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

Title: Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae

Journal Article · · Standards in Genomic Sciences
 [1];  [1];  [2];  [3];  [3];  [3];  [4];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [5];  [5];  [6];  [7];  [8];  [9] more »;  [10];  [1];  [2];  [3];  [11];  [5];  [12];  [1];  [13];  [1] « less
  1. DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig (Germany)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States) ; Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States) ; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States) ; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  8. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  9. Jomo Kenyatta University of Agriculture and Technology, Nairobi (Kenya)
  10. Helmholtz Centre for Infection Research (HZI), Braunschweig (Germany)
  11. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Davis, CA (United States)
  12. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of Queensland, Brisbane (Australia)
  13. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
+ Show Author Affiliations

Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448T, were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
Work for Others (WFO); USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC05-00OR22725; AC02-05CH11231
OSTI ID:
1286834
Alternate ID(s):
OSTI ID: 1511412
Journal Information:
Standards in Genomic Sciences, Vol. 9, Issue 10; ISSN 1944-3277
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 44 works
Citation information provided by
Web of Science

References (95)

Zavarzinella formosa gen. nov., sp. nov., a novel stalked, Gemmata-like planctomycete from a Siberian peat bog journal February 2009
Parsimony, likelihood, and simplicity journal April 2003
The PVC superphylum: exceptions to the bacterial definition? journal August 2013
Phycisphaera mikurensis gen. nov., sp. nov., isolated from a marine alga, and proposal of Phycisphaeraceae fam. nov., Phycisphaerales ord. nov. and Phycisphaerae classis nov. in the phylum Planctomycetes journal January 2009
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis journal April 2000
Phylogenetic Systematics journal January 1965
Approved Lists of Bacterial Names journal January 1980
A Phylogenomic Approach to Resolve the Arthropod Tree of Life journal June 2010
Planktonic microbial community composition across steep physical/chemical gradients in permanently ice-covered Lake Bonney, Antarctica journal March 2006
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs journal September 1997
The Information Content of the Phylogenetic System journal December 1979
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. journal June 1990
Assignment of the genera Planctomyces and Pirella to a new family Planctomycetaceae fam. nov. and description of the order Planctomycetales ord. nov. journal October 1986
Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses journal October 2010
Genome sequence-based species delimitation with confidence intervals and improved distance functions journal January 2013
Prodigal: prokaryotic gene recognition and translation initiation site identification journal March 2010
Cell compartmentalisation in planctomycetes: novel types of structural organisation for the bacterial cell journal June 2001
Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age journal February 2014
VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R journal January 2011
Singulisphaera acidiphila gen. nov., sp. nov., a non-filamentous, Isosphaera-like planctomycete from acidic northern wetlands journal May 2008
Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21T) journal October 2011
An empirical test of the midpoint rooting method: A TEST FOR THE MIDPOINT ROOTING METHOD journal December 2007
Assignment of ATCC 27377 to Pirella gen. nov. as Pirella staleyi comb. nov. journal October 1984
Taxonomic heterogeneity within the Planctomycetales as derived by DNA-DNA hybridization, description of Rhodopirellula baltica gen. nov., sp. nov., transfer of Pirellula marina to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov. and emended description of the genus Pirellula journal September 2004
Planctomyces brasiliensis sp. nov., a Halotolerant Bacterium from a Salt Pit journal October 1989
Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1T), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta journal May 2012
Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects journal May 2013
Singulisphaera rosea sp. nov., a planctomycete from acidic Sphagnum peat, and emended description of the genus Singulisphaera journal February 2011
Re-interpretation of the evidence for the PVC cell plan supports a Gram-negative origin journal December 2013
Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs journal January 2010
Complete genome sequence of Planctomyces limnophilus type strain (Mü 290T) journal July 2010
Genomic Evolution of 11 Type Strains within Family Planctomycetaceae journal January 2014
A Rapid Bootstrap Algorithm for the RAxML Web Servers journal October 2008
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata journal December 2011
Complete genome sequence of Pirellula staleyi type strain (ATCC 27377T) journal December 2009
An efficient algorithm for large-scale detection of protein families journal April 2002
MUSCLE: multiple sequence alignment with high accuracy and high throughput journal March 2004
Phylogenetic diversity, polyamine pattern and DNA base composition of members of the order Planctomycetales journal April 1999
Schlesneria paludicola gen. nov., sp. nov., the first acidophilic member of the order Planctomycetales, from Sphagnum-dominated boreal wetlands journal November 2007
The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation journal December 2012
IMG ER: a system for microbial genome annotation expert review and curation journal June 2009
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea journal December 2009
Chemical composition of the peptidoglycan-free cell envelopes of budding bacteria of the Pirella/Planctomyces group journal September 1986
Planctomyces stranskae (ex Wawrik 1952) sp. nov., nom. rev. and Planctomyces guttaeformis (ex Hortobagyi 1965) sp. nov., nom. rev. journal October 1984
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes journal July 2009
Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology journal December 1971
The DNA Bank Network: The Start from a German Initiative journal March 2011
Characterization of Planctomyces limnophilus and Development of Genetic Tools for Its Manipulation Establish It as a Model Species for the Phylum Planctomycetes journal July 2011
Codivergence of Mycoviruses with Their Hosts journal July 2011
From genome mining to phenotypic microarrays: Planctomycetes as source for novel bioactive molecules journal August 2013
“Who Has First Observed Planctomyces” journal April 2005
Novel Insights into the Diversity of Catabolic Metabolism from Ten Haloarchaeal Genomes journal May 2011
Chemotaxonomic Investigation of Various Prosthecate and/or Budding Bacteria journal April 1993
Complete genome sequence of Isosphaera pallida type strain (IS1BT) journal February 2011
Complete genome sequence of Kytococcus sedentarius type strain (541T) journal July 2009
Planctomyces limnophilus sp. nov., a Stalked and Budding Bacterium from Freshwater journal December 1985
Gene Ontology: tool for the unification of biology journal May 2000
The Information Content of the Phylogenetic System journal December 1979
The Genomic Standards Consortium journal June 2011
Phylogenetic Systematics text January 2000
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models journal August 2006
The budding bacteria, Pirellula and Planctomyces, with atypical 16S rRNA and absence of peptidoglycan, show eubacterial phospholipids and uniquely high proportions of long chain beta-hydroxy fatty acids in the lipopolysaccharide lipid A journal January 1988
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes journal September 2003
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs journal February 2008
Blastopirellula cremea sp. nov., isolated from a dead ark clam journal November 2012
opm: an R package for analysing OmniLog(R) phenotype microarray data journal June 2013
Planctomyces maris sp. nov.: a Marine Isolate of the Planctomyces-Blastocaulis Group of Budding Bacteria journal November 1976
Genome-Scale Phylogeny and the Detection of Systematic Biases journal July 2004
Transposon Mutagenesis of Planctomyces limnophilus and Analysis of a pckA Mutant collection January 2012
Evolutionary trees from DNA sequences: A maximum likelihood approach journal November 1981
Isosphaera pallida, gen. and comb. nov., a gliding, budding eubacterium from hot springs journal April 1987
How Many Bootstrap Replicates Are Necessary? journal March 2010
Planctomyces maris sp. nov., nom. rev. journal October 1980
How Many Bootstrap Replicates Are Necessary? book January 2009
Aquisphaera giovannonii gen. nov., sp. nov., a planctomycete isolated from a freshwater aquarium journal January 2011
The minimum information about a genome sequence (MIGS) specification journal May 2008
RASCAL: rapid scanning and correction of multiple sequence alignments journal June 2003
Comparative analysis of ribonuclease P RNA of the planctomycetes journal July 2004
Pirella marina sp. nov., a budding, peptidoglycan-less bacterium from brackish water journal October 1986
Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology journal December 1971
Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison journal January 2010
En route to a genome-based classification of Archaea and Bacteria? journal June 2010
Isolation and molecular identification of planctomycete bacteria from postlarvae of the giant tiger prawn, Penaeus monodon journal January 1997
Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2T) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010. journal September 2011
Expression of sulfatases in Rhodopirellula baltica and the diversity of sulfatases in the genus Rhodopirellula journal March 2013
The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79 journal January 2005
Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB: List No. 23 journal April 1987
Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB: List No. 32 journal January 1990
Telmatocola sphagniphila gen. nov., sp. nov., a Novel Dendriform Planctomycete from Northern Wetlands journal January 2012
The Genome Sequence of Methanohalophilus mahii SLP T Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments journal January 2010
Phylogenetic Systematics reference-book June 2016
Gemmata obscuriglobus, a new genus and species of the budding bacteria journal May 1984
Genetic basis for the establishment of endosymbiosis in Paramecium journal January 2019
Dietary palmitic acid promotes a prometastatic memory via Schwann cells journal November 2021
Transposon Mutagenesis of Planctomyces limnophilus and Analysis of a pckA Mutant journal July 2012

Cited By (41)

Global and Targeted Lipid Analysis of Gemmata obscuriglobus Reveals the Presence of Lipopolysaccharide, a Signature of the Classical Gram-Negative Outer Membrane journal October 2015
Biochar-induced changes in metal mobility and uptake by perennial plants in a ferralsol of Brazil’s Atlantic forest journal July 2019
Comparative genomics of biotechnologically important yeasts journal August 2016
On the maverick Planctomycetes journal July 2018
Limnoglobus roseus gen. nov., sp. nov., a novel freshwater planctomycete with a giant genome from the family Gemmataceae
  • Kulichevskaya, Irina S.; Naumoff, Daniil G.; Miroshnikov, Kirill K.
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 2 https://doi.org/10.1099/ijsem.0.003904
journal February 2020
Genome-Based Taxonomic Classification of Bacteroidetes journal December 2016
Rubinisphaera italica sp. nov. isolated from a hydrothermal area in the Tyrrhenian Sea close to the volcanic island Panarea journal November 2019
Fuerstia marisgermanicae gen. nov., sp. nov., an Unusual Member of the Phylum Planctomycetes from the German Wadden Sea journal December 2016
Pink‐ and orange‐pigmented Planctomycetes produce saproxanthin‐type carotenoids including a rare C 45 carotenoid journal October 2019
Comparative Genomics of Four Isosphaeraceae Planctomycetes: A Common Pool of Plasmids and Glycoside Hydrolase Genes Shared by Paludisphaera borealis PX4T, Isosphaera pallida IS1BT, Singulisphaera acidiphila DSM 18658T, and Strain SH-PL62 journal March 2017
Alienimonas californiensis gen. nov. sp. nov., a novel Planctomycete isolated from the kelp forest in Monterey Bay journal December 2019
100‐year‐old enigma solved: identification, genomic characterization and biogeography of the yet uncultured Planctomyces bekefii journal November 2019
Tuwongella immobilis gen. nov., sp. nov., a novel non-motile bacterium within the phylum Planctomycetes journal December 2017
Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential journal January 2018
Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T journal December 2017
Assembly of a complete genome sequence for Gemmata obscuriglobus reveals a novel prokaryotic rRNA operon gene architecture journal May 2018
Exemplar Abstract for Planctomyces brasiliensis Schlesner 1990 and Rubinisphaera brasiliensis (Schlesner 1990) Scheuner et al. 2015. dataset January 2013
Exemplar Abstract for Planctomyces limnophilus Hirsch and M??ller 1986, Planctopirus limnophila corrig. (Hirsch and M??ller 1986) Scheuner et al. 2015 and Planctopirus limnophilus (sic) (Hirsch and M??ller 1986) Scheuner et al. 2015. dataset January 2013
Nomenclature Abstract for Singulisphaera acidiphila Kulichevskaya et al. 2008 emend. Scheuner et al. 2014. dataset January 2013
Nomenclature Abstract for Rubinisphaera Scheuner et al. 2015 emend. Kallscheuer et al. 2020. dataset January 2015
Nomenclature Abstract for Rubinisphaera brasiliensis (Schlesner 1990) Scheuner et al. 2015. dataset January 2015
Nomenclature Abstract for Planctopirus Scheuner et al. 2015. dataset January 2015
Nomenclature Abstract for Planctopirus limnophilus (sic) (Hirsch and Muller 1986) Scheuner et al. 2015. dataset January 2015
Nomenclature Abstract for Gimesia Scheuner et al. 2015 emend. Kumar et al. 2020. dataset January 2015
Nomenclature Abstract for Gimesia maris (Bauld and Staley 1980) Scheuner et al. 2015. dataset January 2015
Nomenclature Abstract for Planctopirus limnophila corrig. (Hirsch and Muller 1986) Scheuner et al. 2015. dataset January 2015
Nomenclature Abstract for Planctomycetales Schlesner and Stackebrandt 1987 emend. Dedysh et al. 2020. dataset January 2013
Nomenclature Abstract for Planctomycetaceae Schlesner and Stackebrandt 1987 emend. Dedysh et al. 2020. dataset January 2013
Nomenclature Abstract for Planctomyces brasiliensis Schlesner 1990. dataset January 2013
Nomenclature Abstract for Planctomyces limnophilus Hirsch and Muller 1986. dataset January 2013
Nomenclature Abstract for Planctomyces maris (ex Bauld and Staley 1976) Bauld and Staley 1980. dataset January 2013
Nomenclature Abstract for Gemmata Franzmann and Skerman 1985 emend. Scheuner et al. 2014. dataset January 2013
Taxonomic Abstract for the genera. dataset January 2015
Taxonomic Abstract for the species. dataset January 2015
Taxonomic Abstract for the genera. dataset January 2015
Taxonomic Abstract for the species. dataset January 2015
Taxonomic Abstract for the genera. dataset January 2015
Taxonomic Abstract for the species. dataset January 2015
Taxonomic Abstract for the orders. dataset January 2013
Taxonomic Abstract for the families. dataset January 2013
A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data journal April 2015

Figures / Tables (14)

Figure 1(p. 3)figure Figure 1
Figure 2(p. 3)figure Figure 2
Table 1(p. 4)table Table 1
Table 2(p. 5)table Table 2
Table 3(p. 6)table Table 3
Figure 3(p. 7)figure Figure 3
Table 4(p. 8)table Table 4
Figure 4(p. 9)figure Figure 4
Table 5(p. 9)table Table 5
Table 6(p. 10)table Table 6
Figure 5(p. 11)figure Figure 5
Figure 6(p. 12)figure Figure 6
Table 7(p. 13)table Table 7
Table 8(p. 13)table Table 8

Similar Records

Description of Freudenthalidium gen. nov. and Halluxium gen. nov. to Formally Recognize Clades Fr3 and H as Genera in the Family Symbiodiniaceae (Dinophyceae)
Journal Article · Thu Apr 30 00:00:00 EDT 2020 · Journal of Phycology · OSTI ID:1286834
+5 more
Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae
Journal Article · Tue Dec 19 00:00:00 EST 2017 · Frontiers in Microbiology · OSTI ID:1286834
+7 more
Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2T) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010
Journal Article · Sat Jan 01 00:00:00 EST 2011 · Standards in Genomic Sciences · OSTI ID:1286834
+30 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Non-peptidoglycan bacteria
Stalked bacteria
Halotolerant
Gram-negative
Taxonomic descriptions
Planctomycetales
Planctomycetes
GEBA