Register list for 5 new names including Methylophilus medardensis sp. nov.

Consists of one species, Methylosemipumilus turicensis (GCF_000953015.1), that was initially proposed as ‘Candidatus Methylopumilus turicensis’ in Salcher et. al. 2015 and later changed to Methylosemipumilus turicensis in Salcher et al. 2019. Also known as PRD01a001B from 16S rRNA gene based studies. Methylosemipumilus has a relatively small genome size (<1.8 Mb) but not as small as Methylopumilus (1.3-1.4 Mb), which – together with improved genomic analyses – led to the reclassification to Methylosemipumilus. The closest cultivated relatives are Methylotenera sp. L2L1 (GCF_000744605.1) with an average amino acid identity of 67.45% and average nucleotide identity of 70.55% and Methylovorus sp. MP688 (GCF_000183115.1) with an AAI of 69.37% and an ANI of 69.42%, while the genus Methylopumilus is more distantly related (AAI of 61.5-62.2% and ANI of 66.4-66.9%). Methylosemipumilus are aerobic methylotrophs containing pathways for methanol oxidation (Xox), the RuMP cycle and the tetrahydromethanopterin (H4MPT) pathway for formaldehyde oxidation. Methylosemipumilus are found in the plankton of lakes in relatively low abundances. The so far only strain was isolated via dilution-to extinction cultivation by using autoclaved lake water, no growth is observed in rich medium or on agar plates (Salcher et al. 2015). Therefore, the strain was not submitted to a culture collection because these bacteria are hard to maintain, i.e., they are very slowly growing, reach low densities in liquid culture, and do not grow on agar plates.

Type genome is Methylophilus medardensis MMS-M-51 (GCF_006363915.1), that was isolated by dilution-to-extinction cultivation from the water column of Lake Medard, Czechia. MMS-M-51 has a genome size of 2.6 Mb with a genomic GC content of 49.8%, contains 6 rRNA genes and 42 tRNAs. The genome is complete, consisting of 1 circular chromosome. The closest cultivated relatives are Methylophilus sp. Q8 (GCF_000800115.1) with an average amino acid identity of 85.53% and average nucleotide identity of 78.73% and Methylophilus sp. OH31 (GCF_000576615.1) with an AAI of 85.28% and an ANI of 78.71%.

Type genome is Methylopumilus rimovensis MMS-RI-1 (GCF_006364615.1), an axenic bacterial strain isolated by dilution-to-extinction cultivation from the water column of the Římov Reservoir (Czechia). MMS-RI-1 has a genome size of 1.28 Mb with a genomic GC content of 36.7%, contains 3 rRNA genes and 37 tRNAs. The genome is complete, consisting of 1 circular chromosome. Methylopumilus rimovensis are very small, aerobic, non-motile and methylotrophic. The genome contains genes encoding two rhodopsins (proteorhodopsin and xantho-like rhodopsin) and the biosynthetic pathway for retinal biosynthesis. No genes for flagellar or pilus assembly and chemotaxis were annotated. Pathways for methanol oxidation (Xox) and the RuMP cycle for methylotrophy and the biosynthesis of all amino acids were predicted. Methylopumilus rimovensis are highly abundant only in their isolation source (the Římov Reservoir in Czechia) and recorded in very low abundances in other freshwater lakes, which contrasts with members of other species of the genus that have a global distribution (Methylopumilus planktonicus and Methylopumilus universalis). None of the isolated strains were yet submitted to a culture collection because these bacteria are hard to maintain, i.e., they are very slowly growing, reach low densities in liquid culture, and do not grow on agar plates.

Type genome is Methylopumilus universalis MMS-RVI-51 (GCF_006363895.1), an axenic bacterial strain isolated by dilution-to-extinction cultivation from the water column of the Římov Reservoir (Czechia). MMS-RVI-51 has a genome size of 1.27 Mb with a genomic GC content of 37.2%, contains 3 rRNA genes and 36 tRNAs. The genome is complete, consisting of 1 circular chromosome. Methylopumilus universalis are very small, aerobic, non-motile and methylotrophic. The genome contains genes encoding two rhodopsins (proteorhodopsin and xantho-like rhodopsin) and the biosynthetic pathway for retinal biosynthesis. No genes for flagellar or pilus assembly and chemotaxis were annotated. Pathways for methanol oxidation (Xox) and the RuMP cycle for methylotrophy and the biosynthesis of all amino acids were predicted. Methylopumilus universalis are abundant in the plankton of freshwater lakes with a world-wide distribution and a preference for lakes with a higher nutrient level than members of another species, Methylopumilus planktonicus. None of the isolated strains were yet submitted to a culture collection because these bacteria are hard to maintain, i.e., they are very slowly growing, reach low densities in liquid culture, and do not grow on agar plates.

Type genome is Methylosemipumilus turicensis MMS-10A-171 (GCF_000953015.1), that was initially proposed as ‘Candidatus Methylopumilus turicensis’ in Salcher et. al. 2015 and later changed to Methylosemipumilus turicensis in Salcher et al. 2019. The strain was isolated by dilution-to-extinction cultivation from the water column of Lake Zurich, Switzerland. MMS-10A-171 has a genome size of 1.76 Mb with a genomic GC content of 44.52%, contains 6 rRNA genes and 40 tRNAs. The genome is complete, consisting of 1 circular chromosome. Methylosemipumilus turicensis MMS-10A-171 has a relatively small genome size (1.76 Mb) but not as small as Methylopumilus (1.3-1.4 Mb), which – together with improved genomic analyses – led to the reclassification to Methylosemipumilus. The genome contains genes encoding proteorhodopsins and the biosynthetic pathway for retinal biosynthesis. Pathways for methanol oxidation (Xox), the ribulose monophosphate (RuMP) cycle and the tetrahydromethanopterin (H4MPT) pathway for formaldehyde oxidation were predicted. The closest cultivated relatives are Methylotenera sp. L2L1 (GCF_000744605.1) with an average amino acid identity of 67.45% and average nucleotide identity of 70.55% and Methylovorus sp. MP688 (GCF_000183115.1) with an AAI of 69.37% and an ANI of 69.42%, while the genus Methylopumilus is more distantly related (AAI of 61.5-62.2% and ANI of 66.4-66.9%).