Zwartia hollandica gen. nov., sp. nov., Jezberella montanilacus gen. nov., sp. nov. and Sheuella amnicola gen. nov., comb. nov., representing the environmental GKS98 (betIII) cluster

Abstract

We present two strains affiliated with the GKS98 cluster. This phylogenetically defined cluster is representing abundant, mainly uncultured freshwater bacteria, which were observed by many cultivation-independent studies on the diversity of bacteria in various freshwater lakes and streams. Bacteria affiliated with the GKS98 cluster were detected by cultivation-independent methods in freshwater systems located in Europe, Asia, Africa and the Americas. The two strains, LF4-65T (=CCUG 56422T=DSM 107630T) and MWH-P2sevCIIIbT (=CCUG 56420T=DSM 107629T), are aerobic chemoorganotrophs, both with genome sizes of 3.2 Mbp and G+C values of 52.4 and 51.0 mol%, respectively. Phylogenomic analyses based on concatenated amino acid sequences of 120 proteins suggest an affiliation of the two strains with the family Alcaligenaceae and revealed Orrella amnicola and Orrella marina (= Algicoccus marinus ) as being the closest related, previously described species. However, the calculated phylogenomic trees clearly suggest that the current genus Orrella represents a polyphyletic taxon. Based on the branching order in the phylogenomic trees, as well as the revealed phylogenetic distances and chemotaxonomic traits, we propose to establish the new genus Zwartia gen. nov. and the new species Z. hollandica sp. nov. to harbour strain LF4-65T and the new genus Jezberella gen. nov. and the new species J. montanilacus sp. nov. to harbour strain MWH-P2sevCIIIbT. Furthermore, we propose the reclassification of the species Orrella amnicola in the new genus Sheuella gen. nov. The new genera Zwartia, Jezberella and Sheuella together represent taxonomically the GKS98 cluster.

Adaptive genetic traits in pelagic freshwater microbes

“…can be found in freshwater ecosystems around the globe with abundances varying from <1% up to 67% of the bacterial community (Hahn & Hoetzinger, 2019; Hahn, Kasalický, Jezbera, Brandt, et al, 2010; Hahn, Kasalický, Jezbera, Brandt, Šimek, 2010; Hahn, Lang, et al, 2010; Hahn, Pitt, Schmidt, et al, 2022; Hahn, Pitt, Schmidt, Koll et al, 2022; Salcher et al, 2008). The genus is divided in four subclusters (PnecA, PnecB, PnecC and PnecD; Hahn, 2003) and 31 species have been cultivated and validly described (Hahn, Pitt, Schmidt, et al, 2022; Hahn, Pitt, Schmidt, Koll et al, 2022). Species within subclusters are difficult to delineate based on 16S rRNA sequences as sequence similarities often exceed 99% (Hahn et al, 2016), but strains with near identical 16S rRNA gene sequences are known to show different ecological traits (Boenigk et al, 2004; Hahn et al, 2016).…”

“…Genes encoding these and other environment specific features (e.g. nitrate assimilation, aromatic compound degradation, cell surface proteins likely involved in phage evasion) are usually encoded in genomic islands (Hahn, Pitt, Schmidt, et al, 2022; Hahn, Pitt, Schmidt, Koll et al, 2022; Hoetzinger & Hahn, 2017). In contrast to the core genome, these regions show evidence of high interspecies recombination rates that enable local adaptations (Hoetzinger et al, 2017; Hoetzinger & Hahn, 2017).…”

“…Three genera of the GKS98 lineage have been recently validly described (Hahn, Pitt, Schmidt, et al, 2022; Hahn, Pitt, Schmidt, Koll et al, 2022) and several isolates have been reported from the MWH‐UniP1 lineage (Hahn et al, 2004; Henson et al, 2020; Kim et al, 2020). The three recently described genera of the GKS98 lineage ( Zwartia , Jezberella , and Sheuella ) have relatively large genomes (3.2 Mbp) and intermediate GC contents (50.9%–52.4%) (Hahn, Pitt, Schmidt, et al, 2022; Hahn, Pitt, Schmidt, Koll et al, 2022), similar to what was predicted from MAGs (Cabello‐Yeves, Zemskaya, et al, 2018; Cabello‐Yeves, Picazo, et al, 2018; Linz et al, 2018). GKS98 strains differ in their genomic repertoire with regard to motility, the potential to grow anaerobically, nitrate and nitrate reduction and iron uptake mechanisms (Hahn, Pitt, Schmidt, et al, 2022; Hahn, Pitt, Schmidt, Koll et al, 2022).…”

“…The three recently described genera of the GKS98 lineage ( Zwartia , Jezberella , and Sheuella ) have relatively large genomes (3.2 Mbp) and intermediate GC contents (50.9%–52.4%) (Hahn, Pitt, Schmidt, et al, 2022; Hahn, Pitt, Schmidt, Koll et al, 2022), similar to what was predicted from MAGs (Cabello‐Yeves, Zemskaya, et al, 2018; Cabello‐Yeves, Picazo, et al, 2018; Linz et al, 2018). GKS98 strains differ in their genomic repertoire with regard to motility, the potential to grow anaerobically, nitrate and nitrate reduction and iron uptake mechanisms (Hahn, Pitt, Schmidt, et al, 2022; Hahn, Pitt, Schmidt, Koll et al, 2022). The latter has been proposed to be a specific adaptation to acidic or alkaline environments, respectively.…”

“…Free‐living Polynucleobacter spp. can be found in freshwater ecosystems around the globe with abundances varying from <1% up to 67% of the bacterial community (Hahn & Hoetzinger, 2019; Hahn, Kasalický, Jezbera, Brandt, et al, 2010; Hahn, Kasalický, Jezbera, Brandt, Šimek, 2010; Hahn, Lang, et al, 2010; Hahn, Pitt, Schmidt, et al, 2022; Hahn, Pitt, Schmidt, Koll et al, 2022; Salcher et al, 2008). The genus is divided in four subclusters (PnecA, PnecB, PnecC and PnecD; Hahn, 2003) and 31 species have been cultivated and validly described (Hahn, Pitt, Schmidt, et al, 2022; Hahn, Pitt, Schmidt, Koll et al, 2022).…”