The ISME Journal


Publications
85

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

Recovery and genome reconstruction of novel magnetotactic Elusimicrobiota from bog soil

Citation
Uzun et al. (2023). The ISME Journal 17 (2)
Names
“Obscuribacteriales” “Obscuribacteriaceae” “Obscuribacterium” “Obscuribacterium magneticum” Liberimonas “Liberimonadaceae” Liberimonas magnetica Ts
Abstract
Abstract Studying the minor part of the uncultivated microbial majority (“rare biosphere”) is difficult even with modern culture-independent techniques. The enormity of microbial diversity creates particular challenges for investigating low-abundance microbial populations in soils. Strategies for selective sample enrichment to reduce community complexity can aid in studying the rare biosphere. Magnetotactic bacteria, apart from being a minor part of the microbial community, are al

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

Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily

Citation
Speth et al. (2022). The ISME Journal 16 (7)
Names
Tharpellaceae Tharpella Tharpella aukensis Ts
Abstract
Abstract Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physicochemical data and 16S rRNA gene amplicons to characterize the sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% of those cu

Niche partitioning of the ubiquitous and ecologically relevant NS5 marine group

Citation
Priest et al. (2022). The ISME Journal 16 (6)
Names
“Marisimplicoccus framensis” “Marisimplicoccus” “Marivariicella” “Marivariicella framensis” “Maricapacicella” “Maricapacicella forsetii” “Arcticimaribacter” “Arcticimaribacter forsetii”
Abstract
AbstractNiche concept is a core tenet of ecology that has recently been applied in marine microbial research to describe the partitioning of taxa based either on adaptations to specific conditions across environments or on adaptations to specialised substrates. In this study, we combine spatiotemporal dynamics and predicted substrate utilisation to describe species-level niche partitioning within the NS5 Marine Group. Despite NS5 representing one of the most abundant marine flavobacterial clades

The novel genus, ‘Candidatus Phosphoribacter’, previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide

Citation
Singleton et al. (2022). The ISME Journal 16 (6)
Names
“Phosphoribacter hoenirii” “Phosphoribacter freyrii” “Phosphoribacter thorii” Phosphoribacter baldrii Ts Phosphoribacter hodrii “Phosphoribacter tyrii” Ca. Lutibacillus Phosphoribacter
Abstract
Abstract The bacterial genus Tetrasphaera encompasses abundant polyphosphate accumulating organisms (PAOs) that are responsible for enhanced biological phosphorus removal (EBPR) in wastewater treatment plants. Recent analyses of genomes from pure cultures revealed that 16S rRNA genes cannot resolve the lineage, and that Tetrasphaera spp. are from several different genera within the Dermatophilaceae. Here, we examine 14 recently recovered high-quality metagenome-assembled genomes f

Niche differentiation of sulfur-oxidizing bacteria (SUP05) in submarine hydrothermal plumes

Citation
Dede et al. (2022). The ISME Journal 16 (6)
Names
Ca. Thioglobus plumae Ca. Thioglobus vadi Ca. Thioglobus vulcanius
Abstract
AbstractHydrothermal plumes transport reduced chemical species and metals into the open ocean. Despite their considerable spatial scale and impact on biogeochemical cycles, niche differentiation of abundant microbial clades is poorly understood. Here, we analyzed the microbial ecology of two bathy- (Brothers volcano; BrV-cone and northwest caldera; NWC) and a mesopelagic (Macauley volcano; McV) plumes on the Kermadec intra-oceanic arc in the South Pacific Ocean. The microbial community structure