skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: 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 » 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).« less

Authors:
 [1];  [1];  [2];  [3];  [3];  [4]
  1. Univ. of Innsbruck, Mondsee (Austria). ​Research Dept. for Limnology
  2. Kyambogo Univ., Kyambogo (Uganda). Dept. of Biological Sciences
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Univ. of Georgia, Athens, GA (United States). Department of Microbiology
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory-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

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. doi: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. doi: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}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 3 works
Citation information provided by
Web of Science

Save / Share:

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
  • DOI: 10.1186/s40793-015-0017-x

Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system
journal, April 2016


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
  • DOI: 10.1038/nature21031

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
  • DOI: 10.1016/j.mimet.2004.02.004

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
  • DOI: 10.1099/ijs.0.023929-0

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
  • DOI: 10.1128/AEM.02266-16

Members of a Readily Enriched  -Proteobacterial Clade Are Common in Surface Waters of a Humic Lake
journal, November 2003


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
  • DOI: 10.1186/s40793-015-0077-y

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
  • DOI: 10.1099/ijs.0.059774-0

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
  • DOI: 10.1099/ijsem.0.002096

Genome Sequence of a Freshwater Low-Nucleic-Acid-Content Bacterium, Betaproteobacterium Strain CB
journal, February 2013


Bacterial diversity in an arctic lake: a freshwater SAR11 cluster
journal, January 1996

  • Bahr, M.; Hobbie, Je; Sogin, Ml
  • Aquatic Microbial Ecology, Vol. 11
  • DOI: 10.3354/ame011271

Low Intraspecific Diversity in a Polynucleobacter Subcluster Population Numerically Dominating Bacterioplankton of a Freshwater Pond
journal, August 2005


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
  • DOI: 10.1038/ismej.2015.237

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
  • DOI: 10.1093/molbev/msw054

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
  • DOI: 10.1038/ismej.2015.55

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
  • DOI: 10.1099/ijs.0.031393-0

Genome sequence of the  -rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia
journal, July 2008


Ubiquity of Polynucleobacter necessarius ssp. asymbioticus in lentic freshwater habitats of a heterogenous 2000 km 2 area
journal, March 2010


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
  • DOI: 10.1099/ijs.0.017350-0

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
  • DOI: 10.1093/nar/gkr1044

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
  • DOI: 10.1038/s41559-017-0237-0

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
  • DOI: 10.1073/pnas.0409727102

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
  • DOI: 10.4056/sigs.2395367

The small genome of an abundant coastal ocean methylotroph
journal, July 2008


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
  • DOI: 10.1099/00207713-37-4-456

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
  • DOI: 10.1099/ijs.0.64483-0

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
  • DOI: 10.1073/pnas.1316687110

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
  • DOI: 10.1073/pnas.0906149106

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
  • DOI: 10.1099/ijs.0.010595-0