Species Of Pedobacter Research Articles

Pedobacter schmidteae sp. nov., a new bacterium isolated from the microbiota of the planarian Schmidtea mediterranea

Pedobacter schmidteae sp. nov. strain EGT (Collection de Souches de l’Unité des Rickettsie CSUR P6417 = Colección Española de Cultivos Tipo CECT 9771) is a new Pedobacter species isolated from the planarian Schmidtea mediterranea. Schmidtea mediterranea are flatworms living in freshwater and exhibiting an unusual ability to regenerate amputated parts. To date, the gut microbiota of Schmidtea mediterranea remains poorly studied. Here, via the culturomics strategy that consists in using diversified culture conditions, we isolated a new bacterium, strain EG, that we characterized using the taxono-genomics approach that combines phenotypic assays and genome sequencing and analysis. Strain EG exhibits a 16S rRNA sequence similarity of 98.29% with Pedobacter nyackensis strain NWG-II14T, its closest neighbour with standing in nomenclature. It is an aerobic bacterium belonging to the family Sphingobacteriaceae. Colonies are small, round, smooth and transparent. Bacterial cells are Gram-negative, rod-shaped, motile and non-spore-forming bacilli with positive catalase and oxidase activities. The genome sequence is 6,198,518 bp–long with a G + C content of 41.13%, and the Ortho-ANI and dDDH values when compared to P. nyackensis are 77.34% and 21.50%, respectively. Strain EGT exhibits unique characteristics that classify it as the type strain of new bacterial species for which we propose the name Pedobacter schmidteae sp. nov.

Pedobacter miscanthi sp. nov., isolated from Miscanthus sinensis.

In a survey of endophytic bacteria in Miscanthus sinensis, a strain of Gram-negative, non-endospore-forming, rod-shaped, aerobic bacterium was isolated and designated as RS10T. Phylogenetic analysis based on its 16S rRNA gene sequence showed that the strain RS10T was affiliated with the genus Pedobacter and exhibited the highest sequence similarities to Pedobacter kyungheensis KACC 16221T (97.78 %), Pedobacter roseus KCTC 22187T (97.75 %), Pedobacter humicola KACC 18452T (97.29 %) and Pedobacter soli KACC 14939T (97.23 %). The novel strain contained iso-C15 : 0, iso-C17 : 0-3OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as major fatty acids. The only isoprenoid quinone detected in strain RS10T was MK-7. Strain RS10T contains phosphatidylethanolamine and one kind of aminophospholipid as its major polar lipids. The DNA G+C content for RS10T was 39.8 mol%. Based on the results of phenotypic and genomic characterizations, we concluded that strains RS10T represents a novel species of Pedobacter, for which the name Pedobacter miscanthi sp. nov. is proposed. The type strain is RS10T (=KCTC 62786T=GDMCC 1.1415T).

Proposal of Pedobacter nototheniae sp. nov., isolated from the spleen of a black rock cod (Notothenia coriiceps, Richardson 1844) from the Chilean Antarctica

A pink pigmented, Gram-negative, rod-shaped, non-spore-forming bacterium (strain 36B243T), was isolated from the spleen of a black rock cod (Notothenia coriiceps, Richardson 1844) in the Chilean Antarctica. Strain 36B243T has a 5.26Mb chromosome with a DNA G + C content of 35.4mol%. The draft genome includes the prediction and annotation of 4585 coding genes, and 46 tRNA, 1 tmRNA, and 2735 hypothetical proteins. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain 36B243T into the genus Pedobacter with high sequence similarity to the type strains of Pedobacter sandarakinus (97.5%) and Pedobacter petrophilus (97.1%). Sequence similarities to type strains of all other current Pedobacter species were below 97.1%. Predominant fatty acids are summed feature 3 (C16:1ω7c and/or C16:1ω6c) and iso-C15:0 followed by iso-C17:0 3-OH and C16:0. The major respiratory quinone was menaquinone MK-7. The polar lipid profile contained the major lipids phosphatidylethanolamine, five unidentified aminolipids, two lipids lacking a functional group and two minor glycolipids and one lipid lacking a functional group. An alkali-stable lipid was present. The polyamine pattern contained the predominant compound sym-homospermidine. Characterization by 16S rRNA gene sequence analysis, physiological parameters, pigment analysis, ubiquinone, polar lipid, and fatty acid composition revealed that strain 36B243T represents a new species of the genus Pedobacter. For this reason, we propose the name Pedobacter nototheniae sp. nov. with the type strain 36B243T (= LMG 30634T = CCM 8855T = CIP 111622T).

Environmental superbugs: The case study of Pedobacter spp.

The environment is one of the main reservoirs of antibiotic resistance genes (ARGs) but multidrug resistant (MDR) environmental isolates are barely characterised. As suggested by the name, Pedobacter species have been predominantly isolated from soils, but are also recovered from water (including drinking water), chilled food, fish, compost, sludge, glaciers and other extreme environments. The susceptibility phenotype of Pedobacter lusitanus NL19 (isolated from a deactivated uranium mine), its closely related species and the genus type strain were investigated. All strains are MDR bacteria, resistant to β-lactams, colistin, aminoglycosides and ciprofloxacin. Therefore, Pedobacter spp. are likely intrinsically resistant to β-lactams (including ertapenem) and to other three classes of antibiotics. 6%–8% of their total protein-encoding genes encode a diverse collection of putative ARGs, including β-lactamases. These enzymes are highly abundant in all the other Pedobacter strains with sequenced genomes, especially class C, class B3 and class A. LUS-1 and PLN-1 were further characterised in E. coli. LUS-1 is a class A β-lactamase and it conferred an increase in the MIC of cefotaxime, albeit very low. PLN-1 is a class B3 β-lactamase with carbapenemase activity, conferring resistance to ertapenem and a 66x and 16x increase in the MIC of imipenem and meropenem, respectively. PLN-1 also hydrolyses ampicillin, 1st and 3rd generation cephalosporins, and at a lower extent cephamycins and 4th generation cephalosporins. Therefore, Pedobacter spp. encode a large and diverse arsenal of resistance mechanisms that make them environmental superbugs.

Shifts in spinach microbial communities after chlorine washing and storage at compliant and abusive temperatures

Fresh produce, like spinach, harbors diverse bacterial populations, including spoilage and potentially pathogenic bacteria. This study examined the effects of produce washing in chlorinated water and subsequent storage on the microbiota of spinach. Baby spinach leaves from a commercial fresh-cut produce processor were assessed before and after washing in chlorinated water, and then after one week's storage at 4, 10, and 15 °C. Microbial communities on spinach were analyzed by non-selective plating, qPCR, and 16S rDNA amplicon sequencing. Bacterial populations on spinach, averaging 6.12 ± 0.61 log CFU/g, were reduced by 1.33 ± 0.57 log after washing. However, populations increased by 1.77–3.24 log after storage, with larger increases occurring at higher temperature (15 > 10 > 4 °C). The predominant phylum identified on unwashed spinach leaves was Proteobacteria; dominant genera were Pseudomonas and Sphingomonas. Bacterial communities shifted significantly after chlorine washing and storage. Several Proteobacteria species, such as Stenotrophomonas sp. and Erwinia sp., were relatively tolerant of chlorine treatment, while species of Flavobacterium and Pedobacter (phylum Bacteroidetes) grew rapidly during storage, especially at abusive temperatures. Cupriavidus sp. and Ralstonia sp. showed significant increases after washing. After storage, microbial communities on spinach appeared to shift back toward the pre-washing distributions.

Pedobacter solisilvae sp. nov., isolated from forest soil.

The bacteria strain EN12T was isolated from forest soil in the Republic of Korea. The cells were Gram-negative, non-motile and rod-shaped, and the strain was strictly aerobic. Phylogenetic analysis of its 16S rRNA gene sequences showed that strain EN12T belonged to the class Sphingobacteriia of the phylum Bacteroidetes, and its closest relative is Pedobacter namyangjuensis 5G38T, with a sequence similarity of 95.5 %. The average DNA sequence similarity from validly described species within the genus Pedobacter was 92.5±1.3 %. Chemotaxonomic data including major ubiquinones (menaquinone-7), polar lipids (phosphatidylethanolamine and sphingolipid) and fatty acids (iso-C15 : 0, iso-C17 : 0 3-OH, and C16 : 1ω6c/C16 : 1ω7c) also supported an affiliation of strain EN12T with the genus Pedobacter. Genotypic and phenotypic differentiation of strain EN12T from six published Pedobacter species was revealed through DNA-DNA relatedness and physiological/biochemical tests. Results of these phenotypic, phylogenetic and chemotaxonomic analyses indicated that strain EN12T is a novel species in the genus Pedobacter, for which we propose the name Pedobacter solisilvae sp. nov. (=KCTC 42612T=LMG 28820T).

Pedobacter psychrophilus sp. nov., isolated from fragmentary rock.

Strain P4487AT was isolated during investigation of cultivable bacterial populations of environmental materials sampled at James Ross Island, Antarctica. It revealed Gram-stain-negative short rod-shaped cells producing a pink pigment. Phylogenetic analysis based on 16S rRNA gene sequences allocated strain P4487AT to the genus Pedobacter but showed that the strain represents a distinct intrageneric phylogenetic lineage clearly separated from remaining Pedobacter species. Phylogenetically, strain P4487AT formed a common branch with the Pedobacter arcticus and Pedobacter lignilitoris cluster while the highest value of 94.4 % 16S rRNA gene sequence similarity suggested that Pedobacter lentus is the most closely related species. Biochemical and physiological test results enabled the differentiation of strain P4487AT from all phylogenetically closely related species. Chemotaxonomic analyses of strain P4487AT showed MK-7 as the respiratory menaquinone, sym-homospermidine as the major polyamine, phosphatidylethanolamine and two unidentified lipids as the major polar lipids, presence of sphingolipids, and C16 : 1ω7c/C16 : 1ω6c (summed feature 3), iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids, all of which corresponded with characteristics of the genus Pedobacter. The results showed that strain P4487AT represents a novel species within the genus Pedobacter, for which the name Pedobacter psychrophilus sp. nov. is proposed. The type strain is P4487AT (=CCM 8644T=LMG 29436T).

Pedobacter jamesrossensis sp. nov., Pedobacter lithocola sp. nov., Pedobacter mendelii sp. nov. and Pedobacter petrophilus sp. nov., isolated from the Antarctic environment.

A taxonomic study performed on 17 Gram-stain-negative rod-shaped bacterial strains originating from the Antarctic environment is described. Initial phylogenetic analysis using 16S rRNA gene sequencing differentiated the strains into four groups belonging to the genus Pedobacter but they were separated from all hitherto described Pedobacter species. Group I (n=8) was closest to Pedobacter aquatilis (97.8 % 16S rRNA gene sequence similarity). Group II (n=2) and group III (n=4) were closely related (98.8 % 16S rRNA gene sequence similarity) and had Pedobacter jejuensis as their common nearest neighbour. Group IV (n=3) was distantly delineated from the remaining Pedobacter species. Differentiation of the analysed strains into four clusters was further confirmed by repetitive sequence-based PCR fingerprinting, ribotyping, DNA-DNA hybridization and phenotypic traits. Common to representative strains for the four groups were the presence of major menaquinone MK-7, sym-homospermidine as the major polyamine, phosphatidylethanolamine, two unidentified lipids (L2, L5) and an unidentified aminolipid (AL2) as the major polar lipids, presence of an alkali-stable lipid, and C16:1ω7c/C16:1ω6c (summed feature 3), iso-C15:0 and iso-C 17:0 3-OH as the major fatty acids, which corresponded to characteristics of the genus Pedobacter. The obtained results showed that the strains analysed represent four novel species of the genus Pedobacter, for which the names Pedobacter jamesrossensis sp. nov. (type strain CCM 8689T=LMG 29684T), Pedobacter lithocola sp. nov. (CCM 8691T=LMG 29685T), Pedobacter mendelii sp. nov. (CCM 8685T=LMG 29688T) and Pedobacter petrophilus sp. nov. (CCM 8687T=LMG 29686T) are proposed.

Molecular identification of bacterial endosymbionts of Sappinia strains.

The genus Sappinia comprises free-living amoebae occurring worldwide in a variety of habitats such as soils, plant matter and freshwater ponds, but also animal faeces, and includes at present three species, S. pedata, S. diploidea and S. platani. The genus is potentially pathogenic, as indicated by the identification of S. pedata in a case of human amoebic encephalitis. Electron microscopy studies on some strains already revealed intracellular bacteria in Sappinia. In the current study, we performed 16S ribosomal RNA gene (rDNA) analysis of these bacterial endosymbionts. We first inferred relationships among Sappinia strains on the basis of 18S rDNA, demonstrating that S. pedata emerged as sister to a larger clade including S. diploidea, S. platani and a few 'S. diploidea-like' strains. Thus, bacterial 16S rDNA was searched for in representative strains of each Sappinia species/subgroup. We found that Sappinia strains were associated to distinct species of Flavobacterium or Pedobacter (phylum Bacteroidetes). These appear to be distributed following the amoebal host subgroups, and are not directly related to other Bacteroidetes species known as interacting with free-living amoebae. While all the endosymbionts' close relatives are known to grow on agar, bacteriological media inoculated with amoebal extracts remained negative. Overall, results indicate that the recovered bacteria are likely specific obligate endosymbionts of Sappinia species. Further studies, including additional amoebal strains and deep morphological and molecular analyses, will be necessary to confirm this hypothesis.

Pedobacter humi sp. nov., isolated from a playground soil.

A Gram-stain-negative, aerobic, non-motile, rod-shaped and yellow-pigmented bacterium, designated strain THG S15-2T, was isolated from playground soil in Sindorim-dong, Guro-gu, Seoul, South Korea. According to 16S rRNA gene sequence comparisons, strain THG S15-2T was found to be related most closely to Pedobacter ginsengisoli Gsoil 104T (97.5 % similarity), Pedobacter panaciterrae Gsoil 042T (97.4 %), Pedobacter seoulensis THG-G12T (97.1 %) and Pedobacter caeni LMG 22862T (97.1 %). The level of DNA-DNA relatedness between strain THG S15-2T and its phylogenetically closest neighbours was below 30.0 %. The only isoprenoid quinone detected in strain THG S15-2T was menaquinone-7. The DNA G+C content was 45.9 mol%. The major polar lipid was phosphatidylethanolamine. The major component in the polyamine pattern was sym-homospermidine. The major fatty acids were identified as summed feature 3 (C16:1ω7c and/or C16:1ω6c), iso-C15:0 and C16:0. These data supported the affiliation of strain THG S15-2T to the genus Pedobacter. Strain THG S15-2T was distinguished from related Pedobacter species by physiological and biochemical tests. Therefore, strain THG S15-2T represents a novel species, for which the name Pedobacter humi sp. nov. is proposed. The type strain is THG S15-2T (= KCTC 42735T = CCTCC AB 2015293T).

Aerobic sludge granulation in a Reverse Flow Baffled Reactor (RFBR) operated in continuous-flow mode for wastewater treatment

A novel Reverse Flow Baffled Reactor (RFBR) was constructed to achieve aerobic granulation in continuous-flow process in order to treat the high quantity of influent wastewater. Municipal wastewater was fed to a 120L reactor and successfully produced aerobic granules revealing a sludge volume index (SVI) of 33mL/g. Aerobic granules possessed higher extracellular polymeric substances (EPS) content than seed sludge. The protein/polysaccharide (PN/PS) ratio in the EPS was determined to be about 10:1. Bacterial community analysis revealed that most of the species (Bacteroidetes, Nitrospira and Proteobacteria) found in the seed sludge were preserved in the reactor, except Pedobacter species that was washed out from the reactor. Moreover, different bacterial species were identified in RFBR and SBR (sequencing batch reactor) granules due to different process and operational parameters. Presence of Fe, Ca, Al, Si and P in wastewater were aggregated in granules (acted as a core) and enhanced the granulation. However, the RFBR was operated in periodic feast-famine condition, short settling time, high height/diameter (H/D) ratio, and without sludge return pump, which led to successful granulation in continuous-flow mode.

Diversity of bacterial isolates during full scale rotary drum composting

Bacterial diversity of full scale rotary drum composter from biodegradable organic waste samples were analyzed through two different approaches, i.e., Culture dependent and independent techniques. Culture-dependent enumerations for indigenous population of bacterial isolates mainly total heterotrophic bacteria (Bacillus species, Pseudomonas species and Enterobacter species), Fecal Coliforms, Fecal Streptococci, Escherichia coli, Salmonella species and Shigella species showed reduction during the composting period. On the other hand, Culture-independent method using PCR amplification of specific 16S rRNA sequences identified the presence of Acinetobacter species, Actinobacteria species, Bacillus species, Clostridium species, Hydrogenophaga species, Butyrivibrio species, Pedobacter species, Empedobactor species and Flavobacterium species by sequences clustering in the phylogenetic tree. Furthermore, correlating physico-chemical analysis of samples with bacterial diversity revealed the bacterial communities have undergone changes, possibly linked to the variations in temperature and availability of new metabolic substrates while decomposing organics at different stages of composting.

Pedobacter namyangjuensis sp. nov. isolated from soil and reclassification of Nubsella zeaxanthinifaciens Asker et al. 2008 as Pedobacter zeaxanthinifaciens comb. nov.

A Gram-stain-negative, non-motile, strictly aerobic, yellow-pigmented bacterium, designated strain 5G38(T), was isolated from a field cultivated with Chinese cabbage in Korea. The strain grew at 5-40°C and at pH 6.0-8.0. 16S rRNA gene sequence analysis revealed that strain 5G38(T) represented a distinct lineage within the family Sphingobacteriaceae and showed the highest 16S rRNA gene sequence similarity of 95.2% with Pedobacter koreensis WPCB189(T), followed by Pedobacter agri PB92(T) (94.6%), Pedobacter suwonensis 15-52(T) (94.4%), Pedobacter rhizosphaerae 01-96(T) (94.4%), Pedobacter sandarakinus DS-27(T) (94.4%), and Nubsella zeaxanthinifaciens TDMA-5(T) (94.3%). Strain 5G38(T) formed monophyletic clade with Nubsella zeaxanthinifaciens in the cluster comprised of species of the genus Pedobacter. Chemotaxonomic characteristics of the novel strains, including DNA G+C content of genomic DNA (37.0 mol%), the predominant respiratory quinine (MK-7), and the major fatty acids which were iso-C15:0, summed feature 3 (comprising C16:1 ω7c and/or iso-C15:0 2-OH) and iso-C17:0 3-OH, are similar to those of the genus Pedobacter. However, the novel strains can be distinguished from the other species of Pedobacter by physiological properties. The name Pedobacter namyangjuensis sp. nov. is therefore proposed for strain 5G38(T) (KACC 13938(T) =NBRC 107692(T)) as the type strain. Furthermore, the reclassification of Nubsella zeaxanthinifaciens as Pedobacter zeaxanthinifaciens comb. nov. is proposed.

Pedobacter jeongneungensis sp. nov., isolated from forest soil

Strain BH45(T) was isolated from forest soil of Mt. Bukhan in Jeongneung, Seoul, Korea. The Gram-staining-negative strain BH45(T) grows at 4-30°C (optimum of 25-30°C) and between pH 5-8 (optimum of pH 6-8). Its major cellular fatty acids are C(18:3) ω6c (6,9,12) and C(10:0). The G+C content of genomic DNA was 40.2 mol%. The major respiratory quinone system in strain BH45(T) is menaquinone-7. Phylogenetic analysis based on 16S rRNA gene sequences indicates that strain BH45(T) is closely related to the genus Pedobacter. Sequence similarities with P. terrae KCTC 12762(T), P. suwonensis KACC 11317(T), P. soli KACC 14939(T), P. alluvionis DSM 19624(T), P. roseus KCCM 42272(T), P. yonginense KCTC 22721(T) were 97.5, 97.1, 97.0, 97.0, 97.0, and 96.0%, respectively. DNA-DNA hybridization results distinguish strain BH45(T) from two Pedobacter species with high 16S rRNA gene sequence similarities. According to the phenotypic and molecular data, the strain BH45(T) clearly represents a novel species within the genus Pedobacter; thus, the name Pedobacter jeongneungensis sp. nov. is proposed for this strain. The type strain is BH45(T) (=KACC 15514(T) =JCM 17626(T)).

Pedobacter oryzae sp. nov., isolated from rice paddy soil

A Gram-stain-negative, strictly aerobic bacterium, designated strain N7(T), was isolated from a rice paddy in South Korea. Cells of strain N7(T) were non-motile, non-spore-forming rods. Growth was observed at 15-35 degrees C (optimum of 25-30 degrees C) and between pH 6.0 and 8.0 (optimum of pH 6.5-7.5). The predominant isoprenoid quinone was menaquinone-7. The major cellular fatty acids of strain N7(T) were summed feature 3 (comprising C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH), iso-C(15 : 0), anteiso-C(15 : 0), C(15 : 0) and iso-C(16 : 0). The G+C content of the genomic DNA was 37.7 mol%. Comparative 16S rRNA gene sequence analyses showed that strain N7(T) formed a distinct phyletic line within the genus Pedobacter. Phylogenetic distances from strains of other Pedobacter species with validly published names were greater than 5.0 % (i.e. <95.0 % 16S rRNA gene sequence similarities). On the basis of phenotypic and molecular data, it is clear that strain N7(T) represents a novel species within the genus Pedobacter, for which the name Pedobacter oryzae sp. nov. is proposed. The type strain is N7(T) (=KACC 12821(T) =DSM 19973(T)).

Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil

Three Gram-negative, rod-shaped, non-spore-forming eubacterial strains were isolated in western Montana, USA, and subjected to taxonomic studies. Strains NWG-II14(T) and NWER-II11(T) were isolated from hyporheic sediments of a large alluvial flood plain, whereas strain G-1(T) was isolated from a conifer forest soil. On the basis of 16S rRNA gene sequence similarity, strains NWG-II14(T), NWER-II11(T) and G-1(T) were shown to belong to the family Sphingobacteriaceae and are most closely related to various species of the genus Pedobacter. The results of molecular, physiological and biochemical tests allowed genotypic and phenotypic differentiation of these three strains from 23 Pedobacter species with validly published names. The three isolates therefore represent novel species, for which the names Pedobacter nyackensis sp. nov. (type strain NWG-II14(T) =DSM 19625(T) =LMG 24260(T)), Pedobacter alluvionis sp. nov. (type strain NWER-II11(T) =DSM 19624(T) =LMG 24258(T)) and Pedobacter borealis sp. nov. (type strain G-1(T) =DSM 19626(T) =LMG 24259(T)) are proposed.

Pedobacter daechungensis sp. nov., from freshwater lake sediment in South Korea

A novel bacterial strain, designated Dae 13T, was isolated from sediment from a freshwater lake in Daejeon, South Korea, and was characterized taxonomically by using a polyphasic approach. The isolate was Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the genus Pedobacter in the family Sphingobacteriaceae but was clearly separate from established species of this genus. The 16S rRNA gene sequence similarities between strain Dae 13(T) and type strains of Pedobacter species with validly published names ranged from 91.6 to 97.5 %. The G+C content of the genomic DNA was 33.8 mol%. Chemotaxonomic data, i.e. the presence of MK-7 as the major menaquinone and iso-C(15 : 0), C(16 : 0) and summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c) as the major fatty acids, supported the affiliation of strain Dae 13T to the genus Pedobacter. However, the results of physiological and biochemical tests allowed phenotypic differentiation of the isolate with respect to Pedobacter species with validly published names. Therefore, strain Dae 13T represents a novel species within the genus Pedobacter, for which the name Pedobacter daechungensis sp. nov. is proposed. The type strain is Dae 13T (=KCTC 12637T=LMG 23489T).

Conversion of Lesquerolic Acid to 14-Oxo-11(Z)-Eicosenoic Acid by Genetically Variable Sphingobacterium multivorum Strains

We investigated new microbial systems for their ability to convert lesquerolic acid (LQA; 14-hydroxy-11(Z)-eicosenoic acid) to value-added products. A strain of Sphingobacterium multivorum (NRRL B-23212) was found previously to convert LQA to 14-oxo-11(Z)-eicosenoic acid (14-OEA) as determined by gas chromatography-mass spectrometry and nuclear magnetic resonance analyses. Conversion of LQA was subsequently extended to examine S. multivorum and closely related species of Pedobacter, Spirosoma, Chryseobacterium, and Flavobacterium. Among 25 of such environmental isolates, a group of bacteria, whose identity was further confirmed by 16S rRNA gene sequence analysis as S. multivorum, was the only species found to conduct LQA conversion to produce 14-OEA. Among these strains, however, NRRL B-14797 was a variant strain devoid of the specific biologic activity. A new culture medium at pH 7.0 was defined to include Fe(2+) and Mn(2+) mineral ions, glycerol, and EDTA.2Na to improve the production of 14-OEA from the initial yields of 2% to 13% to approximately > or =75% for the reactive S. multivorum strains. These S. multivorum strains represent the first group of bacteria reported to carry out the functional modification of LQA.

Pedobacter terrae sp. nov., isolated from soil

A Gram-negative, non-motile, rod-shaped bacterial strain, DS-57T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated using a polyphasic approach. It grew optimally at 25 degrees C and in trypticase soy broth without NaCl and trypticase soy broth with 0.5% NaCl. Strain DS-57T contained MK-7 as the predominant menaquinone and iso-C15:0, C16:1omega7c and/or iso-C15:0 2-OH and iso-C17:0 3-OH as the major fatty acids. The DNA G+C content was 39.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-57T was most closely related to the genus Pedobacter of the family Sphingobacteriaceae, clustering coherently with Pedobacter suwonensis, Pedobacter roseus and Pedobacter sandarakinus. Strain DS-57T exhibited 16S rRNA gene sequence similarity values of 99.2, 97.9 and 97.2% with respect to the type strains of P. suwonensis, P. roseus and P. sandarakinus, respectively, and values less than 95.6 % with respect to the type strains of other Pedobacter species. Strain DS-57T exhibited levels of DNA-DNA relatedness of 45, 17 and 15 % with respect to the type strains of P. suwonensis, P. roseus and P. sandarakinus, respectively. Differential phenotypic properties, together with the phylogenetic distinctiveness and the DNA-DNA relatedness data, were sufficient to allow the classification of strain DS-57T as a species that is separate from recognized Pedobacter species. On the basis of phenotypic properties and phylogenetic distinctiveness, therefore, strain DS-57T represents a novel species of the genus Pedobacter, for which the name Pedobacter terrae sp. nov. is proposed. The type strain is DS-57T (=KCTC 12762T=DSM 17933T).

Pedobacter duraquae sp. nov., Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet

Five isolates that were related phylogenetically to members of the genus Pedobacter were isolated from freshwater of the hard-water creek Westerhöfer Bach, North Germany. The five strains (WB 2.1-25(T), WB 2.3-71(T), WB 3.3-3(T), WB 3.3-22(T) and WB 2.3-45(T)) were Gram-negative and chemoheterotrophic, with rod-shaped cells. Most of their metabolic properties matched those given in the description of the genus Pedobacter. Consistent with the genus description, their fatty acids included mainly iso-C(15 : 0) and summed feature 3 (C(16 : 1)omega7c, iso-C(15 : 0) 2-OH or both); C(16 : 1)omega5c, C(16 : 0), iso-C(15 : 0) 3-OH, C(16 : 0) 3-OH and iso-C(17 : 0) 3-OH were present in smaller amounts. The major isoprenoid quinone was menaquinone 7. With one exception, binary similarity values of the almost complete 16S rRNA gene sequences determined among the isolates as well as between the isolates and type strains of Pedobacter species were lower than 98.5 %. The only exception was the close relationship between Pedobacter caeni DSM 16990(T) and strain WB 2.3-45(T) (99.2 % similarity). DNA-DNA reassociation values determined for this pair of strains was 29.8 %, indicating that strain WB 2.3-45(T) represents a unique genospecies. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains WB 2.1-25(T) and WB 2.3-71(T) form a group that is moderately related to P. caeni and strain WB 2.3-45(T) (98.5 % similarity). Strains WB 3.3-3(T) and WB 3.3-22(T) (98.5 % similarity) branched separately from these four organisms. The five phylogenetically isolated strains differed from each other as well as from the type strain of the type species (Pedobacter heparinus DSM 2366(T)) and some related representatives of the genus in several metabolic reactions and cultural parameters. On the basis of phenotypic and phylogenetic distinctiveness, five novel species are proposed: Pedobacter duraquae sp. nov., with WB 2.1-25(T) (=DSM 19034(T)=CIP 109481(T)) as the type strain; Pedobacter westerhofensis sp. nov., with WB 3.3-22(T) (=DSM 19036(T)=CIP 109479(T)) as the type strain; Pedobacter metabolipauper sp. nov., with WB 2.3-71(T) (=DSM 19035(T)=CIP 109480(T)) as the type strain; Pedobacter hartonius sp. nov., with WB 3.3-3(T) (=DSM 19033(T)=CIP 109468(T)) as the type strain; and Pedobacter steynii sp. nov., with WB 2.3-45(T) (=DSM 19110(T)=CIP 109507(T)) as the type strain.