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Machine learning and metagenomics identifies uncharacterized taxa inferred to drive biogeochemical cycles in a subtropical hypereutrophic estuary

Citation
Prabhu et al. (2024). ISME Communications 4 (1)
Names
“Hypereutrophica” “Hypereutrophica brisbanensis” Salinivivens Nitrosopumilus brisbanensis Eutrophomonas brisbanensis Ts Salinivivens marinus Ts Eutrophovita Eutrophosalina Eutrophomonas Salsuginivita brisbanensis Ts Eutrophobiales Eutrophovitaceae Eutrophocola Eutrophocola salsuginis Ts Eutrophobiaceae Eutrophobius Eutrophobius brisbanensis Ts Eutrophomonadaceae Eutrophovita brisbanensis Ts Salivitaceae Salivita Salivita marina Ts Salsuginivita Eutrophosalina marina Ts Marisalimonadaceae Marisalimonas Australimonadales Australimonadaceae Australimonas brisbanensis Ts Marisalimonas marina Ts Australimonas
Abstract
Abstract Anthropogenic influences have drastically increased nutrient concentrations in many estuaries globally, and microbial communities have adapted to the resulting hypereutrophic ecosystems. However, our knowledge of the dominant microbial taxa and their potential functions in these ecosystems has remained sparse. Here, we study prokaryotic community dynamics in a temporal–spatial dataset, from a subtropical hypereutrophic estuary. Screening 54 water samples across brackish t

Candidatus Siderophilus nitratireducens”: a putative nap-dependent nitrate-reducing iron oxidizer within the new order Siderophiliales

Citation
Corbera-Rubio et al. (2024). ISME Communications 4 (1)
Names
Ca. Siderophilus nitratireducens
Abstract
Abstract Nitrate leaching from agricultural soils is increasingly found in groundwater, a primary source of drinking water worldwide. This nitrate influx can potentially stimulate the biological oxidation of iron in anoxic groundwater reservoirs. Nitrate-dependent iron-oxidizing (NDFO) bacteria have been extensively studied in laboratory settings, yet their ecophysiology in natural environments remains largely unknown. To this end, we established a pilot-scale filter on nitrate-ri

Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick

Citation
Rahlff et al. (2023). ISME Communications 3 (1)
Names
“Alishewanella slickus”
Abstract
AbstractVisible surface films, termed slicks, can extensively cover freshwater and marine ecosystems, with coastal regions being particularly susceptible to their presence. The sea-surface microlayer (SML), the upper 1-mm at the air-water interface in slicks (herein slick SML) harbors a distinctive bacterial community, but generally little is known about SML viruses. Using flow cytometry, metagenomics, and cultivation, we characterized viruses and bacteria in a brackish slick SML in comparison t

Expansion of Armatimonadota through marine sediment sequencing describes two classes with unique ecological roles

Citation
Carlton et al. (2023). ISME Communications 3 (1)
Names
“Hebobacteraceae” “Hebobacterales” “Hebobacteria” “Zipacnadaceae” “Zipacnadales” “Zipacnadia” “Hebobacterum abditum” “Hebobacterum” “Zipacnadum vermilionense” “Zipacnadum”
Abstract
AbstractMarine sediments comprise one of the largest environments on the planet, and their microbial inhabitants are significant players in global carbon and nutrient cycles. Recent studies using metagenomic techniques have shown the complexity of these communities and identified novel microorganisms from the ocean floor. Here, we obtained 77 metagenome-assembled genomes (MAGs) from the bacterial phylum Armatimonadota in the Guaymas Basin, Gulf of California, and the Bohai Sea, China. These MAGs

Characterization of a bloom-associated alphaproteobacterial lineage, ‘Candidatus Phycosocius’: insights into freshwater algal-bacterial interactions

Citation
Tanabe et al. (2023). ISME Communications 3 (1)
Names
Ca. Phycosocius Ca. Phycosocius spiralis
Abstract
AbstractMarine bacterial lineages associated with algal blooms, such as the Roseobacter clade, have been well characterized in ecological and genomic contexts, yet such lineages have rarely been explored in freshwater blooms. This study performed phenotypic and genomic analyses of an alphaproteobacterial lineage ‘Candidatus Phycosocius’ (denoted the CaP clade), one of the few lineages ubiquitously associated with freshwater algal blooms, and described a novel species: ‘Ca. Phycosocius spiralis.’

The terrestrial isopod symbiont ‘Candidatus Hepatincola porcellionum’ is a potential nutrient scavenger related to Holosporales symbionts of protists

Citation
Dittmer et al. (2023). ISME Communications 3 (1)
Names
Ca. Hepatincola porcellionum
Abstract
AbstractThe order Holosporales (Alphaproteobacteria) encompasses obligate intracellular bacterial symbionts of diverse Eukaryotes. These bacteria have highly streamlined genomes and can have negative fitness effects on the host. Herein, we present a comparative analysis of the first genome sequences of ‘Ca. Hepatincola porcellionum’, a facultative symbiont occurring extracellularly in the midgut glands of terrestrial isopods. Using a combination of long-read and short-read sequencing, we obtaine

Introducing Candidatus Bathyanammoxibiaceae, a family of bacteria with the anammox potential present in both marine and terrestrial environments

Citation
Zhao et al. (2022). ISME Communications 2 (1)
Names
Ca. Bathyanammoxibiaceae Ca. Brocadiales
Abstract
AbstractAnaerobic ammonium oxidation (Anammox) bacteria are a group of extraordinary bacteria exerting a major impact on the global nitrogen cycle. Their phylogenetic breadth and diversity, however, are not well constrained. Here we describe a new, deep-branching family in the order of Candidatus Brocadiales, Candidatus Bathyanammoxibiaceae, members of which have genes encoding the key enzymes of the anammox metabolism. In marine sediment cores from the Arctic Mid-Ocean Ridge (AMOR), the presenc

Vulcanimicrobium alpinus gen. nov. sp. nov., the first cultivated representative of the candidate phylum “Eremiobacterota”, is a metabolically versatile aerobic anoxygenic phototroph

Citation
Yabe et al. (2022). ISME Communications 2 (1)
Names
Vulcanimicrobium alpinum T Vulcanimicrobium Vulcanimicrobiales
Abstract
Abstract The previously uncultured phylum “Candidatus Eremiobacterota” is globally distributed and often abundant in oligotrophic environments. Although it includes lineages with the genetic potential for photosynthesis, one of the most important metabolic pathways on Earth, the absence of pure cultures has limited further insights into its ecological and physiological traits. We report the first successful isolation of a “Ca. Eremiobacterota” strain from a fumarolic ice cave on M