Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments

Abstract

Geothermal environments, including terrestrial hot springs and deep-sea hydrothermal sediments, often contain many poorly understood lineages of archaea. Here, we recovered ten metagenome-assembled genomes (MAGs) from geothermal sediments and propose that they constitute a new archaeal class within the TACK superphylum, “Candidatus Culexarchaeia”, named after the Culex Basin in Yellowstone National Park. Culexarchaeia harbor distinct sets of proteins involved in key cellular processes that are either phylogenetically divergent or are absent from other closely related TACK lineages, with a particular divergence in cell division and cytoskeletal proteins. Metabolic reconstruction revealed that Culexarchaeia have the capacity to metabolize a wide variety of organic and inorganic substrates. Notably, Culexarchaeia encode a unique modular, membrane associated, and energy conserving [NiFe]-hydrogenase complex that potentially interacts with heterodisulfide reductase (Hdr) subunits. Comparison of this [NiFe]-hydrogenase complex with similar complexes from other archaea suggests that interactions between membrane associated [NiFe]-hydrogenases and Hdr may be more widespread than previously appreciated in both methanogenic and non-methanogenic lifestyles. The analysis of Culexarchaeia further expands our understanding of the phylogenetic and functional diversity of lineages within the TACK superphylum and the ecology, physiology, and evolution of these organisms in extreme environments.

Isolation of a methyl-reducing methanogen outside the Euryarchaeota

“…6), indicating that methanol is almost fully converted into methane. No labeled methane was produced when the co-culture was incubated with 13 C-labeled acetate or 13 C-labeled CO 2 (data not shown). Moreover, nanoscale secondary ion mass spectrometry (NanoSIMS) scanning and lipid stable isotope probing (lipid-SIP) analysis revealed no labeled methanol ows into biomass or lipid of strain LWZ-6 (Figs.…”

“…Thus, these results con rmed that strain LWZ-6 employs hydrogen-dependent methylotrophic methanogenesis as its energy conservation pathway. Lipid-SIP detected 13 C-labeled archaeol and methylated glycerol monoalkyl glycerol tetraether (Me-GMGT) fraction when strain LWZ-6 was incubated with 13 C-labeled acetate, CO 2, or yeast extract, indicating they are required as carbon sources (Fig. 2g).…”

“…In the stable isotope tracer experiment, 1, 2, 4, and 8 % 13 C-labeled methanol (Sigma, USA) was made by mixing 0.1 mL, 0.2 mL, 0.4 mL, and 0.8 mL 0.05 M 13 C-labeled with 0.495 mL, 0.49 mL, 0.48 mL, and 0.46 mL 1 M unlabelled methanol, respectively. 0.5 mL 1 M unlabelled methanol was used as the control group.…”

“…The unlabeled samples were employed for lipid structure identi cation, according to exact molecular mass and MS 2 fragment spectra. The degree of 13 C stable isotope labeling into lipids was estimated based on their MS1 mass spectra following calculations by Thiele and Matsubara 56 . Two representative archaeal lipids 57 , archaeol (C 43 H 88 O 3 ) and Me-GMGT (C 87 H 160 O 6 ) were selected for the calculation of labeling degree.…”

“…The base peak intensity of an isotoplog with i 13 C atoms (BPI i ) was calculated by normalizing it to the highest intensity of all isotoplogs, which was further normalized to the sum BPI of all isotoplogs, resulting in the BPI i(norm) . The degree of 13 C labeling of an isotopolog with i 13 C atoms (DoL i ) and the total degree of 13 C labeling of a lipid (DoL) was calculated with the following equations:…”