Register list for 40 new names including Acidimicrobilacustridaceae fam. nov.

A family of Acidimicrobiales also known as “acIV-D Actinobacteria” or “uncultured Microtrichales” from 16S rRNA gene analyses and as f__UBA8139 in GTDB, that is commonly found in freshwater environments. Consisting of the genus Acidimicrobilacustris and two species, Acidimicrobilacustris thunensis (GCA_965194345.1) and Acidimicrobilacustris europaeus (GCA_965194515.1), both isolated from freshwater lakes. Type species is Acidimicrobilacustris thunensis TE-7 (GCA_965194345.1). The closest cultivated relative is Rhabdothermincola salaria (Iamiaceae, GCF_021246445.1), with an average amino acid identity of 66.55% and an average nucleotide identity of 71.1%. As this related taxon is also included in family UBA8139 in GTDB and not in Iamiaceae, we propose the new family Acidimicrobilacustridaceae. Current GTDB (R220) classification: d__Bacteria; p__Actinomycetota; c__Acidimicrobiia; o__Acidimicrobiales; f__UBA8139.

Type strain is Verrucolacustris abundans MiH-22 (GCA_965194535.1). In contrast to other Methylacidiphilales including the only described genus Methylacidimicrobium (Methylacidiphilaceae, GCF_902143385.2), no genes for C1 metabolism were identified, therefore we suggest the establishment of a new family of non-methanotrophic Methylacidiphilales. The closest cultivated relative is Methylacidimicrobium cyclopophantes 3B_2 (GCF_902143385.2), with an average amino acid identity of 49.5% and average nucleotide identity of 62.8%. Current GTDB classification (R220): d__Bacteria; p__Verrucomicrobiota; c__Verrucomicrobiae; o__Methylacidiphilales; f__UBA3015. 

Type genus of Acidimicrobilacustridaceae also known as “acIV-D Actinobacteria” or “uncultured Microtrichales” from 16S rRNA gene analyses and as g__F1-20-MAGs160 in GTDB, that is commonly found in freshwater environments. Consisting of two species, Acidimicrobilacustris thunensis (GCA_965194345.1) and Acidimicrobilacustris europaeus (GCA_965194515.1), both isolated from freshwater lakes. Type species is Acidimicrobilacustris thunensis TE-7 (GCA_965194345.1). The closest cultivated relative is Rhabdothermincola salaria (GCF_021246445.1), with an average amino acid identity of 66.55% and an average nucleotide identity of 71.1%. Current GTDB (R220) classification: d__Bacteria; p__Actinomycetota; c__Acidimicrobiia; o__Acidimicrobiales; f__UBA8139; g__F1-20-MAGs160.

The genus contains two species, Allorhodoferax aquaticus (GCA_965194715.1) and Allorhodoferax lacus (GCA_965194635.1), both isolated from freshwater lakes. Type species is Allorhodoferax aquaticus MsE-M22 (GCA_965194715.1). The genus is classified as d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; Rhodoferax_C in GTDB (R220) and contains bacteria with various names such as Curvibacter, Rhodoferax, etc. The closest cultivated relative is Curvibacter sp. AEP1-3 (GCF_002163715.1), with average amino acid identities of 86.2-90.7% and average nucleotide identities of 81-9-86.6%. The type strain of the genus Rhodoferax (Rhodoferax fermentans JCM 7819; GCA_002017865.1) is classified as d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__Rhodoferax; s__Rhodoferax fermentans, with AAIs of 66.0-66.8% and ANIs of 72.4-72.6%. We therefore suggest a reclassification of this genus (GTDB genus Rhodoferax_C) with the proposed name Allorhodoferax. 

Type species is Allotabrizicola aquatica RE-M30 (GCA_965194375.1). The closest cultivated relative is Tabrizicola oligotrophica KMS-5 (GCF_011008935.1) with an average amino acid identity of 79.2% and average nucleotide identity of 79.5%. As the closest relative is classified as Tabrizicola_A in GTDB, we propose a new genus that encompasses both species. The type species of the genus Tabrizicola (Tabrizicola aquatica, GCF_002900975.1), has average amino acid identities of 68.4-69.2% and average nucleotide identities of 73.7-74.8% to Tabrizicola oligotrophica KMS-5 (GCF_011008935.1) and Allotabrizicola aquatica RE-M30. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Alphaproteobacteria; o__Rhodobacterales; f__Rhodobacteraceae; g__Tabrizicola_A.

A genus of abundant freshwater bacteria, commonly known from metagenomic and 16S rRNA amplicon studies, often referred to MWH-UniP1 group or betaVI in 16S rRNA based studies. Type species is Lacustribacter communis MsE-M52 (GCA_965194335.1). The closest cultivated relatives are the undescribed Burkholderiales bacterium LSUCC0115 (GCA_009646425.1), with an average amino acid identity of 61.9% and average nucleotide identity of 67.9% and the newly established genus Hahnella, with 60.4-61.7% AAI and 67.2-67.9% ANI. The closest validly described relative is Limnobacter thiooxidans CS-K2 (GCF_036323495.1) with an AAI of 53.95% and an ANI of 66.33%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__UBA954. 

Type species is Novimethylotenera aquatica ME-M6 (GCA_947054645.1). Although the closest cultivated relative (Methylotenera versatilis 7; GCF_000799165.1) has an average amino acid identity of 80.36% and average nucleotide identity of 76.56%, the genus Methylotenera is known to be polyphyletic in phylogenomic trees (e.g., Salcher et al. 2019; https://doi.org/10.1038/s41396-019-0471-3) and some strains that were previously termed Methylotenera should be reclassified. Current GTDB classification of the genus including the closest cultivated relative (GCF_000799165.1) is d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Methylophilaceae; g__Methylotenera_A. We propose a reclassification of the GTDB genus Methylotenera_A to Novimethylotenera, gen. nov.

Type species is Verrucolacustris abundans MiH-22 (GCA_965194535.1). The closest cultivated relative is Methylacidimicrobium cyclopophantes 3B_2 (GCF_902143385.2), with an average amino acid identity of 49.5% and average nucleotide identity of 62.8%. Current GTDB classification (R220): d__Bacteria; p__Verrucomicrobiota; c__Verrucomicrobiae; o__Methylacidiphilales; f__UBA3015; g__UBA3015.

Type strain is Acidimicrobilacustris europaeus KE-4 (GCA_965194515.1), isolated from 5 m depth from Klíčava Reservoir, Czechia (date: 2019-04-25), via high-throughput dilution to extinction cultivation. KE-4 has a genome size of 2.35 Mbp with a genomic GC content of 58.2%, contains 3 rRNA genes and 44 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding rhodopsins but lacks the biosynthetic pathway for retinal biosynthesis. No genes for flagella or pilus assembly and chemotaxis were annotated. Pathways for taurine degradation, assimilatory sulfate reduction and methane/alkanesulfonate oxidation and biosynthesis for all amino acids except histidine and threonine were predicted. Further, pathways for riboflavin, pyridoxal, NAD, coenzyme A, biotin and heme were identified. The closest cultivated relatives are Rhabdothermincola salaria (GCF_021246445.1) with an average amino acid identity of 64.98% and an average nucleotide identity of 69.8% and another newly proposed species, Acidimicrobilacustris thunensis TE-7 (GCA_965194345.1), with an AAI of 73.1% and an ANI of 72%. Current GTDB classification (R220): d__Bacteria; p__Actinomycetota; c__Acidimicrobiia; o__Acidimicrobiales; f__UBA8139; g__F1-20-MAGs160; s__F1-20-MAGs160 sp903827085. 

Type strain is Acidimicrobilacustris thunensis TE-7 (GCA_965194345.1), isolated from 5 m depth from Lake Thun, Switzerland (date: 2019-11-11), via high-throughput dilution to extinction cultivation. TE-7 has a genome size of 2.38 Mbp with a genomic GC content of 60.6%, contains 3 rRNA genes and 46 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding rhodopsins but lacks the biosynthetic pathway for retinal biosynthesis. No genes for flagella or pilus assembly and chemotaxis were annotated. Pathways for taurine degradation, assimilatory sulfate reduction and methane/alkanesulfonate oxidation and biosynthesis for all amino acids except histidine were predicted. Further, pathways for riboflavin, pyridoxal, NAD, coenzyme A, biotin and heme were identified. The closest cultivated relatives are Rhabdothermincola salaria (GCF_021246445.1) with an average amino acid identity of 66.55% and an average nucleotide identity of 71.1% and another newly proposed species, Acidimicrobilacustris europaeus KE-4 (GCA_965194515.1), with an AAI of 73.1% and an ANI of 72%. Current GTDB (R220) classification: d__Bacteria; p__Actinomycetota; c__Acidimicrobiia; o__Acidimicrobiales; f__UBA8139; g__F1-20-MAGs160; s__F1-20-MAGs160 sp945878725. 

Type strain is Allorhodoferax aquaticus MsE-M22 (GCA_965194715.1), isolated from 5 m depth from Lake Most, Czechia (date: 2019-07-30), via high-throughput dilution to extinction cultivation. MsE-M22 has a genome size of 3.7 Mbp with a genomic GC content of 59.3%, contains 6 rRNA genes and 47 tRNAs. The genome is complete, consisting of a circular chromosome. Genes for flagellar and pilus assembly were annotated. Pathways for nitrate reduction, cyanate and urea degradation, glycolate oxidation and the biosynthesis of all amino acids except for aspartate were predicted. Further, pathways for thiamine, riboflavin, NAD, coenzyme A, THF, cobalamin, and heme biosynthesis were identified. The closest cultivated relative is Curvibacter sp. AEP1-3 (GCF_002163715.1), with an average amino acid identity of 90.7% and average nucleotide identity of 86.6%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__Rhodoferax_C; s__Rhodoferax_C sp027488985.

Type strain is Allorhodoferax lacus ZE-M1 (GCA_965194635.1), isolated from 5 m depth from Lake Zurich, Switzerland (date: 2019-04-03), via high-throughput dilution to extinction cultivation. ZE-M1 has a genome size of 3.7 Mbp with a genomic GC content of 60.1%, contains 6 rRNA genes and 46 tRNAs. The genome is a high-quality draft consisting of 2 contigs. Genes for flagellar and pilus assembly were annotated. Pathways for cyanate and urea degradation, glycolate and methane/alkanesulfonate oxidation and the biosynthesis of all amino acids except for aspartate were predicted. Further, pathways for thiamine, riboflavin, NAD, coenzyme A, THF, cobalamin, and heme biosynthesis were identified. The closest cultivated relative is Curvibacter sp. AEP1-3 (GCF_002163715.1), with an average amino acid identity of 86.2% and average nucleotide identity of 81.9%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__Rhodoferax_C; s__. 

Type strain is Allotabrizicola aquatica RE-M30 (GCA_965194375.1), isolated from 0.5 m depth from the Římov Reservoir, Czechia (date: 2019-08-05), via high-throughput dilution to extinction cultivation. RE-M30 has a genome size of 3.6 Mbp with a genomic GC content of 61.9%, contains 6 rRNA genes and 49 tRNAs. The genome is a high-quality draft consisting of 20 contigs. The genome contains genes encoding anoxygenic aerobic phototrophy (pufABLM). Genes for flagellar assembly were annotated in the genome. Pathways for urea and taurine degradation, glycolate oxidation and the biosynthesis of all amino acids were predicted. Further, pathways for riboflavin, pantothenate, coenzyme A, and heme biosynthesis were identified. The closest cultivated relative is Tabrizicola oligotrophica KMS-5 (GCF_011008935.1), with an average amino acid identity of 79.2% and average nucleotide identity of 79.5%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Alphaproteobacteria; o__Rhodobacterales; f__Rhodobacteraceae; g__Tabrizicola_A; s__.

Type strain is Aquidulcibacter miladensis MiH-15 (GCA_965234355.1), isolated from 15 m depth from Lake Milada, Czechia (date: 2019-07-23), via high-throughput dilution to extinction cultivation. MiH-15 has a genome size of 3.2 Mbp with a genomic GC content of 55.7%, contains 3 rRNA genes and 41 tRNAs. The genome is a high-quality draft consisting of 8 contigs. The genome contains genes encoding anoxygenic aerobic phototrophy (pufABLM). Genes for flagellar assembly and chemotaxis were annotated in the genome. Pathways for taurine degradation, assimilatory sulfate reduction and methane/alkanesulfonate oxidation and the biosynthesis of all amino acids were predicted. Further, pathways for riboflavin, NAD, coenzyme A, pimeloyl-ACP, THF, and heme biosynthesis were identified. The closest cultivated relatives are Aquidulcibacter paucihalophilus TH1-2 (GCF_002105465.1) with an average amino acid identity of 87.1% and average nucleotide identity of 80.5% and another newly proposed species, Aquidulcibacter rimovensis RH-10 (GCA_965234525.1), with an AAI of 93.2% and an ANI of 89.4%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Alphaproteobacteria; o__Caulobacterales; f__TH1-2; g__Aquidulcibacter; s__Aquidulcibacter sp945891505.

Type strain is Aquidulcibacter rimovensis RH-10 (GCA_965234525.1), isolated from 30 m depth from Římov Reservoir, Czechia (date: 2019-08-05), via high-throughput dilution to extinction cultivation. RH-10 has a genome size of 3.3 Mbp with a genomic GC content of 55.4%, contains 3 rRNA genes and 42 tRNAs. The genome is a high-quality draft consisting of 2 contigs. The genome contains genes encoding anoxygenic aerobic phototrophy (pufABLM). Genes for flagellar assembly and chemotaxis were annotated in the genome. Pathways for taurine degradation, assimilatory sulfate reduction and methane/alkanesulfonate oxidation and the biosynthesis of all amino acids were predicted. Further, pathways for riboflavin, NAD, coenzyme A, pimeloyl-ACP, THF, and heme biosynthesis were identified. The closest cultivated relatives are Aquidulcibacter paucihalophilus TH1-2 (GCF_002105465.1) with an average amino acid identity of 87.3% and average nucleotide identity of 80.2% and another newly proposed species, Aquidulcibacter miladensis MiH-15 (GCA_965234355.1), with an AAI of 93.2% and an ANI of 89.4%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Alphaproteobacteria; o__Caulobacterales; f__TH1-2; g__Aquidulcibacter; s__Aquidulcibacter sp027532555. 

Type strain is Caulobacter lacus MiH-16 (GCA_965234345.1), isolated from 15 m depth from Lake Milada, Czechia (date: 2019-07-23), via high-throughput dilution to extinction cultivation. MiH-16 has a genome size of 3.6 Mbp with a genomic GC content of 67.6%, contains 3 rRNA genes and 47 tRNAs. The genome is a high-quality draft consisting of 5 contigs. The genome contains genes encoding rhodopsins. Genes for flagellar assembly and chemotaxis were annotated in the genome. Pathways for taurine degradation, assimilatory sulfate reduction and methane/alkanesulfonate oxidation and the biosynthesis of all amino acids were predicted. Further, pathways for thiamine, riboflavin, NAD, coenzyme A, pimeloyl-ACP, THF, and heme biosynthesis were identified. The closest cultivated relative is Caulobacter sp. Root1455 (GCF_001426905.1), with an average amino acid identity of 64% and average nucleotide identity of 74.7%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Alphaproteobacteria; o__Caulobacterales; f__Caulobacteraceae; g__Caulobacter; s__Caulobacter sp903858185.

Type strain is Flavobacterium neuenschwanderi GE-10 (GCA_965234425.1), isolated from 5 m depth from Greifensee, Switzerland (date: 2019-04-03), via high-throughput dilution to extinction cultivation. GE-10 has a genome size of 3.56 Mbp with a genomic GC content of 33.1%, contains 4 rRNA genes and 38 tRNAs. The genome is a high-quality draft consisting of 44 contigs. The genome contains genes encoding rhodopsins. Genes for gliding motility (gldBDHJKLMN, sprA) were annotated in the genome. Pathways for assimilatory sulfate reduction and the biosynthesis of all amino acids were predicted. Further, pathways for riboflavin, NAD, coenzyme A, biotin, THF, menaquinone, and heme were identified. The closest cultivated relative is Flavobacterium psychrotolerans RB1R5 (GCF_003097635.1), with an average amino acid identity of 74.81% and average nucleotide identity of 74.37%. Current GTDB classification (R220): d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Flavobacteriales; f__Flavobacteriaceae; g__Flavobacterium; s__.

Type strain is Flavobacterium rarum TH-M1 (GCA_965234445.1), isolated from 180 m from Lake Thun, Switzerland (date: 2019-04-08), via high-throughput dilution to extinction cultivation. TH-M1 has a genome size of 4.26 Mbp with a genomic GC content of 33.4%, contains 6 rRNA genes and 51 tRNAs. The genome is a high-quality draft consisting of 29 contigs. The genome contains genes encoding rhodopsins. Genes for gliding motility (gldBDHJKLMN, sprA) were annotated in the genome. Pathways for taurine degradation, assimilatory sulfate reduction and the biosynthesis of all amino acids were predicted. Further, pathways for thiamine, riboflavin, NAD, pantothenate, coenzyme A, biotin, THF, menaquinone, and heme were identified. The closest cultivated relative is Flavobacterium praedii IMCC34515 (GCF_026810365.1), with an average amino acid identity of 85.51% and average nucleotide identity of 83.7%. Current GTDB classification (R220): d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Flavobacteriales; f__Flavobacteriaceae; g__Flavobacterium; s__.

Type strain is Fontibacterium abundans MiE-29 (GCA_965235095.1), isolated from 5 m depth from Lake Milada, Czechia (date: 2019-10-15), via high-throughput dilution to extinction cultivation. MiE-29 has a genome size of 1.1 Mbp with a genomic GC content of 29.4%, contains 3 rRNA genes and 31 tRNAs. The genome is a high-quality draft consisting of 2 contigs. The genome contains genes encoding rhodopsins and the biosynthetic pathway for retinal biosynthesis. No genes for flagella or pilus assembly and chemotaxis were annotated. Pathways for glycolate oxidation and the biosynthesis of 16 amino acids were predicted. Further, pathways for riboflavin, NAD, coenzyme A, and heme biosynthesis were identified. The closest cultivated relatives are Fontibacterium commune, syn. ‘Candidatus Fonsibacter ubiquis’ LSUCC0530 (GCF_002688585.1; later reclassified to ‘Ca. Allofontibacter communis’), with an average amino acid identity of 86.5% and average nucleotide identity of 85.2% and another newly proposed species, Fontibacterium medardicum ME-17 (GCA_965235075.1), with an AAI of 92.7% and an ANI of 91.1%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Alphaproteobacteria; o__Pelagibacterales; f__Pelagibacteraceae; g__Fonsibacter; s__.

Type strain is Allofontibacter medardicus ME-17 (GCA_965235075.1), isolated from 5 m depth from Lake Medard, Czechia (date: 2019-10-22), via high-throughput dilution to extinction cultivation. ME-17 has a genome size of 1.1 Mbp with a genomic GC content of 29.6%, contains 3 rRNA genes and 31 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding rhodopsins and the biosynthetic pathway for retinal biosynthesis. No genes for flagella or pilus assembly and chemotaxis were annotated. Pathways for glycolate oxidation and the biosynthesis of 16 amino acids were predicted. Further, pathways for riboflavin, NAD, coenzyme A, and heme biosynthesis were identified. The closest cultivated relatives are ‘Candidatus Fonsibacter ubiquis’ LSUCC0530 (GCF_002688585.1; later reclassified to ‘Ca. Allofontibacter communis’), with an average amino acid identity of 87.2% and average nucleotide identity of 85.2% and another newly proposed species, Allofontibacter abundans MiE-29 (GCA_965235095.1), with an AAI of 92.7% and an ANI of 91.1%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Alphaproteobacteria; o__Pelagibacterales; f__Pelagibacteraceae; g__Fonsibacter; s__Fonsibacter sp018882565.

Type strain is Hydrogenophaga miladensis MiE-M28 (GCA_965234585.1), isolated from 5 m depth from Lake Milada, Czechia (date: 2019-10-15), via high-throughput dilution to extinction cultivation. MiE-M28 has a genome size of 2.4 Mbp with a genomic GC content of 60.6%, contains 6 rRNA genes and 43 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding anoxygenic aerobic phototrophy (pufABLM) and the complete Calvin cycle for carbon fixation via RuBisCO. Genes for flagellar and pilus assembly were annotated. Pathways for thiosulfate oxidation (Sox pathway), glycolate and methane/alkanesulfonate oxidation and the biosynthesis of all amino acids were predicted. Further, pathways for thiamine, riboflavin, NAD, coenzyme A, pimeloyl-ACP, and heme biosynthesis were identified. The closest cultivated relative is Hydrogenophaga intermedia MER 62 (GCF_001571205.1), with an average nucleotide identity of 74.2%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Burkholderiaceae_B; g__Hydrogenophaga; s__Hydrogenophaga intermedia_C.

Type strain is Lacustribacter communis MsE-M52 (GCA_965194335.1), isolated from 5 m depth from Lake Most, Czechia (date: 2019-10-01), via high-throughput dilution to extinction cultivation. MsE-M52 has a genome size of 2.1 Mbp with a genomic GC content of 53.3%, contains 3 rRNA genes and 42 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding anoxygenic aerobic phototrophy (pufABLM). Genes for flagellar assembly were annotated. Pathways for urea and taurine degradation, thiosulfate oxidation (Sox pathway), glycolate oxidation, and the biosynthesis of all amino acids except for aspartate were predicted. Further, pathways for thiamine, riboflavin, NAD, pantothenate, coenzyme A, THF, and heme biosynthesis were identified. The closest cultivated relatives are the undescribed Burkholderiales bacterium LSUCC0115 (GCA_009646425.1), with an average amino acid identity of 61.9% and average nucleotide identity of 67.9% and the newly established genus Hahnella, with 60.4-61.7% AAI and 67.2-67.9% ANI. The closest validly described relative is Limnobacter thiooxidans CS-K2 (GCF_036323495.1) with an AAI of 53.95% and an ANI of 66.33%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__UBA954; s__UBA954 sp002293155.

Type strain is Leadbetterella lacustris RE-19 (GCA_965234335.1), isolated from 0.5 m depth from the Římov reservoir, Czechia (date: 2019-08-05), via high-throughput dilution to extinction cultivation. RE-19 has a genome size of 5 Mbp with a genomic GC content of 37.48 %, contains 9 rRNA genes and 36 tRNAs. The genome is a high-quality draft consisting of 36 contigs. The genome contains genes encoding rhodopsins. Genes for gliding motility (gldBDHJKLMN, sprA) were annotated in the genome. Pathways for assimilatory sulfate reduction, methane/alkanesulfonate oxidation and the biosynthesis of all amino acids were predicted. Further, pathways for riboflavin, NAD, coenzyme A, THF, menaquinone, and heme biosynthesis were identified. The closest cultivated relative is Lacihabitans soyangensis KCTC23259 (GCF_024343775.1), with an average amino acid identity of 85.5% and average nucleotide identity of 82.97%. Lacihabitans is grouped with the genus Leadbetterella in GTDB. Current GTDB classification (R220): d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Cytophagales; f__Spirosomaceae; g__Leadbetterella; s__Leadbetterella fluviale_A. 

Type strain is Limnohabitans kasalickyi MaE-M4 (GCA_965234325.1), isolated from 5 m depth from Lake Maggiore, Italy (date: 2019-04-09), via high-throughput dilution to extinction cultivation. MaE-M4 has a genome size of 3.7 Mbp with a genomic GC content of 56.3%, contains 6 rRNA genes and 44 tRNAs. The genome is a high-quality draft consisting of 16 contigs. The genome contains genes encoding anoxygenic aerobic phototrophy (pufABLM). Genes for flagellar and pilus assembly were annotated. Pathways for cyanate, urea, and taurine degradation, thiosulfate oxidation (Sox pathway), methane/alkanesulfonate and glycolate oxidation, and the biosynthesis of all amino acids except for aspartate were predicted. Further, pathways for thiamine, riboflavin, pantothenate, coenzyme A, pimeloyl-ACP, THF, and heme biosynthesis were identified. The closest cultivated relative is Limnohabitans sp. Jir61 (GCF_003063545.1), with an average amino acid identity of 77.9% and average nucleotide identity of 80.1%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Burkholderiaceae_B; g__Limnohabitans; s__Limnohabitans sp002778325.

Type strain is Limnohabitans rimovensis RE-1 (GCA_965234775.1), isolated from 0.5 m depth from the Římov Reservoir, Czechia (date: 2019-04-23), via high-throughput dilution to extinction cultivation. RE-1 has a genome size of 3.5 Mbp with a genomic GC content of 58.7%, contains 3 rRNA genes and 43 tRNAs. The genome is a high-quality draft consisting of 12 contigs. The genome contains genes encoding anoxygenic aerobic phototrophy (pufABLM). Genes for flagellar and pilus assembly were annotated. Pathways for urea degradation, thiosulfate oxidation (Sox pathway), methane/alkanesulfonate and glycolate oxidation, benzoate, salicylate, and phthalate degradation, and the biosynthesis of all amino acids except for aspartate were predicted. Further, pathways for thiamine, riboflavin, pantothenate, coenzyme A, THF, and heme biosynthesis were identified. The closest cultivated relative is Limnohabitans sp. JirII-31 (GCF_002778315.1), with an average amino acid identity of 65.1% and average nucleotide identity of 72.4%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Burkholderiaceae_B; g__Limnohabitans; s__.

Type strain is Methylotenera hypolimnetica RH-M31 (GCA_947054635.1), isolated from 30 m depth from the Římov Reservoir, Czechia (date: 15.08.2019), via high-throughput dilution to extinction cultivation. RH-M31 has a genome size of 1.8 Mbp with a genomic GC content of 49.2%, contains 6 rRNA genes and 38 tRNAs. The genome is complete, consisting of a circular chromosome. No genes for flagellar or pilus assembly and chemotaxis were annotated. Pathways for methanol oxidation (Xox), the RuMP and methylcitric acid (MCA) cycle for methylotrophy and the biosynthesis of all amino acids were predicted. Further, pathways for thiamine, riboflavin, NAD, coenzyme A, pimeloyl-ACP, biotin, THF, ubiquinone, and heme biosynthesis were identified. The closest cultivated relatives are Methylotenera versatilis 301 (GCF_000093025.1) with an average amino acid identity of 75.7% and average nucleotide identity of 72.6% and another newly proposed species, Methylotenera profunda RH-M32 (GCA_947054625.1), with an AAI of 94.2% and an ANI of 92%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Methylophilaceae; g__Methylotenera; s__Methylotenera sp903951385.

Type strain is Methylotenera profunda RH-M32 (GCA_947054625.1), isolated from 30 m depth from the Římov Reservoir, Czechia (date: 15.08.2019), via high-throughput dilution to extinction cultivation. RH-M32 has a genome size of 1.7 Mbp with a genomic GC content of 47.9%, contains 6 rRNA genes and 38 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding rhodopsins and the biosynthetic pathway for retinal biosynthesis. No genes for flagellar or pilus assembly and chemotaxis were annotated. Pathways for methanol oxidation (Xox), the RuMP and methylcitric acid (MCA) cycle for methylotrophy and the biosynthesis of all amino acids were predicted. Further, pathways for thiamine, riboflavin, NAD, coenzyme A, pimeloyl-ACP, biotin, THF, ubiquinone, and heme biosynthesis were identified. The closest cultivated relatives are Methylotenera versatilis 301 (GCF_000093025.1) with an average amino acid identity of 75.9% and average nucleotide identity of 72.8% and another newly proposed species, Methylotenera hypolimnetica RH-M31 (GCA_947054635.1), with an AAI of 94.2% and an ANI of 92%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Methylophilaceae; g__Methylotenera; s__Methylotenera oryzisoli_A.

Type strain is Mycobacterium aquicola MiE-22 (GCA_965234515.1), isolated from 5 m depth from Lake Milada, Czechia (date: 2019-10-15), via high-throughput dilution to extinction cultivation. MiE-22 has a genome size of 3.4 Mbp with a genomic GC content of 66.3%, contains 3 rRNA genes and 57 tRNAs. The genome is a high-quality draft consisting of 3 contigs. The genome contains genes encoding rhodopsins. No genes for flagella or pilus assembly and chemotaxis were annotated. Pathways for taurine degradation, assimilatory sulfate reduction and the biosynthesis of all amino acids except for histidine and aspartate were predicted. Further, pathways for many vitamins and cofactors (riboflavin, pyridoxal, NAD, coenzyme A, biotin, tetrahydrofolate, heme, cobalamine and menaquinone) were identified. The closest cultivated relative is Mycobacterium massilipolynesiensis M26 (GCF_001494595.1), with an average amino acid identity of 71.31% and average nucleotide identity of 76.47%. Current GTDB classification (R220): d__Bacteria; p__Actinomycetota; c__Actinomycetia; o__Mycobacteriales; f__Mycobacteriaceae; g__Mycobacterium; s__Mycobacterium sp945897705.

Type strain is Novamethylotenera aquatica ME-M6 (GCA_947054645.1), isolated from 5 m depth from Lake Medard, Czechia (date: 09.07.2019), via high-throughput dilution to extinction cultivation. ME-M6 has a genome size of 2.1 Mbp with a genomic GC content of 41.7%, contains 6 rRNA genes and 37 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding rhodopsins and the biosynthetic pathway for retinal biosynthesis. No genes for flagellar assembly and chemotaxis were annotated. Pathways for methanol oxidation (Xox), the RuMP and methylcitric acid (MCA) cycle for methylotrophy and the biosynthesis of all amino acids were predicted. Further, pathways for thiamine, riboflavin, NAD, coenzyme A, pimeloyl-ACP, biotin, THF, ubiquinone, and heme biosynthesis were identified. The closest cultivated relative is Methylotenera versatilis 7 (GCF_000799165.1) with an average amino acid identity of 80.36% and average nucleotide identity of 76.56%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Methylophilaceae; g__Methylotenera_A; s__Methylotenera_A oryzisoli_A.

Type strain is Planktophila warneckii RE-8 (GCA_965234675.1), isolated from 0.5 m depth from the Římov reservoir, Czechia (date: 2019-04-23), via high-throughput dilution to extinction cultivation. RE-8 has a genome size of 1.4 Mbp with a genomic GC content of 46.2%, contains 3 rRNA genes and 38 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding rhodopsins. No genes for flagella or pilus assembly and chemotaxis were annotated. Pathways for the biosynthesis of all amino acids except for histidine were predicted. Further, pathways for riboflavin, pyridoxal, coenzyme A, and menaquinone biosynthesis were identified. The closest cultivated relative is Actinobacteria bacterium IMCC26103 (GCA_002284875.1), with an average amino acid identity of 72.2% and average nucleotide identity of 70.96%. Current GTDB classification (R220): d__Bacteria; p__Actinomycetota; c__Actinomycetia; o__Nanopelagicales; f__Nanopelagicaceae; g__Planktophila; s__.

Type strain is Polynucleobacter hahnii ZE-4 (GCA_965234415.1), isolated from 5 m depth from Lake Zurich, Switzerland (date: 2019-04-03), via high-throughput dilution to extinction cultivation. ZE-4 has a genome size of 2.3 Mbp with a genomic GC content of 43.7%, contains 3 rRNA genes and 38 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding anoxygenic aerobic phototrophy (pufABLM). No genes for flagellar assembly and chemotaxis were annotated. Pathways for nitrate reduction, thiosulfate oxidation (Sox pathway), glycolate oxidation and the biosynthesis of all amino acids except for aspartate were predicted. Further, pathways for thiamine, riboflavin, NAD, pantothenate, coenzyme A, biotin, THF, ubiquinone, and heme biosynthesis were identified. The closest cultivated relative is Polynucleobacter sp. IMCC 30228 (GCF_021395205.1), with an average amino acid identity of 86.6% and average nucleotide identity of 82.8%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__Polynucleobacter; s__Polynucleobacter sp903944725.

Type strain is Polynucleobacter hoetzingeranus RE-M21 (GCA_965234555.1), isolated from 0.5 m depth from the Římov Reservoir, Czechia (date: 2019-08-05), via high-throughput dilution to extinction cultivation. RE-M21 has a genome size of 1.8 Mbp with a genomic GC content of 46.6%, contains 3 rRNA genes and 40 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding anoxygenic aerobic phototrophy (pufABLM). No genes for flagellar assembly and chemotaxis were annotated. Pathways for cyanate degradation, thiosulfate oxidation (Sox pathway), glycolate oxidation and the biosynthesis of all amino acids except for aspartate were predicted. Further, pathways for thiamine, riboflavin, NAD, pantothenate, coenzyme A, biotin, THF, ubiquinone, and heme biosynthesis were identified. The closest cultivated relative is Polynucleobacter sp. MWH-UH24A (GCF_018687475.1), with an average amino acid identity of 82.7% and average nucleotide identity of 74.9%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__Polynucleobacter; s__Polynucleobacter sp027486235.

Type strain is Rhabdoaerophilum aquaticum MsE-M23 (GCA_965234495.1), isolated from 5 m depth from Lake Most, Czechia (date: 2019-07-30), via high-throughput dilution to extinction cultivation. MsE-M23 has a genome size of 34 Mbp with a genomic GC content of 58.6%, contains 3 rRNA genes and 46 tRNAs. The genome is complete, consisting of a circular chromosome and one circular plasmid. Genes for flagellar assembly and chemotaxis were annotated in the genome. Pathways for cyanate and urea degradation, thiosulfate oxidation (Sox pathway), glycolate oxidation and the biosynthesis of all amino acids were predicted. Further, pathways for thiamine, riboflavin, NAD, coenzyme A, THF, and heme biosynthesis were identified. The closest cultivated relative is Rhabdaerophilum calidifontis SYSU G02060 (GCF_008641065.1), with an average amino acid identity of 66.3% and average nucleotide identity of 70.3%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Alphaproteobacteria; o__Rhizobiales; f__Beijerinckiaceae; g__Rhabdaerophilum; s__.

Type strain is Rhodoluna miladensis MiE-23b (GCA_965234705.1), isolated from 5 m depth from Lake Milada, Czechia (date: 2019-10-15), via high-throughput dilution to extinction cultivation. MiE-23b has a genome size of 1.28 Mbp with a genomic GC content of 50.2%, contains 3 rRNA genes and 40 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding rhodopsins but lacks the biosynthetic pathway for retinal biosynthesis. No genes for flagella or pilus assembly and chemotaxis were annotated. Pathways for the biosynthesis of all amino acids except for methionine and histidine were predicted. Further, pathways for riboflavin, pyridoxal, coenzyme A, and menaquinone were identified. The closest cultivated relative is Rhodoluna lacicola MWH-Ta8 (GCF_000699505), with an average amino acid identity of 65.06% and average nucleotide identity of 67.72%. Current GTDB classification (R220): d__Bacteria; p__Actinomycetota; c__Actinomycetia; o__Actinomycetales; f__Microbacteriaceae; g__Rhodoluna; s__. 

Type strain is Sphingorhabdus commune GE-11 (GCA_965234695.1), isolated from 5 m depth from Lake Greifensee, Switzerland (date: 2019-04-03), via high-throughput dilution to extinction cultivation. GE-11 has a genome size of 2.4 Mbp with a genomic GC content of 54.9%, contains 3 rRNA genes and 42 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding rhodopsins and the biosynthetic pathway for retinal biosynthesis. No genes for flagellar or pilus assembly and chemotaxis were annotated. Pathways for assimilatory sulfate reduction and methane/alkanesulfonate oxidation and the biosynthesis of all amino acids were predicted. Further, pathways for riboflavin, NAD, coenzyme A, THF, and heme biosynthesis were identified. The closest cultivated relative is Sphingorhabdus wooponensis 03SU3-P (GCF_003933235.1), with an average amino acid identity of 87.4% and average nucleotide identity of 80.5%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Alphaproteobacteria; o__Sphingomonadales; f__Sphingomonadaceae; g__Sphingorhabdus_B; s__Sphingorhabdus_B sp903821685.

Type strain is Sphingorhabdus rara RE-M21a (GCA_965234565.1), isolated from 0.5 m depth from the Římov Reservoir, Czechia (date: 2019-08-05), via high-throughput dilution to extinction cultivation. RE-M21a has a genome size of 3.2 Mbp with a genomic GC content of 57.5%, contains 3 rRNA genes and 45 tRNAs. The genome is a high-quality draft consisting of 4 contigs. The genome contains genes encoding rhodopsins and the biosynthetic pathway for retinal biosynthesis. No genes for flagellar or pilus assembly and chemotaxis were annotated. Pathways for taurine degradation, assimilatory sulfate reduction and methane/alkanesulfonate oxidation and the biosynthesis of all amino acids were predicted. Further, pathways for thiamine, riboflavin, pantothenate, NAD, coenzyme A, THF, and heme biosynthesis were identified. The closest cultivated relative is Sphingorhabdus pulchriflava GY_G (GCF_003367235.1), with an average amino acid identity of 76.8% and average nucleotide identity of 75.4%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Alphaproteobacteria; o__Sphingomonadales; f__Sphingomonadaceae; g__Sphingorhabdus_B; s__Sphingorhabdus_B sp021298455. 

Type strain is Tabrizicola rara LH-M10 (GCA_965234505.1), isolated from 50 m depth from Lake Lugano, Switzerland (date: 2019-11-05), via high-throughput dilution to extinction cultivation. LH-M10 has a genome size of 4.2 Mbp with a genomic GC content of 62.8%, contains 4 rRNA genes and 48 tRNAs. The genome is a high-quality draft consisting of 22 contigs. The genome contains the complete Calvin cycle for carbon fixation via RuBisCO. Genes for flagellar assembly were annotated in the genome. Pathways for urea and taurine degradation, glycolate oxidation and the biosynthesis of all amino acids were predicted. Further, pathways for riboflavin, coenzyme A, cobalamin, and heme biosynthesis were identified. The closest cultivated relative is Rhodobacter thermarum YIM 73036 (GCF_003574395.1; Basonym: Tabrizicola thermarum Khan et al. 2019), with an average amino acid identity of 75.7% and average nucleotide identity of 77.1%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Alphaproteobacteria; o__Rhodobacterales; f__Rhodobacteraceae; g__Tabrizicola; s__Tabrizicola sp903917595.

Type strain is Verrucolacustris abundans MiH-22 (GCA_965194535.1), isolated from 15 m depth from Lake Milada, Czechia (date: 2019-10-15), via high-throughput dilution to extinction cultivation. MiH-22 has a genome size of 2.0 Mbp with a genomic GC content of 52.8%, contains 3 rRNA genes and 46 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding rhodopsins. No genes for flagellar assembly and chemotaxis were annotated. In contrast to other Methylacidiphilales members, no genes for C1 metabolism (methanotrophy) were identified. Pathways for assimilatory sulfate reduction and the biosynthesis of all amino acids except for methionine, histidine and tryptophan were predicted. Further, pathways for only three vitamins (thiamine, riboflavin, and biotin biosynthesis) were identified. The closest cultivated relative is Methylacidimicrobium cyclopophantes 3B_2 (GCF_902143385.2), with an average amino acid identity of 49.5% and average nucleotide identity of 62.8%. Current GTDB classification (R220): d__Bacteria; p__Verrucomicrobiota; c__Verrucomicrobiae; o__Methylacidiphilales; f__UBA3015; g__UBA3015; s__UBA3015 sp030054195.

Type strain is Zwartia lucis GE-14 (GCA_965234455.1), isolated from 5 m depth from Greifensee, Switzerland (date: 2019-04-03), via high-throughput dilution to extinction cultivation. GE-14 has a genome size of 3.7 Mbp with a genomic GC content of 50.9%, contains 6 rRNA genes and 41 tRNAs. The genome is a high-quality draft consisting of 7 contigs. In contrast to other Zwartia sp., the genome contains genes encoding rhodopsins and the biosynthetic pathway for retinal biosynthesis. No genes for flagellar or pilus assembly and chemotaxis were annotated. Pathways for nitrate reduction, cyanate, urea and taurine degradation, thiosulfate oxidation (Sox pathway), glycolate and methane/alkanesulfonate oxidation, and the biosynthesis of all amino acids were predicted. Further, pathways for thiamine, riboflavin, pantothenate, coenzyme A, THF, ubiquinone, and heme biosynthesis were identified. The closest cultivated relative is Zwartia panacis strain KCTC42751 (GCF_030410395.1), with an average amino acid identity of 82.1% and average nucleotide identity of 77.6%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__Zwartia; s__.

Type strain is Zwartia planktonica RE-10 (GCA_965234315.1), isolated from 0.5 m depth from the Římov Reservoir, Czechia (date: 2019-04-23), via high-throughput dilution to extinction cultivation. RE-10 has a genome size of 4.5 Mbp with a genomic GC content of 52%, contains 6 rRNA genes and 44 tRNAs. The genome is complete, consisting of a circular chromosome. No genes for flagellar or pilus assembly and chemotaxis were annotated. Pathways for cyanate, urea and taurine degradation, thiosulfate oxidation (Sox pathway), glycolate oxidation, and the biosynthesis of all amino acids were predicted. Further, pathways for thiamine, riboflavin, NAD, pantothenate, coenzyme A, THF, ubiquinone, and heme biosynthesis were identified. The closest cultivated relative is Zwartia hollandica LF4-65 (GCF_019923725.1), with an average amino acid identity of 71.2% and average nucleotide identity of 71.6%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__Zwartia; s__Zwartia sp030832095.