Gene expression and ultrastructure of meso‐ and thermophilic methanotrophic consortia

Abstract

SummaryThe sulfate‐dependent, anaerobic oxidation of methane (AOM) is an important sink for methane in marine environments. It is carried out between anaerobic methanotrophic archaea (ANME) and sulfate‐reducing bacteria (SRB) living in syntrophic partnership. In this study, we compared the genomes, gene expression patterns and ultrastructures of three phylogenetically different microbial consortia found in hydrocarbon‐rich environments under different temperature regimes: ANME‐1a/HotSeep‐1 (60°C), ANME‐1a/Seep‐SRB2 (37°C) and ANME‐2c/Seep‐SRB2 (20°C). All three ANME encode a reverse methanogenesis pathway: ANME‐2c encodes all enzymes, while ANME‐1a lacks the gene for N5,N10‐methylene tetrahydromethanopterin reductase (mer) and encodes a methylenetetrahydrofolate reductase (Met). The bacterial partners contain the genes encoding the canonical dissimilatory sulfate reduction pathway. During AOM, all three consortia types highly expressed genes encoding for the formation of flagella or type IV pili and/or c‐type cytochromes, some predicted to be extracellular. ANME‐2c expressed potentially extracellular cytochromes with up to 32 hemes, whereas ANME‐1a and SRB expressed less complex cytochromes (≤ 8 and ≤ 12 heme respectively). The intercellular space of all consortia showed nanowire‐like structures and heme‐rich areas. These features are proposed to enable interspecies electron exchange, hence suggesting that direct electron transfer is a common mechanism to sulfate‐dependent AOM, and that both partners synthesize molecules to enable it.

Diverse anaerobic methane‐ and multi‐carbon alkane‐metabolizing archaea coexist and show activity in Guaymas Basin hydrothermal sediment

“…To construct the heat map, we first downloaded the protein sequences related to the MAO pathways of ANME-1 (Hallam et al, 2003;Meyerdierks et al, 2010), ANME-2 (a/b, c, d, Wang et al, 2014;Krukenberg et al, 2018;Haroon et al, 2013), ANME-3 (Niemann et al, 2006, no genomic data), Ca. To construct the heat map, we first downloaded the protein sequences related to the MAO pathways of ANME-1 (Hallam et al, 2003;Meyerdierks et al, 2010), ANME-2 (a/b, c, d, Wang et al, 2014;Krukenberg et al, 2018;Haroon et al, 2013), ANME-3 (Niemann et al, 2006, no genomic data), Ca.…”

“…A heat map of genes involved in reverse methanogenesis, coenzyme recycling and electron transfer, onecarbon compounds and acetyl-CoA metabolism from the current M8 metagenomic and metatranscriptomic datasets was constructed based on calculations of the average sequencing depth and FPKM values of each gene described above, with multi-subunit enzymes displayed as the average of these values for all subunits. To construct the heat map, we first downloaded the protein sequences related to the MAO pathways of ANME-1 (Hallam et al, 2003;Meyerdierks et al, 2010), ANME-2 (a/b, c, d, Wang et al, 2014;Krukenberg et al, 2018;Haroon et al, 2013), ANME-3 (Niemann et al, 2006, no genomic data), Ca. Syntrophoarchaeum spp.…”

Microbial interactions in the anaerobic oxidation of methane: model simulations constrained by process rates and activity patterns

“…It has been shown that methane‐oxidation by ANME‐2 archaea in deep‐sea sediments can be catabolically and anabolically decoupled from sulfate‐reduction and the activity of their deltaproteobacterial partners using soluble oxidants, including anthraquinone‐2,6‐disulfonate (AQDS), humic acids and iron(III)‐citrate (Scheller et al, ), consistent with a syntrophic electron exchange between Archaea and Bacteria in the consortia (McGlynn et al, ; Wegener et al, ). Moreover, large S‐layer associated multiheme cytochromes were observed to be encoded by ANME‐2 genomes, and appear to be related to electron transfer in ANME‐2/SRB consortia as observed by transmission electron microscopy (TEM) (McGlynn et al, ; Krukenberg et al, ). TEM on thin sections of thermophilic AOM consortia further reported pili‐like structures with diameters of 10 nm and apparent lengths of 100 nm to > 1000 nm, which connect SRB HotSeep‐1 and ANME‐1 cells (Wegener et al, ), suggestive of DIET.…”

A Membrane-Bound Cytochrome EnablesMethanosarcina acetivoransto Conserve Energy to Support Growth from Extracellular Electron Transfer

“…Methanogens such as Methanothrix (formerly Methanosaeta ) and Methanosarcina species can accept electrons via direct interspecies electron transfer from electron-donating partners, such as Geobacter species in important methanogenic environments such as anaerobic digesters and rice paddy soils (10–12). Anaerobic methane oxidation also plays an important role in the global carbon cycle and diverse anaerobic methane-oxidizing archaea (ANME) transfer electrons derived from methane oxidation to extracellular electron acceptors, such as other microbial species, Fe(III), or extracellular quinones (13–19). The electrical contacts for extracellular electron exchange have yet to be definitively identified in any of these Archaea.…”

“…It has been hypothesized that outer-surface cytochromes enable electron transfer to electron-accepting microbial partners or Fe(III) in some ANME (13–19). Genes for multi-heme c -type cytochromes that are present in ANME genomes can be highly expressed and in some instances the proteins have been detected.…”