Page 191 - Microbial methane cycling in a warming world From biosphere to atmosphere Michiel H in t Zandt

translocating Rnf complex that is linked to energy conservation could not be detected in MAG 9 (Welte and Deppenmeier 2014).
All Methanosarcinales contain c-type cytochromes (Thauer et al. 2008). All MAGs contained cytochrome c biogenesis proteins (CcmE & CcdA) from the cytochrome c maturation system I, but genes encoding cytochrome c proteins were only found in MAG 4 and 5 (Stevens et al. 2011). Alcohol dehydrogenases for potential use of alcohols as electron donors were detected in all MAGs. Specific for MAG 5, an isopropanol dehydrogenase gene was identified. All Methanosarcinaceae MAGs encoded genes for several toxin-antitoxin system II proteins which are proposed to provide an antiviral defense mechanism (Makarova, Wolf and Koonin 2013). The putative RNA-targeting HicAB cassette was found in all three genomes (Makarova, Grishin and Koonin 2006). The mRNA targeting interferase RelE and DNA gyrase inhibiting ParE was detected in all MAGs (Makarova, Wolf and Koonin 2009). VapC with predicted nuclease activity was not found in MAG 9, YefM that is part of the YefM-YoeB toxin-antitoxin system was only detected in MAG 5 (Cherny and Gazit 2004; Makarova, Wolf and Koonin 2009).
Catalase and peroxidase, which are involved in oxidative defense, were present in all three Methanosarcinaceae. All MAGs encode a NADH peroxidase. Furthermore a cytochrome c peroxidase was detected in MAG 4 and MAG 9, which encodes a catalase/peroxidase HPI, a 8 bifunctional enzyme with both catalase and broad-spectrum peroxidase activity (Hillar et al.
2000).
The chemotaxis gene cluster encoding CheRDCABYW was found in MAG 4 and 5, with the absence of CheY in MAG 5. The cluster is structurally similar to the one described in Methanosarcina acetivorans and other archaea (Galagan et al. 2002; Schlesner et al. 2009). Type IV pilin and flagellar assembly proteins were found in all MAGs. However, genes encoding for flagellin were only detected in MAG 4 and MAG 5. Together with cytochrome c proteins, pili and flagella can play a role in direct interspecies electron transfer reactions that support a syntrophic lifestyle (Shimoyama et al. 2009; Shrestha et al. 2013).
Overall, we observed clear distinctions between the three annotated Methanosarcinaceae MAGs. To investigate MAG-specific differences we performed genome-wide nucleotide, amino acid and gene-based analyses (Fig. 3, Supplementary Table S4). Due to the close identity
189