Opening a next‐generation black box: Ecological trends for hundreds of species‐like taxa uncovered within a single bacterial &gt;99% 16S rRNA operational taxonomic unit

Hahn, Martin W.; Huemer, Andrea; Pitt, Alexandra; Hoetzinger, Matthias

doi:10.1111/1755-0998.13444

Cited by 14 publications

(22 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…3h). A shift in bacterial ecotype diversity along a calcium gradient was previously reported (Hahn et al, 2021), but how calcium directly influences community composition is unclear. Perhaps the effect is indirect and calcium influences ecological interaction in the plankton community, as low calcium levels were previously shown to limit zooplankton productivity and diversity (Azan & Arnott, 2018).…”

Section: Lake Conditions Shape the Structure And Function Of Bacteria...mentioning

confidence: 87%

A genome catalogue of lake bacteria across watershed land use gradients at a continental scale

Garner

Kraemer

Onana

et al. 2022

Preprint

View full text Add to dashboard Cite

Lakes are highly heterogenous ecosystems inhabited by a rich microbiome whose genomic diversity remains poorly defined compared to other major biomes. Here, we present a continental-scale study of metagenomes collected across one of the most lake-rich landscapes on Earth. Analysis of 308 Canadian lakes resulted in a metagenome-assembled genome (MAG) catalogue of 1,008 bacterial genomospecies spanning a broad phylogenetic and metabolic diversity. Lake trophic state was a significant determinant of taxonomic and functional turnover of MAG assemblages. We detected a role for resource availability, particularly carbohydrate diversity, in driving biogeographic patterns. Coupling the MAG catalogue with geomatics information on watershed characteristics revealed an influence of soil properties and human land use on MAG assemblages. Agriculture and human population density were particularly influential on MAG functional turnover, signifying a detectable human footprint in lake bacterial communities. Overall, the Canadian lake MAG catalogue greatly expands the freshwater microbial genomic landscape, bringing us closer to an integrative view of bacterial genome diversity across Earth's biomes.

show abstract

Section: Lake Conditions Shape the Structure And Function Of Bacteria...mentioning

confidence: 87%

A genome catalogue of lake bacteria across watershed land use gradients at a continental scale

Garner

Kraemer

Onana

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Furthermore, an approximate boarder between habitats characterized by water with low Ca 2+ (<12 mg l −1 Ca 2+ ) and high Ca 2+ concentration (>12 mg l −1 Ca 2+ ) is indicated. It has been shown that planktonic Polynucleobacter species either prefer low or higher Ca 2+ concentrations [19]. The numbers identifying the respective type strains can be found in .…”

Section: Ecology and Biogeographymentioning

confidence: 99%

“…Thus, it has to be assumed that all 14 proposed type strains represent free-living, planktonic freshwater bacteria, but distinct ecological adaptations of the strains have to be expected. Further knowledge on the ecology of the proposed species and biogeographical aspects can be gained from a previously published amplicon sequencing study [19] and from previously published metagenome data [52] characterizing bacterioplankton of a lake representing the home habitat of two type strains described here. [34]); 3, P. sinensis MWH-HuW1 T (data from [18]); 4, P. aenigmaticus MWH-K35W1 T (data from [26]) and P. duraquae MWH-MoK4 T (data from [18]).…”

Section: Ecology and Biogeographymentioning

confidence: 99%

“…1. World map depicting the geographic origin of the type strains of the newly proposed Polynucleobacter species (numbers 1-14) and of the previously described species (numbers [15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31]. The colour code indicates the current annual mean temperatures at terrestrial locations predicted by the WorldClim model (version 1.3, with a resolution of 2.5 min) [58].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Fourteen new Polynucleobacter species: P. brandtiae sp. nov., P. kasalickyi sp. nov., P. antarcticus sp. nov., P. arcticus sp. nov., P. tropicus sp. nov., P. bastaniensis sp. nov., P. corsicus sp. nov., P. finlandensis sp. nov., P. ibericus sp. nov., P. hallstattensis sp. nov., P. alcilacus sp. nov., P. nymphae sp. nov., P. paludilacus sp. nov. and P. parvulilacunae sp. nov.

Hahn

Pitt

Schmidt

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

Self Cite

View full text Add to dashboard Cite

Fourteen strains, all isolated from the surface of freshwater habitats, were genomically, phylogenetically and phenotypically characterized. The strains were obtained from geographically and climatically broadly scattered sites. This included two lakes in Antarctica, one arctic pond located on the Svalbard archipelago (Norway), a tropical habitat located in Uganda, some lakes in Southern Europe (Spain and France), lakes, ponds and a puddle in Central Europe (Austria, Czech Republic and Germany), and lakes in Northern Europe (Finland). Most of the investigated strains were characterized by rather small cell sizes and rather slow growth on media such as nutrient broth–soyotone–yeast extract (NSY) medium. Phylogenomic analyses indicated that all fourteen strains are affiliated with the genus Polynucleobacter ( Burkholderiaceae , Pseudomonadota ). Thirteen of the strains were found to be affiliated with subcluster PnecC of the genus. All these strains were characterized by genome sizes in the range of 1.7–2.3 Mbp and G+C values of 44.9–46.5 mol%. Furthermore, all PnecC-affiliated strains shared 16S rRNA gene sequence similarities >99 %. Only one strain characterized by a larger genome size of 2.9 Mbp and a lower G+C value of 41.0 mol% was found to be affiliated with subcluster PnecA. Whole genome sequence comparisons revealed that all 14 strains shared among each other, as well as with the type strains of the previously described 17 Polynucleobacter species, whole-genome average nucleotide identities values <95 %. This suggested that the 14 investigated strains represent 14 different new species. We propose the establishment of 14 new Polynucleobacter species represented by the following type strains: UB-Domo-W1T (=DSM 103491T=CIP 111598T=JCM 32562T), VK13T (=DSM 103488T=JCM 32564T), LimPoW16T (=DSM 24085T=CIP 111098T), UK-Long2-W17T (=DSM 103489T=CIP 111328T=JCM 32563T), UK-Pondora-W15T (=DSM 103423T=JCM 32939T), MWH-Mekk-B1T (=DSM 106779T=JCM 32556T), MWH-Mekk-C3T (=DSM 103415T=JCM 32557T), Ross1-W9T (=DSM 103416T=JCM 32561T), MWH-Hall10T (=DSM 107042T=JCM 32938T), AP-Basta-1000A-D1T (=DSM 107039T=JCM 32933T), AP-Melu-1000-A1T (=DSM 107036T=JCM 32935T), es-MAR-2T (=DSM 103424T=JCM 32554T), AP-Mumm-500A-B3T (=DSM 107037T=JCM 32936T), MWH-UH21BT (=DSM 23884T=LMG 29707T).

show abstract

“…These differences in pH adaptation suggests that it could have been one of the driving forces for the evolution of two lineages. However, in other genera of freshwater bacteria, species adapted to acidic and alkaline conditions are present in a single genus [50]. Genome sequencing and analysis of more strains affiliated with the GKS98 cluster, and more environmental investigations are needed to confirm the suggested ecological tendencies.…”

Section: Ecologymentioning

confidence: 99%

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

Hahn

Pitt

Schmidt

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Opening a next‐generation black box: Ecological trends for hundreds of species‐like taxa uncovered within a single bacterial >99% 16S rRNA operational taxonomic unit

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 14 publications

References 49 publications

A genome catalogue of lake bacteria across watershed land use gradients at a continental scale

A genome catalogue of lake bacteria across watershed land use gradients at a continental scale

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

Contact Info

Product

Resources

About