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Hahn MW, Pitt A, Schmidt J, Camacho A. 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. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005408] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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).
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Affiliation(s)
- Martin W. Hahn
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Antonio Camacho
- Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, E-46980 Paterna, Spain
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Betiku OC, Sarjeant KC, Ngatia LW, Aghimien MO, Odewumi CO, Latinwo LM. Evaluation of microbial diversity of three recreational water bodies using 16S rRNA metagenomic approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 771:144773. [PMID: 33548724 DOI: 10.1016/j.scitotenv.2020.144773] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 06/12/2023]
Abstract
Surface water plays a significant role in world development by promoting economic growth and health benefits to humans and animals whose lives depend on good water quality in the ecosystem. Thus, this study investigated the differences in physical and chemical properties of surface water from two lakes (Lakes Jackson and Talquin) and a pond (Pedrick Pond). Also, the influence of environmental factors on the microbial communities that live within the water environment was examined. Genomic DNA was extracted from the water samples collected and 16S rRNA sequencing method was employed to characterize the microbial community compositions across the three locations. The results obtained suggest that the water sources met the recommended recreational water quality criteria standard for clean water. Overall, Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes were the main bacterial phyla present in the communities, while Archaea was mainly dominated by Euryachaeota. Pressure, conductivity, temperature, dissolved oxygen (DO), and pH accounted for 74.2% of the variation in the distribution of the microbial community in the three locations (P < 0.05), while 58.2% of the variation in the microbial community distribution was accounted for by pressure and conductivity. The high temperature observed in the Pedrick Pond correlated with the distribution of genera hgcl_clades and Legionella. While in Lake Talquin, water conductivity was significantly associated with the abundance of Cyanobium_PCC_6307, Sediminibacterium, and Conexibacter. The results from this study indicate that the microbial communities in the two lakes are different from the pond and all the environmental variables accounted for a significant portion of the total variation, but pressure, conductivity, and temperature are more important factors due to significant correlation with the distribution of the microbial communities.
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Affiliation(s)
- Omolola C Betiku
- Center for Water Resources, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL 32307, USA; Division of Agriculture Science, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL 32307, USA.
| | - Keawin C Sarjeant
- Division of Agriculture Science, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL 32307, USA
| | - Lucy W Ngatia
- Center for Water Resources, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL 32307, USA
| | - Monica O Aghimien
- Department of Biological Sciences, Florida A&M University, Tallahassee, FL 32307, USA
| | - Caroline O Odewumi
- Department of Biological Sciences, Florida A&M University, Tallahassee, FL 32307, USA
| | - Lekan M Latinwo
- Department of Biological Sciences, Florida A&M University, Tallahassee, FL 32307, USA
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Hoetzinger M, Schmidt J, Pitt A, Koll U, Lang E, Hahn MW. Polynucleobacter paneuropaeus sp. nov., characterized by six strains isolated from freshwater lakes located along a 3000 km north-south cross-section across Europe. Int J Syst Evol Microbiol 2018; 69:203-213. [PMID: 30465643 DOI: 10.1099/ijsem.0.003130] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Six Polynucleobacter (Burkholderiaceae, Betaproteobacteria) strains isolated from different freshwater lakes located across Europe were taxonomically investigated. Phylogenetic analyses based on 16S rRNA gene sequences assigns all six strains to the cryptic species complex PnecC within the genus Polynucleobacter. Analyses of partial glutamine synthetase (glnA) genes suggests that all six strains belong to the species-like taxon designated F15 in previous papers. Comparative genome analyses reveal that the six strains form a genomically coherent group characterized by whole-genome average nucleotide identity (gANI) values of >98 % but separated by gANI values of <88 % from the type strains and representatives of the 16 previously described Polynucleobacter species. In phylogenetic analyses based on nucleotide sequences of 319 orthologous genes, the six strains represent a monophyletic cluster that is clearly separated from all other described species. Genome sizes of the six strains range from 1.61 to 1.83 Mbp, which is smaller than genome sizes of the majority of type strains representing previously described Polynucleobacter species. By contrast, the G+C content of the DNA of the strains is well in the range of 44.8-46.6 mol% previously found for other type strains of species affiliated with the subgroup PnecC. Variation among the six strains representing the new species is evident in a number of traits. These include gene content differences, for instance regarding a gene cluster encoding anoxygenic photosynthesis, as well as phenotypic traits. We propose to name the new species represented by the six strains Polynucleobacter paneuropaeus sp. nov. and designate strain MG-25-Pas1-D2T (=DSM 103454T =CIP 111323T) as the type strain.
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Affiliation(s)
- Matthias Hoetzinger
- 1Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- 1Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Alexandra Pitt
- 1Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Ulrike Koll
- 1Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Elke Lang
- 2Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - Martin W Hahn
- 1Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
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Hahn MW, Koll U, Schmidt J, Huymann LR, Karbon G, Lang E. Polynucleobacter hirudinilacicola sp. nov. and Polynucleobacter campilacus sp. nov., both isolated from freshwater systems. Int J Syst Evol Microbiol 2018; 68:2593-2601. [PMID: 29939120 DOI: 10.1099/ijsem.0.002880] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains MWH-EgelM1-30-B4T and MWH-Feld-100T were isolated from the water columns of two freshwater systems. Both strains represent delicate bacteria not easy to work with in laboratory experiments. Phylogenetic analyses of the 16S rRNA genes suggested that both strains were affiliated with the genus Polynucleobacter. Both strains share 16S rRNA gene sequence similarities of >99 % with eight free-living Polynucleobacter type strains, all affiliated with the cryptic species complex PnecC. The full-length 16S rRNA gene sequences of the two strains differ only in two and three positions, respectively, from the sequence of the closest related Polynucleobacter type strain. Genome sequencing of both strains revealed relatively small genome sizes of 2.0 Mbp and G+C contents of 45 mol%. Phylogenetic analyses based on nucleotide sequences of 319 shared protein-encoding genes consistently placed the two strains in taxon PnecC but did not suggest an affiliation with one of the previously described species. Pairwise analyses of whole genome average nucleotide identities (gANI) with representatives of all previously described Polynucleobacter species resulted in both cases throughout in values <80 %. Pairwise comparison of the genomes of the two new strains resulted in gANI values of 83.3 %. All gANI analyses clearly suggested that strains MWH-EgelM1-30-B4T and MWH-Feld-100T represent two novel Polynucleobacter species. We propose for these novel species the names Polynucleobacter hirudinilacicola sp. nov. and Polynucleobacter campilacus sp. nov. and strains MWH-EgelM1-30-B4T (=DSM 23911T=LMG 30144T) and MWH-Feld-100T (=DSM 24007T=LMG 29705T) as the type strains, respectively.
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Affiliation(s)
- Martin W Hahn
- 1Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Ulrike Koll
- 1Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- 1Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Lesley R Huymann
- 1Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Gerlinde Karbon
- 1Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Elke Lang
- 2Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
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Pitt A, Schmidt J, Lang E, Whitman WB, Woyke T, Hahn MW. Polynucleobacter meluiroseus sp. nov., a bacterium isolated from a lake located in the mountains of the Mediterranean island of Corsica. Int J Syst Evol Microbiol 2018; 68:1975-1985. [PMID: 29688164 DOI: 10.1099/ijsem.0.002777] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain AP-Melu-1000-B4 was isolated from a lake located in the mountains of the Mediterranean island of Corsica (France). Phenotypic, chemotaxonomic and genomic traits were investigated. Phylogenetic analyses based on 16S rRNA gene sequencing referred the strain to the cryptic species complex PnecC within the genus Polynucleobacter. The strain encoded genes for biosynthesis of proteorhodopsin and retinal. When pelleted by centrifugation the strain showed an intense rose colouring. Major fatty acids were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and summed feature 2 (C16 : 1 isoI and C14 : 0-3OH). The sequence of the 16S rRNA gene contained an indel which was not present in any previously described Polynucleobacter species. Genome sequencing revealed a genome size of 1.89 Mbp and a G+C content of 46.6 mol%. In order to resolve the phylogenetic position of the new strain within subcluster PnecC, its phylogeny was reconstructed from sequences of 319 shared genes. To represent all currently described Polynucleobacter species by whole genome sequences, three type strains were additionally sequenced. Our phylogenetic analysis revealed that strain AP-Melu-100-B4 occupied a basal position compared with previously described PnecC strains. Pairwise determined whole genome average nucleotide identity (gANI) values suggested that strain AP-Melu-1000-B4 represents a new species, for which we propose the name Polynucleobacter meluiroseus sp. nov. with the type strain AP-Melu-1000-B4T (=DSM 103591T=CIP 111329T).
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Affiliation(s)
- Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Elke Lang
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - William B Whitman
- Department of Microbiology, 527 Biological Sciences Building, University of Georgia, Athens, GA, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
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Hahn MW, Schmidt J, Asiyo GS, Kyrpides NC, Woyke T, Whitman WB. Reclassification of a Polynucleobacter cosmopolitanus strain isolated from tropical Lake Victoria as Polynucleobacter victoriensis sp. nov. Int J Syst Evol Microbiol 2017; 67:5087-5093. [PMID: 29068276 DOI: 10.1099/ijsem.0.002421] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Polynucleobacter (family Burkholderiaceae) is phylogenetically subdivided into at least four subclusters. One of those, subcluster PnecC, was recognized as a cryptic species complex. Here we test by comparative genome analyses whether subcluster PnecD, currently solely represented by the species Polynucleobactercosmopolitanus, also represents such a cryptic species complex. The genome sequences of the two P. cosmopolitanus strains, MWH-MoIso2T and MWH-VicM1, were determined. The latter strain was also characterized in the previous description of P. cosmopolitanus. These two strains originate from a temperate lake located in Austria and from the large tropical Lake Victoria located in East Africa, respectively. Strains MWH-MoIso2T and MWH-VicM1 possess quite small genomes of 1.78 and 1.63 Mbp, respectively, and share similar G+C values of 44.1 and 43.1 mol%, respectively. Both strains encode only a single copy of the ribosomal operon, and their 16S rRNA genes differ only in four positions, equalling a sequence similarity of 99.74 %. Both genomes possess characteristics indicating evolutionary genome streamlining, such as high coding densities of 93.9 and 94.6 % of bases, respectively. Average nucleotide identity (ANI) comparisons of the genomes of the two strains resulted in a value of 78.4 %, suggesting that each of the strains represents a separate species. Our investigation suggests that PnecD represents an additional cryptic species complex within the genus Polynucleobacter that was not resolved by 16S rRNA gene sequence analyses. We propose reclassification of strain MWH-VicM1 as Polynucleobacter victoriensis sp. nov., with type strain MWH-VicM1T(=DSM 21486T=JCM 32005T).
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Affiliation(s)
- Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Grace Ssanyu Asiyo
- Department of Biological Sciences, Kyambogo University, P.O Box 1, Kyambogo, Uganda
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - William B Whitman
- Department of Microbiology, University of Georgia, 527 Biological Sciences Building, Athens, GA, USA
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