The ISME Journal


Publications
71

Tissue-associated and vertically transmitted bacterial symbiont in the coral Pocillopora acuta

Citation
Maire et al. (2024). The ISME Journal 18 (1)
Names
Sororendozoicomonas aggregata Ts Sororendozoicomonas
Abstract
Abstract Coral microhabitats are colonized by a myriad of microorganisms, including diverse bacteria which are essential for host functioning and survival. However, the location, transmission, and functions of individual bacterial species living inside the coral tissues remain poorly studied. Here, we show that a previously undescribed bacterial symbiont of the coral Pocillopora acuta forms cell-associated microbial aggregates (CAMAs) within the mesenterial filaments. CAMAs were f

Flexible genomic island conservation across freshwater and marine Methylophilaceae

Citation
Layoun et al. (2024). The ISME Journal 18 (1)
Names
“Methylopumilus” “Methylopumilus planktonicus”
Abstract
Abstract The evolutionary trajectory of Methylophilaceae includes habitat transitions from freshwater sediments to freshwater and marine pelagial that resulted in genome reduction (genome-streamlining) of the pelagic taxa. However, the extent of genetic similarities in the genomic structure and microdiversity of the two genome-streamlined pelagic lineages (freshwater “Ca. Methylopumilus” and the marine OM43 lineage) has so far never been compared. Here, we analyzed complete genome

Members of the class Candidatus Ordosarchaeia imply an alternative evolutionary scenario from methanogens to haloarchaea

Citation
Zhao et al. (2024). The ISME Journal 18 (1)
Names
Ca. Hikarchaeia Ca. Ordosarchaeia
Abstract
Abstract The origin of methanogenesis can be traced to the common ancestor of non-DPANN archaea, whereas haloarchaea (or Halobacteria) are believed to have evolved from a methanogenic ancestor through multiple evolutionary events. However, due to the accelerated evolution and compositional bias of proteins adapting to hypersaline habitats, Halobacteria exhibit substantial evolutionary divergence from methanogens, and the identification of the closest methanogen (either Methanonatr

Cultivation and genomic characterization of novel and ubiquitous marine nitrite-oxidizing bacteria from the Nitrospirales

Citation
Mueller et al. (2023). The ISME Journal 17 (11)
Names
“Nitronereus thalassa” “Nitronereus”
Abstract
Abstract Nitrospirales, including the genus Nitrospira, are environmentally widespread chemolithoautotrophic nitrite-oxidizing bacteria. These mostly uncultured microorganisms gain energy through nitrite oxidation, fix CO2, and thus play vital roles in nitrogen and carbon cycling. Over the last decade, our understanding of their physiology has advanced through several new discoveries, such as alternative energy metabolisms and complete ammonia oxidizers (comammox Nitrospira). Thes

Cuticle supplementation and nitrogen recycling by a dual bacterial symbiosis in a family of xylophagous beetles

Citation
Kiefer et al. (2023). The ISME Journal 17 (7)
Names
Bostrichidicola ureolyticus Ts Shikimatogenerans bostrichidophilus Shikimatogenerans silvanidophilus Ts Bostrichidicola
Abstract
AbstractMany insects engage in stable nutritional symbioses with bacteria that supplement limiting essential nutrients to their host. While several plant sap-feeding Hemipteran lineages are known to be simultaneously associated with two or more endosymbionts with complementary biosynthetic pathways to synthesize amino acids or vitamins, such co-obligate symbioses have not been functionally characterized in other insect orders. Here, we report on the characterization of a dual co-obligate, bacter

Water column dynamics control nitrite-dependent anaerobic methane oxidation by Candidatus “Methylomirabilis” in stratified lake basins

Citation
Su et al. (2023). The ISME Journal 17 (5)
Names
Methylomirabilis
Abstract
AbstractWe investigated microbial methane oxidation in the water column of two connected but hydrodynamically contrasting basins of Lake Lugano, Switzerland. Both basins accumulate large amounts of methane in the water column below their chemoclines, but methane oxidation efficiently prevents methane from reaching surface waters. Here we show that in the meromictic North Basin water column, a substantial fraction of methane was eliminated through anaerobic methane oxidation (AOM) coupled to nitr

Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria

Citation
Sereika et al. (2023). The ISME Journal 17 (4)
Names
Electronema halotolerans Electrothrix laxa Electronema Electronema aureum Ts Electrothrix Electrothrix gigas Electrothrix arhusiensis Electrothrix communis Ts
Abstract
AbstractCable bacteria of theDesulfobulbaceaefamily are centimeter-long filamentous bacteria, which are capable of conducting long-distance electron transfer. Currently, all cable bacteria are classified into two candidate genera:CandidatusElectronema, typically found in freshwater environments, andCandidatusElectrothrix, typically found in saltwater environments. This taxonomic framework is based on both 16S rRNA gene sequences and metagenome-assembled genome (MAG) phylogenies. However, most of

Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species

Citation
Bizic et al. (2023). The ISME Journal 17 (3)
Names
Ca. Thiovulum karukerense Ca. Thiovulum stygium Ca. Thiovulum imperiosus
Abstract
AbstractThiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O2 (~7%). The cave’s surface-water microbial community is dominated by bacteria we identified as Thiovulum. We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum. We asse

Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae

Citation
Dharamshi et al. (2022). The ISME Journal 16 (12)
Names
“Parasimkaniaceae”
Abstract
AbstractSponge microbiomes contribute to host health, nutrition, and defense through the production of secondary metabolites.Chlamydiae, a phylum of obligate intracellular bacteria ranging from animal pathogens to endosymbionts of microbial eukaryotes, are frequently found associated with sponges. However, sponge-associated chlamydial diversity has not yet been investigated at the genomic level and host interactions thus far remain unexplored. Here, we sequenced the microbiomes of three sponge s