Herbold, Craig W.

Abstract Background Tramway Ridge, a geothermal Antarctic Specially Protected Area (1) (elevation 3340 m) located near the summit of Mount Erebus, is home to a unique community composed of cosmopolitan surface-associated micro-organisms and abundant, poorly understood subsurface-associated microorganisms (2–5). Here, we use shotgun metagenomics to compare the functional capabilities of this community to those found elsewhere on Earth and to infer endemism and metabolic capabilities of abundant subsurface taxa. Results We found that the functional potential in this community is most similar to that found in terrestrial hydrothermal environments (hot springs, sediments) and that the two dominant organisms in the subsurface are primarily endemic. They were found to be facultative anaerobic heterotrophs that likely share a pool of nitrogenous organic compounds while specializing in different carbon compounds. Conclusions Metagenomic insights have provided a detailed understanding of the microbe-based ecosystem found in geothermally heated fumaroles at Tramway Ridge. This approach enabled us to compare Tramway Ridge with other microbial systems, identify endemic taxa and elucidate the key metabolic pathways that may enable specific organisms to dominate the ecosystem.

AbstractTaurine-respiring gut bacteria produce H2S with ambivalent impact on host health. We report the isolation and ecophysiological characterization of a taurine-respiring mouse gut bacterium. Taurinivorans muris strain LT0009 represents a new widespread species that differs from the human gut sulfidogen Bilophila wadsworthia in its sulfur metabolism pathways and host distribution. T. muris specializes in taurine respiration in vivo, seemingly unaffected by mouse diet and genotype, but is dependent on other bacteria for release of taurine from bile acids. Colonization of T. muris in gnotobiotic mice increased deconjugation of taurine-conjugated bile acids and transcriptional activity of a sulfur metabolism gene-encoding prophage in other commensals, and slightly decreased the abundance of Salmonella enterica, which showed reduced expression of galactonate catabolism genes. Re-analysis of metagenome data from a previous study further suggested that T. muris can contribute to protection against pathogens by the commensal mouse gut microbiota. Together, we show the realized physiological niche of a key murine gut sulfidogen and its interactions with selected gut microbiota members.

AbstractMany marine sponges host highly diverse microbiomes that contribute to various aspects of host health. Although the putative function of individual groups of sponge symbionts has been increasingly described, the extreme diversity has generally precluded in‐depth characterization of entire microbiomes, including identification of syntrophic partnerships. The Indo‐Pacific sponge Ianthella basta is emerging as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other low abundance or transitory taxa. Here, we retrieved metagenome assembled genomes (MAGs) representing >90% of I. basta's microbial community, facilitating the metabolic reconstruction of the sponge's near complete microbiome. Through this analysis, we identified metabolic complementarity between microbes, including vitamin sharing, described the importance of low abundance symbionts, and characterized a novel microbe–host attachment mechanism in the Alphaproteobacterium. We further identified putative viral sequences, highlighting the role viruses can play in maintaining symbioses in I. basta through the horizontal transfer of eukaryotic‐like proteins, and complemented this data with metaproteomics to identify active metabolic pathways in bacteria, archaea, and viruses. This data provide the framework to adopt I. basta as a model organism for studying host–microbe interactions and provide a basis for in‐depth physiological experiments.

AbstractExtracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus, nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of DNA-foraging microorganisms in marine sediments are largely unknown. Here, we combined microcosm experiments, DNA stable isotope probing (SIP), single-cell SIP using nano-scale secondary isotope mass spectrometry (NanoSIMS) and genome-centric metagenomics to study microbial catabolism of DNA and its subcomponents in marine sediments.13C-DNA added to sediment microcosms was largely degraded within 10 d and mineralized to13CO2. SIP probing of DNA revealed diverse ‘CandidatusIzemoplasma’,Lutibacter,Shewanellaand Fusibacteraceae incorporated DNA-derived13C-carbon. NanoSIMS confirmed incorporation of13C into individual bacterial cells of Fusibacteraceae sorted from microcosms. Genomes of the13C-labelled taxa all encoded enzymatic repertoires for catabolism of DNA or subcomponents of DNA. Comparative genomics indicated that diverse ‘CandidatusIzemoplasmatales’ (former Tenericutes) are exceptional because they encode multiple (up to five) predicted extracellular nucleases and are probably specialized DNA-degraders. Analyses of additional sediment metagenomes revealed extracellular nuclease genes are prevalent among Bacteroidota at diverse sites. Together, our results reveal the identities and functional properties of microorganisms that may contribute to the key ecosystem function of degrading and recycling DNA in the seabed.

For Thaumarchaeota , the ratio of their glycerol dialkyl glycerol tetraether (GDGT) lipids depends on growth temperature, a premise that forms the basis of the widely applied TEX 86 paleotemperature proxy. A thorough understanding of which GDGTs are produced by which Thaumarchaeota and what the effect of temperature is on their GDGT composition is essential for constraining the TEX 86 proxy. “ Ca . Nitrosotenuis uzonensis” is a moderately thermophilic thaumarchaeote enriched from a thermal spring, setting it apart in its environmental niche from the other marine mesophilic members of its order. Indeed, we found that the GDGT composition of “ Ca . Nitrosotenuis uzonensis” cultures was distinct from those of other members of its order and was more similar to those of other thermophilic, terrestrial Thaumarchaeota . This suggests that while phylogeny has a strong influence on GDGT distribution, the environmental niche that a thaumarchaeote inhabits also shapes its GDGT composition.

Summary Marine sponges represent one of the few eukaryotic groups that frequently harbour symbiotic members of the Thaumarchaeota , which are important chemoautotrophic ammonia‐oxidizers in many environments. However, in most studies, direct demonstration of ammonia‐oxidation by these archaea within sponges is lacking, and little is known about sponge‐specific adaptations of ammonia‐oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope‐based functional assays. ‘ Candidatus Nitrosospongia ianthellae’ is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbour nitrite‐oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin‐like proteases, a metalloprotease unique among archaea, as well as a putative branched‐chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge‐associated, but not in free‐living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic‐like proteins, and a DNA‐phosporothioation system, represent important adaptations of AOA to life within these ancient filter‐feeding animals.

Abstract Ni.tro.so.te.nu.a.ce'ae. N.L. adj nitrosus nitrous; L. adj. tenuis slender; ‐aceae ending to denote a family; N.L. fem. pl. n. Nitrosotenuaceae the Nitrosotenuis family. Candidatus Nitrosotenuaceae: A family of slender nitrite producers Candidatus Nitrosotenuaceae is a family of Thaumarchaeota that consists of a single genus, Ca . Nitrosotenuis, which can be found widely distributed in soils, freshwater, hot springs, the subsurface, and activated sludge. They may be rods or spheres and may or may not have flagella. Similar to other known and described Thaumarchaeota , Ca . Nitrosotenuaceae are aerobic chemolithautotrophs that use energy gained from the oxidation of ammonia to nitrite to fix carbon via modified 3‐hydroxypropionate/4‐hydroxybutyrate carbon fixation pathway. At this time, no pure culture of Ca . Nitrosotenuaceae exists, but some of the six available enrichments with members of the genus are almost pure. It remains to be demonstrated whether the remaining bacterial contaminants provide essential compounds to Ca . Nitrosotenuaceae. Enrichments of Ca . Nitrosotenuaceae are intolerant to high salinity (>0.3%), although they are phylogenetically related to the Group I.1a Thaumarchaeota ( Ca . Nitrosopumilaceae), which includes taxa that are widely distributed in the ocean. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the family Candidatus Nitrosotenuaceae is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Thermoproteati / Thermoproteota / Nitrososphaeria / Nitrosopumilales / Candidatus Nitrosotenuaceae The family Candidatus Nitrosotenuaceae can also be recovered in the Genome Taxonomy Database (GTDB) as f__Nitrosopumilaceae (version v220) ** . GTDB classification: d__Archaea / p__Thermoproteota / c__Nitrososphaeria / o__Nitrososphaerales / f__Nitrosopumilaceae * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776