Silvimonas terrae gen. nov., sp. nov., a novel chitin-degrading facultative anaerobe belonging to the ‘Betaproteobacteria’

A novel endo-type chitinase possessing chitobiase activity derived from the chitinolytic bacterium, Chitiniphilus shinanonensis SAY3T

One of the chitinases (ChiG) derived from the chitinolytic bacterium Chitiniphilus shinanonensis SAY3T exhibited chitobiase activity cleaving dimers of N-acetyl-D-glucosamine (GlcNAc) into monomers, which is not detected in typical endo-type chitinases. Analysis of the reaction products for GlcNAc hexamers revealed that all the five internal glycosidic bonds were cleaved at the initial stage. The overall reaction catalyzed by chitobiases toward GlcNAc dimers was similar to that catalyzed by N-acetyl-D-glucosaminidases (NAGs). SAY3 possesses two NAGs (ChiI and ChiT) that are thought to be important in chitin catabolism. Unexpectedly, a triple gene-disrupted mutant (ΔchiIΔchiTΔchiG) was still able to grow on synthetic medium containing GlcNAc dimers or powdered chitin, similar to the wild-type SAY3, although it exhibited only 3% of total cellular NAG activity compared to the wild-type. This indicates the presence of unidentified enzyme(s) capable of supporting normal bacterial growth on the chitin medium by NAG activity compensation.

Silvimonas soli sp. nov., a new member of Chromobacteriaceae isolated from soil in Norrbyskär island, Sweden

A novel bacterial species is described that was isolated from the soil of Norrbyskär island (Sweden). This Gram-negative, facultatively anaerobic and motile rod, designated 17-6T, was classified in the family Chromobacteriaceae, class Betaproteobacteria, and further characterized by a polyphasic approach. Comparative 16S rRNA gene analysis revealed the potential species novelty of the strain, with Silvimonas terrae (98.20 % similarity) and Silvimonas amylolytica (98.13 %) being its closest type strains. The phylogenetic novelty of the isolate at the level of species was confirmed using phylogenetic analyses based on the whole genome: average nucleotide identity values ranged from 79 to 81 %, average amino acid identity values from 75 to 81 % and percentage of conserved proteins values from 69-81 % with the members of genera Silvimonas and Amantichitinum. On the basis of phenotypic, phylogenetic, functional and genotypic analyses, we propose the isolate as the type strain of a novel species within the genus Silvimonas with the designation Silvimonas soli 17-6T (=DSM 115342T=CCM 9308T).

Phylogenomics and molecular signatures support division of the order Neisseriales into emended families Neisseriaceae and Chromobacteriaceae and three new families Aquaspirillaceae fam. nov., Chitinibacteraceae fam. nov., and Leeiaceae fam. nov

The order Neisseriales contains 37 genera harboring 122 species with validly published names, which are placed into two families, Neisseriaceae and Chromobacteriaceae. Genome sequences are now available for 35 of the 37 Neisseriales genera for reliably determining their evolutionary relationships and taxonomy. We report here comprehensive phylogenomic and comparative analyses on protein sequences from 110 Neisseriales genomes plus 3 Chitinimonas genomes using multiple approaches. In a phylogenomic tree based on 596 core proteins, Neisseriales species formed 5 strongly supported clades. In addition to the clades for Neisseriaceae and Chromobacteriaceae families, three novel species clades designated as the "Chitinibacteraceae", "Aquaspirillaceae", and "Leeiaceae" were observed. The genus Chitinimonas grouped reliably with members of the "Chitinibacteraceae" clade. The major clades within the order Neisseriales can also be distinguished based on average amino acid identity analysis. In parallel, our comparative genomic studies have identified 30 conserved signature indels (CSIs) that are specific for members of the order Neisseriales or its five main clades. One of these CSIs is uniquely shared by all Neisseriales, whereas 8, 4, 9, 3 and 5 CSIs are distinctive characteristics of the Neisseriaceae, Chromobacteriaceae, "Chitinibacteraceae", "Aquaspirillaceae" and "Leeiaceae" clades, respectively. Based on the strong phylogenetic and molecular evidence presented here, we are proposing that the three newly identified clades should be recognized as novel families (Chitinibacteraceae fam. nov., Aquaspirillaceae fam. nov. and Leeiaceae fam. nov.) within the order Neisseriales. In addition, we are also emending descriptions of the families Neisseriaceae and Chromobacteriaceae regarding their constituent genera and other distinguishing characteristics.

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

Community assembly processes generate shifts in species abundances that influence ecosystem cycling of carbon and nutrients, yet our understanding of assembly remains largely separate from ecosystem-level functioning. Here, we investigate relationships between assembly and changes in microbial metabolism across space and time in hyporheic microbial communities. We pair sampling of two habitat types (i.e., attached and planktonic) through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally explicit multivariate statistics. We demonstrate that multiple selective pressures-imposed by sediment and porewater physicochemistry-integrate to generate changes in microbial community composition at distinct timescales among habitat types. These changes in composition are reflective of contrasting associations of Betaproteobacteria and Thaumarchaeota with ecological selection and with seasonal changes in microbial metabolism. We present a conceptual model based on our results in which metabolism increases when oscillating selective pressures oppose temporally stable selective pressures. Our conceptual model is pertinent to both macrobial and microbial systems experiencing multiple selective pressures and presents an avenue for assimilating community assembly processes into predictions of ecosystem-level functioning.

Rivicola pingtungensis gen. nov., sp. nov., a new member of the family Neisseriaceae isolated from a freshwater river

A bacterial strain, designated Npb-03(T), was isolated from a freshwater river in Taiwan and was characterized using a polyphasic taxonomic approach. The cells were Gram-reaction-negative, straight rod-shaped, non-motile, non-spore-forming and facultatively anaerobic. Growth occurred at 10-37 °C (optimum, 30-35 °C), at pH 6.0-8.0 (optimum, pH 6.0-7.0) and with 0-1.0% NaCl (optimum, 0%). The predominant fatty acids were summed feature 3 (comprising C(16 : 1)ω7c and/or C(16 : 1)ω6c) and C(16 : 0). The major isoprenoid quinone was Q-8 and the DNA G+C content was 64.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminolipid and three uncharacterized phospholipids. The major polyamines were putrescine, 2-hydroxyputrescine, cadaverine and spermidine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-03(T) forms a distinct lineage with respect to closely related genera within the family Neisseriaceae of the class Betaproteobacteria, most closely related to the genera Aquaspirillum, Laribacter, Leeia and Microvirgula, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93%. On the basis of the genotypic and phenotypic data, strain Npb-03(T) represents a novel genus and species of the family Neisseriaceae, for which the name Rivicola pingtungensis gen. nov., sp. nov. is proposed. The type strain is Npb-03(T) ( = BCRC 80376(T) = LMG 26668(T) = KCTC 23712(T)).

Phylogenomics and molecular signatures for the order Neisseriales: proposal for division of the order Neisseriales into the emended family Neisseriaceae and Chromobacteriaceae fam. nov

The species from the order Neisseriales are currently distinguished from other bacteria on the basis of branching in 16S rRNA gene trees. For this order containing a single family, Neisseriaceae, no distinctive molecular, biochemical, or phenotypic characters are presently known. We report here detailed phylogenetic and comparative analyses on the 27 genome sequenced species of the order Neisseriales. Our comparative genomic analyses have identified 54 conserved signature indels (CSIs) in widely distributed proteins that are specific for either all of the sequenced Neisseriales species or a number of clades within this order that are also supported by phylogenetic analyses. Of these CSIs, 11 are specifically present in all of the sequenced species from this order, but are not found in homologous proteins from any other bacteria. These CSIs provide novel molecular markers specific for, and delimiting, this order. Twenty-one CSIs in diverse proteins are specific for a group comprised of the genera Neisseria, Eikenella, Kingella, and Simonsiella (Clade I), which are obligate host-associated organisms, lacking flagella and exhibiting varied morphology. The species from these genera also formed a strongly supported clade in phylogenetic trees based upon concatenated protein sequences; a monophyletic grouping of these genera and other genera displaying similar morphological characteristics was also observed in the 16S rRNA gene tree. A second clade (Clade II), supported by seven of the identified CSIs and phylogenetic trees based upon concatenated protein sequences, grouped together species from the genera Chromobacterium, Laribacter, and Pseudogulbenkiania that are rod-shaped bacteria, which display flagella-based motility and are capable of free living. The remainder of the CSIs were uniquely shared by smaller groups within these two main clades. Our analyses also provide novel insights into the evolutionary history of the Neisseriales and suggest that the CSIs that are specific for the Clade I species may play an important role in the evolution of obligate host-association within this order. On the basis of phylogenetic analysis, the identified CSIs, and conserved phenotypic characteristics of different Neisseriales genera, we propose a division of this order into two families: an emended family Neisseriaceae (corresponding to Clade I) containing the genera Alysiella, Bergeriella, Conchiformibius, Eikenella, Kingella, Neisseria, Simonsiella, Stenoxybacter, Uruburuella and Vitreoscilla and a new family, Chromobacteriaceae fam. nov., harboring the remainder of the genera from this order (viz. Andreprevotia, Aquaspirillum, Aquitalea, Chitinibacter, Chitinilyticum, Chitiniphilus, Chromobacterium, Deefgea, Formivibrio, Gulbenkiania, Iodobacter, Jeongeupia, Laribacter, Leeia, Microvirgula, Paludibacterium, Pseudogulbenkiania, Silvimonas, and Vogesella).

Amantichitinum ursilacus gen. nov., sp. nov., a chitin-degrading bacterium isolated from soil

A bacterial strain named IGB-41(T) was isolated from a soil sample from an ant hill near Stuttgart, Germany. The strain was Gram-negative, rod-shaped, motile and facultatively anaerobic. Phylogenetic analysis based on 16S rRNA grouped the strain IGB-41(T) within the class Betaproteobacteria into the family Neisseriaceae together with Silvimonas amylolytica NBRC 103189(T), Silvimonas iriomotensis NBRC 103188(T) and Silvimonas terrae KM-45(T) as the closest relatives with sequence similarities of 96.7, 96.6 and 96.1 %, respectively. The G+C content of the genomic DNA was determined to be 61.5 mol% and quinone analysis revealed Q-8 as the only detectable quinone. Major cellular fatty acids were identified as C(16 : 0), summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c) and C(18 : 1)ω7c . Strain IGB-41(T) was unique in harbouring phosphoaminolipids, aminolipids and glycoaminolipids when compared with Silvimonas amylolytica NBRC 103189(T) in polar lipid analysis. On the basis of the physiological, phenotypic and genotypic characteristics of strain IGB-41(T), we suggest that the novel strain should be assigned to a new genus Amantichitinum and novel species Amantichitinum ursilacus. The type species of the genus Amantichitinum is Amantichitinum ursilacus and the type strain is IGB-41(T) (=DSM 23761(T) =CIP 110167(T)).

Variability of soil organic carbon reservation capability between coastal salt marsh and riverside freshwater wetland in Chongming Dongtan and its microbial mechanism

Two representative zones in Chongming Dongtan which faced the Yangtze River and East China Sea respectively were selected to study the variability of soil organic carbon (SOC) reservation capability between coastal wetland and riverside wetland in the Chongming Dongtan wetland as well as its mechanism by analyzing soil characteristics and plant biomass. The results showed the SOC content of riverside wetland was only 48.61% (P = 0.000 < 0.05) that of coastal wetland. As the organic matter inputs from plant litter of the coastal wetland and riverside wetland were approximately the same, the higher soil microbial respiration (SMR) of riverside wetland led to its lower SOC reservation capability. In the riverside wetland, the high soil microbial biomass, higher proportion of beta-Proteobacteria, which have strong carbon metabolism activity and the existence of some specific aerobic heterotrophic bacteria such as Bacilli and uncultured Lactococcus, were the important reasons for the higher SMR compared to the coastal wetland. There were additional differences in soil physical and chemical characteristics between the coastal wetland and riverside wetlands. Path analysis of predominant bacteria and microbial biomass showed that soil salinity influenced beta-Proteobacteria and microbial biomass most negatively among these physical and chemical factors. Therefore the low salinity of the riverside area was suitable for the growth of microorganisms, especially beta-Proteobacteria and some specific bacteria, which led to the high SMR and low SOC reservation capability when compared to the coastal area.

Endogeic earthworms shape bacterial functional communities and affect organic matter mineralization in a tropical soil

Priming effect (PE) is defined as a stimulation of the mineralization of soil organic matter (SOM) following a supply of fresh organic matter. This process can have important consequences on the fate of SOM and on the management of residues in agricultural soils, especially in tropical regions where soil fertility is essentially based on the management of organic matter. Earthworms are ecosystem engineers known to affect the dynamics of SOM. Endogeic earthworms ingest large amounts of soil and assimilate a part of organic matter it contains. During gut transit, microorganisms are transported to new substrates and their activity is stimulated by (i) the production of readily assimilable organic matter (mucus) and (ii) the possible presence of fresh organic residues in the ingested soil. The objective of our study was to see (i) whether earthworms impact the PE intensity when a fresh residue is added to a tropical soil and (ii) whether this impact is linked to a stimulation/inhibition of bacterial taxa, and which taxa are affected. A tropical soil from Madagascar was incubated in the laboratory, with a (13)C wheat straw residue, in the presence or absence of a peregrine endogeic tropical earthworm, Pontoscolex corethrurus. Emissions of (12)CO(2) and (13)CO(2) were followed during 16 days. The coupling between DNA-SIP (stable isotope probing) and pyrosequencing showed that stimulation of both the mineralization of wheat residues and the PE can be linked to the stimulation of several groups especially belonging to the Bacteroidetes phylum.

Chitinivorax tropicus gen. nov., sp. nov., a chitinolytic bacterium isolated from a freshwater lake

A facultatively anaerobic, chitinolytic bacterium, strain KL-9(T), was isolated from a freshwater lake in Taiwan and characterized by using a polyphasic taxonomic approach. Cells of strain KL-9(T) were gram-negative, rod-shaped, motile by means of a single polar flagellum and non-spore-forming. Growth occurred at 15-40 °C (optimum, 30-37 °C), at pH 7.0-9.0 (optimum, pH 8.0) and with 0-1.0 % NaCl (optimum, 0 %). The predominant fatty acids were summed feature 3 (comprising C(16 : 1)ω7c and/or C(16 : 1)ω6c) and C(16 : 0). The major isoprenoid quinone was Q-8. The DNA G+C content of strain KL-9(T) was 64.6 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine and several uncharacterized phospholipids and aminolipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KL-9(T) formed a distinct lineage with respect to closely related genera within the class Betaproteobacteria, being most closely related to members of the genera Leeia, Chitinimonas, Silvimonas and Andreprevotia. Levels of 16S rRNA gene sequence similarity with respect to the type strains of type species of these genera were below 91 %. On the basis of genotypic and phenotypic data, strain KL-9(T) is thus considered to represent a novel species of a new genus within the class Betaproteobacteria, for which the name Chitinivorax tropicus gen. nov., sp. nov. is proposed. The type strain of Chitinivorax tropicus is KL-9(T) ( = BCRC 80168(T) = LMG 25530(T)).

Chitinolyticbacter meiyuanensis SYBC-H1T, gen. nov., sp. nov., a chitin-degrading bacterium isolated from soil

A novel aerobic mesophilic bacterial strain SYBC-H1(T) capable of degrading chitin was isolated and classified in this study. The strain exhibited strong chitinolytic activity and was a Gram-negative, curved, rod-shaped, and motile bacterium. Growth of this strain was observed between 10 and 41°C and between pH 3.5 and 9.5. The DNA G + C content of strain SYBC-H1(T) was 53.25 mol%. The cellular fatty acids (>5%) were 12:0 iso 3-OH (5.87%), 16:0 (28.16%), and 18:1ω7c (20.48%). Phylogenetic analysis based on 16S rRNA gene sequence similarity revealed that strain SYBC-H1(T) belonged to the family Neisseriaceae, and was distantly related (95.0% similarity) to the genus Chitiniphilus. Its phenotype was unique and genetic and phylogenetic analysis experiments suggested that strain SYBC-H1(T) represented the type strain (CGMCC 3438(T), ATCC BAA-2140(T)) of a novel genus, for which the name Chitinolyticbacter meiyuanensis SYBC-H1(T) gen. nov., sp. nov. was proposed. The highest enzymatic activity of chitinase (9.6 U/ml) was obtained at 72 h in 250 ml shake flasks. The 16S rRNA gene sequence of SYBC-H1(T) has been deposited in GenBank under the accession number GQ981314.

Detection of Deefgea chitinilytica in freshwater ornamental fish

AIM

To identify and characterize six chitinolytic bacterial strains isolated from ornamental fish.

METHODS AND RESULTS

Six different isolates of Deefgea chitinilytica were detected in healthy as well as diseased ornamental fish in Germany over a period of 2 years. Bacterial strains were identified using 16S rRNA partial gene sequencing and further characterized using different biochemical microtest systems and additional standard biochemical tests.

CONCLUSION

We show that commercially available biochemical microtest systems are useful for identification of D. chitinilytica, supplemented by 16S rRNA partial gene sequencing. Furthermore, this study provides new information about the occurrence of D. chitinilytica, as this is the first isolation of D. chitinilytica from animals and first described isolation in Europe.

SIGNIFICANCE AND IMPACT OF THE STUDY

Deefgea chitinilytica may be isolated regularly in fish diagnostic laboratories. Therefore, accurate identification of this bacterial species is important. Involvement of D. chitinilytica in opportunistic infections of aquatic organisms cannot be excluded and has to be further investigated.

Silvimonas iriomotensis sp. nov. and Silvimonas amylolytica sp. nov., new members of the class Betaproteobacteria isolated from the subtropical zone in Japan

The taxonomic positions of two bacterial strains, ir6-1T and ir6-4T, isolated from soil collected in Iriomote Island in Japan, were determined by using a polyphasic taxonomic approach. The strains were facultatively anaerobic, motile and Gram-stain-negative rods and their optimum pH for growth was pH 4.0. Their major respiratory quinone was ubiquinone-8 and the predominant cellular fatty acids were C14 : 0, C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. The G+C content of the genomic DNA of ir6-1T and ir6-4T was 59.9 and 57.5 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strains clustered with the genus Silvimonas in the class Betaproteobacteria. DNA–DNA similarities were lower than 53 % among ir6-1T, ir6-4T and Silvimonas terrae NBRC 100961T, and these strains could be differentiated from each other by several phenotypic characters. Based on these results, we propose the emendation of the genus Silvimonas and inclusion of two novel species, Silvimonas iriomotensis sp. nov. (type strain ir6-1T=NBRC 103188T =CGMCC 1.8859T =KCTC 22513T) and Silvimonas amylolytica sp. nov. (ir6-4T =NBRC 103189T =CGMCC 1.8860T =KCTC 22514T).

Chitiniphilus shinanonensis gen. nov., sp. nov., a novel chitin-degrading bacterium belonging to Betaproteobacteria

A bacterial strain capable of degrading chitin, strain SAY3T, was isolated from moat water of Ueda Castle in Nagano Prefecture, Japan. The strain was gram-negative, curved rod-shaped, facultatively anaerobic, and motile with a single polar flagellum. It grew well with chitin as a sole carbon source. The cellular fatty acids profiles showed the presence of C16:1 omega7c and C16:0 as the major components. The G+C content of DNA was 67.6 mol% and Q-8 was the major respiratory quinone. A 16S rRNA gene sequence-based phylogenetic analysis showed the strain belonged to the family Neisseriaceae but was distantly related (94% identity) to any previously known species. Since the strain was clearly distinct from closely related genera in phenotypic and chemotaxonomic characteristics, it should be classified under a new genus and a new species. We propose the name Chitiniphilus shinanonensis gen. nov., sp. nov. The type strain is SAY3T (=NBRC 104970T=NICMB 14509T).

Jeongeupia naejangsanensis gen. nov., sp. nov., a cellulose-degrading bacterium isolated from forest soil from Naejang Mountain in Korea

A Gram-stain-negative, motile, rod-shaped, cellulose-degrading bacterial strain, BIO-TAS4-2(T), which belongs to the Betaproteobacteria , was isolated from forest soil from Naejang Mountain, Korea, and its taxonomic position was investigated by using a polyphasic study. Strain BIO-TAS4-2(T) grew optimally at pH 7.0-8.0, at 30 degrees C and in the presence of 0-1.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain BIO-TAS4-2(T) clustered with members of the genera Andreprevotia, Silvimonas and Deefgea of the family Neisseriaceae, with which it exhibited 16S rRNA gene sequence similarities of 93.5-94.2 %. Strain BIO-TAS4-2(T) contained Q-8 as the predominant ubiquinone and summed feature 3 (C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH) and C(16 : 0) as the major fatty acids. The DNA G+C content was 63.8 mol%. Strain BIO-TAS4-2(T) could be differentiated from members of phylogenetically related genera by differences in fatty acid composition, DNA G+C content and some phenotypic properties. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain BIO-TAS4-2(T) is considered to represent a novel species in a new genus, for which the name Jeongeupia naejangsanensis gen. nov., sp. nov. is proposed, with BIO-TAS4-2(T) (=KCTC 22633(T)=CCUG 57610(T)) as the type strain.

Chitinilyticum aquatile gen. nov., sp. nov., a chitinolytic bacterium isolated from a freshwater pond used for Pacific white shrimp culture

Strain c14T, originally isolated from surface water of a freshwater pond located in Pingtung (southern Taiwan) used for culture of Pacific white shrimp (Litopenaeus vannamei), was subjected to a polyphasic taxonomic approach. The strain exhibited strong chitinolytic activity and was able to grow under aerobic and anaerobic conditions by utilizing chitin exclusively as the carbon, nitrogen and energy source. Phylogenetic analysis of the 16S rRNA gene sequence revealed a clear affiliation of the proposed bacterium to the Betaproteobacteria, most closely related to Chitinibacter tainanensis S1T, Deefgea rivuli WB 3.4-79T and Silvimonas terrae KM-45T, with 94.6, 93.6 and 92.9 % 16S rRNA gene sequence similarity, respectively. The predominant fatty acids detected in cells of strain c14T were C16 : 0, C18 : 1 ω7c and summed feature 3 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH). The G+C content of the genomic DNA was 69.5 (±1.0) mol%. Biochemical, physiological, chemotaxonomic and phylogenetic analyses showed that strain c14T could not be assigned to any known genus of the Betaproteobacteria. Therefore, strain c14T is classified within a novel genus and species, for which the name Chitinilyticum aquatile gen. nov., sp. nov. is proposed. The type strain of Chitinilyticum aquatile is c14T (=LMG 23346T =BCRC 17533T).

Andreprevotia chitinilytica gen. nov., sp. nov., isolated from forest soil from Halla Mountain, Jeju Island, Korea

A motile, Gram-negative, rod-shaped bacterium, designated strain JS11-7T, was isolated from forest soil from Halla Mountain, Jeju Island, Korea. It grew optimally at 28 °C, pH 6–7 and in the presence of 0–2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JS11-7T belongs to the family Neisseriaceae, with Silvimonas terrae as its closest relative (95.0 % similarity). It contained Q-8 as the predominant quinone and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω6c), C16 : 0 and C18 : 1 ω7c as the major fatty acids. The DNA G+C content was 62 mol%. On the basis of phenotypic and genotypic characteristics and the results of 16S rRNA gene sequence analysis, strain JS11-7T represents a novel genus and species, for which the name Andreprevotia chitinilytica gen. nov., sp. nov. is proposed. The type species is Andreprevotia chitinilytica and the type strain is JS11-7T (=KACC 11608T=DSM 18519T).

Leeia oryzae gen. nov., sp. nov., isolated from a rice field in Korea

A strictly aerobic, non-spore-forming, Gram-negative bacterium, designated strain HW7T, was isolated from a rice field in Korea. Cells of strain HW7T were short rod-shaped and motile with single polar flagella. The major cellular fatty acids of strain HW7T were C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). The genomic DNA G+C content was 56 mol% and the major isoprenoid quinone was Q-8. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HW7T forms a distinct lineage with respect to closely related genera within the class Betaproteobacteria and that the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93 %. On the basis of the physiological and phylogenetic data, strain HW7T represents a novel genus and species of the Betaproteobacteria, for which the name Leeia oryzae gen. nov., sp. nov. is proposed. The type strain is HW7T (=KCTC 12585T=DSM 17879T).

Deefgea rivuli gen. nov., sp. nov., a member of the class Betaproteobacteria

Two strains, designated WB 3.4-79(T) and WB 3.3-25, were isolated from a hard-water sample collected from the Westerhöfer Bach, Lower Saxony, Germany. The strains shared 100 % DNA-DNA relatedness, indicating membership of the same genospecies. This close relationship was supported by identical 16S rRNA gene sequences and high similarities in fatty acid composition and biochemical characteristics. The G+C content of the genomic DNA of strain WB 3.4-79(T) was 48.5 mol% and the predominant ubiquinone was Q-8. Major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Major fatty acids (>10 %) were C(16 : 0) and C(16 : 1)omega7c. Polyhydroxybutyrate and polyphosphate granules as well as unidentified enterosomes and a polar organelle are visible by electron microscopy. Comparative 16S rRNA gene sequence analysis indicated that the isolates were placed within the class Betaproteobacteria, remotely related to Chitinibacter tainanensis DSM 15459(T), Silvimonas terrae KCTC 12358(T), Formivibrio citricus DSM 6150(T) and Iodobacter fluviatilis DSM 3764(T). On the basis of phylogenetic and phenotypic distinctness, we propose a novel genus, Deefgea gen. nov., with Deefgea rivuli sp. nov. as the type species. The type strain of Deefgea rivuli is strain WB 3.4-79(T) (=DSM 18356(T)=CIP 109326(T)).

Gulbenkiania mobilis gen. nov., sp. nov., isolated from treated municipal wastewater

A bacterial strain (E4FC31T) isolated from treated municipal wastewater was characterized phenotypically and phylogenetically. Cells were Gram-negative, curved rods with a polar flagellum. The isolate was catalase-, oxidase- and arginine dihydrolase-positive, and able to grow between 15 and 45 °C and between pH 5.5 and 9.0. The predominant fatty acids were C16 : 1/iso-C15 : 02-OH and C16 : 0, the major respiratory quinone was ubiquinone 8 and the G+C content of the genomic DNA was 63 mol%. 16S rRNA gene sequence analysis indicated that strain E4FC31Tbelonged to the classBetaproteobacteriaand was a member of the familyNeisseriaceae. Its closest phylogenetic neighbours wereAquitalea magnusoniiandChromobacterium violaceum(<94 % 16S rRNA gene sequence similarity). Phylogenetic analysis and phenotypic characteristics of strain E4FC31Tsuggest that it represents a novel species of a new genus, for which the nameGulbenkiania mobilisgen. nov., sp. nov. is proposed. The type strain ofGulbenkiania mobilisis E4FC31T(=DSM 18507T=LMG 23770T).