The ammonia-producing bacteria B55T , CA73, SA69 and SA72 were isolated from the waterweeds Ludwigia adscendens (B55 T ) and Eleocharis dulcis (CA73, SA69 and SA72) grown in highly acidic swamps (pH 2-4) in actual acid sulfate soil areas of Vietnam. The isolates were Gram-positive, irregular rod-shaped, non-spore-forming bacteria. On the basis of 16S rRNA gene sequence similarity, strain B55 T was shown to belong to the genus Curtobacterium of the class Actinobacteria. Chemotaxonomic data (MK-9 as major isoprenoid quinone, D-ornithine as cell-wall diamino acid, acetyl as the acyl type of peptidoglycan) supported the affiliation of all four strains to this genus. Although their 16S rRNA gene sequence similarity was 99 % to species with validly published names within the genus, they formed a group that was distinct in the phylogenetic tree, and DNA-DNA relatedness values to these established species were less than 10 %. The results of physiological and biochemical tests and major fatty acids (cyclohexyl-C 17 : 0 , anteiso-C 17 : 0 and cyclohexyl-C 19 : 0 ) allowed phenotypic differentiation of these strains from the species of Curtobacterium with validly published names. Therefore, strains B55 T , CA73, SA69 and SA72 represent a novel species, for which the name Curtobacterium ammoniigenes sp. nov. is proposed. The type strain is B55 T (=NBRC 101786The genus Curtobacterium was first described by Yamada & Komagata (1972) and, at present, the genus comprises six recognized species, isolated from rice (Curtobacterium citreum, the type species; Komagata & Iizuka, 1964;Yamada & Komagata, 1972) Strains were grown on one-tenth-strength tryptic soy (1/10 TS) agar plates [3.0 g tryptic soy broth l 21 solidified with 15.0 g agar l 21 (Difco), pH 4.1] at 28 uC under aerobic conditions followed by selection on the basis of neutralization of 1/10 TS liquid medium (pH 4) determined by measuring the pH of culture supernatants after a 3 day cultivation period. Strain B55T was obtained from a stem of L. adscendens, and strains CA73, SA69 and SA72 were isolated from stems of E. dulcis. All strains showed growth between pH 3.5 and 8.0, with an optimum at pH 4-5. On 1/10 TS liquid medium (pH 4.1), the strains alkalinized the medium to pH 7.2 and the concentration of ammonium ions in the medium was increased from 0.14 to 0.61 mM. This increase seemed to be responsible for the neutralization since, by the addition of ammonium to fresh acidic medium to a final concentration of 0.61 mM, the pH increased from pH 4.1 to 7.2. No or little alkalinization or increase in the ammonium ion concentration was observed on 1/10 TS liquid medium of pH 7 or above. All strains showed good growth on 1/10 TS (pH 4.1) at 25-37 u C with an optimum at 30 u C, but did not grow at 4 or 45 u C. On 1/10 TS agar (pH 4.1), the organisms formed smooth, round, convex, pale-yellow colonies. The strains were Gram-positive (Ryu, 1938), non-endospore-forming and aerobic. Motility was not observed.The 16S rRNA gene of each strain was amplified by PCR using universal pr...

Nitrogen-fixing bacteria, strains SA41T, SA42 and SA53, were isolated from an aquatic plant, Eleocharis dulcis, that grows in highly acidic swamps (pH 2–4) in actual acid sulfate soil areas of Vietnam. The isolates were Gram-negative, aerobic, non-spore-forming, rod-shaped bacteria, having a cell width of 0.6–0.7 μm and a length of 1.5–1.7 μm. They showed good growth between pH 3.0 and 7.0, and between 17 and 37 °C. The organisms contained ubiquinone Q-8 as the predominant isoprenoid quinone, and C16 : 0, C17 : 0 cyclo, C18 : 1 ω7c and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) as major fatty acids. Their fatty acid profiles are similar to those reported for other Burkholderia species. The DNA G+C content of these strains was 64 mol%. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the genus Burkholderia. Although their calculated 16S rRNA gene sequence similarity values to Burkholderia silvatlantica, Burkholderia mimosarum, Burkholderia ferrariae and Burkholderia tropica were 98.5, 98.2, 98.0 and 97.0 %, respectively, the isolates formed a distinct group in phylogenetic trees, and the DNA–DNA relatedness values of strain SA41T to these species were 39, 41, 39 and 33 %, respectively. The results of physiological and biochemical tests, including whole-cell protein pattern analysis, allowed phenotypic differentiation of these strains from the published Burkholderia species. Therefore, strains SA41T, SA42 and SA53 represent a novel species for which the name Burkholderia heleia sp. nov. is proposed. The type strain is SA41T (=NBRC 101817T=VTCC-D6-7T).

Burkholderia acidipaludis sp. nov., aluminiumtolerant bacteria isolated from Chinese water chestnut (Eleocharis dulcis) growing in highly acidic swamps in South-East Asia Two strains of aluminium-tolerant bacteria, SA33 T and 7A078, were isolated from Chinese water chestnut (Eleocharis dulcis) growing in highly acidic swamps (pH 2-4) in actual acid sulfate soil areas of Vietnam (SA33 T ) and Thailand (7A078). The strains were Gram-negative, aerobic, nonspore-forming rods, 0.6-0.7 mm wide and 1.3-1.7 mm long. These strains showed good growth at pH 3.0-8.0 and 17-37 6C. The organisms contained ubiquinone Q-8 as the predominant isoprenoid quinone and C 16 : 0 , C 18 : 1 v7c and C 17 : 0 cyclo as the major fatty acids. Their fatty acid profiles were similar to those reported for other Burkholderia species. The DNA G+C content of these strains was 64 mol%. On the basis of 16S rRNA gene sequence similarity, the strains were shown to belong to the genus Burkholderia. Although the 16S rRNA gene sequence similarity values calculated for strain SA33 T to 7A078 and the type strains of Burkholderia kururiensis, B.sacchari and B. tuberum were 100, 97.3, 97.1 and 97.0 %, respectively, strains SA33 T and 7A078 formed a group that was distinct in the phylogenetic trees; the DNA-DNA relatedness of strain SA33 T to 7A078 and these three type strains were respectively 90, 47, 46 and 45 %. The results of physiological and biochemical tests, including whole-cell protein pattern analysis, allowed phenotypic differentiation of these strains from described Burkholderia species. Therefore, strains SA33 T and 7A078 represent a novel species, for which the name Burkholderia acidipaludis sp. nov. is proposed. The type strain is SA33 T (5NBRC 101816 T 5VTCC-D6-6 T ). Strain 7A078 (5NBRC 103872 5BCC 36999) is a reference strain. Yabuuchi et al. (1992) created the genus Burkholderia by the transfer of seven species from Pseudomonas, with Burkholderia cepacia as the type species. During the course of a study to develop bioremediation measures for actual acid sulfate soils (AASS; Aizawa et al., 2008;Sasaki et al., 2008), we isolated a number of bacteria associated with plants growing in highly acidic aquatic environments (pH 2-4) of AASS in South-east Asia (Aizawa et al., 2007Kimoto et al., 2010). In this present study, we characterized two pH-neutralizing bacteria, strain SA33 T , isolated from Chinese water chestnut (Eleocharis dulcis) growing in highly acidic swamps (pH 2-4) in AASS areas in Vietnam, and 7A078, isolated from E. dulcis growing in similar areas in Thailand. By a polyphasic approach, including 16S rRNA gene sequence analysis, DNA-DNA hybridization, whole-cell protein analysis, fatty acid methyl ester analysis and phenotypic and biochemical characterization, the strains were shown to be affiliated with the genus Burkholderia. The data obtained suggest that the strains represent a novel species of the genus Burkholderia.Abbreviation: AASS, actual acid sulfate soil.The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequ...

An aluminium-tolerant bacterium, strain AL46 T , was isolated from a waterweed, Panicum repens, grown in a highly acidic swamp (pH 3) at an actual acid sulfate soil area of Vietnam. Cells were Gram-negative, aerobic, non-spore-forming, non-motile rods (0.3 mm wide and 1.2-1.6 mm long). 16S rRNA gene sequence analysis indicated that strain AL46 T belongs to the genus Acidocella, class Alphaproteobacteria. Strain AL46 T was related most closely to the type strains of Acidocella facilis and Acidocella aminolytica (99.4 and 97.8 % 16S rRNA gene sequence similarity, respectively). Levels of DNA-DNA relatedness between strain AL46 T and the above type strains were 40 %. The results of physiological and biochemical tests allowed the novel strain to be differentiated phenotypically from the two recognized Acidocella species. Data for predominant cellular fatty acids (cyclopropyl C 19 : 0 and C 18 : 1 ), major isoprenoid quinone (Q-10) and DNA G+C content (65.6 mol%) were in accordance with those reported for the genus Acidocella. Therefore, strain AL46 T is considered to represent a novel species of the genus Acidocella, for which the name Acidocella aluminiidurans sp. nov. is proposed. The type strain is AL46 T (5NBRC 104303 T 5VTCC-D9-1 T ).

Although the chemical nature of soil organic matter (SOM) is thought to affect the mineralization rate of N bound in SOM, little direct evidence exists for such effects. To test the hypothesis that the N mineralization rate is affected by the degree of SOM humification, we added equivalent amounts of humic acid (HA) N as either the labile mobile humic acid (MHA) fraction or the more humified calcium humate (CaHA) fraction to two lowland rice (Oryza sativa L.) soils, which were subsequently incubated under anaerobic conditions for 6 wk. The HA fractions had been chemically extracted from seven irrigated lowland rice soils from Vietnam and the Philippines. In both incubation soils, the amount of N mineralized from the added HA fractions decreased exponentially as the optical density of the HA at 465 nm (E4, index of humification) increased (R2 = 0.94–0.98). Mineralization of humic N was also strongly negatively associated with the amount of N or C contained in each HA fraction per kilogram of soil extracted, suggesting a more recalcitrant nature of the fractions in those soils where conditions allowed them to accumulate. Nitrogen mineralization was less for both the MHA (by 26%) and CaHA (by 41%) when incubated in the International Rice Research Institute (IRRI) soil compared with the Tanhoi soil. The most plausible explanation for this decrease is increased stabilization of the added HA by the relatively abundant Ca+2 in the IRRI soil. We conclude that the degree of humification of the MHA and CaHA fractions plays an important role in governing the rate of N mineralization in lowland rice soils because (i) N mineralization from these fractions was affected by their degree of humification, and (ii) the fractions are a small but important component of total soil N.