Rinke, Christian


Publications
18

Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific

Citation
Sun et al. (2025). Microbial Genomics 11 (3)
Names
“Tangaroaeota” “Tangaroaeaceae” “Tangaroaeales” “Tangaroaeia” “Tangaroaea” “Tangaroaea hikurangi” “Spongiamicia” “Spongiamicales” “Spongiamicaceae” “Spongiamicota” “Ryujiniota” “Ryujiniia” “Ryujiniales” “Ryujiniaceae” “Ryujinia” “Ryujinia shimokita” “Spongiamicus weybense” “Spongiamicus”
Abstract
Marine sediments are vast, underexplored habitats and represent one of the largest carbon deposits on our planet. Microbial communities drive nutrient cycling in these sediments, but the full extent of their taxonomic and metabolic diversity remains to be explored. Here, we analysed shallow coastal and deep subseafloor sediment cores from 0.01 to nearly 600 metres below the seafloor, in the Western Pacific Region. Applying metagenomics, we identified several taxonomic clusters across all samples

Proposal of Patescibacterium danicum gen. Nov., sp. nov. in the ubiquitous ultrasmall bacterial phylum Patescibacteriota phyl. Nov

Citation
Dutkiewicz et al. (2024). ISME Communications
Names
Patescibacterium danicum Ts Ca. Patescibacteria Patescibacteriota Patescibacteriia Patescibacteriales Patescibacteriaceae Patescibacterium
Abstract
Abstract Candidatus Patescibacteria is a diverse bacterial phylum that is notable for members with ultrasmall cell size, reduced genomes, limited metabolic capabilities and dependence on other prokaryotic hosts. Despite the prevalence of the name Ca. Patescibacteria in the scientific literature, it is not officially recognized under the International Code of Nomenclature of Prokaryotes (ICNP) and lacks a nomenclatural type. Here, we rectify this situation by describing two closely

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

Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes

Citation
Chuvochina et al. (2023). FEMS Microbiology Letters 370
Names
“Paceibacteraceae” “Paceibacterales” “Bradymonadia” Brachyspiria Thermoplasmatota Francisellales Piscirickettsiales Acetobacterales Methyloligellaceae Rhodomicrobiaceae Leptospiria Alicyclobacillia Natranaerobiia Jeotgalibacillaceae Brevinematia Amphibacillaceae Chitinimonas Chitinimonadaceae Marinicellaceae Ahniellaceae Pseudohongiellaceae Methanoculleaceae Methanofollaceae Methanosphaerulaceae Methanocellia Methanosarcinia Methanonatronarchaeia Methanoliparia Halobacteriota Exiguobacteriales Exiguobacteriaceae Salinicoccaceae Staphylococcales Gemellaceae Thermicanales Thermicanaceae Neiellaceae Oceanococcaceae Wohlfahrtiimonadaceae Thermaerobacteria Thermaerobacterales Thermaerobacteraceae Sedimentibacteraceae Proteiniboraceae Monoglobaceae Monoglobales Lutisporaceae Lutisporales Lachnospirales Christensenellales Caldicoprobacterales Caldicellulosiruptoraceae Caldicellulosiruptorales Oxobacteraceae Caloramatoraceae Acetivibrionaceae Acetivibrio Acetivibrionales Clostridiisalibacter Clostridiisalibacteraceae Caldisalinibacter Dethiosulfatibacteraceae Thermincolales Thermincolia Carboxydocellales Carboxydocellaceae Tindalliaceae Thermotaleaceae Natronincolaceae Filifactoraceae Caminicellaceae Anaerovoracaceae Peptostreptococcales Acidaminobacteraceae Mahellales Mahellaceae Thermosulfidibacterota Thermosulfidibacteria Thermosulfidibacterales Thermosulfidibacteraceae Elainellaceae Elainellales Phormidesmidaceae Phormidesmidales Hydrogenothermales Desulfurobacteriia “Paceibacteria” Vampirovibrionaceae Vampirovibrionales Vampirovibrionia Binataceae Binatales Binatia Hydrothermia Hydrothermales Hydrothermaceae Azobacteroidaceae Bipolaricaulales Bipolaricaulaceae Bipolaricaulia Hepatobacteraceae Hepatoplasmataceae Johnevansiaceae Johnevansiales Kapaibacteriaceae Kapaibacteriales Magnetobacteriaceae Methylomirabilaceae Methylomirabilales Methylomirabilia Muiribacteriaceae Muiribacteriales Muiribacteriia Nucleicultricaceae Obscuribacteraceae Promineifilaceae Promineifilales Pseudothioglobaceae Puniceispirillaceae Puniceispirillales Saccharimonadaceae Saccharimonadales Tenderiaceae Tenderiales Thermobaculaceae Thermobaculales Desulforudaceae Methylomirabilota Cloacimonadia Cloacimonadales Cloacimonadaceae Kapaibacteriia “Poriferisulfidales” Leptolyngbyaceae
Abstract
Abstract The Genome Taxonomy Database (GTDB) is a taxonomic framework that defines prokaryotic taxa as monophyletic groups in concatenated protein reference trees according to systematic criteria. This has resulted in a substantial number of changes to existing classifications (https://gtdb.ecogenomic.org). In the case of union of taxa, GTDB names were applied based on the priority of publication. The division of taxa or change in rank led to the formation of new Latin names above

Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages

Citation
Sun et al. (2021). ISME Communications 1 (1)
Names
Ca. Borrarchaeum weybense Jordiarchaeum Jordiarchaeum madagascariense Ts “Sifarchaeaceae” Jordiarchaeaceae “Sifarchaeales” Jordiarchaeales “Sifarchaeia” Jordiarchaeia “Borrarchaeaceae” Ca. Borrarchaeum “Sifarchaeum” Ca. Sifarchaeum marinoarchaea Ca. Sifarchaeum subterraneus “Sifarchaeota”
Abstract
AbstractAsgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative heterotrophs contributing to carbon cycling in sediment ecosystems. Here, we double the genomic catalogue of Asgardarchaeota by obtaining 71 MAGs from a range of habitats around the globe, including the deep subsurface,

Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution

Citation
Dombrowski et al. (2020). Nature Communications 11 (1)
Names
“Undinarchaeia” “Undinarchaeota” “Naiadarchaeales” “Undinarchaeales” “Naiadarchaeaceae” “Undinarchaeaceae” “Undinarchaeum marinum”
Abstract
AbstractThe recently discovered DPANN archaea are a potentially deep-branching, monophyletic radiation of organisms with small cells and genomes. However, the monophyly and early emergence of the various DPANN clades and their role in life’s evolution are debated. Here, we reconstructed and analysed genomes of an uncharacterized archaeal phylum (CandidatusUndinarchaeota), revealing that its members have small genomes and, while potentially being able to conserve energy through fermentation, like

A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)

Citation
Rinke et al. (2019). The ISME Journal 13 (3)
Names
Poseidoniia Thalassarchaeum betae Ts Thalassarchaeum Poseidoniaceae Poseidonia Poseidonia alphae Ts Thalassarchaeaceae Poseidoniales Ca. Poseidonaceae “Nanohalarchaeota” “Poseidoniota”
Abstract
Abstract Marine Group II (MGII) archaea represent the most abundant planktonic archaeal group in ocean surface waters, but our understanding of the group has been limited by a lack of cultured representatives and few sequenced genomes. Here, we conducted a comparative phylogenomic analysis of 270 recently available MGII metagenome-assembled genomes (MAGs) to investigate their evolution and ecology. Based on a rank-normalised genome phylogeny, we propose that MGII is an order-level