Peter Schumann

Publications of Peter Schumann

• Saccharothrix hoggarensis sp. nov., a novel actinomycete isolated from Saharan soil.

  Authors: Dalila Boubetra, Abdelghani Zitouni, Noureddine Bouras, Florence Mathieu, Ahmed Lebrihi, Peter Schumann, Cathrin Spröer, Hans-Peter Klenk, Nasserdine Sabaou

  International journal of systematic and evolutionary microbiology. 04/2012;

  An actinomycete strain designated SA181T, was isolated from Saharan soil in the Hoggar region (South Algeria) and was characterized taxonomically by using a polyphasic approach. The morphological andAn actinomycete strain designated SA181T, was isolated from Saharan soil in the Hoggar region (South Algeria) and was characterized taxonomically by using a polyphasic approach. The morphological and chemotaxonomic characteristics of the strain were consistent with the members of the genus Saccharothrix, and 16S rRNA gene sequence analysis confirmed that strain SA181T was a novel member of the genus Saccharothrix. DNA-DNA hybridization values between strain SA181T and the nearest Saccharothrix species, Saccharothrix longispora, S. texasensis and S. xinjiangenesis were clearly below the 70 % threshold. The genotypic and phenotypic data showed that the organism represents a novel species of the genus Saccharothrix for which the name Saccharothrix hoggarensis sp. nov. is proposed, with the type strain SA181T (DSM 45457T = CCUG 60214T).

• Saliterribacillus persicus gen. nov., sp. nov., a moderately halophilic bacterium isolated from the Iranian hypersaline lake Aran-Bidgol.

  Authors: Mohammad Ali Amoozegar, Maryam Bagheri, Maryam Didari, Seyed Abolhassan Shahzedeh Fazeli, Peter Schumann, Cristina Sánchez-Porro, Antonio Ventosa

  International journal of systematic and evolutionary microbiology. 03/2012;

  A novel Gram-positive, moderately halophilic bacterium, designated strain X4BT, was isolated from soil around the hypersaline lake Aran-Bidgol in Iran and characterized taxonomically using aA novel Gram-positive, moderately halophilic bacterium, designated strain X4BT, was isolated from soil around the hypersaline lake Aran-Bidgol in Iran and characterized taxonomically using a polyphasic approach. Cells of strain X4BT were motile rods and formed ellipsoidal endospores at a terminal or subterminal position in swollen sporangia. Strain X4BT was a strictly aerobic bacterium, catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5-22.5 % (w/v), with optimum growth occurring at 7.5 % (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. Analysis of 16S rRNA gene sequence revealed that strain X4BT is a member of the family Bacillaceae, constituting a novel phyletic lineage within this family. Highest sequence similarities were obtained with the 16S rRNA gene sequences of the type strains of Sediminibacillus albus (96.0 %), Paraliobacillus ryukyuensis (95.9 %), Paraliobacillus quinghaiensis (95.8 %) and Sediminibacillus halophilus (95.7%), respectively. The DNA G+C content of this new isolate was 35.2 mol%. The major cellular fatty acids of strain X4BT were anteiso-C15:0 and anteiso-C17:0 and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, two aminolipids, an aminophospholipid and an unknown phospholipid. The isoprenoid quinones were MK-7 (89 %) and MK-6 (11 %). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of 16S rRNA gene sequence analysis in combination with chemotaxonomic and phenotypic data, strain X4BT represents a new genus and species in the family Bacillaceae, order Bacillales for which the name Saliterribacillus persicus gen. nov., sp. nov. is proposed. The type strain of Saliterribacillus persicus is X4BT (= IBRC-M 10629T = KCTC 13827T).

• Description of Budvicia diplopodorum sp. nov. and emendation of the genus description.

  Authors: Elke Lang, Peter Schumann, Brigitte A Knapp, Ramesh Kumar, Cathrin Spröer, Heribert Insam

  International journal of systematic and evolutionary microbiology. 03/2012;

  A Gram-negative, rod shaped, weakly motile, non-spore-forming bacterium (D9T) was isolated from the gut of Cylindrioulus fulviceps (Diplopoda) on 1/3 concentrated nutrient agar plates (Knapp et al.,A Gram-negative, rod shaped, weakly motile, non-spore-forming bacterium (D9T) was isolated from the gut of Cylindrioulus fulviceps (Diplopoda) on 1/3 concentrated nutrient agar plates (Knapp et al., 2010). On the basis of 16S rRNA gene sequence similarity, strain D9T was shown to be phylogenetically closely related to the species Budvicia aquatica, the sole species of the genus Budvicia, family Enterobacteriaceae. The similarity of the 16S rRNA gene sequences of strain D9T and the type strain of B. aquatica was 98.4 %. Other species showing high pairwise similarities with the isolate belonged to the genus Yersinia, namely Y. frederiksenii, Y. massiliensis, Y. pestis, Y. pseudotuberculosis, Y. similis and Y. ruckeri (similarities of the type strains with strain D9T were 96.8 % for the first four species, 96.7 % and 96.5 %, respectively). The sequence similarities of the housekeeping genes rpoB, hsp60 and gyrB of strainD9T with those of B. aquatica and other members of the Enterobacteriaceae were less than 94 %. The trees constructed from sequences of these genes univocally grouped the isolate with the type strain of B. aquatica and separate from Yersinia species. The G+C content of the DNA (48.3 %) and the whole cell fatty acid pattern of strain D9 T (C14:0 , feature 3 including C16:1w7c and iso-C15:0 2OH, C16:0, cyclo-C17:0 and C18:1w7c as major components) were typical for members of the Enterobacteriaceae. DNA-DNA hybridization of strain D9T with the type strain of B. aquatica, DSM 5075T, resulted in a relatedness of 30.3 mol% indicating that the isolate does not belong to the species B. aquatica. Physiological tests allowed the phenotypic differentiation of strain D9T from its sister species as well as from phylogenetically related species of the genus Yersinia. From these results it is concluded that D9T represents a new species for which the name Budvicia diplopodorum sp. nov. is proposed with D9T (= DSM 21983T = CCM 7845T) as its type strain.

• Reclassification of Koreibacter algae as a later heterotypic synonym of Paraoerskovia marina and emended descriptions of the genus Paraoerskovia (Khan et al. 2009) and of Paraoerskovia marina (Khan et al. 2009).

  Authors: Peter Schumann, Ruediger Pukall, Cathrin Spröer, Erko Stackebrandt

  International journal of systematic and evolutionary microbiology. 03/2012;

  16S rRNA gene sequences deposited for the type strains of Paraoerskovia marina CTT-37(T) (AB445007) and Koreibacter algae DSW-2(T) (FM995611) show a similarity of 100 %. Consequently, the type16S rRNA gene sequences deposited for the type strains of Paraoerskovia marina CTT-37(T) (AB445007) and Koreibacter algae DSW-2(T) (FM995611) show a similarity of 100 %. Consequently, the type strains were subjected to a polyphasic re-characterization under direct comparison in order to clarify their taxonomic position. PvuII RiboPrint patterns and the quantitative ratios of cellular fatty acids revealed strain-specific differences between the strains DSM 21750(T) (=CTT-37(T)) and DSM 22126(T) (=DSW-2(T)). The percentage of DNA-DNA binding of 94 % indicated that both type strains belong to the same genomospecies. Agreement in the peptidoglycan structure, highly similar fatty acid profiles and MALDI-TOF mass spectra, the ability to produce acid from the same carbon sources, corresponding enzymatic activities and G+C values of 70.8±0.3 mol% in addition to the consistent characteristics reported in the original descriptions support the view that both strains should be affiliated to the same species. According to Rules 38 and 42 of the Bacteriological Code, Koreibacter algae should be reclassified as later heterotypic synonym of Paraoerskovia marina and the descriptions of the genus Paraoerskovia (Khan et al. 2009) and of Paraoerskovia marina (Khan et al. 2009) are emended.

• Bifidobacterium reuteri sp. nov., Bifidobacterium callitrichos sp. nov., Bifidobacterium saguini sp. nov., Bifidobacterium stellenboschense sp. nov. and Bifidobacterium biavatii sp. nov. isolated from faeces of common marmoset (Callithrix jacchus) and red-handed tamarin (Saguinus midas).

  Authors: Akihito Endo, Yuka Futagawa-Endo, Peter Schumann, Rüdiger Pukall, Leon M T Dicks

  Systematic and applied microbiology. 03/2012; 35(2):92-7.

  Five strains of bifidobacteria were isolated from faeces of a common marmoset (Callithrix jacchus) and a red-handed tamarin (Saguinus midas). The five isolates clustered inside the phylogenetic groupFive strains of bifidobacteria were isolated from faeces of a common marmoset (Callithrix jacchus) and a red-handed tamarin (Saguinus midas). The five isolates clustered inside the phylogenetic group of the genus Bifidobacterium but did not show high sequence similarities between the isolates and to known species in the genus by phylogenetic analysis based on 16S rRNA gene sequences. Sequence analyses of dnaJ1 and hsp60 also indicated their independent phylogenetic positions to each other in the Bifidobacterium cluster. DNA G+C contents of the species ranged from 57.3 to 66.3mol%, which is within the values recorded for Bifidobacterium species. All isolates showed fructose-6-phosphate phosphoketolase activity. Based on the data provided, the five isolates represent five novel species, for which the names Bifidobacterium reuteri sp. nov. (type strain: AFB22-1(T)=JCM 17295(T)=DSM 23975(T)), Bifidobacterium callitrichos sp. nov. (type strain: AFB22-5(T)=JCM 17296(T)=DSM 23973(T)), Bifidobacterium saguini sp. nov. (type strain: AFB23-1(T)=JCM 17297(T)=DSM 23967(T)), Bifidobacterium stellenboschense sp. nov. (type strain: AFB23-3(T)=JCM 17298(T)=DSM 23968(T)) and Bifidobacterium biavatii sp. nov. (type strain: AFB23-4(T)=JCM 17299(T)=DSM 23969(T)) are proposed.

• Lactobacillus pasteurii sp. nov. and Lactobacillus hominis sp. nov. two novel species.

  Authors: Sylvie Cousin, Laurence Motreff, Marie-Laure Gulat-Okalla, Catherine Gouyette, Cathrin Spröer, Peter Schumann, Evelyne Begaud, Christiane Bouchier, Dominique Clermont, Chantal Bizet

  International journal of systematic and evolutionary microbiology. 02/2012;

  The strains 1517T and 61DT were characterised by phenotypic and molecular taxonomic methods. The Gram-positive lactic acid bacteria were homo-fermentative, facultative anaerobes with short rods. TheyThe strains 1517T and 61DT were characterised by phenotypic and molecular taxonomic methods. The Gram-positive lactic acid bacteria were homo-fermentative, facultative anaerobes with short rods. They were phylogenetically related to the genus Lactobacillus according to the 16S rDNA gene sequence analysis with 99 % similarity values between strain 1517T and Lactobacillus gigeriorum and 98.6, 98.5 and 98.4 % between strain 61D T and Lactobacillus gasseri, L. taiwanensis and L. johnsonii, respectively. Multilocus sequence analysis (MLSA) and metabolic analysis of both strains showed variation from the strains and their close relatives with variation of position for the genes pheS and rpoA. The DNA-DNA relatedness with 43.5 % between strain 1517 T and Lactobacillus gigeriorum and 38.6, 29.9 and 39.7 % between strain 61DT, L. johnsonii, L. taiwanensis and L. gasseri, respectively, confirmed status as a novel species. Based on phenotypic and genotypic characteristics, two novel species of Lactobacillus are proposed: Lactobacillus pasteurii sp. nov., with 1517T (CRBIP 24.76T=DSM 23907T) as the type strain and Lactobacillus hominis sp. nov., with 61DT (CRBIP 24.179T=DSM 23910T) as the type strain.

• Alpinimonas psychrophila gen. nov., sp. nov., a novel actinobacterium of the family Microbacteriaceae isolated from alpine glacier cryoconite.

  Authors: Peter Schumann, De-Chao Zhang, Mersiha Redzic, Rosa Margesin

  International journal of systematic and evolutionary microbiology. 01/2012;

  A Gram-type positive, non-motile, psychrophilic actinobacterium, designated Cr8-25T, was isolated from alpine glacier cryoconite and was able to grow well over a temperature range of 1-15 °C.A Gram-type positive, non-motile, psychrophilic actinobacterium, designated Cr8-25T, was isolated from alpine glacier cryoconite and was able to grow well over a temperature range of 1-15 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Cr8-25T belonged to the family Microbacteriaceae and showed highest 16S rRNA gene sequence similarity with Klugiella xanthotipulae 44C3T (97.0 %). However, strain Cr8-25T was differentiated from the type strain of K. xanthotipulae on the level of genomospecies by a DNA-DNA relatedness of only 37.2 %. Strain Cr8-25T contained a peptidoglycan cross-linked according to the B-type which is based on 2,4-diaminobutyric acid. The cell wall contained the sugars galactose, fucose and rhamnose. The predominant cellular fatty acids of strain Cr8-25T were C15:0 anteiso (64.6 %) and iso-C16:0 (22.5 %) and the major menaquinones were MK-11 and MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and unknown glycolipids. The G+C content of the genomic DNA was 58.8 mol%. On the basis of the phenotypic characteristics, phylogenetic and chemotaxonomic analyses and DNA-DNA relatedness data, strain Cr8-25T represents a novel species of a new genus in the family Microbacteriaceae, for which the name Alpinimonas psychrophila is proposed. The type strain is Cr8-25T (=DSM 23737T = LMG 26215T).

• Alteribacillus bidgolensis gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline Iranian lake, and reclassification of Bacillus persepolensis as Alteribacillus persepolensis comb. nov.

  Authors: Maryam Didari, Mohammad Ali Amoozegar, Maryam Bagheri, Peter Schumann, Cathrin Spröer, Cristina Sánchez-Porro, Antonio Ventosa

  International journal of systematic and evolutionary microbiology. 01/2012;

  A novel Gram-positive, moderately halophilic bacterium, designated strain P4BT, was isolated from water of the hypersaline lake Aran-Bidgol in Iran and characterized taxonomically using a polyphasicA novel Gram-positive, moderately halophilic bacterium, designated strain P4BT, was isolated from water of the hypersaline lake Aran-Bidgol in Iran and characterized taxonomically using a polyphasic approach. Cells of strain P4BT were rod-shaped, nonmotile rods and producing ellipsoidal endospores at a central position in non-swollen sporangia. Strain P4BT was a strictly aerobic bacterium and catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5-12.5 % (w/v), with optimum growth occurring at 5-7.5 % (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain P4BT was shown to belong to the phylum Firmicutes and the closest phylogenetic similarities were with the species Bacillus persepolensis HS136T (97.1 %) and Bacillus salarius BH169T (95.1 %); however, the 16S rRNA gene sequence similarity with Bacillus subtilis subsp. subtilis DSM 10T was only 91.3%, indicating that it might not be a member of the genus Bacillus. The DNA G+C content of this new isolate was 38.9 mol%. DNA-DNA hybridization experiments revealed a low level of relatedness between strain P4BT and Bacillus persepolensis HS136T (6 %). The major cellular fatty acids of strain P4BT were iso-C15:0 (24.4 %) and anteiso-C15:0 (24.3 %), similarly to those determined for Bacillus persepolensis HS136T but different to those determined for Bacillus salarius DSM 16461T or Bacillus subtilis subsp. subtilis DSM 10T. Its polar lipid pattern consisted of phosphatidylglycerol, an aminoglycolipid, and an unknown phospholipid. This polar lipid profile was quite similar to that obtained for Bacillus persepolensis DSM 21632T but different to those of Bacillus salarius DSM 16461T or Bacillus subtilis subsp. subtilis DSM 10T. The isoprenoid quinones were MK-7 (88 %) and MK-8 (2 %). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All these features reveal the placement of isolate P4BT within Firmicutes, closely related to Bacillus persepolensis but with features that clearly distinct them from those of the genus Bacillus or other related genera. On the basis of polyphasic evidence from this study, we propose the placement of strain P4BT within a new genus, as Alteribacillus bidgolensis gen. nov., sp. nov. (type strain P4BT = DSM 25260T = IBRC-M 10614T = KCTC 13821T) and the transfer of Bacillus persepolensis to this new genus, as Alteribacillus persepolensis comb. nov. The type strain of Alteribacillus persepolensis is HS136T (=CCM 7595T =DSM 21632T = JCM 15720T = LMG 25222T).

• Microbacterium immunditiarum sp. nov., a novel actinobacterium isolated from a landfill surface soil.

  Authors: Srinivasan Krishnamurthi, Amit Bhattacharya, Peter Schumann, Syed G Dastager, Shu-Kun Tang, Wen-Jun Li, Tapan Chakrabarti

  International journal of systematic and evolutionary microbiology. 11/2011;

  A Gram-positive, non-endospore forming bacterium designated as strain SK 18T was isolated from surface soil of a landfill by dilution plating on tryptic soy broth agar (TSBA). PreliminaryA Gram-positive, non-endospore forming bacterium designated as strain SK 18T was isolated from surface soil of a landfill by dilution plating on tryptic soy broth agar (TSBA). Preliminary characterization of strain SK 18T using biochemical tests, FAME analysis and partial 16S rRNA gene sequencing placed it within the genus Microbacterium. Analysis of the cell wall indicated that the peptidoglycan was of the B-type of cross-linkage containing amino acids lysine and ornithine with muramic acid in the N-glycolyl form. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. The major fatty acids of the cell membrane were anteiso-C17:0, anteiso-C15:0 and iso-C16:0. All these data further strengthened the placement of the strain within the genus Microbacterium. Strain SK 18T showed closest 16S rRNA gene sequence similarity (97.2 %) with Microbacterium ulmi. The similarity with all other Microbacterium species was less than 97.0 %. DNA-DNA hybridization of the strain with its closest relative M. ulmi revealed a low reassociation value of 39.0 %. Moreover, strain SK 18T showed a number of differences in phenotypic characteristics (colony color, catalase, hydrolysis of polymers, acid production from sugars and oxidation of various substrates) and its DNA G + C mol % was also higher when compared with M. ulmi. These data indicated that strain SK 18T could not be placed within any existing species and deserves to be treated as a new species within the genus Microbacterium. The name Microbacterium immunditiarum sp. nov. is proposed. The type strain is SK 18T (=MTCC 7185T = JCM 14034T).

• Gaiella occulta gen. nov., sp. nov., a novel representative of a deep branching phylogenetic lineage within the class Actinobacteria and proposal of Gaiellaceae fam. nov. and Gaiellales ord. nov.

  Authors: Luciana Albuquerque, Luís França, Fred A Rainey, Peter Schumann, M Fernanda Nobre, Milton S da Costa

  Systematic and applied microbiology. 09/2011; 34(8):595-9.

  Two isolates, with an optimum growth temperature of about 35-37°C and an optimum pH for growth between 6.5 and 7.5, were recovered from a deep mineral water aquifer in Portugal. Strains formTwo isolates, with an optimum growth temperature of about 35-37°C and an optimum pH for growth between 6.5 and 7.5, were recovered from a deep mineral water aquifer in Portugal. Strains form rod-shaped cells and were non-motile. These strains were non-pigmented, strictly aerobic, catalase and oxidase positive. Strains F2-233(T) and F2-223 assimilated carbohydrates, organic acids and amino acids. Major fatty acids were novel iso internally branched such as 17:0 iso 10-methyl, 17:0 iso and 15:0 iso 8-methyl. The peptidoglycan contained meso-diaminopimelic acid and menaquinone MK-7 was the major respiratory quinone. Analysis of the 16S rRNA gene shows the strains to cluster with species of the genera Thermoleophilum, Patulibacter, Conexibacter and Solirubrobacter to which they have pairwise sequence similarity in the range 87-88%. Based on 16S rRNA gene sequence analysis, physiological and biochemical characteristics we describe a new species of a novel genus represented by strain F2-233(T) (=CECT 7815(T)=LMG 26412(T)) for which we propose the name Gaiella occulta gen. nov., sp. nov. We also propose that this organism represents a novel family named Gaiellaceae fam. nov. of a novel order named Gaiellales ord. nov.

• Melghirimyces algeriensis gen. nov., sp. nov., a member of the family Thermoactinomycetaceae, isolated from a salt lake.

  Authors: Ammara Nariman Addou, Peter Schumann, Cathrin Spröer, Hocine Hacene, Jean-Luc Cayol, Marie-Laure Fardeau

  International journal of systematic and evolutionary microbiology. 08/2011;

  A novel filamentous bacterium designated NariEXT was isolated from soil collected from a salt lake named Chott Melghir located in south east of Algeria. The strain is an aerobic, halotolerant,A novel filamentous bacterium designated NariEXT was isolated from soil collected from a salt lake named Chott Melghir located in south east of Algeria. The strain is an aerobic, halotolerant, thermotolerant, Gram positive bacterium, growing at NaCl concentrations up to 21% w/v and temperature and pH ranges between 37-60° C and 5.0-9.5, respectively. The major fatty acids were iso and anteiso 15:0. The G+C value was 47.3 mol %. Major menaquinone was MK7, but MK 6 and MK 8 were also present. Polar lipids profile consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylmonomethylethanolamine. Results of molecular and phenotypic analysis led to the description of the strain as a new member to the family Thermoactinomycetaceae. Strain NariEXT is distinct from recognized genera of this family by morphological, biochemical and chemotaxonomic characteristics. Strain NariEXT shows a 16S rRNA gene sequence similarity of 95.38 % and 94.28% with Desmospora activa and Kroppenstedtia eburnea, respectively, but differs from both type strains in its sugars, polar lipids and in the presence of methyl-PE. On the basis of physiological and phylogenetical data the type strain NariEXT (=DSM 45474T =CCUG 59620T) represents a new species in a new genus of the family Thermoactinomycetaceae for which the name Melghirimyces algeriensis gen. nov., sp. nov. is proposed.

• Thermus composti sp. nov., isolated from oyster mushroom compost.

  Authors: Balázs Vajna, Szilvia Kanizsai, Zsuzsa Kéki, Károly Márialigeti, Peter Schumann, Erika M Tóth

  International journal of systematic and evolutionary microbiology. 08/2011;

  A Gram-negative, rod-shaped bacterium strain (K-39(T)) was isolated from the thermophilic phase of the composting process for oyster mushroom substrate preparation. The strain grew at 40-80 °CA Gram-negative, rod-shaped bacterium strain (K-39(T)) was isolated from the thermophilic phase of the composting process for oyster mushroom substrate preparation. The strain grew at 40-80 °C (optimum, 65-75 °C), at pH 5-9 (optimum, pH 7), in media containing up to 1.5% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain K-39(T) formed a distinct lineage within the genus Thermus. Its closest cultivated relative was Thermus islandicus PRI 3838(T) (96.8% similarity). The DNA G+C content of strain K-39(T) was 71.3 mol%. The new strain could be differentiated from the related taxa by not being able to hydrolyze starch. The predominant fatty acids of strain K-39(T) were iso-C(17:0) and anteiso-C(17:0). Strain K-39(T) contained a lower amount of the fatty acid iso-C(15:0) as compared to related Thermus species. The predominant respiratory quinone of the new isolate was menaquinone MK-8. On the basis of a polyphasic taxonomic study, strain K-39(T) is considered to represent a novel species of the genus Thermus, for which the name Thermus composti sp. nov. is proposed. The type strain is K-39(T) (=DSM 21686(T)=NCAIM B 02340(T)).

• Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons.

  Authors: Rainer Borriss, Xiao-Hua Chen, Christian Rueckert, Jochen Blom, Anke Becker, Birgit Baumgarth, Ben Fan, Rüdiger Pukall, Peter Schumann, Cathrin Spröer, Helmut Junge, Joachim Vater, Alfred Pühler, Hans-Peter Klenk

  International journal of systematic and evolutionary microbiology. 08/2011; 61(Pt 8):1786-801.

  The whole-genome-sequenced rhizobacterium Bacillus amyloliquefaciens FZB42(T) (Chen et al., 2007) and other plant-associated strains of the genus Bacillus described as belonging to the speciesThe whole-genome-sequenced rhizobacterium Bacillus amyloliquefaciens FZB42(T) (Chen et al., 2007) and other plant-associated strains of the genus Bacillus described as belonging to the species Bacillus amyloliquefaciens or Bacillus subtilis are used commercially to promote the growth and improve the health of crop plants. Previous investigations revealed that a group of strains represented a distinct ecotype related to B. amyloliquefaciens; however, the exact taxonomic position of this group remains elusive (Reva et al., 2004). In the present study, we demonstrated the ability of a group of Bacillus strains closely related to strain FZB42(T) to colonize Arabidopsis roots. On the basis of their phenotypic traits, the strains were similar to Bacillus amyloliquefaciens DSM 7(T) but differed considerably from this type strain in the DNA sequences of genes encoding 16S rRNA, gyrase subunit A (gyrA) and histidine kinase (cheA). Phylogenetic analysis performed with partial 16S rRNA, gyrA and cheA gene sequences revealed that the plant-associated strains of the genus Bacillus, including strain FZB42(T), formed a lineage, which could be distinguished from the cluster of strains closely related to B. amyloliquefaciens DSM 7(T). DNA-DNA hybridizations (DDH) performed with genomic DNA from strains DSM 7(T) and FZB42(T) yielded relatedness values of 63.7-71.2 %. Several methods of genomic analysis, such as direct whole-genome comparison, digital DDH and microarray-based comparative genomichybridization (M-CGH) were used as complementary tests. The group of plant-associated strains could be distinguished from strain DSM 7(T) and the type strain of B. subtilis by differences in the potential to synthesize non-ribosomal lipopeptides and polyketides. Based on the differences found in the marker gene sequences and the whole genomes of these strains, we propose two novel subspecies, designated B. amyloliquefaciens subsp. plantarum subsp. nov., with the type strain FZB42(T) ( = DSM 23117(T) = BGSC 10A6(T)), and B. amyloliquefaciens subsp. amyloliquefaciens subsp. nov., with the type strain DSM 7(T)( = ATCC 23350(T) = Fukumoto Strain F(T)), for plant-associated and non-plant-associated representatives, respecitvely. This is in agreement with results of DDH and M-CGH tests and the MALDI-TOF MS of cellular components, all of which suggested that the ecovars represent two different subspecies.

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• Peptoniphilus methioninivorax sp. nov., a Gram-positive anaerobic coccus isolated from retail ground beef.

  Authors: Alejandro P Rooney, James L Swezey, Rüdiger Pukall, Peter Schumann, Stefan Spring

  International journal of systematic and evolutionary microbiology. 08/2011; 61(Pt 8):1962-7.

  Strain NRRL B-23883(T) was isolated from retail ground beef as part of a study on the genetic diversity of Clostridium perfringens. The strain was found to be a strictly anaerobic, Gram-positiveStrain NRRL B-23883(T) was isolated from retail ground beef as part of a study on the genetic diversity of Clostridium perfringens. The strain was found to be a strictly anaerobic, Gram-positive coccus that was able to utilize peptone as a sole carbon source. Analysis of the 16S rRNA gene sequence revealed that the strain was closely related to species within the genera Peptoniphilus and Anaerosphaera, but it was substantially different from the closest recognized species by nearly 10 % sequence divergence. The strain was also found to be closely related (>99 % sequence similarity) to an uncultured bacterial strain that was sequenced from a 16S rRNA gene clone library constructed to characterize the bacterial community of faeces from a captive spotted hyena. Strain NRRL B-23883(T) shared the peptidoglycan type A4β, l-Orn-d-Glu with members of the genus Peptoniphilus. Further phenotypic analysis revealed that strain NRRL B-23883(T) was able to utilize glycyl l-methionine as a sole carbon source, in contrast to other species of the genus Peptoniphilus. Therefore, it is proposed that the isolate represents a novel species, Peptoniphilus methioninivorax sp. nov.; the type strain is NRRL B-23883(T) ( = DSM 22461(T)).

• Bacillus alkalisediminis sp. nov., an alkaliphilic and moderately halophilic bacterium isolated from sediment of extremely shallow soda ponds.

  Authors: Andrea K Borsodi, Beatrix Pollák, Zsuzsa Kéki, Anna Rusznyák, Attila L Kovács, Cathrin Spröer, Peter Schumann, Károly Márialigeti, Erika M Tóth

  International journal of systematic and evolutionary microbiology. 08/2011; 61(Pt 8):1880-6.

  Alkaliphilic strains characterized by optimal growth at pH 9.0 and 5 % (w/v) NaCl designated K1-25(T) and H3-93 were isolated from extremely shallow soda ponds located in Hungary. Cells of bothAlkaliphilic strains characterized by optimal growth at pH 9.0 and 5 % (w/v) NaCl designated K1-25(T) and H3-93 were isolated from extremely shallow soda ponds located in Hungary. Cells of both strains were Gram-stain-positive, non-motile, straight rods and formed central, ellipsoidal endospores with swollen sporangia. The isolates were aerobic, catalase-positive, oxidase-negative and contained a peptidoglycan of type A1γ based on meso-diaminopimelic acid. In both strains, menaquinone-7 (MK-7) was the predominant isoprenoid quinone and the major cellular fatty acids were anteiso-C(15 : 0) and iso-C(15 : 0). The DNA G+C contents of strains K1-25(T) and H3-93 were 39.0 and 36.3 mol%, respectively. 16S rRNA gene sequence-based phylogenetic analysis revealed 99.2 % similarity between strains K1-25(T) and H3-93 and the novel isolates had the highest similarities to Bacillus akibai 1139(T) (97.8 and 98.3 %, respectively), Bacillus wakoensis N-1(T) (97.0 and 97.4 %), Bacillus okhensis Kh10-101(T) (97.1 and 97.4 %) and Bacillus krulwichiae AM31D(T) (96.9 and 97.1 %). DNA-DNA hybridization between our strains and the type strains of closely related Bacillus species was lower than 70 %. Although DNA-DNA hybridization between strains K1-25(T) and H3-93 was 27 %, the phenotypic and chemotaxonomic data did not support the differentiation of these two strains into separate species. Therefore, they represent genomovars of a novel species, for which the name Bacillus alkalisediminis sp. nov. is proposed. The type strain is K1-25(T) ( = DSM 21670(T)  = NCAIM B02301(T)).

• Cellulomonas phragmiteti sp. nov., a cellulolytic bacterium isolated from reed (Phragmites australis) periphyton in a shallow soda pond.

  Authors: Anna Rusznyák, Erika M Tóth, Peter Schumann, Cathrin Spröer, Judit Makk, Gitta Szabó, Péter Vladár, Károly Márialigeti, Andrea K Borsodi

  International journal of systematic and evolutionary microbiology. 07/2011; 61(Pt 7):1662-6.

  An alkalitolerant and moderately halophilic strain, designated KB23(T), characterized by optimal growth at pH 8.0-9.0 and in the presence of 5-7 % (w/v) NaCl, was isolated from a reed (PhragmitesAn alkalitolerant and moderately halophilic strain, designated KB23(T), characterized by optimal growth at pH 8.0-9.0 and in the presence of 5-7 % (w/v) NaCl, was isolated from a reed (Phragmites australis) periphyton sample originating from an extremely shallow, alkaline soda pond located in Hungary. Cells of strain KB23(T) were Gram-stain-positive, motile straight rods. Strain KB23(T) was facultatively anaerobic, catalase-positive, oxidase-negative and contained peptidoglycan type A4β (L-Orn-D-Asp). MK-9(H4) was the predominant isoprenoid quinone and anteiso-C(15 : 0), C(16 : 0) and anteiso-C(15 : 1) were the major cellular fatty acids. The DNA G+C content of strain KB23(T) was 74.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that this strain belongs to the genus Cellulomonas and that it is related most closely to Cellulomonas flavigena DSM 20109(T) (97.35 % similarity), Cellulomonas terrae DB5(T) (96.81 %), Cellulomonas iranensis O(T) (96.75), Cellulomonas chitinilytica X.bu-b(T) (96.60 %), Cellulomonas persica I(T) (96.53 %), Cellulomonas composti TR7-06(T) (96.45 %), Cellulomonas biazotea DSM 20112(T) (96.34 %) and Cellulomonas fimi DSM 20113(T) (96.20 %). According to these results, together with DNA-DNA hybridization and physiological data, strain KB23(T) is considered to represent a novel species of the genus Cellulomonas, for which the name Cellulomonas phragmiteti sp. nov. is proposed. The type strain is KB23(T) ( = DSM 22512(T)  = NCAIM B002303(T)).

• Agrococcus carbonis sp. nov., isolated from soil of a coal mine.

  Authors: Soniya Dhanjal, Ishwinder Kaur, Suresh Korpole, Peter Schumann, Swaranjit Singh Cameotra, Rüdiger Pukall, Hans-Peter Klenk, Shanmugam Mayilraj

  International journal of systematic and evolutionary microbiology. 06/2011; 61(Pt 6):1253-8.

  An actinobacterial strain, designated G4(T), isolated from a coal mine was subjected to polyphasic taxonomic characterization. Cells were Gram-stain-positive, yellow-pigmented, non-motile andAn actinobacterial strain, designated G4(T), isolated from a coal mine was subjected to polyphasic taxonomic characterization. Cells were Gram-stain-positive, yellow-pigmented, non-motile and non-spore-forming cocci. This organism possessed a type B peptidoglycan with diaminobutyric acid as diagnostic diamino acid. The major respiratory quinones were MK-9, MK-10 and MK-11. The major fatty acids were anteiso-C(15 : 0) (41.6 %) and anteiso-C(17 : 0) (32.8 %). The predominant cellular polar lipids were diphosphatidylglycerol and phosphatidylglycerol. Cell wall sugars comprised galactose, glucose, ribose and rhamnose. 16S rRNA gene sequence analysis of strain G4(T) showed high similarity with Agrococcus baldri (98.9 %), Agrococcus citreus (97.8 %), Agrococcus jenensis (97.3 %) and Agrococcus terreus (97.0 %). Sequence similarity with the type strains of the other species of the genus Agrococcus was less than 97.0 %. The DNA-DNA relatedness of strain G4(T) with the type strains of Agrococcus baldri, Agrococcus citreus, Agrococcus jenensis and Agrococcus terreus was less than 70 %. On the basis of the physiological, biochemical and chemotaxonomic characteristics, strain G4(T) should be classified as the type strain of a novel species of the genus Agrococcus, for which the name Agrococcus carbonis sp. nov. is proposed. The type strain is G4(T) ( = MTCC 10213(T)  = DSM 22965(T)).

• Bacillus iranensis sp. nov., a moderately halophilic bacterium from Aran-Bidgol Lake, a hypersaline Iranian lake.

  Authors: Maryam Bagheri, Maryam Didari, Mohammad Ali Amoozegar, Peter Schumann, Cristina Sanchez-Porro, Malieh Mehrshad, Antonio Ventosa

  International journal of systematic and evolutionary microbiology. 05/2011;

  A novel Gram-positive, moderately halophilic, designated strain X5BT, was isolated from saline mud of the hypersaline lake Aran-Bidgol in Iran. Strain X5BT, a strictly aerobic motile bacterium,A novel Gram-positive, moderately halophilic, designated strain X5BT, was isolated from saline mud of the hypersaline lake Aran-Bidgol in Iran. Strain X5BT, a strictly aerobic motile bacterium, produced ellipsoidal endospores at a central-subterminal position in non-swollen sporangia. The strain grew between pH 7.0 and 10.0 (optimal growth at pH 7.5), between 25 and 45°C (optimal growth at 35°C) and at salinities of 2.5 to 15 % (w/v) NaCl, growing optimally at 5-7.5 % (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain X5BT was shown to belong to the genus Bacillus and showed the closest phylogenetic similarity with the species Bacillus persepolensis HS136T (95.6 %) and Bacillus salarius BH159T (95.5 %). The DNA G+C content of this new isolate was 42.4 mol%. The major cellular fatty acids of strain X5BT were anteiso-C15:0 and iso-C15:0, and its polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, three phospholipids and two glycolipids. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid and the isoprenoid quinones were MK-7 (92 %), MK-6 (6 %) and MK-5 (2 %). On the basis of polyphasic evidence from this study, a new species of the genus Bacillus, Bacillus iranensis sp. nov. is proposed, with strain X5BT (=IBRC10446T =DSM 23995T) as the type strain.

• Nocardiopsis arvandica sp. nov., isolated from sandy soil.

  Authors: Javad Hamedi, Fatemeh Mohammadipanah, Gabriele Pötter, Cathrin Spröer, Peter Schumann, Markus Göker, Hans-Peter Klenk

  International journal of systematic and evolutionary microbiology. 05/2011; 61(Pt 5):1189-94.

  An actinomycete strain, HM7(T), was isolated from sandy soil from the banks of the Arvand River, Khoramshahr, Iran. In a study conducted using a polyphasic taxonomic approach, it was found that thisAn actinomycete strain, HM7(T), was isolated from sandy soil from the banks of the Arvand River, Khoramshahr, Iran. In a study conducted using a polyphasic taxonomic approach, it was found that this strain represented a novel species in the genus Nocardiopsis. Strain HM7(T) had long, branched substrate mycelia and the aerial mycelium completely fragmented to long chains of rod-shaped spores. The cell wall of strain HM7(T) contained meso-diaminopimelic acid, galactose and ribose. The predominant phospholipids were phosphatidylglycerol, phosphatidylethanolamine diphosphatidylglycerol, and phosphatidylcholine. The main menaquinones were MK-10(H(2)), MK-10(H(4)), MK-10(H(0)) and MK-9(H(2)). Strain HM7(T) showed the highest degree of 16S rRNA gene sequence similarity with Nocardiopsis sinuspersici UTMC 00102(T) (99.8 %) and Nocardiopsis quinghaiensis YIM 28A4(T) (99.3 %), but differed significantly from these type strains based on DNA-DNA hybridization data (37.6 and 38.9 % relatedness, respectively). Physiological, biochemical and phenotypic characteristics allowed strain HM7(T) to be differentiated from related species. On the basis of results from phenotypic and phylogenetic analyses, strain HM7(T) is considered to represent a novel species of the genus Nocardiopsis, for which the name Nocardiopsis arvandica sp. nov. is proposed; the type strain of this species is HM7(T) ( = UTMC 00103(T) = DSM 45278(T) = CCUG 58831(T)).

• Reclassification of Leifsonia ginsengi (Qiu et al. 2007) as Herbiconiux ginsengi gen. nov., comb. nov. and description of Herbiconiux solani sp. nov., an actinobacterium associated with the phyllosphere of Solanum tuberosum L.

  Authors: Undine Behrendt, Peter Schumann, Moriyuki Hamada, Ken-Ichiro Suzuki, Cathrin Spröer, Andreas Ulrich

  International journal of systematic and evolutionary microbiology. 05/2011; 61(Pt 5):1039-47.

  In the context of studying the effects of transgenic fructan-producing potatoes on the community structure of phyllosphere bacteria, a group of strains closely related to the species LeifsoniaIn the context of studying the effects of transgenic fructan-producing potatoes on the community structure of phyllosphere bacteria, a group of strains closely related to the species Leifsonia ginsengi was isolated. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the new isolates and L. ginsengi DSM 19088(T) formed a lineage at the genus level and this finding was supported by chemotaxonomic characterization. The peptidoglycan type of the representative isolate, K134/01(T), and L. ginsengi DSM 19088(T) was B2γ, with d- and l-diaminobutyric acid as the diagnostic diamino acid and glycine, alanine and threo-3-hydroxyglutamic acid. The almost-complete substitution of glutamic acid by threo-3-hydroxyglutamic acid supported the differentiation of the new strains from recognized species of the genus Leifsonia. Furthermore, the detection of substantial amounts of the fatty acid cyclohexyl-C(17 : 0) in the new isolates and L. ginsengi DSM 19088(T) was a prominent chemotaxonomic feature for a clear demarcation of these strains from all genera of the family Microbacteriaceae that display the B2γ cell-wall type. Comparative phylogenetic and phenotypic analyses of the isolates and L. ginsengi DSM 19088(T) revealed the separate species status of the isolates. On the basis of these results, it is proposed that L. ginsengi should be classified as the type species of a novel genus, Herbiconiux gen. nov., with the name Herbiconiux ginsengi gen. nov., comb. nov. (type strain wged11(T) = CGMCC 4.3491(T) = JCM 13908(T) = DSM 19088(T) = NBRC 104580(T)). The phyllosphere isolates are assigned to a novel species, Herbiconiux solani sp. nov. (type strain K134/01(T) = DSM 19813(T) = LMG 24387(T) = NBRC 106740(T)).