Tomoko Aizawa

Mucilaginibacter kameinonensis sp., nov., isolated from garden soil.

An extracellular polysaccharide-producing bacterium, strain SCK(T), was isolated from a soil sample taken from Kameino, Fujisawa, Japan. The isolate was Gram-negative and cells were non-motile, irregular-shaped rods that grew optimally at 25 degrees C and grew between pH 5 and 8. Strain SCK(T) contained MK-7 as the major isoprenoid quinone, iso-C(15:0) and C(16:1)omega7c and/or iso-C(15:0) 2-OH as the major fatty acids and sphingolipids, with d-17:0 as the main dihydrosphingosine. Flexirubin-type pigments were also present. The DNA G+C content was 43.7 mol%. On the basis of 16S rRNA gene sequence analysis, strain SCK(T) was shown to belong to the genus Mucilaginibacter. The 16S rRNA gene sequence similarity between strain SCK(T) and the two type strains of Mucilaginibacter was 93%. The results of physiological and biochemical tests allowed phenotypic differentiation of the strain from published Mucilaginibacter species. Therefore, strain SCK(T) represents a novel species, for which the name Mucilaginibacter kameinonensis sp. nov. is proposed. The type strain is SCK(T) (=NBRC 102645(T) =KCTC 22227(T)).

Burkholderia acidipaludis sp. nov., aluminium- tolerant 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, non-spore-forming rods, 0.6-0.7 mum wide and 1.3-1.7 mum long. These strains showed good growth at pH 3.0-8.0 and 17-37 degrees C. The organisms contained ubiquinone Q-8 as the predominant isoprenoid quinone and C(16 : 0), C(18 : 1) ω 7c 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) (=NBRC 101816(T) =VTCC-D6-6(T)). Strain 7A078 (=NBRC 103872 =BCC 36999) is a reference strain.

Burkholderia heleia sp. nov., a nitrogen-fixing bacterium isolated from an aquatic plant, Eleocharis dulcis, that grows in highly acidic swamps in actual acid sulfate soil areas of Vietnam

Nitrogen-fixing bacteria, strains SA41(T), 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 microm and a length of 1.5-1.7 microm. They showed good growth between pH 3.0 and 7.0, and between 17 and 37 degrees C. The organisms contained ubiquinone Q-8 as the predominant isoprenoid quinone, and C(16 : 0), C(17 : 0) cyclo, C(18 : 1) omega7c and summed feature 3 (C(16 : 1) omega7c and/or iso-C(15 : 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 SA41(T) 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 SA41(T), SA42 and SA53 represent a novel species for which the name Burkholderia heleia sp. nov. is proposed. The type strain is SA41(T) (=NBRC 101817(T)=VTCC-D6-7(T)).

Acidocella aluminiidurans sp. nov., an aluminium-tolerant bacterium isolated from Panicum repens grown in a highly acidic swamp in actual acid sulfate soil area of Vietnam.

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 microm wide and 1.2-1.6 microm 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) (=NBRC 104303(T) =VTCC-D9-1(T)).

Burkholderia bannensis sp. nov., an acid- neutralizing bacterium isolated from torpedo grass (Panicum repens) growing in highly acidic swamps

Two strains of acid-neutralizing bacteria, E25(T) and E21, were isolated from torpedo grass (Panicum repens) growing in highly acidic swamps (pH 2-4) in actual acid sulfate soil areas of Thailand. Cells of the strains were gram-negative, aerobic, non-spore-forming rods, 0.6-0.8 µm wide and 1.6-2.1 µm long. The strains showed good growth at pH 4.0-8.0 and 17-37 °C. The organisms contained ubiquinone Q-8 as the predominant isoprenoid quinone and C(16 : 0), C(17 : 0) cyclo and C(18 : 1)ω7c as the major fatty acids. Their fatty acid profiles were similar to those reported for other Burkholderia species. The DNA G+C content of the strains was 65 mol%. On the basis of 16S rRNA gene sequence similarity, the strains were shown to belong to the genus Burkholderia. Although the calculated 16S rRNA gene sequence similarity of E25(T) to strain E21 and the type strains of Burkholderia unamae, B. tropica, B. sacchari, B. nodosa and B. mimosarum was 100, 98.7, 98.6, 97.6, 97.4 and 97.3 %, respectively, strains E25(T) and E21 formed a group that was distinct in the phylogenetic tree; the DNA-DNA relatedness of E25(T) to E21 and B. unamae CIP 107921(T), B. tropica LMG 22274(T), B. sacchari LMG 19450(T), B. nodosa LMG 23741(T) and B. mimosarum LMG 23256(T) was 90, 42, 42, 42, 45 and 35 %, respectively. The results of physiological and biochemical tests including whole-cell protein pattern analysis allowed phenotypic differentiation of these strains from previously described Burkholderia species. Therefore, strains E25(T) and E21 represent a novel species, for which the name Burkholderia bannensis sp. nov. is proposed. The type strain is E25(T) ( = NBRC 103871(T)  = BCC 36998(T)).

Bacillus trypoxylicola sp. nov., xylanase-producing alkaliphilic bacteria isolated from the guts of Japanese horned beetle larvae (Trypoxylus dichotomus septentrionalis)

Three xylanase-producing alkaliphilic strains, SU1(T), 36AC4 and 36AC6, were isolated from the guts of larvae of the Japanese horned beetle (Trypoxylus dichotomus septentrionalis). The isolates stained Gram-positive and were aerobic, spore-forming, non-motile and rod-shaped and grew optimally at 30 degrees C and pH 9. They contained MK-7 as the major isoprenoid quinone and iso-C(15 : 0), anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(17 : 0) as the major fatty acids. The DNA G+C contents of the strains were 37.4-37.7 mol%. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the genus Bacillus. Although their 16S rRNA gene sequence similarity to the type strains of the alkaliphilic species Bacillus pseudalcaliphilus and B. alcalophilus was 97 %, the novel isolates formed a distinct group in the phylogenetic trees and DNA-DNA relatedness values to the type strains of these species were less than 30 %. Results of physiological and biochemical tests, including salt preference, enabled these strains to be differentiated phenotypically from described Bacillus species. Therefore, strains SU1(T), 36AC4 and 36AC6 represent a novel species for which the name Bacillus trypoxylicola sp. nov. is proposed; the type strain is SU1(T) (=NBRC 102646(T) =KCTC 13244(T)).

Evasion of Innate Immune Responses by the Highly Virulent Cryptococcus gattii by Altering Capsule Glucuronoxylomannan Structure.

Cryptococcus neoformans causes life-threatening diseases mainly in immunosuppressed hosts such as AIDS patients; C. gattii causes disseminated infections even in healthy hosts. To identify the possible molecular mechanisms underlying this difference in virulence, we investigated the survival and histopathology of lung tissue in wild-type and CD4-depleted mice infected with C. neoformans H99 and C. gattii JP02 (the highly virulent strain isolated in Japan); we then compared dendritic cell (DC) cytokine release responses to different cell fractions from these two strains. JP02-infected mice exhibited shorter survival and fewer inflammatory cells in the lung than H99-infected control mice. Depletion of CD4-related cellular immunity reduced survival of H99-infected mice but had no effect on the survival or inflammatory cell infiltration in JP02-infected mice, suggesting that JP02 evades immune detection. To identify the molecule(s) conferring this difference, we measured cytokine production from murine DCs co-cultured with H99 and JP02 in vitro. The levels of inflammatory cytokines from DCs treated with intact JP02 cells, the extracted capsule, secreted extracellular polysaccharides, and purified glucuronoxylomannan (GXM) were markedly lower than those induced by intact H99 cells and corresponding H99 fractions. Structural analysis of GXM indicated that JP02 altered one of two O-acetyl groups detected in the H99 GXM. Deacetylated GXM lost the ability to induce inflammatory cytokine release from DCs, implicating these O-acetyl groups in immune recognition. We conclude that the highly virulent C. gattii processes a structural alteration in GXM that allows this pathogen to evade the immune response and therefore elimination.

High Aluminum Tolerance of Rhodotorula sp. RS1 is Associated with Thickening of the Cell Wall Rather than Chelation of Aluminum Ions

Abstract Aluminum (Al) is very toxic to many living organisms, including plants, animals and microorganisms. However, despite many studies on Al tolerance in plants, little has been reported concerning these mechanisms in microorganisms. In this study, a red yeast, which could tolerate Al 3+ concentrations as high as 200 mmol L −1 , was isolated from acidic soils, identified as Rhodotorula sp. and designated as RS1. As the medium compositions can greatly affect the responses of microorganisms to Al, two culture mediums, glucose medium (GM) and lysogeny broth medium containing soil extract (S-LBM), were used. During growth of RS1, the pH of medium decreased in GM but increased in S-LBM. These changes in the pH of the media were not induced by Al addition. No or little secretion of organic acids was observed in RS1 growth media. Importantly, the thickness of the cell walls and the ratio of cell wall to biomass of RS1 significantly increased in GM with high Al 3+ concentrations. In the presence of 100 mmol Al L −1 , 78.0% of the total Al of whole cells was present in the thickened cell walls. The Al in cell walls was mostly bound to OH, amide and CO groups of polysaccharides. These results suggest that thickening of the cell wall in response to the high Al 3+ concentrations may play an important role in the high tolerance of RS1 to Al and that pH increase of the medium and chelation of Al ions are not involved in Al tolerance of this organism.

Complete mitochondrial genome of the aluminum-tolerant fungus Rhodotorula taiwanensis RS1 and comparative analysis of Basidiomycota mitochondrial genomes

The complete mitochondrial genome of Rhodotorula taiwanensis RS1, an aluminum‐tolerant Basidiomycota fungus, was determined and compared with the known mitochondrial genomes of 12 Basidiomycota species. The mitochondrial genome of R. taiwanensis RS1 is a circular DNA molecule of 40,392 bp and encodes the typical 15 mitochondrial proteins, 23 tRNAs, and small and large rRNAs as well as 10 intronic open reading frames. These genes are apparently transcribed in two directions and do not show syntenies in gene order with other investigated Basidiomycota species. The average G+C content (41%) of the mitochondrial genome of R. taiwanensis RS1 is the highest among the Basidiomycota species. Two introns were detected in the sequence of the atp9 gene of R. taiwanensis RS1, but not in that of other Basidiomycota species. Rhodotorula taiwanensis is the first species of the genus Rhodotorula whose full mitochondrial genome has been sequenced; and the data presented here supply valuable information for understanding the evolution of fungal mitochondrial genomes and researching the mechanism of aluminum tolerance in microorganisms.

Genome sequence determination and metagenomic characterization of a Dehalococcoides mixed culture grown on cis-1,2-dichloroethene

A Dehalococcoides-containing bacterial consortium that performed dechlorination of 0.20 mM cis-1,2-dichloroethene to ethene in 14 days was obtained from the sediment mud of the lotus field. To obtain detailed information of the consortium, the metagenome was analyzed using the short-read next-generation sequencer SOLiD 3. Matching the obtained sequence tags with the reference genome sequences indicated that the Dehalococcoides sp. in the consortium was highly homologous to Dehalococcoides mccartyi CBDB1 and BAV1. Sequence comparison with the reference sequence constructed from 16S rRNA gene sequences in a public database showed the presence of Sedimentibacter, Sulfurospirillum, Clostridium, Desulfovibrio, Parabacteroides, Alistipes, Eubacterium, Peptostreptococcus and Proteocatella in addition to Dehalococcoides sp. After further enrichment, the members of the consortium were narrowed down to almost three species. Finally, the full-length circular genome sequence of the Dehalococcoides sp. in the consortium, D. mccartyi IBARAKI, was determined by analyzing the metagenome with the single-molecule DNA sequencer PacBio RS. The accuracy of the sequence was confirmed by matching it to the tag sequences obtained by SOLiD 3. The genome is 1,451,062 nt and the number of CDS is 1566, which includes 3 rRNA genes and 47 tRNA genes. There exist twenty-eight RDase genes that are accompanied by the genes for anchor proteins. The genome exhibits significant sequence identity with other Dehalococcoides spp. throughout the genome, but there exists significant difference in the distribution RDase genes. The combination of a short-read next-generation DNA sequencer and a long-read single-molecule DNA sequencer gives detailed information of a bacterial consortium.