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Complete Genome Sequences of Polynucleobacter sp. Subcluster PnecA Strains SHI2 and SHI8, Isolated from an Oligotrophic-Dystrophic Lake in Japan. Microbiol Resour Announc 2023; 12:e0003023. [PMID: 36856406 PMCID: PMC10112219 DOI: 10.1128/mra.00030-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
Members of the genus Polynucleobacter belonging to the subcluster PnecA comprise freshwater bacterioplankton with worldwide distribution. Here, we report the complete genome sequences of two Polynucleobacter sp. strains (PnecA), SHI2 and SHI8, isolated from the surface water of an oligotrophic-dystrophic lake in a humid continental climate in Japan.
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2
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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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3
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Shabarova T, Salcher MM, Porcal P, Znachor P, Nedoma J, Grossart HP, Seďa J, Hejzlar J, Šimek K. Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession. Nat Microbiol 2021; 6:479-488. [PMID: 33510474 DOI: 10.1038/s41564-020-00852-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023]
Abstract
Small lakes and ponds occupy an enormous surface area of inland freshwater and represent an important terrestrial-water interface. Disturbances caused by extreme weather events can have substantial effects on these ecosystems. Here, we analysed the dynamics of nutrients and the entire plankton community in two flood events and afterwards, when quasi-stable conditions were established, to investigate the effect of such disturbances on a small forest pond. We show that floodings result in repeated washout of resident organisms and hundredfold increases in nutrient load. Despite this, the microbial community recovers to a predisturbance state within two weeks of flooding through four well-defined succession phases. Reassembly of phytoplankton and especially zooplankton takes up to two times longer and features repetitive and adaptive patterns. Release of dissolved nutrients from the pond is associated with inflow rates and community recovery, and returns to predisturbance levels before microbial compositions recover. Our findings shed light on the mechanisms underlying functional resilience of small waterbodies and are relevant to global change-induced increases in weather extremes.
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Affiliation(s)
- Tanja Shabarova
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Petr Porcal
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Petr Znachor
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Jiří Nedoma
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute of Freshwater Biology and Inland Fisheries (IGB), Stechlin, Germany.,Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Jaromír Seďa
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Josef Hejzlar
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Karel Šimek
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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4
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Nuy JK, Hoetzinger M, Hahn MW, Beisser D, Boenigk J. Ecological Differentiation in Two Major Freshwater Bacterial Taxa Along Environmental Gradients. Front Microbiol 2020; 11:154. [PMID: 32117171 PMCID: PMC7031163 DOI: 10.3389/fmicb.2020.00154] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/22/2020] [Indexed: 12/05/2022] Open
Abstract
Polynucleobacter (Burkholderiaceae, Betaproteobacteria) and Limnohabitans (Comamonadaceae, Betaproteobacteria) are abundant freshwater bacteria comprising large genetic and taxonomic diversities, with species adapted to physico-chemically distinct types of freshwater systems. The relative importance of environmental drivers, i.e., physico-chemistry, presence of microeukaryotes and geographic position for the diversity and prevalence has not been investigated for both taxa before. Here, we present the first pan-European study on this topic, comprising 255 freshwater lakes. We investigated Limnohabitans and Polynucleobacter using an amplicon sequencing approach of partial 16S rRNA genes along environmental gradients. We show that physico-chemical factors had the greatest impact on both genera. Analyses on environmental gradients revealed an exceptionally broad ecological spectrum of operational taxonomic units (OTUs). Despite the coarse resolution of the genetic marker, we found OTUs with contrasting environmental preferences within Polynucleobacter and Limnohabitans subclusters. Such an ecological differentiation has been characterized for PnecC and LimC before but was so far unknown for less well studied subclusters such as PnecA and PnecB. Richness and abundance of OTUs are geographically clustered, suggesting that geographic diversity patterns are attributable to region-specific physico-chemical characteristics (e.g., pH and temperature) rather than latitudinal gradients or lake sizes.
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Affiliation(s)
- Julia K Nuy
- Department of Biodiversity, University of Duisburg Essen, Essen, Germany
| | - Matthias Hoetzinger
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Daniela Beisser
- Department of Biodiversity, University of Duisburg Essen, Essen, Germany
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg Essen, Essen, Germany
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5
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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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6
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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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7
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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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8
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Hoetzinger M, Hahn MW. Genomic divergence and cohesion in a species of pelagic freshwater bacteria. BMC Genomics 2017; 18:794. [PMID: 29037158 PMCID: PMC5644125 DOI: 10.1186/s12864-017-4199-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 10/08/2017] [Indexed: 11/15/2022] Open
Abstract
Background In many prokaryotic genera a clustered phylogeny is observed, akin to the occurrence of species in sexually reproducing organisms. For some taxa, homologous recombination has been invoked as the underlying mechanism providing genomic cohesion among conspecific individuals. Whether this mechanism is applicable to prokaryotes in freshwaters with low habitat connectivity – i.e. elevated geographic barriers to gene flow – is unclear. To investigate further we studied genomic trends within the globally abundant PnecC cluster (genus Polynucleobacter, Betaproteobacteria) and analyzed homologous recombination within the affiliated species P. asymbioticus. Results Comparisons among 20 PnecC genomes revealed a clearly discontinuous distribution of nucleotide sequence similarities. Among the nine conspecific individuals (P. asymbioticus) all average nucleotide identity (ANI) values were greater than 97%, whereas all other comparisons exhibited ANI values lower than 85%. The reconstruction of recombination and mutation events for the P. asymbioticus core genomes yielded an r/m ratio of 7.4, which is clearly above estimated thresholds for recombination to act as a cohesive force. Hotspots of recombination were found to be located in the flanking regions of genomic islands. Even between geographically separated habitats a high flux of recombination was evident. While a biogeographic population structure was suggested from MLST data targeting rather conserved loci, such a structure was barely visible when whole genome data was considered. However, both MLST and whole genome data showed evidence of differentiation between two lineages of P. asymbioticus. The ratios of non-synonymous to synonymous substitution rates as well as growth rates in transplantation experiments suggested that this divergence was not selectively neutral. Conclusions The high extent of homologous recombination among P. asymbioticus bacteria can act as a cohesive force that effectively counteracts genetic divergence. At least on a regional scale, homologous recombination can act across geographically separated ecosystems and therefore plays an important role in the evolution and consistency of bacterial freshwater species. A species model akin to the biological species concept may be applicable for P. asymbioticus. Nonetheless, two genetically distinct lineages have emerged and further research may clarify if their divergence has been initiated by reinforced geographical barriers or has been evolving in sympatry. Electronic supplementary material The online version of this article (10.1186/s12864-017-4199-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthias Hoetzinger
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310, Mondsee, Austria.
| | - Martin W Hahn
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310, Mondsee, Austria
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9
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Hahn MW, Koll U, Karbon G, Schmidt J, Lang E. Polynucleobacter aenigmaticus sp. nov. isolated from the permanently anoxic monimolimnion of a temperate meromictic lake. Int J Syst Evol Microbiol 2017; 67:4646-4654. [PMID: 29022553 DOI: 10.1099/ijsem.0.002347] [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: 01/08/2023] Open
Abstract
The bacterial strain MWH-K35W1T was isolated from a permanently anoxic water layer of a meromictic lake located in the Austrian Salzkammergut area. The basically chemo-organoheterotrophic strain was isolated and maintained under aerobic conditions. Phylogenetic analyses of the 16S rRNA gene and the glutamine synthetase gene (glnA) of the strain suggested an affiliation to the genus Polynucleobacter and the cryptic species complex PnecC. Strain MWH-K35W1T shares with the type strains of the six free-living species of the genus Polynucleobacter affiliated with this species complex 16S rRNA gene sequence similarities of 99.6-99.9 %, while the type material of the obligate endosymbiont Polynucleobacternecessarius, which is also affiliated with this species complex, shares a gene sequence similarity of 99.1 %. Genome sequencing resulted in a genome size of 2.14 Mbp and a DNA G+C content of 45.98 mol%. Major fatty acids were C16 : 1ω7c, C18 : 1ω7c and C16 : 0. This strain is the first strain of the genus Polynucleobacter found to encode a proteorhodopsin-like protein but, in contrast to some other strains affiliated to this genus, it does not encode a putative anoxygenic photosynthesis system. Multilocus sequence analysis based on partial sequences of eight housekeeping genes, as well as average nucleotide identity (ANI) analyses, did not suggest that strain MWH-K35W1T belongs to a previously described species. We propose the name Polynucleobacter aenigmaticus for a novel species with strain MWH-K35W1T (=DSM 24006T=LMG 29706T) as the type strain.
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Affiliation(s)
- Martin W Hahn
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Ulrike Koll
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Gerlinde Karbon
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Institute 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
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10
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Hahn MW, Karbon G, Koll U, Schmidt J, Lang E. Polynucleobacter sphagniphilus sp. nov. a planktonic freshwater bacterium isolated from an acidic and humic freshwater habitat. Int J Syst Evol Microbiol 2017; 67:3261-3267. [PMID: 28829016 DOI: 10.1099/ijsem.0.002096] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain MWH-Weng1-1T, isolated from an acidic freshwater habitat located in the Wenger Moor, Austria, was characterized by investigating its phenotypic, chemotaxonomic and genomic traits. Phylogenetic analyses based on 16S rRNA gene sequencing placed the strain in the cryptic species complex PnecC within the genus Polynucleobacter. The strain had a genome of 2.04 Mbp with a G+C content of 45.6 mol%. The major fatty acids of the strain were C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. In order to resolve the systematic position of the strain within the species complex PnecC, concatenated partial sequences of eight housekeeping genes were used for phylogenetic analyses. The obtained trees did not place strain MWH-Weng1-1T close to any of the six previously described species within this cryptic species complex. Pairwise whole genome average nucleotide identity comparisons with genome sequences of strains representing the six previously described species of the subcluster resulted throughout in values <78 %, which clearly suggested that strain MWH-Weng1-1T (DSM 24018T=CIP 111099T) represents a novel species. We propose the name Polynucleobacter sphagniphilus sp. nov. and strain MWH-Weng1-1T as the type strain for this new species.
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Affiliation(s)
- Martin W Hahn
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Gerlinde Karbon
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Ulrike Koll
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Institute 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
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11
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Pernthaler J. Competition and niche separation of pelagic bacteria in freshwater habitats. Environ Microbiol 2017; 19:2133-2150. [PMID: 28370850 DOI: 10.1111/1462-2920.13742] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/19/2017] [Accepted: 03/23/2017] [Indexed: 11/29/2022]
Abstract
Freshwater bacterioplankton assemblages are composed of sympatric populations that can be delineated, for example, by ribosomal RNA gene relatedness and that differ in key ecophysiological properties. They may be free-living or attached, specialized for particular concentrations or subsets of substrates, or invest a variable amount of their resources in defence traits against protistan predators and viruses. Some may be motile and tactic whereas others are not, with far-reaching implications for their respective life styles and niche partitioning. The co-occurrence of competitors with overlapping growth requirements has profound consequences for the stability of community functions; it can to some extent be explained by habitat factors such as the microscale complexity and spatiotemporal variability of the lacustrine environments. On the other hand, the composition and diversity of freshwater microbial assemblages also reflects non-equilibrium states, dispersal and the stochasticity of community assembly processes. This review synoptically discusses the competition and niche separation of heterotrophic bacterial populations (defined at various levels of phylogenetic resolution) in the pelagic zone of inland surface waters from a variety of angles, focusing on habitat heterogeneity and the resulting biogeographic distribution patterns, the ecophysiological adaptations to the substrate field and the interactions of prokaryotes with predators and viruses.
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Affiliation(s)
- Jakob Pernthaler
- Limnological Station Kilchberg, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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12
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Hahn MW, Huymann LR, Koll U, Schmidt J, Lang E, Hoetzinger M. Polynucleobacter wuianus sp. nov., a free-living freshwater bacterium affiliated with the cryptic species complex PnecC. Int J Syst Evol Microbiol 2017; 67:379-385. [PMID: 27902302 DOI: 10.1099/ijsem.0.001637] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain QLW-P1FAT50C-4T, isolated from a shallow, acidic freshwater pond located in the Austrian Alps at an altitude of 1300 m, was characterized by investigation of phenotypic, chemotaxonomic and genomic traits. As shown previously, phylogenetic analyses based on 16S rRNA gene sequences placed the strain in the cryptic species complex PnecC within the genus Polynucleobacter. The major fatty acids of the strain were C16 : 1ω7c and C18 : 1ω7c. The strain has a genome of 2.23 Mbp with a DNA G+C content of 44.9 mol%. The strain encodes a seemingly complete gene cluster for anoxygenic photosynthesis but lacks typical genes for CO2 assimilation. In order to resolve the phylogenetic position of the strain within the species complex PnecC, concatenated partial sequences of eight housekeeping genes were analysed. The phylogenetic reconstruction obtained did not place strain QLW-P1FAT50C-4T close to any of the five previously described species within subcluster PnecC. Pairwise average nucleotide identity (ANI) comparisons of whole-genome sequences suggested that strain QLW-P1FAT50C-4T (=DSM 24008T=CIP 111100T) represents a novel species, for which we propose the name Polynucleobacter wuianus sp. nov.
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Affiliation(s)
- Martin W Hahn
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, Mondsee A-5310, Austria
| | - Lesley R Huymann
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, Mondsee A-5310, Austria
| | - Ulrike Koll
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, Mondsee A-5310, Austria
| | - Johanna Schmidt
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, Mondsee A-5310, Austria
| | - Elke Lang
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - Matthias Hoetzinger
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, Mondsee A-5310, Austria
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13
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Formosimonas limnophila gen. nov., sp. nov., a new member of the family Burkholderiaceae isolated from a freshwater lake. Int J Syst Evol Microbiol 2017; 67:17-24. [DOI: 10.1099/ijsem.0.001561] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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14
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Hahn MW, Schmidt J, Pitt A, Taipale SJ, Lang E. Reclassification of four Polynucleobacter necessarius strains as representatives of Polynucleobacter asymbioticus comb. nov., Polynucleobacter duraquae sp. nov., Polynucleobacter yangtzensis sp. nov. and Polynucleobacter sinensis sp. nov., and emended description of Polynucleobacter necessarius. Int J Syst Evol Microbiol 2016; 66:2883-2892. [PMID: 27064460 PMCID: PMC5018217 DOI: 10.1099/ijsem.0.001073] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genome comparisons based on average nucleotide identity (ANI) values of four strains currently classified as Polynucleobacter necessarius subsp. asymbioticus resulted in ANI values of 75.7-78.4 %, suggesting that each of those strains represents a separate species. The species P. necessarius was proposed by Heckmann and Schmidt in 1987 to accommodate obligate endosymbionts of ciliates affiliated with the genus Euplotes. The required revision of this species is, however, hampered by the fact, that this species is based only on a description and lacks a type strain available as pure culture. Furthermore, the ciliate culture Euplotes aediculatus ATCC 30859, on which the description of the species was based, is no longer available. We found another Euplotes aediculatus culture (Ammermann) sharing the same origin with ATCC 30859 and proved the identity of the endosymbionts contained in the two cultures. A multilocus sequence comparison approach was used to estimate if the four strains currently classified as Polynucleobacternecessarius subsp. asymbioticus share ANI values with the endosymbiont in the Ammermann culture above or below the threshold for species demarcation. A significant correlation (R2 0.98, P<0.0001) between multilocus sequence similarity and ANI values of genome-sequenced strains enabled the prediction that it is highly unlikely that these four strains belong to the species P. necessarius. We propose reclassification of strains QLW-P1DMWA-1T (=DSM 18221T=CIP 109841T), MWH-MoK4T (=DSM 21495T=CIP 110977T), MWH-JaK3T (=DSM 21493T=CIP 110976T) and MWH-HuW1T (=DSM 21492T=CIP 110978T) as Polynucleobacter asymbioticus comb. nov., Polynucleobacter duraquae sp. nov., Polynucleobacter yangtzensis sp. nov. and Polynucleobacter sinensis sp. nov., respectively.
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Affiliation(s)
- Martin W Hahn
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Alexandra Pitt
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Sami J Taipale
- Lammi Biological Station, University of Helsinki, Pääjärventie 320, 16900 Lammi, Finland
| | - Elke Lang
- Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
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15
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Paver SF, Youngblut ND, Whitaker RJ, Kent AD. Phytoplankton succession affects the composition of Polynucleobacter subtypes in humic lakes. Environ Microbiol 2014; 17:816-28. [PMID: 24912130 DOI: 10.1111/1462-2920.12529] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 06/03/2014] [Indexed: 11/27/2022]
Abstract
Phytoplankton influence the composition of bacterial communities, but the taxonomic specificity of algal-bacterial interactions is unclear due to the aggregation of ecologically distinct bacterial populations by community characterization methods. Here we examine whether phytoplankton seasonal succession affects the composition of subtypes within the cosmopolitan freshwater bacterial genus Polynucleobacter. Changes in the composition of Polynucleobacter subtypes were characterized in samples collected weekly from May to August in 2003 and 2008 from three humic lakes using terminal restriction fragment length polymorphism fingerprinting of the protein-encoding cytochrome c oxidase ccoN gene. Changes in phytoplankton population abundances explained, on average, 30% of temporal variation in the composition of Polynucleobacter subtypes and the interaction between phytoplankton and the environment explained an additional 18% of temporal variation. The effect of phytoplankton on specific Polynucleobacter subtypes was experimentally confirmed by changes in Polynucleobacter subtype composition following incubation with different phytoplankton assemblages or a no-phytoplankton control. Phytoplankton-associated subtypes and differentiation in substrate use among subtypes likely contribute to the effects of phytoplankton on Polynucleobacter subtype composition. Interactions between unique Polynucleobacter populations and phytoplankton highlight the ecological significance and specificity of species interactions in freshwater communities.
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Affiliation(s)
- Sara F Paver
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, IL, 61801, USA
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16
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Di Maiuta N, Schwarzentruber P, Schenker M, Schoelkopf J. Microbial population dynamics in the faeces of wood-eating loricariid catfishes. Lett Appl Microbiol 2013; 56:401-7. [DOI: 10.1111/lam.12061] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/15/2013] [Accepted: 02/19/2013] [Indexed: 11/30/2022]
Affiliation(s)
- N. Di Maiuta
- Omya Development AG; R&D-Microbiology; Oftringen Switzerland
| | | | - M. Schenker
- Omya Development AG; R&D-Surface Chemistry; Oftringen Switzerland
| | - J. Schoelkopf
- Omya Development AG; R&D-Surface Chemistry; Oftringen Switzerland
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17
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Watanabe K, Komatsu N, Kitamura T, Ishii Y, Park HD, Miyata R, Noda N, Sekiguchi Y, Satou T, Watanabe M, Yamamura S, Imai A, Hayashi S. Ecological niche separation in the Polynucleobacter subclusters linked to quality of dissolved organic matter: a demonstration using a high sensitivity cultivation-based approach. Environ Microbiol 2012; 14:2511-25. [PMID: 22759205 DOI: 10.1111/j.1462-2920.2012.02815.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The free-living, cosmopolitan, freshwater betaproteobacterial bacterioplankton genus Polynucleobacter was detected in different years in 11 lakes of varying types and a river using the size-exclusion assay method (SEAM). Of the 350 strains isolated, 228 (65.1%) were affiliated with the Polynucleobacter subclusters PnecC (30.0%) and PnecD (35.1%). Significant positive correlations between fluorescence in situ hybridization and SEAM data were observed in the relative abundance of PnecC and PnecD bacteria to Polynucleobacter communities (PnecC + PnecD). Isolates were mainly PnecC bacteria in the samples with a high specific UV absorbance at 254 nm (SUVA(254) ), and a low total hydrolysable neutral carbohydrate and amino acid (THneutralCH + THAA) content of the dissolved organic matter (DOM) fraction, which is known to be correlated with a high humic content. In contrast, the PnecD bacteria were abundant in samples with high chlorophyll a and/or THneutralCH + THAA concentrations, indicative of primary productivity. With few exceptions, differences in the relative abundance of PnecC and PnecD in each sample, determined using a high-sensitivity cultivation-based approach, were due to DOM quality. These results suggest that the major DOM component in the field, which is allochthonously or autochthonously derived, is a key factor for ecological niche separation between PnecC and PnecD subclusters.
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Affiliation(s)
- Keiji Watanabe
- National Institute for Environmental Studies, Tsukuba, Ibaraki 305-8506, Japan.
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18
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Jezbera J, Jezberová J, Koll U, Horňák K, Šimek K, Hahn MW. Contrasting trends in distribution of four major planktonic betaproteobacterial groups along a pH gradient of epilimnia of 72 freshwater habitats. FEMS Microbiol Ecol 2012; 81:467-79. [PMID: 22452571 DOI: 10.1111/j.1574-6941.2012.01372.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 03/16/2012] [Accepted: 03/16/2012] [Indexed: 12/22/2022] Open
Abstract
The distribution and abundance of Betaproteobacteria and three of its genera - Limnohabitans (R-BT065 lineage), Polynucleobacter (including subclusters Polynucleobacter necessarius and Polynucleobacter acidiphobus/Polynucleobacter difficilis), and Methylophilus - across the epilimnia of 72 limnologically diverse freshwater habitats were investigated using fluorescence in situ hybridization. Moreover, seasonal development of Betaproteobacteria subgroups along the longitudinal axis of a reservoir was followed. Betaproteobacteria comprised on average 29.1%, Polynucleobacter 11.6%, P. necessarius 10.1%, P. acidiphobus/difficilis 0.5%, Limnohabitans 8.9%, and Methylophilus 0.9% of total bacterioplankton cells in the investigated habitats. Polynucleobacter necessarius and Limnohabitans coexisted in the majority of habitats but showed contrasting abundance patterns along the pH gradient of habitats (pH, 3.8-8.5). The observed distribution patterns could theoretically be explained by different preferences for substrate sources, that is, substances of humic origin in acidic waters and algal-derived substances in alkaline waters. However, substrate utilization patterns observed in laboratory experiments indicate no coherent group-specific differences in substrate preferences. Interestingly, similar distribution patterns were revealed for Limnohabitans and P. acidiphobus/difficilis, suggesting similar ecological adaptations of these distantly related taxa. Our findings further emphasize that at least two taxa of freshwater Betaproteobacteria represent ecologically diversified groups. Investigations at higher phylogenetic resolution are required for obtaining further insights into their ecology.
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Affiliation(s)
- Jan Jezbera
- Institute for Limnology, Austrian Academy of Sciences, Mondsee, Austria.
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19
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Meincke L, Copeland A, Lapidus A, Lucas S, Berry KW, Del Rio TG, Hammon N, Dalin E, Tice H, Pitluck S, Richardson P, Bruce D, Goodwin L, Han C, Tapia R, Detter JC, Schmutz J, Brettin T, Larimer F, Land M, Hauser L, Kyrpides NC, Ivanova N, Göker M, Woyke T, Wu QL, Pöckl M, Hahn MW, Klenk HP. Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1(T)). Stand Genomic Sci 2012; 6:74-83. [PMID: 22675600 PMCID: PMC3368402 DOI: 10.4056/sigs.2395367] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Polynucleobacter necessarius subsp. asymbioticus strain QLW-P1DMWA-1(T) is a planktonic freshwater bacterium affiliated with the family Burkholderiaceae (class Betaproteobacteria). This strain is of interest because it represents a subspecies with cosmopolitan and ubiquitous distribution in standing freshwater systems. The 16S-23S ITS genotype represented by the sequenced strain comprised on average more than 10% of bacterioplankton in its home habitat. While all strains of the subspecies P. necessarius asymbioticus are free-living freshwater bacteria, strains belonging to the only other subspecies, P. necessarius subsp. necessarius are obligate endosymbionts of the ciliate Euplotes aediculatus. The two subspecies of P. necessarius are the instances of two closely related subspecies that differ in their lifestyle (free-living vs. obligate endosymbiont), and they are the only members of the genus Polynucleobacter with completely sequenced genomes. Here we describe the features of P. necessarius subsp. asymbioticus, together with the complete genome sequence and annotation. The 2,159,490 bp long chromosome with a total of 2,088 protein-coding and 48 RNA genes is the first completed genome sequence of the genus Polynucleobacter to be published and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2006.
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Affiliation(s)
- Linda Meincke
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Nancy Hammon
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Eileen Dalin
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - David Bruce
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lynne Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - John C. Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Jeremy Schmutz
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Thomas Brettin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Frank Larimer
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | | | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Qinglong L. Wu
- Austrian Academy of Sciences, Institute for Limnology, Mondsee, Austria
| | - Matthias Pöckl
- Austrian Academy of Sciences, Institute for Limnology, Mondsee, Austria
| | - Martin W. Hahn
- Austrian Academy of Sciences, Institute for Limnology, Mondsee, Austria
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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20
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Saw JHW, Yuryev A, Kanbe M, Hou S, Young AG, Aizawa SI, Alam M. Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium. Stand Genomic Sci 2012; 6:84-93. [PMID: 22675601 PMCID: PMC3368406 DOI: 10.4056/sigs.2445005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Saprospira grandis is a coastal marine bacterium that can capture and prey upon other marine bacteria using a mechanism known as ‘ixotrophy’. Here, we present the complete genome sequence of Saprospira grandis str. Lewin isolated from La Jolla beach in San Diego, California. The complete genome sequence comprises a chromosome of 4.35 Mbp and a plasmid of 54.9 Kbp. Genome analysis revealed incomplete pathways for the biosynthesis of nine essential amino acids but presence of a large number of peptidases. The genome encodes multiple copies of sensor globin-coupled rsbR genes thought to be essential for stress response and the presence of such sensor globins in Bacteroidetes is unprecedented. A total of 429 spacer sequences within the three CRISPR repeat regions were identified in the genome and this number is the largest among all the Bacteroidetes sequenced to date.
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Affiliation(s)
- Jimmy H. W. Saw
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, USA
| | | | - Masaomi Kanbe
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics, and Bioinformatics, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Aaron G. Young
- Advanced Studies in Genomics, Proteomics, and Bioinformatics, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Shin-Ichi Aizawa
- Prefectural University of Hiroshima, Department of Biosciences, 562 Nanatsuka, Shobara, Hiroshima 727-0023, Japan
| | - Maqsudul Alam
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
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21
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Hahn MW, Minasyan A, Lang E, Koll U, Spröer C. Polynucleobacter difficilis sp. nov., a planktonic freshwater bacterium affiliated with subcluster B1 of the genus Polynucleobacter. Int J Syst Evol Microbiol 2011; 62:376-383. [PMID: 21441373 DOI: 10.1099/ijs.0.031393-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain AM-8B5(T), isolated from Lake Sevan in Armenia, was characterized phenotypically, chemotaxonomically and phylogenetically. This chemo-organoheterotrophic, aerobic, facultatively anaerobic, catalase- and oxidase-positive, non-motile strain grew on NSY medium at NaCl concentrations of 0.0-0.2 % (w/v) and at 4-30 °C. Whole-cell fatty acids were dominated by summed feature 3 (including C(16 : 1)ω7c and iso-C(15 : 0) 2-OH), C(16 : 0) and C(18 : 1)ω7c. C(12 : 0) 2-OH and C(16 : 1) 2-OH were the only hydroxylated fatty acids detected. Phylogenetic analysis as well as phenotypic and chemotaxonomic similarities indicated that the novel isolate was affiliated with the genus Polynucleobacter. 16S rRNA gene similarity values with the four previously described Polynucleobacter species ranged from 96.2 to 98.7 %. DNA-DNA hybridization experiments showed that the isolate did not belong to any of the previously described Polynucleobacter species. The isolate could be distinguished from all previously established Polynucleobacter species based on chemotaxonomic and phenotypic traits. The bacterium possessed a free-living lifestyle and represents a group of bacteria inhabiting the water column of many freshwater lakes. Based on the revealed phylogeny, and chemotaxonomic and phenotypic differences to previously described Polynucleobacter species, it is proposed that the isolate represents a novel species, Polynucleobacter difficilis sp. nov.; the type strain is AM-8B5(T) ( = DSM 22349(T) = CIP 110078(T)).
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Affiliation(s)
- Martin W Hahn
- Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Arevik Minasyan
- Institute of Hydroecology and Ichthyology of Scientific Centre of Zoology and Hydroeocology of National Academy of Sciences of Republic of Armenia, St Paruyr Sevak 7, 0014 Yerevan, Armenia.,Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Elke Lang
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstr. 7b, D-38124 Braunschweig, Germany
| | - Ulrike Koll
- Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Catrin Spröer
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstr. 7b, D-38124 Braunschweig, Germany
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22
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Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S. A guide to the natural history of freshwater lake bacteria. Microbiol Mol Biol Rev 2011; 75:14-49. [PMID: 21372319 PMCID: PMC3063352 DOI: 10.1128/mmbr.00028-10] [Citation(s) in RCA: 867] [Impact Index Per Article: 66.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies.
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Affiliation(s)
- Ryan J. Newton
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
| | - Stuart E. Jones
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
| | - Alexander Eiler
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
| | - Katherine D. McMahon
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
| | - Stefan Bertilsson
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
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23
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Hahn MW, Lang E, Brandt U, Spröer C. Polynucleobacter acidiphobus sp. nov., a representative of an abundant group of planktonic freshwater bacteria. Int J Syst Evol Microbiol 2010; 61:788-794. [PMID: 20435747 DOI: 10.1099/ijs.0.023929-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The heterotrophic, aerobic, facultatively anaerobic, catalase- and oxidase-positive, non-motile strain MWH-PoolGreenA3(T), isolated from a rock pool filled with freshwater, was characterized. The strain grew on NSY medium over a NaCl range of 0.0-0.3 % (w/v). Whole-cell fatty acids were dominated by C(16 : 1)ω7c (feature 3), C(18 : 1)ω7c and straight-chain C(16 : 0); furthermore, the components C(12 : 0) and C(14 : 0) 2-OH were present. The DNA G+C content was 48.3 mol%. Phylogenetic analysis as well as strong similarities in phenotypic and chemotaxonomic traits indicated the affiliation with the genus Polynucleobacter. 16S rRNA gene similarity values with the three described species of the genus Polynucleobacter ranged from 96.7 to 97.8 %. DNA-DNA hybridization experiments did not reveal that the strain belongs to a previously described species of the genus Polynucleobacter. The strain can be discriminated from previously established species of the genus Polynucleobacter by chemotaxonomic and phenotypic traits. The bacterium possesses a free-living lifestyle and represents a group of planktonic freshwater bacteria occurring with high cell numbers in many freshwater lakes. Based on the phylogeny revealed and the chemotaxonomic and phenotypic differences from previously described species of the genus Polynucleobacter, we propose to establish the novel species Polynucleobacter acidiphobus sp. nov. with the type strain MWH-PoolGreenA3(T) ( = DSM 21994(T) = CIP 110079(T)).
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Affiliation(s)
- Martin W Hahn
- Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, 5310 Mondsee, Austria
| | - Elke Lang
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7b, D-38124 Braunschweig, Germany
| | - Ulrike Brandt
- Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, 5310 Mondsee, Austria
| | - Cathrin Spröer
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7b, D-38124 Braunschweig, Germany
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