Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake

Abstract

The potential metabolism and ecological roles of many microbial taxa remain unknown because insufficient genomic data are available to assess their functional potential. Two such microbial “dark matter” taxa are the Candidatus bacterial phyla Cloacimonadota and Omnitrophota, both of which have been identified in global anoxic environments, including (but not limited to) organic-carbon-rich lakes. Using 24 metagenome-assembled genomes (MAGs) obtained from an Antarctic lake (Ace Lake, Vestfold Hills), novel lineages and novel metabolic traits were identified for both phyla. The Cloacimonadota MAGs exhibited a capacity for carbon fixation using the reverse tricarboxylic acid cycle driven by oxidation of hydrogen and sulfur. Certain Cloacimonadota MAGs encoded proteins that possess dockerin and cohesin domains, which is consistent with the assembly of extracellular cellulosome-like structures that are used for degradation of polypeptides and polysaccharides. The Omnitrophota MAGs represented phylogenetically diverse taxa that were predicted to possess a strong biosynthetic capacity for amino acids, nucleosides, fatty acids, and essential cofactors. All of the Omnitrophota were inferred to be obligate fermentative heterotrophs that utilize a relatively narrow range of organic compounds, have an incomplete tricarboxylic acid cycle, and possess a single hydrogenase gene important for achieving redox balance in the cell. We reason that both Cloacimonadota and Omnitrophota form metabolic interactions with hydrogen-consuming partners (methanogens and Desulfobacterota, respectively) and, therefore, occupy specific niches in Ace Lake.

Into the darkness: the ecologies of novel ‘microbial dark matter’ phyla in an Antarctic lake

“…MAGs of the other four Ace Lake species encode an incomplete TCA cycle in both the oxidative and reductive directions: genes for 2‐oxoglutarate:ferredoxin oxidoreductase, succinyl‐CoA synthetase, succinate dehydrogenase and fumarate reductase are all absent. Given the estimated completeness (88%–98%) of these MAGs, we regard the incomplete TCA cycle as a likely metabolic trait, and consistent with these species having a ‘horse‐shoe’‐type TCA pathway, as found in certain other anaerobic bacteria, where this pathway functions solely in biosynthesis (Wood et al ., 2004; Herlemann et al ., 2009; Marco‐Urrea et al ., 2011; Williams et al ., 2021a). Thus, the right branch terminates at 2‐oxoglutarate, the amino acceptor for ammonia assimilation and transamination reactions (see below), and the left branch allows the interconversion of oxaloacetate, malate, and fumarate (Herlemann et al ., 2009).…”

“…Thus, these new phyla add to the repertoire of Ace Lake bacteria inferred to degrade recalcitrant organic material and particulate matter, including Bacteroidota, Verrucomicrobiota, Planctomycetota, Gammaproteobacteria, and Ca . Cloacimonadota (Panwar et al ., 2020; Williams et al ., 2021a). We inferred the presence of a Wood–Ljungdahl pathway in certain MAGs belonging to Ca .…”

Cloacimonadota metabolisms include adaptations in engineered environments that are reflected in the evolutionary history of the phylum

“…Clade II is a monophyletic group of 10 genomes from environmental ecosystems (Fig. 1; bootstrap = 100), including the anoxic, brackish Sakinaw Lake (Rinke et al ., 2013), an Antarctic lake (Williams et al ., 2021), and the deep sea water column in the Black Sea (Villanueva et al ., 2021) (See Supporting Information S1 Results for full details).…”

“…The majority of Cloacimonadota genomes contain full glycolysis pathways with pyruvate orthophosphate dikinase replacing or complementing pyruvate kinase in 91% (42/46) of genomes (see Supporting Information S1 text for additional detail). A recent examination of seven novel MAGs from Antarctic lake‐dwelling Cloacimonadota identified the capacity for carbon fixation using the reverse tricarboxylic acid cycle (Williams et al ., 2021). In contrast, Cloacimonadota genomes generally encode highly incomplete tricarboxylic acid (TCA) cycles, with only two TCA cycle genes present in more than 22% of the genomes: fumarate hydratase (EC: 4.2.1.2) in 89% of the genomes (41/46) and oxoglutarate ferredoxin oxidoreductase (EC: 1.2.7.3 or 1.2.7.11) in 96% of the genomes (44/45).…”

“…Previous analyses have suggested Cloacimonadota ferment amino acids to generate energy, pointing to five ferredoxin oxidoreductases as key markers for this activity (Pelletier et al ., 2008; Williams et al ., 2021). Neither study discussed amino acid degradation pathways, which generate the necessary 2‐oxoacid substrates.…”