Aquabacterium fontiphilum sp. nov., isolated from spring water

A short-rod-shaped, Gram-negative, motile bacterial strain, designated CS-6(T), was isolated from a water sample collected from a spring located inside Nature Valley, Hsinchu County, Taiwan, and was characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Aquabacterium in the class Betaproteobacteria. The closest neighbours were Aquabacterium parvum B6(T) (96.7 % sequence similarity), Aquabacterium commune B8(T) (96.6 %) and Aquabacterium citratiphilum B4(T) (95.9 %). The predominant fatty acids were 18 : 1omega7c (30.5 %), 16 : 0 (27.9 %) and summed feature 3 (16 : 1omega7c and/or iso-15 : 0 2-OH) (22.7 %). The DNA-DNA relatedness of the strain with respect to recognized species of the genus Aquabacterium was less than 70 %. The isolate was also distinguishable from members of the genus Aquabacterium on the basis of phenotypic and biochemical characteristics. It is evident from the genotypic, chemotaxonomic and phenotypic data, therefore, that strain CS-6(T) represents a novel species of the genus Aquabacterium, for which the name Aquabacterium fontiphilum sp. nov. is proposed. The type strain is CS-6(T) (=LMG 24215(T)=BCRC 17729(T)).

Molecular detection and phylogenetic analysis of the catechol 1,2-dioxygenase gene from Gordonia spp

The C12O gene (catA gene) encodes for catechol 1,2-dioxygenase, which is a key enzyme involved in the first step catalysis of the aromatic ring in the ortho-cleavage pathway. This functional gene can be used as a marker to assess the catabolic potential of bacteria in bioremediation. C12OF and C12OR primers were designed based on the conserved regions of the CatA amino acid sequence of Actinobacteria for amplifying the catA gene from the genus Gordonia (16 Gordonia representing 11 species). The amplified catA genes (382bp) were sequenced and analyzed. In the phylogenetic tree based on the translated catA amino acid sequences, all the Gordonia segregated clearly from other closely related genera. The sequence similarity of the catA gene in Gordonia ranged from 72.4% to 99.5%, indicating that the catA gene might have evolved faster than rrn operons or the gyrB gene at the inter-species level. A single nucleotide deletion of the catA gene was observed in Gordonia amicalis CC-MJ-2a, Gordonia rhizosphera and Gordonia sputi at nucleotide position 349. This deletion led to an encoding frame shift downstream of 11 amino acid residues, from WPSVAARAPAP to GHPWRPAHLHL, which was similar to most of the non-Gordonia Actinobacteria. Such variations might influence the catabolic activities or substrate utilization patterns of catechol 1,2-dioxygenase among Gordonia.

Vogesella perlucida sp. nov., a non-pigmented bacterium isolated from spring water

A transparent, non-pigmented, Gram-negative, rod-shaped bacterium, designated strain DS-28(T), was isolated from water samples collected from a spring located in Tainan County, Taiwan. 16S rRNA gene sequence analysis indicated that the novel strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Vogesella; the only sole close neighbour of the novel strain was Vogesella indigofera ATCC 19706(T) (97.4 % 16S rRNA gene sequence similarity). The isolate was distinguished from V. indigofera on the basis of genotypic data, several phenotypic properties and an inability to produce characteristic blue-pigmented colonies on peptone agar. The fatty acid profile was slightly different from that reported for V. indigofera ATCC 19706(T). It was evident from the genotypic and phenotypic data that strain DS-28(T) represents a novel species of the genus Vogesella, for which the name Vogesella perlucida sp. nov. is proposed. The type strain is DS-28(T) (=BCRC 17730(T)=LMG 24214(T)).

Luteimonas aquatica sp. nov., isolated from fresh water from Southern Taiwan

A yellow-pigmented bacterial strain, designated RIB1-20(T), isolated from fresh water was investigated by means of a polyphasic taxonomic approach. The cells were Gram-negative, rod-shaped and non-spore-forming. Phylogenetic analyses with the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Luteimonas, its two closest neighbours being Luteimonas composti CC-YY255(T) (96.1% sequence similarity) and Luteimonas mephitis B1953/27.1(T) (95.8%). Strain RIB1-20(T) was clearly distinguished from both of those type strains using phylogenetic analysis, DNA-DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that strain RIB1-20(T) represents a novel species of the genus Luteimonas, for which the name Luteimonas aquatica sp. nov. is proposed. The type strain is RIB1-20(T) (=BCRC 17731(T) =LMG 24212(T)).

Sphingobium rhizovicinum sp. nov., isolated from rhizosphere soil of Fortunella hindsii (Champ. ex Benth.) Swingle

The taxonomic status of a pale-yellow-coloured bacterial isolate from rhizosphere soil of Fortunella hindsii (Champ. ex Benth.) Swingle was characterized using a polyphasic taxonomic approach. Comparative analysis of the 16S rRNA gene sequence showed that the isolate constituted a distinct branch within the genus Sphingobium. The generic assignment was confirmed by chemotaxonomic data, which revealed the presence of a fatty acid profile that was characteristic for the genus Sphingobium, consisting of straight-chain saturated and unsaturated as well as 2-OH fatty acids and the lack of 3-OH fatty acids, ubiquinone with ten isoprene units (Q-10) as the predominant respiratory quinone, and a polar lipid pattern that consisted of the predominant compounds phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, diphosphatidylglycerol, sphingoglycolipid and an unknown glycolipid. Spermidine was the major polyamine component. The genotypic and phenotypic data (physiology and fatty acid and polar lipid profiles) showed that the isolate merits classification as representing a novel species of the genus Sphingobium, for which the name Sphingobium rhizovicinum sp. nov. is proposed. The type strain is CC-FH12-1T (=CCM 7491(T)=BCRC 17770T) [corrected]

Application of wastewater from paper and food seasoning industries with green manure to increase soil organic carbon: a laboratory study

This laboratory scale experiment was designed to study the suitability of organic wastes from paper and food seasoning industries to improve the soil organic carbon for rice cultivation. Lignin-rich wastewater from paper industry and nitrogen-rich effluent from a food industry at suitably lower concentrations were used at two levels of green manure to enhance the soil organic carbon fraction over time. Both the groups of soils with or without Sesbania were incubated under submerged condition at 25 degrees C for 15 days. Wastewaters from paper industry (WP), food industry (WS), and a combination of WP+WS were added separately to both the treatment groups in flasks. After 103 days of incubation, from all the three treatments and control, total organic carbon and alkali-soluble organic carbon fractions were analyzed. Results indicated that in all the three treatments containing green manure amended with industrial wastewaters, the organic carbon content increased significantly. The alkali-soluble organic carbon fraction was increased by 59% in the soil amended with green manure containing WS and by 31% in the treatment without green manure compared to control. The paper mill waste water namely, WP, increased the organic carbon only in the soil containing green manure by 63%. The combined treatment of WP+WS with green manure increased alkali-soluble organic carbon fraction by 90% compared to control, while in the treatment without green manure, the organic carbon increase was 71%. Overall, the combined treatment WP+WS with green manure could increase the alkali-soluble organic carbon fraction more than all other treatments. Hence, wastewater rich in organics from paper and food industries can be efficiently used to temporarily increase the soil organic carbon content.

Chromobacterium aquaticum sp. nov., isolated from spring water samples

Strain CC-SEYA-1T, a motile, Gram-negative, non-violet-pigmented bacterium, was isolated on nutrient agar from spring-water samples collected from Yang-Ming Mountain, Taipei County, Taiwan. 16S rRNA gene sequence studies showed that the strain clustered with Chromobacterium violaceum (96.8 % similarity) and Chromobacterium subtsugae (96.5 % similarity), followed by Aquitalea magnusonii (95.8 % similarity). The fatty acid profile was slightly different from those reported for C. violaceum, C. subtsugae and A. magnusonii. The results of DNA-DNA hybridization, and physiological and biochemical tests allowed both genotypic and phenotypic differentiation of the isolate from the described Chromobacterium species. It is evident from the data obtained that the strain should be classified as a novel species in the genus Chromobacterium. The name proposed for this taxon is Chromobacterium aquaticum sp. nov.; the type strain is CC-SEYA-1T (=CCUG 55175T=BCRC 17769T).

Brachybacterium phenoliresistens sp. nov., isolated from oil-contaminated coastal sand

A coccoid- to ovoid-shaped, Gram-positive, non-motile bacterial strain, designated phenol-AT, was isolated from an oil-contaminated coastal sand sample collected from Pingtung County, southern Taiwan, and characterized by use of a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Brachybacterium in the family Dermabacteraceae, class Actinobacteria. The closest neighbours were Brachybacterium rhamnosum LMG 19848T (96.9% 16S rRNA gene sequence similarity), Brachybacterium nesterenkovii DSM 9573T (97.0%) and Brachybacterium muris C3H-21T (96.3%). The peptidoglycan type of strain phenol-AT was variation A4gamma with meso-diaminopimelic acid as the diagnostic cell-wall diamino acid. The isolate contained MK-7 as the major component of the quinone system. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, and unidentified phospholipids and glycolipids. The predominant fatty acid was anteiso-C15:0 (59.5%); significant amounts of iso-C16:0 (9.4%), iso-C14:0 (9.5%) and anteiso-C17:0 (10.8%) were also present. The isolate was also distinguished from recognized members of the genus Brachybacterium on the basis of several phenotypic and biochemical characteristics. It is evident from the genotypic, chemotaxonomic and phenotypic data that isolate phenol-AT represents a novel species of the genus Brachybacterium, for which the name Brachybacterium phenoliresistens sp. nov. is proposed. The type strain is phenol-AT (=LMG 23707T=BCRC 17589T).