Flavobacterium arsenitoxidans sp. nov., an arsenite-oxidizing bacterium from Thai soil

Bacterial Community Structure Responds to Soil Management in the Rhizosphere of Vine Grape Vineyards

The microbial communities of the rhizospheres of vineyards have been subject to a considerable body of research, but it is still unclear how the applied soil cultivation methods are able to change the structure, composition, and level of diversity of their communities. Rhizosphere samples were collected from three neighbouring vineyards with the same time of planting and planting material (rootstock: Teleki 5C; Vitis vinifera: Müller Thurgau). Our objective was to examine the diversity occurring in bacterial community structures in vineyards that differ only in the methods of tillage procedure applied, namely intensive (INT), extensive (EXT), and abandoned (AB). For that we took samples from two depths (10-30 cm (shallow = S) and 30-50 cm (deep = D) of the grape rhizosphere in each vineyard and the laboratory and immediately prepared the slices of the roots for DNA-based analysis of the bacterial communities. Bacterial community structure was assessed by means of PCR-DGGE analysis carried out on the v3 region of 16S rRNA gene. Based on the band composition of the DGGE profiles thus obtained, the diversity of the microbial communities was evaluated and determined by the Shannon-Weaver index (H'). Between the AB and EXT vineyards at the S depth, the similarity of the community structure was 55%; however, the similarity of the D samples was more than 80%, while the difference between the INT samples and the other two was also higher than 80%. Based on our results, we can conclude that intensive cultivation strongly affects the structure and diversity of the bacterial community.

Start-Up and Performance of a Full Scale Passive System In-Cluding Biofilters for the Treatment of Fe, as and Mn in a Neutral Mine Drainage

Passive mine drainage treatment plants are the scene of many chemical and biological reactions. Here, the establishment of iron (Fe), arsenic (As), and manganese (Mn) removal was monitored immediately after the commissioning of the Lopérec (Brittany, France) passive water treatment plant, composed of aeration cascades and settling ponds followed by pozzolana biofilters. Iron and As were almost completely removed immediately after commissioning, while Mn removal took more than 28 days to reach its maximum performance. Investigations were performed during two periods presenting strong variations in feeding flow-rates: from 2.8 m3.h−1 to 8.6 m3.h−1 and from 13.2 m3.h−1 to 31.3 m3.h−1. Design flow rate was reached during the first week of the second period. Dissolved Fe and As were not affected by the decrease in residence time while Mn was only slightly affected. Microbial communities in biofilter presented similarities with those of the pond sludge, and genera including Mn-oxidizing species were detected. Proportion of bacteria carrying the aioA gene encoding for As(III)-oxidase enzyme increased in communities during the second period. Results suggest Mn removal is mainly associated with bio-oxidation whereas removal of Fe and As could be mainly attributed to chemical oxidation and precipitation of Fe, possibly helped by As(III) bio-oxidation.

Flavobacterium agrisoli sp. nov., a novel bacterium isolated from soil

A Gram-stain negative, rod shaped, motile by gliding, yellow-pigmented, aerobic bacterium, designated SE-1-e^T, was isolated from a soil sample collected on Dokdo Island, South Korea. The isolate was characterized taxonomically using a polyphasic approach based on the phenotypic and genomic analyses. The phylogenetic analysis based on 16S rRNA gene sequence revealed that strain SE-1-e^T belonged to the genus Flavobacterium in the family Flavobacteriaceae and had the highest sequence similarity with Flavobacterium cheongpyeongense IMCC34759^T (97.5%), Flavobacterium arsenitoxidans S2-3H^T (97.4%), Flavobacterium resistens BD-b365^T (97.4%), and Flavobacterium chungangense CJ7^T (97.4%). The predominant respiratory quinone of the isolate was found to be MK-6; the main polar lipid was phosphatidylethanolamine; and the major fatty acids were identified as summed feature 3 (C_16:1 ω7c/C_16:1 ω6c), C_15:0 iso, and C_16:0. The draft genome of strain SE-1-e^T had a length of 3,715,609 bp and a DNA G + C content of 34.8 mol%. The nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the novel isolate and F. cheongpyeongense IMCC34759^T, F. resistens BD-b365^T, and Flavobacterium chungangense CJ7^T ranged from 74.9 to 75.3% and from 20.2 to 20.9%, respectively. On the basis of its phenotypic properties, genotypic distinctiveness, and chemotaxonomic features, strain SE-1-e^T represents a novel species in the genus Flavobacterium, for which the name Flavobacterium agrisoli sp. nov. is proposed. The type strain is SE-1-e^T (= KCTC 82352 ^T = JCM 34302 ^T).

Flavobacterium limi sp. nov., isolated from forest mud

A Gram-stain-negative, aerobic, non-motile, yellow and rod-shaped bacterial strain was isolated from forest mud located at Kyung Hee University, South Korea. Strain THG-AG6.4^T grew at 10-35 °C, pH 6.0-9.5 and in the presence of 0-1.5 % (w/v) NaCl. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that strain THG-AG6.4^T was most closely related to Flavobacterium gyeonganense HME 7524^T (97.66 %), Flavobacterium defluvii EMB 117^T (96.93 %) and Flavobacterium arsenitoxidans S2-3H^T (96.80 %). The DNA G+C content of strain THG-AG6.4^T was 30.2 mol%. The DNA-DNA relatedness values between strain THG-AG6.4^T and its closest phylogenetic neighbour, F. gyeonganense HME 7524^T, were below 61.0 %. The predominant quinone of strain THG-AG6.4^T was MK-6. The major polar lipids were phosphatidylethanolamine, an unidentified phospholipid, five unidentified glycolipids, phosphatidylserine, an unidentified lipid, an unidentified aminophospholipid, two unidentified aminolipids and two unidentified aminoglycolipids. The major fatty acids were C16 : 0, C18 : 0 10-methyl, summed feature 3 and C18 : 1ω9c. The major polyamine was homospermidine. On the basis of the phenotypic, genotypic and phylogenetic characterization of strain THG-AG6.4^T, it is concluded that the isolate represents a novel species of the genus Flavobacterium, for which the name Flavobacterium limi sp. nov. is proposed, with THG-AG6.4^T as the type strain (=KACC 18851^T=CGMCC 1.16060^T).

Development of Culture Medium for the Isolation of Flavobacterium and Chryseobacterium from Rhizosphere Soil

An effective medium designated phosphate separately autoclaved Reasoner’s 2A supplemented with cycloheximide and tobramycin (PSR2A-C/T) has been developed for the isolation of Flavobacterium and Chryseobacterium strains from the plant rhizosphere. It consists of Reasoner’s 2A agar (R2A) prepared by autoclaving phosphate and agar separately and supplementing with 50 mg L⁻¹ cycloheximide and 1 mg L⁻¹ tobramycin. A comparison was made among the following nine media: PSR2A-C/T, PSR2A-C/T supplemented with NaCl, R2A agar, R2A agar supplemented with cycloheximide and tobramycin, 1/4-strength tryptic soy agar (TSA), 1/10-strength TSA, soil-extract agar, Schaedler anaerobe agar (SAA), and SAA supplemented with gramicidin, for the recovery of Flavobacterium and Chryseobacterium strains from the Welsh onion rhizosphere. Flavobacterium strains were only isolated on PSR2A-C/T, and the recovery rate of Chryseobacterium strains was higher from PSR2A-C/T than from the eight other media. In order to confirm the effectiveness of PSR2A-C/T, bacteria were isolated from onion rhizosphere soil with this medium. Flavobacterium and Chryseobacterium strains were successfully isolated from this sample at a similar rate to that from the Welsh onion rhizosphere.

Flavobacterium notoginsengisoli sp. nov., isolated from the rhizosphere of Panax notoginseng

Two novel bacterial strains, designated SYP-B540(T) and SYP-B556, were isolated from rhizospheric soil of Panax notoginseng located at Yunnan Province, China. Both strains were Gram-staining negative, aerobic, non-motile, elongated rod shaped and yellow coloured. They grew optimally at 28 °C and pH 7.0. Analysis of 16S rRNA gene sequences showed that the two strains shared 99.8 % sequence similarity to each other, but lower than 97.6 % to the other known species of the genus Flavobacterium. The predominant respiratory quinone for the two strains was MK-6, and the major fatty acids were iso-C15:0 and summed Feature 3 (comprising 16:1 ω7c and/or 16:1 ω6c). The polar lipids consisted of phosphatidylethanolamine, two unidentified polar lipids and three unidentified amino-phospholipids. The DNA G+C contents of strains SYP-B540(T) and SYP-B556 were 33.3 and 32.7 mol%, respectively. In addition, the DNA-DNA hybridization values of strains SYP-B540(T) and SYP-B556 to their closest phylogenetic neighbors were significantly lower than 70 %. On the basis of the polyphasic taxonomy studies, strains SYP-B540(T) and SYP-B556 represent a novel species of the genus Flavobacterium, for which the name Flavobacterium notoginsengisoli sp. nov. is proposed. The type strain is SYP-B540(T) (=KCTC 32505(T) = NBRC 110012(T) = BCRC 80724(T)).