanomethylovorans dominated. Metagenomics data analysis also showed the dominance of Methanomethylovorans and Methanosarcina. DMS-specific methyltransferase genes (mts) were found in very low relative abundances whilst the methanol-, trimethylamine- and dimethylamine-specific methyltransferase genes (mtaA, mttB and mtbB) had the highest relative abundances, suggesting their involvement in DMS-dependent methanogenesis. CONCLUSIONS: This is the first study demonstrating a significant potential for DMS-dependent methanogenesis in river sediments with contrasting geologies. Methanomethylovorans were the dominant methylotrophic methanogen in all river sediment microcosms. Methyltransferases specific to methylotrophic substrates other than DMS are likely key enzymes in DMS-dependent methanogenesis, highlighting their versatility and importance in the methane cycle in freshwater sediments, which would warrant further study.

Methanolobus use unspecific methyltransferases to produce methane from dimethylsulphide in Baltic Sea sediments.

BACKGROUND: In anoxic coastal and marine sediments, degradation of methylated compounds is the major route to the production of methane, a powerful greenhouse gas. Dimethylsulphide (DMS) is the most abundant biogenic organic sulphur compound in the environment and an abundant methylated compound leading to methane production in anoxic sediments. However, understanding of the microbial diversity driving DMS-dependent methanogenesis is limited, and the metabolic pathways underlying this process in the environment remain unexplored. To address this, we used anoxic incubations, amplicon sequencing, genome-centric metagenomics and metatranscriptomics of brackish sediments collected along the depth profile of the Baltic Sea with varying sulphate concentrations. RESULTS: We identified Methanolobus as the dominant methylotrophic methanogens in all our DMS-amended sediment incubations (61-99%) regardless of their sulphate concentrations. We also showed that the mtt and mta genes (trimethylamine- and methanol-methyltransferases) from Methanolobus were highly expressed when the sediment samples were incubated with DMS. Furthermore, we did not find mtsA and mtsB (methylsulphide-methyltransferases) in metatranscriptomes, metagenomes or in the Methanolobus MAGs, whilst mtsD and mtsF were found 2-3 orders of magnitude lower in selected samples. CONCLUSIONS: Our study demonstrated that the Methanolobus genus is likely the key player in anaerobic DMS degradation in brackish Baltic Sea sediments. This is also the first study analysing the metabolic pathways of anaerobic DMS degradation in the environment and showing that methylotrophic methane production from DMS may not require a substrate-specific methyltransferase as was previously accepted. This highlights the versatility of the key enzymes in methane production in anoxic sediments, which would have significant implications for the global greenhouse gas budget and the methane cycle. Video Abstract.

Monitoring the abundance and the activity of ammonia-oxidizing bacteria in a full-scale nitrifying activated sludge reactor.

Cell-specific ammonia oxidation rate (AOR) has been suggested to be an indicator of the performance of nitrification reactors and to be used as an operational parameter previously. However, published AOR values change by orders of magnitude and studies investigating full-scale nitrification reactors are limited. Therefore, this study aimed at quantifying ammonia-oxidizing bacteria (AOB) and estimating their in situ cell-specific AOR in a full-scale activated sludge reactor treating combined domestic and industrial wastewaters. Results showed that cell-specific AOR changed between 5.30 and 9.89 fmol cell(-1) h(-1), although no significant variation in AOB cell numbers were obtained (1.54E + 08 ± 0.22 cell/ml). However, ammonia-removal efficiency varied largely (52-79 %) and was proportional to the cell-specific AOR in the reactor. This suggested that the cell-specific AOR might be the factor affecting the biological ammonia-removal efficiency of nitrification reactors independent of the AOB number. Further investigation is needed to establish an empirical relationship to use cell-specific AOR as a parameter to operate full-scale nitrification systems more effectively.

Methanogenic and sulphate reducing bacterial population levels in a full-scale anaerobic reactor treating pulp and paper industry wastewater using fluorescence in situ hybridisation.

In this study, specific methanogenic activity (SMA) test and fluorescence in situ hybridisation (FISH) were respectively used to determine acetoclastic methanogenic capacity, and composition and number of methanogenic and sulphate reducing bacterial (SRB) populations within a full scale anaerobic contact reactor treating a pulp and paper industry effluent. The sludge samples were collected from three different heights along the anaerobic reactor having a difficulty of completely stirring. Performance of the anaerobic reactor in terms of COD removal efficiency varied between 47 and 55% at organic loading rates in a range of 1.6-1.8 kg COD m(-3) d(-1) and methane yield varied between 0.18 and 0.20 m3CH4kg CODrem(-1). The anaerobic reactor was not operated for 2 weeks during the monitoring period. According to SMA test results, potential methane production rate was 276 mLCH4 gVSS(-1) d(-1) before the off period of the reactor, however it decreased to 159 mL CH4 gVSS(-1) d(-1) after this period. SMA test and FISH results along the reactor height showed that the acetoclastic methanogenic activity of the sludge samples, the relative abundance of acetoclastic methanogens, hydrogenotrophic methanogens and acetate oxidising SRB decreased as the reactor height increased, however the relative abundance of non-acetate oxidising SRB increased.