Reclassification of a Polynucleobacter cosmopolitanus strain isolated from tropical Lake Victoria as Polynucleobacter victoriensis sp. nov.
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 Polynucleobacter cosmopolitanus , 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 ofmore »
- Authors:
-
- Univ. of Innsbruck, Mondsee (Austria). Research Dept. for Limnology
- Kyambogo Univ., Kyambogo (Uganda). Dept. of Biological Sciences
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Univ. of Georgia, Athens, GA (United States). Department of Microbiology
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
- Sponsoring Org.:
- USDOE Office of Science (SC); Austrian Science Fund (FWF); European Science Foundation (ESF)
- OSTI Identifier:
- 1527027
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- International Journal of Systematic and Evolutionary Microbiology
- Additional Journal Information:
- Journal Volume: 67; Journal Issue: 12; Journal ID: ISSN 1466-5026
- Publisher:
- International Union of Microbiological Societies
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Hahn, Martin W., Schmidt, Johanna, Asiyo, Grace Ssanyu, Kyrpides, Nikos C., Woyke, Tanja, and Whitman, William B. Reclassification of a Polynucleobacter cosmopolitanus strain isolated from tropical Lake Victoria as Polynucleobacter victoriensis sp. nov.. United States: N. p., 2017.
Web. doi:10.1099/ijsem.0.002421.
Hahn, Martin W., Schmidt, Johanna, Asiyo, Grace Ssanyu, Kyrpides, Nikos C., Woyke, Tanja, & Whitman, William B. Reclassification of a Polynucleobacter cosmopolitanus strain isolated from tropical Lake Victoria as Polynucleobacter victoriensis sp. nov.. United States. https://doi.org/10.1099/ijsem.0.002421
Hahn, Martin W., Schmidt, Johanna, Asiyo, Grace Ssanyu, Kyrpides, Nikos C., Woyke, Tanja, and Whitman, William B. Fri .
"Reclassification of a Polynucleobacter cosmopolitanus strain isolated from tropical Lake Victoria as Polynucleobacter victoriensis sp. nov.". United States. https://doi.org/10.1099/ijsem.0.002421. https://www.osti.gov/servlets/purl/1527027.
@article{osti_1527027,
title = {Reclassification of a Polynucleobacter cosmopolitanus strain isolated from tropical Lake Victoria as Polynucleobacter victoriensis sp. nov.},
author = {Hahn, Martin W. and Schmidt, Johanna and Asiyo, Grace Ssanyu and Kyrpides, Nikos C. and Woyke, Tanja and Whitman, William B.},
abstractNote = {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 Polynucleobacter cosmopolitanus , 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).},
doi = {10.1099/ijsem.0.002421},
journal = {International Journal of Systematic and Evolutionary Microbiology},
number = 12,
volume = 67,
place = {United States},
year = {2017},
month = {12}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 4 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains
journal, May 2015
- Whitman, William B.; Woyke, Tanja; Klenk, Hans-Peter
- Standards in Genomic Sciences, Vol. 10, Issue 1
The Complete Genome Sequence of Cupriavidus metallidurans Strain CH34, a Master Survivalist in Harsh and Anthropogenic Environments
journal, May 2010
- Janssen, Paul J.; Van Houdt, Rob; Moors, Hugo
- PLoS ONE, Vol. 5, Issue 5
Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system
journal, April 2016
- Chen, I-Min A.; Markowitz, Victor M.; Palaniappan, Krishna
- BMC Genomics, Vol. 17, Issue 1
Asgard archaea illuminate the origin of eukaryotic cellular complexity
journal, January 2017
- Zaremba-Niedzwiedzka, Katarzyna; Caceres, Eva F.; Saw, Jimmy H.
- Nature, Vol. 541, Issue 7637
The filtration–acclimatization method for isolation of an important fraction of the not readily cultivable bacteria
journal, June 2004
- Hahn, Martin W.; Stadler, Peter; Wu, Qinglong L.
- Journal of Microbiological Methods, Vol. 57, Issue 3
Polynucleobacter acidiphobus sp. nov., a representative of an abundant group of planktonic freshwater bacteria
journal, April 2010
- Hahn, M. W.; Lang, E.; Brandt, U.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 61, Issue 4
Effective isolation of bacterioplankton genus Polynucleobacter from freshwater environments grown on photochemically degraded dissolved organic matter: Isolation and ecological aspects of Polynucleobacter
journal, January 2009
- Watanabe, Keiji; Komatsu, Nobuyuki; Ishii, Yuichi
- FEMS Microbiology Ecology, Vol. 67, Issue 1
Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool
journal, November 2016
- Hoetzinger, Matthias; Schmidt, Johanna; Jezberová, Jitka
- Applied and Environmental Microbiology, Vol. 83, Issue 3
Members of a Readily Enriched -Proteobacterial Clade Are Common in Surface Waters of a Humic Lake
journal, November 2003
- Burkert, U.; Warnecke, F.; Babenzien, D.
- Applied and Environmental Microbiology, Vol. 69, Issue 11
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
journal, October 2015
- Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos
- Standards in Genomic Sciences, Vol. 10, Issue 1
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
journal, February 2014
- Kim, M.; Oh, H. -S.; Park, S. -C.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 2
Differences in structure and dynamics of Polynucleobacter communities in a temperate and a subtropical lake, revealed at three phylogenetic levels: Structure and dynamics of Polynucleobacter communities
journal, July 2006
- Wu, Qinglong L.; Hahn, Martin W.
- FEMS Microbiology Ecology, Vol. 57, Issue 1
Endosymbiosis in statu nascendi: close phylogenetic relationship between obligately endosymbiotic and obligately free-living Polynucleobacter strains (Betaproteobacteria)
journal, February 2007
- Vannini, Claudia; Pöckl, Matthias; Petroni, Giulio
- Environmental Microbiology, Vol. 9, Issue 2
Polynucleobacter sphagniphilus sp. nov. a planktonic freshwater bacterium isolated from an acidic and humic freshwater habitat
journal, September 2017
- Hahn, Martin W.; Karbon, Gerlinde; Koll, Ulrike
- International Journal of Systematic and Evolutionary Microbiology, Vol. 67, Issue 9
Genome Sequence of a Freshwater Low-Nucleic-Acid-Content Bacterium, Betaproteobacterium Strain CB
journal, February 2013
- Hao, Z.; Li, L.; Liu, J.
- Genome Announcements, Vol. 1, Issue 2
Bacterial diversity in an arctic lake: a freshwater SAR11 cluster
journal, January 1996
- Bahr, M.; Hobbie, Je; Sogin, Ml
- Aquatic Microbial Ecology, Vol. 11
Global phylogeography of pelagic P olynucleobacter bacteria: Restricted geographic distribution of subgroups, isolation by distance and influence of climate : Phylogeography of
journal, July 2014
- Hahn, Martin W.; Koll, Ulrike; Jezberová, Jitka
- Environmental Microbiology, Vol. 17, Issue 3
Low Intraspecific Diversity in a Polynucleobacter Subcluster Population Numerically Dominating Bacterioplankton of a Freshwater Pond
journal, August 2005
- Hahn, M. W.; Pockl, M.; Wu, Q. L.
- Applied and Environmental Microbiology, Vol. 71, Issue 8
Complete ecological isolation and cryptic diversity in Polynucleobacter bacteria not resolved by 16S rRNA gene sequences
journal, March 2016
- Hahn, Martin W.; Jezberová, Jitka; Koll, Ulrike
- The ISME Journal, Vol. 10, Issue 7
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
journal, March 2016
- Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro
- Molecular Biology and Evolution, Vol. 33, Issue 7
The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign
journal, May 2015
- Salcher, Michaela M.; Neuenschwander, Stefan M.; Posch, Thomas
- The ISME Journal, Vol. 9, Issue 11
Emended description of the genus Polynucleobacter and the species Polynucleobacter necessarius and proposal of two subspecies, P. necessarius subsp. necessarius subsp. nov. and P. necessarius subsp. asymbioticus subsp. nov.
journal, June 2009
- Hahn, M. W.; Lang, E.; Brandt, U.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 8
Polynucleobacter difficilis sp. nov., a planktonic freshwater bacterium affiliated with subcluster B1 of the genus Polynucleobacter
journal, March 2011
- Hahn, M. W.; Minasyan, A.; Lang, E.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 62, Issue 2
Genome sequence of the -rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia
journal, July 2008
- Amadou, C.; Pascal, G.; Mangenot, S.
- Genome Research, Vol. 18, Issue 9
Ubiquity of Polynucleobacter necessarius ssp. asymbioticus in lentic freshwater habitats of a heterogenous 2000 km 2 area
journal, March 2010
- Jezberová, Jitka; Jezbera, Jan; Brandt, Ulrike
- Environmental Microbiology, Vol. 12, Issue 3
Polynucleobacter rarus sp. nov., a free-living planktonic bacterium isolated from an acidic lake
journal, April 2010
- Hahn, M. W.; Lang, E.; Tarao, M.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 61, Issue 4
IMG: the integrated microbial genomes database and comparative analysis system
journal, December 2011
- Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K.
- Nucleic Acids Research, Vol. 40, Issue D1
The Passive Yet Successful Way of Planktonic Life: Genomic and Experimental Analysis of the Ecology of a Free-Living Polynucleobacter Population
journal, March 2012
- Hahn, Martin W.; Scheuerl, Thomas; Jezberová, Jitka
- PLoS ONE, Vol. 7, Issue 3
Parallel genome reduction in symbionts descended from closely related free-living bacteria
journal, July 2017
- Boscaro, Vittorio; Kolisko, Martin; Felletti, Michele
- Nature Ecology & Evolution, Vol. 1, Issue 8
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
journal, August 2016
- Hahn, Martin W.; Schmidt, Johanna; Pitt, Alexandra
- International Journal of Systematic and Evolutionary Microbiology, Vol. 66, Issue 8
Genomic insights that advance the species definition for prokaryotes
journal, February 2005
- Konstantinidis, K. T.; Tiedje, J. M.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 7
Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1T)
journal, March 2012
- Meincke, Linda; Copeland, Alex; Lapidus, Alla
- Standards in Genomic Sciences, Vol. 6, Issue 1
The small genome of an abundant coastal ocean methylotroph
journal, July 2008
- Giovannoni, Stephen J.; Hayakawa, Darin H.; Tripp, H. James
- Environmental Microbiology, Vol. 10, Issue 7
Polynucleobacter necessarius gen. nov., sp. nov., an Obligately Endosymbiotic Bacterium Living in the Cytoplasm of Euplotes aediculatus
journal, October 1987
- Heckmann, K.; Schmidt, H. J.
- International Journal of Systematic Bacteriology, Vol. 37, Issue 4
Ecotypes of Planktonic Actinobacteria with Identical 16S rRNA Genes Adapted to Thermal Niches in Temperate, Subtropical, and Tropical Freshwater Habitats
journal, February 2005
- Hahn, M. W.; Pockl, M.
- Applied and Environmental Microbiology, Vol. 71, Issue 2
DNA–DNA hybridization values and their relationship to whole-genome sequence similarities
journal, January 2007
- Klappenbach, Joel A.; Goris, Johan; Vandamme, Peter
- International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 1
Isolation of Strains Belonging to the Cosmopolitan Polynucleobacter necessarius Cluster from Freshwater Habitats Located in Three Climatic Zones
journal, September 2003
- Hahn, M. W.
- Applied and Environmental Microbiology, Vol. 69, Issue 9
Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria
journal, October 2013
- Boscaro, V.; Felletti, M.; Vannini, C.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 46
Ecological niche separation in the Polynucleobacter subclusters linked to quality of dissolved organic matter: a demonstration using a high sensitivity cultivation-based approach: Niche separation of Polynucleobacter communities
journal, July 2012
- Watanabe, Keiji; Komatsu, Nobuyuki; Kitamura, Tatsumi
- Environmental Microbiology, Vol. 14, Issue 9
Circumpolar synchrony in big river bacterioplankton
journal, November 2009
- Crump, Byron C.; Peterson, Bruce J.; Raymond, Peter A.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 50
Polynucleobacter cosmopolitanus sp. nov., free-living planktonic bacteria inhabiting freshwater lakes and rivers
journal, July 2009
- Hahn, M. W.; Lang, E.; Brandt, U.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 1
Complex Evolution of the Mismatch Repair System in Eukaryotes is Illuminated by Novel Archaeal Genomes
journal, January 2021
- Hofstatter, Paulo G.; Lahr, Daniel J. G.
- Journal of Molecular Evolution, Vol. 89, Issue 1-2
An SHR–SCR module specifies legume cortical cell fate to enable nodulation
journal, December 2020
- Dong, Wentao; Zhu, Yayun; Chang, Huizhong
- Nature, Vol. 589, Issue 7843
Alcohol pretreatment of stools effect on culturomics
journal, March 2020
- Afouda, Pamela; Hocquart, Marie; Pham, Thi-Phuong-Thao
- Scientific Reports, Vol. 10, Issue 1
The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign
text, January 2015
- Salcher, Michaela M.; Neuenschwander, Stefan M.; Posch, Thomas
- Nature Publishing Group
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
journal, May 2014
- Kim, M.; Oh, H. -S.; Park, S. -C.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 5
Works referencing / citing this record:
Polynucleobacter meluiroseus sp. nov., a bacterium isolated from a lake located in the mountains of the Mediterranean island of Corsica
journal, June 2018
- Pitt, Alexandra; Schmidt, Johanna; Lang, Elke
- International Journal of Systematic and Evolutionary Microbiology, Vol. 68, Issue 6
Polynucleobacter hirudinilacicola sp. nov. and Polynucleobacter campilacus sp. nov., both isolated from freshwater systems
journal, August 2018
- Hahn, Martin W.; Koll, Ulrike; Schmidt, Johanna
- International Journal of Systematic and Evolutionary Microbiology, Vol. 68, Issue 8
Polynucleobacter paneuropaeus sp. nov., characterized by six strains isolated from freshwater lakes located along a 3000 km north–south cross-section across Europe
journal, January 2019
- Hoetzinger, Matthias; Schmidt, Johanna; Pitt, Alexandra
- International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 1