Verrucomicrobia

14,000,000 Leading Edge Experts on the ideXlab platform

Scan Science and Technology

Contact Leading Edge Experts & Companies

Scan Science and Technology

Contact Leading Edge Experts & Companies

The Experts below are selected from a list of 5076 Experts worldwide ranked by ideXlab platform

Akira Yokota - One of the best experts on this subject based on the ideXlab platform.

  • cerasicoccus maritimus sp nov and cerasicoccus frondis sp nov two peptidoglycan less marine Verrucomicrobial species and description of Verrucomicrobia phyl nov nom rev
    Journal of General and Applied Microbiology, 2010
    Co-Authors: Jaewoo Yoon, Yoshihide Matsuo, Satoru Matsuda, Hiroaki Kasai, Akira Yokota
    Abstract:

    Three Gram-negative, pale-pink-pigmented, spherical, chemoheterotrophic bacteria were isolated from seawater and a dystrophic leaf in the Republic of Palau. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the novel isolates YM31-114T, YM31-066T and YM31-067 shared approximately 97-100% sequence similarity with members of the genus Cerasicoccus of the family Puniceicoccaceae within the phylumVerrucomicrobia.’ The hybridization values for DNA-DNA relatedness between the novel isolates and Cerasicoccus arenae YM26-026T were less than 70%, which is accepted as a phylogenetic definition of a species. β-Lactam antibiotic susceptibility test and amino acid analysis of cell-wall hydrolysates revealed that the novel isolates did not contain muramic acid or diaminopimelic acid in their cell walls, suggesting that these strains lack peptidoglycan. The DNA G+C contents of the three strains were 55-56 mol%; MK-7 was the major menaquinone. The presence of C14:0 and C18:1ω9c as the major cellular fatty acids supported the identification of the novel isolates as members of the genus Cerasicoccus. On the basis of polyphasic taxonomic evidence, it was concluded that these strains should be classified as representing two novel, separate species in the genus Cerasicoccus within the phylumVerrucomicrobia,’ for which the names Cerasicoccus maritimus sp. nov. (type strain YM31-114T=MBIC24844T) and Cerasicoccus frondis sp. nov. (type strain YM31-066T=MBIC24796T) are proposed. Proposal for designation of the Verrucomicrobia phyl. nov., nom. rev. is also presented.

  • description of persicirhabdus sediminis gen nov sp nov roseibacillus ishigakijimensis gen nov sp nov roseibacillus ponti sp nov roseibacillus persicicus sp nov luteolibacter pohnpeiensis gen nov sp nov and luteolibacter algae sp nov six marine members of the phylum Verrucomicrobia and emended descriptions of the class Verrucomicrobiae the order Verrucomicrobiales and the family Verrucomicrobiaceae
    International Journal of Systematic and Evolutionary Microbiology, 2008
    Co-Authors: Jaewoo Yoon, Yoshihide Matsuo, Kyoko Adachi, Midori Nozawa, Satoru Matsuda, Hiroaki Kasai, Akira Yokota
    Abstract:

    Ten pale-pink- and pale-yellow-pigmented, Gram-negative, non-motile, rod-shaped, chemoheterotrophic bacteria designated strains YM20-087T, YM21-151, MN1-741T, YM27-120T, YM26-010T, YM24-184, YM20-122, A4T-83T, A5J-41-2T and A5J-40 were isolated from various marine environments and were subjected to a polyphasic taxonomic investigation. Phylogenetic analyses based on 16S rRNA gene sequences indicated that these isolates belonged to the phylumVerrucomicrobia’ (subdivision 1) and represented three independent lineages that were distinct from species of genera of the family Verrucomicrobiaceae with validly published names. The cell-wall peptidoglycan of these strains contained muramic acid and meso-diaminopimelic acid. Strains MN1-741T, YM27-120T, YM26-010T, YM24-184 and YM20-122 produced pinkish carotenoid pigments. On the basis of polyphasic taxonomic evidence, it was concluded that these strains should be classified within three new genera, Persicirhabdus gen. nov. (with one species, the type species Persicirhabdus sediminis sp. nov.), Roseibacillus gen. nov. (with three species; type species Roseibacillus ishigakijimensis sp. nov.) and Luteolibacter gen. nov. (with two species; type species Luteolibacter pohnpeiensis sp. nov.), of the family Verrucomicrobiaceae within the phylumVerrucomicrobia’. The names Persicirhabdus sediminis gen. nov., sp. nov. (type strain YM20-087T =MBIC08313T =KCTC 22039T), Roseibacillus ishigakijimensis gen. nov., sp. nov. (type strain MN1-741T =MBIC08315T =KCTC 12986T), Roseibacillus ponti sp. nov. (type strain YM27-120T =MBIC08316T =KCTC 12987T), Roseibacillus persicicus sp. nov. (type strain YM26-010T =MBIC08317T =KCTC 12988T), Luteolibacter pohnpeiensis gen. nov., sp. nov. (type strain A4T-83T =MBIC08322T =KCTC 22041T) and Luteolibacter algae sp. nov. (type strain A5J-41-2T =MBIC08320T =KCTC 22040T) are therefore proposed. Emended descriptions of the class Verrucomicrobiae, the order Verrucomicrobiales and the family Verrucomicrobiaceae are also presented.

  • cerasicoccus arenae gen nov sp nov a carotenoid producing marine representative of the family puniceicoccaceae within the phylum Verrucomicrobia isolated from marine sand
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Jaewoo Yoon, Yoshihide Matsuo, Kyoko Adachi, Satoru Matsuda, Hiroaki Kasai, Akira Yokota
    Abstract:

    A polyphasic taxonomic study was performed on strain YM26-026T, which was isolated from acid-treated sediment in Kamaishi, Japan. The bacterial cells were pale-pink-pigmented, Gram-negative, obligately aerobic, non-spore-forming, spherical and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel isolate was a member of the phylumVerrucomicrobia’ and shared approximately 84–87 % sequence similarity with strains of the class Opitutae that have been cultivated to date. Strain YM26-026T produced pale-pink pigments of carotenoid. β-Lactam antibiotic susceptibility tests and amino acid analysis of cell-wall hydrolysates indicated that the novel isolate did not contain muramic acid or diaminopimelic acid in the cell wall, suggesting that the strain lacks peptidoglycan. The G+C content of the DNA of strain YM26-026T was 54.0 mol%. Menaquinone-7 was the major quinone and C14 : 0 and C18 : 1 ω9c were the major fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that strain YM26-026T represents a new genus of the family Puniceicoccaceae within the phylumVerrucomicrobia’, for which the name Cerasicoccus arenae gen. nov., sp. nov. is proposed. The type strain is YM26-026T (=MBIC08280T=KCTC 12870T).

  • coraliomargarita akajimensis gen nov sp nov a novel member of the phylum Verrucomicrobia isolated from seawater in japan
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Jaewoo Yoon, Satoru Matsuda, Hiroaki Kasai, Mina Yasumotohirose, Atsuko Katsuta, Hiroshi Sekiguchi, Akira Yokota
    Abstract:

    An obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium, designated strain 04OKA010-24(T), was isolated from seawater surrounding the hard coral Galaxea fascicularis L., collected at Majanohama, Akajima, Japan, and was subjected to a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that the new strain represented a member of the phylum 'Verrucomicrobia' and shared 84-95 % sequence similarity with cultivated strains of 'Verrucomicrobia' subdivision 4. Amino acid analysis of the cell-wall hydrolysate indicated the absence of muramic acid and diaminopimelic acid, which suggested that the strain did not contain peptidoglycan in the cell wall. The G+C content of the DNA was 53.9 mol%. MK-7 was the major menaquinone and C(14 : 0), C(18 : 1)omega9c and C(18 : 0) were the major fatty acids. On the basis of these data, it was concluded that strain 04OKA010-24(T) represents a novel species in a new genus in subdivision 4 of the phylum 'Verrucomicrobia', for which the name Coraliomargarita akajimensis gen. nov., sp. nov. is proposed. The type strain of Coraliomargarita akajimensis is 04OKA010-24(T) (=MBIC06463(T)=IAM 15411(T)=KCTC 12865(T)).

Jorge L M Rodrigues - One of the best experts on this subject based on the ideXlab platform.

  • second correction for wertz et al genomic and physiological characterization of the Verrucomicrobia isolate geminisphaera colitermitum gen nov sp nov reveals microaerophily and nitrogen fixation genes
    Applied and Environmental Microbiology, 2017
    Co-Authors: John T Wertz, Thomas M Schmidt, Eunji Kim, John A Breznak, Jorge L M Rodrigues
    Abstract:

    Volume 78, no. 5, p. 1544–1555, 2012, [https://doi.org/10.1128/AEM.06466-11][1], and volume 83, no. 13, e00987-17, 2017, [https://doi.org/10.1128/AEM.00987-17][2]. The name Diplosphaera, the proposed genus name for Verrucomicrobia strain TAV2, was previously used for a microalga. Subsequently, we

  • Forest-to-pasture conversion increases the diversity of the phylum Verrucomicrobia in Amazon rainforest soils.
    Frontiers in microbiology, 2015
    Co-Authors: Kshitij Ranjan, Rebecca C Mueller, Brendan J M Bohannan, Fabiana S Paula, Klaus Nüsslein, Ederson Da Conceição Jesus, Karina Cenciani, Jorge L M Rodrigues
    Abstract:

    The Amazon rainforest is well known for its rich plant and animal diversity, but its bacterial diversity is virtually unexplored. Due to ongoing and widespread deforestation followed by conversion to agriculture, there is an urgent need to quantify the soil biological diversity within this tropical ecosystem. Given the abundance of the phylum Verrucomicrobia in soils, we targeted this group to examine its response to forest-to-pasture conversion. Both taxonomic and phylogenetic diversities were higher for pasture in comparison to primary and secondary forests. The community composition of Verrucomicrobia in pasture soils was significantly different from those of forests, with a 11.6% increase in the number of sequences belonging to subphylum 3 and a proportional decrease in sequences belonging to the class Spartobacteria. Based on 99% operational taxonomic unit identity, 40% of the sequences have not been detected in previous studies, underscoring the limited knowledge regarding the diversity of microorganisms in tropical ecosystems. The abundance of Verrucomicrobia, measured with quantitative PCR, was strongly correlated with soil C content (r = 0.80, P = 0.0016), indicating their importance in metabolizing plant-derived carbon compounds in soils.

  • genomic and physiological characterization of the Verrucomicrobia isolate diplosphaera colitermitum gen nov sp nov reveals microaerophily and nitrogen fixation genes
    Applied and Environmental Microbiology, 2012
    Co-Authors: John T Wertz, Thomas M Schmidt, Eunji Kim, John A Breznak, Jorge L M Rodrigues
    Abstract:

    Previously we reported the cultivation of novel Verrucomicrobia, including strain TAV2 (93% 16S rRNA gene identity to its nearest cultivated representative, Opitutus terreae PB90-1) from the gut of the termite Reticulitermes flavipes. To gain better insight into the Verrucomicrobia as a whole and understand the role of Verrucomicrobia within the termite gut ecosystem, we analyzed a draft genome and undertook a physiological characterization of TAV2. Strain TAV2 is an autochthonous member of the R. flavipes gut microbiota and groups phylogenetically among diverse Verrucomicrobia from R. flavipes and other termites that are represented by 16S rRNA gene sequences alone. TAV2 is a microaerophile, possessing a high-affinity cbb3-type terminal oxidase-encoding gene and exhibiting an optimum growth rate between 2 and 8% (vol/vol) oxygen. It has the genetic potential to degrade cellulose, an important function within termite guts, but its in vitro substrate utilization spectrum was limited to starch and a few mono- and disaccharides. Growth occurred on nitrogen-free medium, and genomic screening revealed genes for dinitrogenases, heretofore detected in only a few members of the Verrucomicrobia. This represents the first (i) characterization of a Verrucomicrobial species from the termite gut, (ii) report of nif and anf genes in a nonacidophilic Verrucomicrobial species, and (iii) description of a microaerophilic genotype and phenotype in this phylum of bacteria. The genetic and physiological distinctiveness of TAV2 supports its recognition as the type strain of a new genus and species, for which the name Diplosphaera colitermitum gen. nov., sp. nov., is proposed.

  • phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil
    FEMS Microbiology Ecology, 2010
    Co-Authors: Anna M Kielak, Jorge L M Rodrigues, Eiko E Kuramae, Patrick S G Chain, Johannes A Van Veen, George A Kowalchuk
    Abstract:

    The bacterial phylum Verrucomicrobia has a widespread distribution, and is known to be one of the most common and diverse phyla in soil habitats. However, members of this phylum have typically been recalcitrant to cultivation methods, hampering the study of this presumably important bacterial group. In this study, we examine the phylogenetic diversity of the Verrucomicrobia in a former agricultural field and gain access to genomic information via a metagenomic approach. We examined Verrucomicrobia-like 16S rRNA gene sequences recovered from general bacterial and phylum-specific libraries, revealing a dominance of subdivisions 1 and 2. A PCR-based screening method was developed to identify inserts containing Verrucomicrobial 16S rRNA genes within a large-insert metagenomic library, and on screening of 28,800 clones, four fosmids were identified as containing Verrucomicrobial genomic DNA. Full-length sequencing of fosmid inserts and gene annotation identified a total of 98 ORFs, representing a range of functions. No conservation of gene order was observed adjacent to the ribosomal operons. Fosmid inserts were further analyzed for tetranucleotide frequencies to identify remnants of past horizontal gene transfer events. The metagenomic approach utilized proved to be suitable for the recovery of Verrucomicrobial genomic DNA, thereby providing a window into the genomes of members of this important, yet poorly characterized, bacterial phylum.

Jaewoo Yoon - One of the best experts on this subject based on the ideXlab platform.

  • cerasicoccus maritimus sp nov and cerasicoccus frondis sp nov two peptidoglycan less marine Verrucomicrobial species and description of Verrucomicrobia phyl nov nom rev
    Journal of General and Applied Microbiology, 2010
    Co-Authors: Jaewoo Yoon, Yoshihide Matsuo, Satoru Matsuda, Hiroaki Kasai, Akira Yokota
    Abstract:

    Three Gram-negative, pale-pink-pigmented, spherical, chemoheterotrophic bacteria were isolated from seawater and a dystrophic leaf in the Republic of Palau. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the novel isolates YM31-114T, YM31-066T and YM31-067 shared approximately 97-100% sequence similarity with members of the genus Cerasicoccus of the family Puniceicoccaceae within the phylumVerrucomicrobia.’ The hybridization values for DNA-DNA relatedness between the novel isolates and Cerasicoccus arenae YM26-026T were less than 70%, which is accepted as a phylogenetic definition of a species. β-Lactam antibiotic susceptibility test and amino acid analysis of cell-wall hydrolysates revealed that the novel isolates did not contain muramic acid or diaminopimelic acid in their cell walls, suggesting that these strains lack peptidoglycan. The DNA G+C contents of the three strains were 55-56 mol%; MK-7 was the major menaquinone. The presence of C14:0 and C18:1ω9c as the major cellular fatty acids supported the identification of the novel isolates as members of the genus Cerasicoccus. On the basis of polyphasic taxonomic evidence, it was concluded that these strains should be classified as representing two novel, separate species in the genus Cerasicoccus within the phylumVerrucomicrobia,’ for which the names Cerasicoccus maritimus sp. nov. (type strain YM31-114T=MBIC24844T) and Cerasicoccus frondis sp. nov. (type strain YM31-066T=MBIC24796T) are proposed. Proposal for designation of the Verrucomicrobia phyl. nov., nom. rev. is also presented.

  • description of persicirhabdus sediminis gen nov sp nov roseibacillus ishigakijimensis gen nov sp nov roseibacillus ponti sp nov roseibacillus persicicus sp nov luteolibacter pohnpeiensis gen nov sp nov and luteolibacter algae sp nov six marine members of the phylum Verrucomicrobia and emended descriptions of the class Verrucomicrobiae the order Verrucomicrobiales and the family Verrucomicrobiaceae
    International Journal of Systematic and Evolutionary Microbiology, 2008
    Co-Authors: Jaewoo Yoon, Yoshihide Matsuo, Kyoko Adachi, Midori Nozawa, Satoru Matsuda, Hiroaki Kasai, Akira Yokota
    Abstract:

    Ten pale-pink- and pale-yellow-pigmented, Gram-negative, non-motile, rod-shaped, chemoheterotrophic bacteria designated strains YM20-087T, YM21-151, MN1-741T, YM27-120T, YM26-010T, YM24-184, YM20-122, A4T-83T, A5J-41-2T and A5J-40 were isolated from various marine environments and were subjected to a polyphasic taxonomic investigation. Phylogenetic analyses based on 16S rRNA gene sequences indicated that these isolates belonged to the phylumVerrucomicrobia’ (subdivision 1) and represented three independent lineages that were distinct from species of genera of the family Verrucomicrobiaceae with validly published names. The cell-wall peptidoglycan of these strains contained muramic acid and meso-diaminopimelic acid. Strains MN1-741T, YM27-120T, YM26-010T, YM24-184 and YM20-122 produced pinkish carotenoid pigments. On the basis of polyphasic taxonomic evidence, it was concluded that these strains should be classified within three new genera, Persicirhabdus gen. nov. (with one species, the type species Persicirhabdus sediminis sp. nov.), Roseibacillus gen. nov. (with three species; type species Roseibacillus ishigakijimensis sp. nov.) and Luteolibacter gen. nov. (with two species; type species Luteolibacter pohnpeiensis sp. nov.), of the family Verrucomicrobiaceae within the phylumVerrucomicrobia’. The names Persicirhabdus sediminis gen. nov., sp. nov. (type strain YM20-087T =MBIC08313T =KCTC 22039T), Roseibacillus ishigakijimensis gen. nov., sp. nov. (type strain MN1-741T =MBIC08315T =KCTC 12986T), Roseibacillus ponti sp. nov. (type strain YM27-120T =MBIC08316T =KCTC 12987T), Roseibacillus persicicus sp. nov. (type strain YM26-010T =MBIC08317T =KCTC 12988T), Luteolibacter pohnpeiensis gen. nov., sp. nov. (type strain A4T-83T =MBIC08322T =KCTC 22041T) and Luteolibacter algae sp. nov. (type strain A5J-41-2T =MBIC08320T =KCTC 22040T) are therefore proposed. Emended descriptions of the class Verrucomicrobiae, the order Verrucomicrobiales and the family Verrucomicrobiaceae are also presented.

  • cerasicoccus arenae gen nov sp nov a carotenoid producing marine representative of the family puniceicoccaceae within the phylum Verrucomicrobia isolated from marine sand
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Jaewoo Yoon, Yoshihide Matsuo, Kyoko Adachi, Satoru Matsuda, Hiroaki Kasai, Akira Yokota
    Abstract:

    A polyphasic taxonomic study was performed on strain YM26-026T, which was isolated from acid-treated sediment in Kamaishi, Japan. The bacterial cells were pale-pink-pigmented, Gram-negative, obligately aerobic, non-spore-forming, spherical and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel isolate was a member of the phylumVerrucomicrobia’ and shared approximately 84–87 % sequence similarity with strains of the class Opitutae that have been cultivated to date. Strain YM26-026T produced pale-pink pigments of carotenoid. β-Lactam antibiotic susceptibility tests and amino acid analysis of cell-wall hydrolysates indicated that the novel isolate did not contain muramic acid or diaminopimelic acid in the cell wall, suggesting that the strain lacks peptidoglycan. The G+C content of the DNA of strain YM26-026T was 54.0 mol%. Menaquinone-7 was the major quinone and C14 : 0 and C18 : 1 ω9c were the major fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that strain YM26-026T represents a new genus of the family Puniceicoccaceae within the phylumVerrucomicrobia’, for which the name Cerasicoccus arenae gen. nov., sp. nov. is proposed. The type strain is YM26-026T (=MBIC08280T=KCTC 12870T).

  • coraliomargarita akajimensis gen nov sp nov a novel member of the phylum Verrucomicrobia isolated from seawater in japan
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Jaewoo Yoon, Satoru Matsuda, Hiroaki Kasai, Mina Yasumotohirose, Atsuko Katsuta, Hiroshi Sekiguchi, Akira Yokota
    Abstract:

    An obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium, designated strain 04OKA010-24(T), was isolated from seawater surrounding the hard coral Galaxea fascicularis L., collected at Majanohama, Akajima, Japan, and was subjected to a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that the new strain represented a member of the phylum 'Verrucomicrobia' and shared 84-95 % sequence similarity with cultivated strains of 'Verrucomicrobia' subdivision 4. Amino acid analysis of the cell-wall hydrolysate indicated the absence of muramic acid and diaminopimelic acid, which suggested that the strain did not contain peptidoglycan in the cell wall. The G+C content of the DNA was 53.9 mol%. MK-7 was the major menaquinone and C(14 : 0), C(18 : 1)omega9c and C(18 : 0) were the major fatty acids. On the basis of these data, it was concluded that strain 04OKA010-24(T) represents a novel species in a new genus in subdivision 4 of the phylum 'Verrucomicrobia', for which the name Coraliomargarita akajimensis gen. nov., sp. nov. is proposed. The type strain of Coraliomargarita akajimensis is 04OKA010-24(T) (=MBIC06463(T)=IAM 15411(T)=KCTC 12865(T)).

Ute Hentschel - One of the best experts on this subject based on the ideXlab platform.

  • rubritalea marina gen nov sp nov a marine representative of the phylum Verrucomicrobia isolated from a sponge porifera
    International Journal of Systematic and Evolutionary Microbiology, 2006
    Co-Authors: Matthias Scheuermayer, Tobias A M Gulder, Gerhard Bringmann, Ute Hentschel
    Abstract:

    A marine bacterium, strain Pol012T, was isolated from the Mediterranean sponge Axinella polypoides and subsequently characterized as belonging to subphylum 1 of the phylumVerrucomicrobia’. Strain Pol012T was non-motile, Gram-negative, coccoid or rod-shaped and red in colour. The menaquinones MK-8 and MK-9 were detected. The G+C content of the genomic DNA was 50.9 mol%. Growth was possible at temperatures between 8 and 30 °C and at pH values between 6.8 and 8.2. The closest cultured relative of strain Pol012T was Akkermansia muciniphila (83 % sequence similarity), while the closest environmental 16S rRNA gene sequence was the marine clone Arctic96BD-2 (95 % sequence similarity). Strain Pol012T is the first marine pure-culture representative of ‘Verrucomicrobia’ subphylum 1 and represents a novel genus and species, for which the name Rubritalea marina gen. nov., sp. nov. is proposed. The type strain is Pol012T (=DSM 177716T=CIP 108984T). The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain Pol012T is DQ302104, and those for Verrucomicrobial 16S rRNA gene sequences from sponges and seawater are DQ302105–DQ302120.

  • rubritalea marina gen nov sp nov a marine representative of the phylum Verrucomicrobia isolated from a sponge porifera
    International Journal of Systematic and Evolutionary Microbiology, 2006
    Co-Authors: Matthias Scheuermayer, Tobias A M Gulder, Gerhard Bringmann, Ute Hentschel
    Abstract:

    A marine bacterium, strain Pol012(T), was isolated from the Mediterranean sponge Axinella polypoides and subsequently characterized as belonging to subphylum 1 of the phylum 'Verrucomicrobia'. Strain Pol012(T) was non-motile, Gram-negative, coccoid or rod-shaped and red in colour. The menaquinones MK-8 and MK-9 were detected. The G+C content of the genomic DNA was 50.9 mol%. Growth was possible at temperatures between 8 and 30 degrees C and at pH values between 6.8 and 8.2. The closest cultured relative of strain Pol012(T) was Akkermansia muciniphila (83 % sequence similarity), while the closest environmental 16S rRNA gene sequence was the marine clone Arctic96BD-2 (95 % sequence similarity). Strain Pol012(T) is the first marine pure-culture representative of 'Verrucomicrobia' subphylum 1 and represents a novel genus and species, for which the name Rubritalea marina gen. nov., sp. nov. is proposed. The type strain is Pol012(T) (=DSM 177716(T)=CIP 108984(T)).

James T. Staley - One of the best experts on this subject based on the ideXlab platform.

  • Phylum Verrucomicrobia representatives share a compartmentalized cell plan with members of bacterial phylum Planctomycetes
    BMC microbiology, 2009
    Co-Authors: Kuo-chang Lee, Parveen Sangwan, Richard I Webb, Peter H Janssen, James T. Staley, Tony Romeo, John A. Fuerst
    Abstract:

    The phylum Verrucomicrobia is a divergent phylum within domain Bacteria including members of the microbial communities of soil and fresh and marine waters; recently extremely acidophilic members from hot springs have been found to oxidize methane. At least one genus, Prosthecobacter, includes species with genes homologous to those encoding eukaryotic tubulins. A significant superphylum relationship of Verrucomicrobia with members of phylum Planctomycetes possessing a unique compartmentalized cell plan, and members of the phylum Chlamydiae including human pathogens with a complex intracellular life cycle, has been proposed. Based on the postulated superphylum relationship, we hypothesized that members of the two separate phyla Planctomycetes and Verrucomicrobia might share a similar ultrastructure plan differing from classical prokaryote organization. The ultrastructure of cells of four members of phylum Verrucomicrobia – Verrucomicrobium spinosum, Prosthecobacter dejongeii, Chthoniobacter flavus, and strain Ellin514 – was examined using electron microscopy incorporating high-pressure freezing and cryosubstitution. These four members of phylum Verrucomicrobia, representing 3 class-level subdivisions within the phylum, were found to possess a compartmentalized cell plan analogous to that found in phylum Planctomycetes. Like all planctomycetes investigated, they possess a major pirellulosome compartment containing a condensed nucleoid and ribosomes surrounded by an intracytoplasmic membrane (ICM), as well as a ribosome-free paryphoplasm compartment between the ICM and cytoplasmic membrane. A unique compartmentalized cell plan so far found among Domain Bacteria only within phylum Planctomycetes, and challenging our concept of prokaryote cell plans, has now been found in a second phylum of the Domain Bacteria, in members of phylum Verrucomicrobia. The planctomycete cell plan thus occurs in at least two distinct phyla of the Bacteria, phyla which have been suggested from other evidence to be related phylogenetically in the proposed PVC (Planctomycetes-Verrucomicrobia-Chlamydiae) superphylum. This planctomycete cell plan is present in at least 3 of 6 subdivisions of Verrucomicrobia, suggesting that the common ancestor of the Verrucomicrobial phylum was also compartmentalized and possessed such a plan. The presence of this compartmentalized cell plan in both phylum Planctomycetes and phylum Verrucomicrobia suggest that the last common ancestor of these phyla was also compartmentalized.

  • a canonical ftsz protein in verrucomicrobium spinosum a member of the bacterial phylum Verrucomicrobia that also includes tubulin producing prosthecobacter species
    BMC Evolutionary Biology, 2007
    Co-Authors: Benjamin Yee, James T. Staley, Feras F Lafi, Brian B Oakley, John A. Fuerst
    Abstract:

    Background The origin and evolution of the homologous GTP-binding cytoskeletal proteins FtsZ typical of Bacteria and tubulin characteristic of eukaryotes is a major question in molecular evolutionary biology. Both FtsZ and tubulin are central to key cell biology processes – bacterial septation and cell division in the case of FtsZ and in the case of tubulins the function of microtubules necessary for mitosis and other key cytoskeleton-dependent processes in eukaryotes. The origin of tubulin in particular is of significance to models for eukaryote origins. Most members of domain Bacteria possess FtsZ, but bacteria in genus Prosthecobacter of the phylum Verrucomicrobia form a key exception, possessing tubulin homologs BtubA and BtubB. It is therefore of interest to know whether other members of phylum Verrucomicrobia possess FtsZ or tubulin as their FtsZ-tubulin gene family representative.

  • a canonical ftsz protein in verrucomicrobium spinosum a member of the bacterial phylum Verrucomicrobia that also includes tubulin producing prosthecobacter species
    BMC Evolutionary Biology, 2007
    Co-Authors: Benjamin K Yee, James T. Staley, Feras F Lafi, Brian B Oakley, John A. Fuerst
    Abstract:

    The origin and evolution of the homologous GTP-binding cytoskeletal proteins FtsZ typical of Bacteria and tubulin characteristic of eukaryotes is a major question in molecular evolutionary biology. Both FtsZ and tubulin are central to key cell biology processes – bacterial septation and cell division in the case of FtsZ and in the case of tubulins the function of microtubules necessary for mitosis and other key cytoskeleton-dependent processes in eukaryotes. The origin of tubulin in particular is of significance to models for eukaryote origins. Most members of domain Bacteria possess FtsZ, but bacteria in genus Prosthecobacter of the phylum Verrucomicrobia form a key exception, possessing tubulin homologs BtubA and BtubB. It is therefore of interest to know whether other members of phylum Verrucomicrobia possess FtsZ or tubulin as their FtsZ-tubulin gene family representative. Verrucomicrobium spinosum, a member of Phylum Verrucomicrobia of domain Bacteria, has been found to possess a gene for a protein homologous to the cytoskeletal protein FtsZ. The deduced amino acid sequence has sequence signatures and predicted secondary structure characteristic for FtsZ rather than tubulin, but phylogenetic trees and sequence analysis indicate that it is divergent from all other known FtsZ sequences in members of domain Bacteria. The FtsZ gene of V. spinosum is located within a dcw gene cluster exhibiting gene order conservation known to contribute to the divisome in other Bacteria and comparable to these clusters in other Bacteria, suggesting a similar functional role. Verrucomicrobium spinosum has been found to possess a gene for a protein homologous to the cytoskeletal protein FtsZ. The results suggest the functional as well as structural homology of the V. spinosum FtsZ to the FtsZs of other Bacteria implying its involvement in cell septum formation during division. Thus, both bacteria-like FtsZ and eukaryote-like tubulin cytoskeletal homologs occur in different species of the phylum Verrucomicrobia of domain Bacteria, a result with potential major implications for understanding evolution of tubulin-like cytoskeletal proteins and the origin of eukaryote tubulins.

  • eukaryotic signature proteins of prosthecobacter dejongeii and gemmata sp wa 1 as revealed by in silico analysis
    Fems Microbiology Letters, 2005
    Co-Authors: James T. Staley, Heather Bouzek, Cheryl Jenkins
    Abstract:

    The genomes of representatives of three bacterial phyla have been compared with the list of 347 eukaryotic signature proteins (ESPs) derived by Hartman and Fedorov [Proc. Natl. Acad. Sci. USA 99 (2002) 1420]. The species included Prosthecobacter dejongeii of the Verrucomicrobia phylum, Gemmata sp. Wa-1 of the Planctomycetes phylum and Caulobacter crescentus of the Proteobacteria. The protist Trypanosoma brucei was used as a eukaryotic control. P. dejongeii had unique ERGO blast matches to α-, β-, and γ-tubulin, to Set2, a transciptional factor associated with eukaryotic DNA, and to LAMMER protein kinase for a total of 10 high-scoring ESP matches altogether. Gemmata sp. Wa-1 shared four of its 17 high-scoring ESP matches with P. dejongeii, and that information coupled with other genomic data provides strong support that these two phyla are related to one another. If the ESP list is an accurate listing of unique eukaryotic proteins, then the low number of high-scoring matches between the proteins of these two bacteria with the list raises doubts about these phyla being direct ancestors of the Eucarya. However, this does not rule out the possibility that ancestral members of either the Verrucomicrobia or Planctomycetes may have played an important role in the evolution of a proto-eukaryotic organism.

  • eukaryotic signature proteins of prosthecobacter dejongeii and gemmata sp wa 1 as revealed by in silico analysis
    Fems Microbiology Letters, 2005
    Co-Authors: James T. Staley, Heather Bouzek, Cheryl Jenkins
    Abstract:

    The genomes of representatives of three bacterial phyla have been compared with the list of 347 eukaryotic signature proteins (ESPs) derived by Hartman and Fedorov [Proc. Natl. Acad. Sci. USA 99 (2002) 1420]. The species included Prosthecobacter dejongeii of the Verrucomicrobia phylum, Gemmata sp. Wa-1 of the Planctomycetes phylum and Caulobacter crescentus of the Proteobacteria. The protist Trypanosoma brucei was used as a eukaryotic control. P. dejongeii had unique ERGO blast matches to α-, β-, and γ-tubulin, to Set2, a transciptional factor associated with eukaryotic DNA, and to LAMMER protein kinase for a total of 10 high-scoring ESP matches altogether. Gemmata sp. Wa-1 shared four of its 17 high-scoring ESP matches with P. dejongeii, and that information coupled with other genomic data provides strong support that these two phyla are related to one another. If the ESP list is an accurate listing of unique eukaryotic proteins, then the low number of high-scoring matches between the proteins of these two bacteria with the list raises doubts about these phyla being direct ancestors of the Eucarya. However, this does not rule out the possibility that ancestral members of either the Verrucomicrobia or Planctomycetes may have played an important role in the evolution of a proto-eukaryotic organism.