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26


Genetic potential for aerobic respiration and denitrification in globally distributed respiratory endosymbionts

Citation
Speth et al. (2024). Nature Communications 15 (1)
Names
Azoamicus ciliaticola Ts “Azosocius agrarius” “Azoamicus soli” “Azosocius aquiferis” “Azoamicus viridis” “Azoamicaceae” “Azosocius” “Azoamicales”
Abstract
AbstractThe endosymbiont Candidatus Azoamicus ciliaticola was proposed to generate ATP for its eukaryotic host, an anaerobic ciliate of the Plagiopylea class, fulfilling a function analogous to mitochondria in other eukaryotic cells. The discovery of this respiratory endosymbiosis has major implications for both evolutionary history and ecology of microbial eukaryotes. However, with only a single species described, knowledge of its environmental distribution and diversity is limited. Here we rep

Asgard archaea modulate potential methanogenesis substrates in wetland soil

Citation
Valentin-Alvarado et al. (2024). Nature Communications 15 (1)
Names
Freyarchaeum deiterrae Ts Atabeyarchaeum deiterrae Ts Atabeyarchaeia Atabeyarchaeum Freyarchaeum Atabeyarchaeaceae Atabeyarchaeales Freyarchaeaceae Freyarchaeales Freyarchaeia
Abstract
AbstractThe roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions in soil ecosystems remain unknown. Of particular interest are Asgard archaeal contributions to methane cycling in wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new Asgard lineage, and a complete genome of Freyarchaeia, and predicted their metabolism in situ. Metatranscriptomics reveals expression of gene

Sustained bacterial N2O reduction at acidic pH

Citation
He et al. (2024). Nature Communications 15 (1)
Names
Desulfosporosinus nitrosoreducens
Abstract
AbstractNitrous oxide (N2O) is a climate-active gas with emissions predicted to increase due to agricultural intensification. Microbial reduction of N2O to dinitrogen (N2) is the major consumption process but microbial N2O reduction under acidic conditions is considered negligible, albeit strongly acidic soils harbor nosZ genes encoding N2O reductase. Here, we study a co-culture derived from acidic tropical forest soil that reduces N2O at pH 4.5. The co-culture exhibits bimodal growth with a Ser

The protein interactome of the citrus Huanglongbing pathogen Candidatus Liberibacter asiaticus

Citation
Carter et al. (2023). Nature Communications 14 (1)
Names
Ca. Liberibacter asiaticus
Abstract
AbstractThe bacterium Candidatus Liberibacter asiaticus (CLas) causes citrus Huanglongbing disease. Our understanding of the pathogenicity and biology of this microorganism remains limited because CLas has not yet been cultivated in artificial media. Its genome is relatively small and encodes approximately 1136 proteins, of which 415 have unknown functions. Here, we use a high-throughput yeast-two-hybrid (Y2H) screen to identify interactions between CLas proteins, thus providing insights into th

Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle

Citation
Li et al. (2023). Nature Communications 14 (1)
Names
“Houyibacterium oceanica” “Houyibacterium” “Houyibacteriaceae” “Houyihalomonas phototrophica” “Xihehalomonas phototrophica” “Xihemonas sinensis” “Kuafubacteria” “Kuafubacterium phototrophica” “Kuafucaenimonas phototrophica” “Kuafuhalomonas phototrophica” “Xihepedomonas phototrophica” “Xihelimnomonas phototrophica” “Xihecaenimonas phototrophica” “Kuafubacteriales” “Kuafubacteriaceae” “Xihehalomonas” “Xihemonas” “Xihecaenibacterium” “Houyihalomonas” “Xihelimnobacterium phototrophica” “Xihelimnobacterium” “Xihemonas phototrophica” “Xihecaenibacterium phototrophica” “Xihebacterium phototrophica” “Xihebacterium glacialis” “Xihebacterium aquatica” “Xihemicrobium phototrophica” “Xihemicrobium aquatica” “Kuafubacterium” “Xihebacterium” “Xihemicrobium” “Xihecaenimonas” “Xihelimnomonas” “Xihepedomonas” “Kuafuhalomonas” “Kuafucaenimonas”
Abstract
AbstractPhotosynthesis is a fundamental biogeochemical process, thought to be restricted to a few bacterial and eukaryotic phyla. However, understanding the origin and evolution of phototrophic organisms can be impeded and biased by the difficulties of cultivation. Here, we analyzed metagenomic datasets and found potential photosynthetic abilities encoded in the genomes of uncultivated bacteria within the phylum Myxococcota. A putative photosynthesis gene cluster encoding a type-II reaction cent

Multi-heme cytochrome-mediated extracellular electron transfer by the anaerobic methanotroph ‘Candidatus Methanoperedens nitroreducens’

Citation
Zhang et al. (2023). Nature Communications 14 (1)
Names
Ca. Methanoperedens nitroreducens
Abstract
AbstractAnaerobic methanotrophic archaea (ANME) carry out anaerobic oxidation of methane, thus playing a crucial role in the methane cycle. Previous genomic evidence indicates that multi-heme c-type cytochromes (MHCs) may facilitate the extracellular electron transfer (EET) from ANME to different electron sinks. Here, we provide experimental evidence supporting cytochrome-mediated EET for the reduction of metals and electrodes by ‘Candidatus Methanoperedens nitroreducens’, an ANME acclimated to

Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut

Citation
Ye et al. (2023). Nature Communications 14 (1)
Names
Taurinivorans muris Ts Taurinivorans
Abstract
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 dep

Cultivation of marine bacteria of the SAR202 clade

Citation
Lim et al. (2023). Nature Communications 14 (1)
Names
Lucifugimonas marina Ts Lucifugimonas Lucifugimonadales Lucifugimonadaceae
Abstract
AbstractBacteria of the SAR202 clade, within the phylum Chloroflexota, are ubiquitously distributed in the ocean but have not yet been cultivated in the lab. It has been proposed that ancient expansions of catabolic enzyme paralogs broadened the spectrum of organic compounds that SAR202 bacteria could oxidize, leading to transformations of the Earth’s carbon cycle. Here, we report the successful cultivation of SAR202 bacteria from surface seawater using dilution-to-extinction culturing. The grow

New globally distributed bacterial phyla within the FCB superphylum

Citation
Gong et al. (2022). Nature Communications 13 (1)
Names
“Orphanbacterum longqiense” “Joyebacterota” “Arandabacteraceae” “Arandabacterota” “Arandabacterales” “Arandabacteria” “Orphanbacterum” “Arandabacterum bohaiense” “Blakebacterota” “Orphanbacteraceae” “Joyebacterum haimaense” “Blakebacterum guaymasense” “Orphanbacterales” “Joyebacterum” “Blakebacterum” “Orphanbacteria” “Joyebacteraceae” “Blakebacteraceae” “Orphanbacterota” “Joyebacterales” “Blakebacterales” “Arandabacterum” “Joyebacteria” “Blakebacteria”
Abstract
AbstractMicrobes in marine sediments play crucial roles in global carbon and nutrient cycling. However, our understanding of microbial diversity and physiology on the ocean floor is limited. Here, we use phylogenomic analyses of thousands of metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments to identify 55 MAGs that are phylogenetically distinct from previously described bacterial phyla. We propose that these MAGs belong to 4 novel bacterial phyla (Blakebacterota, Orphanbact