Complete genome sequence of Bacillus subtilis NA05 (=NBRC 116153), a phosphate-solubilizing bacterium isolated from crop field soil.

We report the complete genome sequence of the phosphate-solubilizing bacterium Bacillus subtilis NA05 (=NBRC 116153), consisting of a circular chromosome of ~3.8 M bp and two circular plasmids. The data presented here provide further insight into the genetic and functional potential of B. subtilis and the mechanism of phosphate solubilization.

Bacterial and fungal community composition and community-level physiological profiles in forest soils.

We characterized the potential functioning and composition of the bacterial and fungal communities in the O and A horizons of forest soils using community-level physiological profile (CLPP) based on BIOLOG analysis, and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis of 16S and 18S rDNA fragments, respectively. In addition, relationships between the potential functioning and the community composition in each horizon, and between the O and A horizons, were assessed using Procrustes analysis. For the bacterial and fungal communities, the CLPP and DGGE profile were clearly separated between the O and A horizons in a principal coordinate analysis except for the fungal CLPP. No significant links for CLPP and DGGE profile between the O and A horizons were observed for either bacterial or fungal communities, suggesting that different factors had considerable influence on the microbial communities between the O and A horizons. Significant couplings between bacterial and fungal DGGE profiles (p <0.05 for O horizon; p <0.01 for A horizon), and between bacterial and fungal CLPPs (p = 0.001 for O horizon; p <0.01 for A horizon), were observed in the O and A horizons, implying that common factors strongly influenced the bacterial and fungal communities in each horizon. Although a significant correlation was observed between bacterial community composition and the potential functioning in the A horizon (p <0.01), such a correlation was not observed for the fungal community in the A horizon, and for the bacterial and fungal communities in the O horizon. This finding suggested that potential functioning, which would reflect only rapidly growing microorganisms, was not strongly associated with the composition of the entire microbial community. Further studies are needed to unravel the factors shaping the composition and functioning of microbial communities in forest soils.

Prokaryotic Community Structure of Long-Term Fertilization Field Andisols in Central Japan.

Long-term fertilization experiments are a useful way to elucidate the impacts of fertilization on soil ecosystems. Here, we report the prokaryotic community structure in experimental field soil after 80 years of successive fertilization. Our 16S rRNA gene sequencing detected 20,996 amplicon sequence variants, including major phyla such as Proteobacteria, Acidobacteria, and Actinobacteria.

Phosphorus-mineralizing Communities Reflect Nutrient-Rich Characteristics in Japanese Arable Andisols.

Elucidating the soil phosphorus cycle driven by soil microbes is a vital question in soil microbial ecology. The Japanese arable Andisols, occupying half of the Japanese cropland, are known for their high phosphorus sorption capacity. However, limited information is currently available on microbially driven phosphorus mineralization in arable Andisols. We herein report that the phosphorus-mineralizing community in the Japanese arable Andisols showed characteristic distribution and composition patterns, from those in other types of soils. We performed a chemical analysis and microbial community analysis of 43 arable Andisols along the Japanese archipelago. Soil phosphomonoesterase activities measured at pH 11 were approximately 70% of those at pH 6.5, which indicates that alkaline phosphatase contributes to phosphorus cycling, although most soil samples were acidic. Functional gene predictions based on 16S rRNA gene sequencing indicated that the alkaline phosphatase gene phoD was more abundant than other alkaline phosphatase genes and, thus, plays major roles. Hence, amplicon sequencing targeting phoD was performed and the results obtained showed that alphaproteobacterial phoD was dominant. This is in contrast to previously reported phoD compositions in other soils and may be attributed to the nutrient conditions in arable Andisols, which favor copiotrophic Alphaproteobacteria. Furthermore, the composition of phoD correlated with soil pH and bioavailable phosphorus concentrations rather than carbon or nitrogen concentrations. These results were partly different from previous findings, varying in the soil types and geographic ranges of sampling sites. Collectively, the present results indicate that the phosphorus-mineralizing community in the Japanese arable Andisols is regulated differently from those in other soil types.

Nitrogen supply rate regulates microbial resource allocation for synthesis of nitrogen-acquiring enzymes.

Although microorganisms will preferentially allocate resources to synthesis of nitrogen (N)-acquiring enzymes when soil N availability is low according to the resource allocation model for extracellular enzyme synthesis, a robust link between microbial N-acquiring enzyme activity and soil N concentration has not been reported. To verify this link, we measured several indices of soil N availability and enzyme activity of four N-acquiring enzymes [N-acetyl-ß-glucosaminidase (NAG), protease (PR), urease (UR), and L-asparaginase (LA)] and a carbon (C)-acquiring enzyme [ß-D-glucosidase (BG)] in arable and forest soils. Although the ratios of NAG/BG and PR/BG were not significantly related with indices of soil N availability, ratios of LA/BG and UR/BG were strongly and negatively related with potentially mineralizable N estimated by aerobic incubation but not with pools of labile inorganic N and organic N. These results suggest that microorganisms might allocate their resources to LA and UR synthesis in response to N supply rate rather than the size of the easily available N pools. It was also suggested that the underlying mechanism for synthesis was different between these N-acquiring enzymes in soil microorganisms: microbial LA and UR were primarily synthesized to acquire N, whereas NAG and PR syntheses were regulated not only by N availability but also by other factors.

Evaluating the Effects of Metals on Microorganisms in Flooded Paddy Soils Using the SEM/AVS-Based Approach and Measurements of Exchangeable Metal Concentrations.

We examined possible adverse effects of heavy metals on microbial activity, biomass, and community composition using the simultaneously extracted metals (SEM)/acid-volatile sulfide (AVS)-based approach and measurements of exchangeable metal concentrations in three paddy soils (wastewater-contaminated soil, mine-contaminated soil, and noncontaminated soil) incubated for 60 days under flooded conditions. Incubation under flooding increased pH and decreased Eh in all samples. AVS increased when Eh decreased to approximately -200 mV for the mine-contaminated and noncontaminated soils, while the wastewater-contaminated soil originally had a high concentration of AVS despite its air-dried condition. Addition of rice straw or alkaline material containing calcium carbonate and gypsum increased AVS levels under flooded conditions. We observed no apparent relationship between soil enzyme activity (ß-D-glucosidase and acid phosphatase) and concentrations of SEM, [∑SEM - AVS], and exchangeable metals. Bacterial and fungal community composition, assessed using polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) analysis targeting rRNA genes, was largely influenced by site of collection and incubation time, but metal contamination did not influence community composition. We observed significant negative correlations between biomass C and [∑SEM - AVS] and between biomass C and ∑SEM, suggesting that [∑SEM - AVS] and ∑SEM might reflect the bioavailability of organic matter to microorganisms in these soils.

[Relationship between Arsenic (+3 Oxidation State) Methyltransferase Genetic Polymorphisms and Methylation Capacity of Inorganic Arsenic].

Arsenic metabolism affects the susceptibility of humans to arsenic toxicity; therefore, clarification of the factors associated with individual variations in arsenic metabolism is an important task. Genetic polymorphisms such as single nucleotide polymorphisms (SNPs) in arsenic (+3 oxidation state) methyltransferase (AS3MT), which can methylate arsenic compounds using S-adenosyl-l-methionine (AdoMet), have been reported to modify arsenic methylation. In this review, we summarize studies conducted by us in Vietnam and by others on the association of AS3MT genetic polymorphisms with arsenic metabolism as well as human health effects. Most of the SNPs in AS3MT showed inconsistent results in terms of genotype-dependent differences in arsenic metabolism among the studies. However, AS3MT 12390 (rs3740393) and 14458 (rs11191439) were consistently related to arsenic methylation regardless of the study population: AS3MT 12390 (rs3740393) affected the second step of methylation of arsenic, whereas 14458 (rs11191439) affected the first methylation step.

Haptoglobin genotyping of Vietnamese: global distribution of HP del, complete deletion allele of the HP gene.

The haptoglobin (HP) gene deletion allele (HP(del)) is responsible for anhaptoglobinemia and a genetic risk factor for anaphylaxis reaction after transfusion due to production of the anti-HP antibody. The distribution of this allele has been explored by several groups including ours. Here, we studied the frequency of HP(del) in addition to the distribution of common HP genotypes in 293 Vietnamese. The HP(del) was encountered with the frequency of 0.020. The present result suggested that this deletion allele is restricted to East and Southeast Asians. Thus, this allele seems to be a potential ancestry informative marker for these populations.

Individual variations in arsenic metabolism in Vietnamese: the association with arsenic exposure and GSTP1 genetic polymorphism.

We investigated the association of As exposure and genetic polymorphism in glutathione S-transferase π1 (GSTP1) with As metabolism in 190 local residents from the As contaminated groundwater areas in the Red River Delta, Vietnam. Total As concentrations in groundwater ranged from <0.1 to 502 µg l(-1). Concentrations of dimethylarsinic acid (DMA(V)), monomethylarsonic acid (MMA(V)), and arsenite (As(III)) in human urine were positively correlated with total As levels in the groundwater, suggesting that people in these areas may be exposed to As through the groundwater. The concentration ratios of urinary As(III)/arsenate (As(V)) and MMA(V)/inorganic As (IA; As(III) + As(V))(M/I), which are indicators of As metabolism, increased with the urinary As level. Concentration and proportion of As(III) were high in the wild type of GSTP1 Ile105Val compared with the hetero type, and these trends were more pronounced in the higher As exposure group (>56 µg l(-1) creatinine in urine), but not in the lower exposure group. In the high As exposure group, As(III)/As(V) ratios in the urine of wild type of GSTP1 Ile105Val were significantly higher than those of the hetero type, while the opposite trend was observed for M/I. These results suggest that the excretion and metabolism of IA may depend on both the As exposure level and the GSTP1 Ile105Val genotype.

Polymorphic trial in oxidative damage of arsenic exposed Vietnamese.

Arsenic causes DNA damage and changes the cellular capacity for DNA repair. Genes in the base excision repair (BER) pathway influence the generation and repair of oxidative lesions. Single nucleotide polymorphisms (SNPs) in human 8-oxoguanine DNA glycosylase (hOGG1) Ser326Cys; apurinic/apyrimidinic endonuclease (APE1) Asp148Glu; X-ray and repair and cross-complementing group 1 (XRCC1) Arg280His and Arg399Gln in the BER genes were analyzed, and the relationship between these 4 SNPs and the urinary 8-hydroxy-2'-deoxyguanosine (8-OHdG) concentrations of 100 Vietnamese population exposed to arsenic was investigated. Individuals with hOGG1 326Cys/Cys showed significantly higher urinary 8-OHdG concentrations than did those with 326 Ser/Cys and Ser/Ser. As for APE1 Asp148Glu, heterozygous subjects showed significantly higher urinary 8-OHdG concentrations than did those homozygous for Asp/Asp. Moreover, global ethnic comparison of the allelic frequencies of the 4SNPs was performed in 10 population and previous reported data. The mutant allele frequencies of hOGG1 Ser326Cys in the Asian populations were higher than those in the African and Caucasian populations. As for APE1 Asp148Glu, Caucasians showed higher mutant frequencies than those shown by African and Asian populations. Among Asian populations, the Bangladeshi population showed relatively higher mutant allele frequencies of the APE1 Asp148Glu polymorphism. This study is the first to demonstrate the existence of genetic heterogeneity in a worldwide distribution of SNPs (hOGG1 Ser326Cys, APE1 Asp148Glu, XRCC1 Arg280His, and XRCC1 Arg399Gln) in the BER genes.

Effect of Tris-HCl buffer on DNA adsorption by a variety of soil constituents.

We investigated the effect of tris(hydroxymethyl)aminomethane hydrochloride (Tris-HCl) buffer (pH 7.0) as a bulk solution on the adsorption of DNA by gibbsite, goethite, montmorillonite, kaolinite, synthetic and natural allophanes, two humic acids and two andosols. The natural allophane, gibbsite, kaolinite and an andosol adsorbed significantly more DNA in a 0.1 M Tris-HCl buffer than in a 0.1 M NaCl solution (t-test, P<0.005). In contrast, montmorillonite adsorbed significantly less DNA in the Tris-HCl than NaCl solution (P<0.05). Care should be taken when using Tris-HCl in studies on the adsorption of extracellular DNA molecules by soil particles.

Silver speciation in liver of marine mammals by synchrotron X-ray absorption fine structure and X-ray fluorescence spectroscopies.

The chemical form of Ag in the livers of five species of marine mammals was examined using X-ray absorption fine structure (XAFS) and X-ray fluorescence (XRF) spectroscopies. The XAFS analysis suggested that Ag(2)Se was present in the livers of the Franciscana dolphin (Pontoporia blainvillei), Dall's porpoise (Phocoenoides dalli), and Baird's beaked whale (Berardius bairdii), whereas Ag(2)S was present in the livers of the striped dolphin (Stenella coeruleoalba) and pygmy killer whale (Feresa attenuata). XRF spectroscopy results revealed that the distribution patterns of Ag and Se in a thin section of the liver of the Franciscana dolphin were the same; this also implied that Ag was associated with Se in the liver. Thus, the interaction of Ag with Se or S may offer significant protection against the toxicity of Ag in marine mammals. The formation of either Ag(2)Se or Ag(2)S might depend on the Hg levels in the liver. Ag(2)Se was observed in liver samples with relatively high Ag/Hg ratio, whereas liver samples with low Ag/Hg ratio contained Ag(2)S.

The presence of mercury selenide in various tissues of the striped dolphin: evidence from µ-XRF-XRD and XAFS analyses.

Marine mammals accumulate mercury in their tissues at high concentration and detoxify by forming mercury selenide (HgSe, tiemannite) mainly in the liver. We investigated the possibility of formation of HgSe in various tissues (liver, kidney, lung, spleen, pancreas, muscle and brain) other than the liver of the striped dolphin (Stenella coeruleoalba). We applied a combination method of micro-X-ray fluorescence (µ-XRF) imaging and micro-X-ray diffraction (µ-XRD) using a synchrotron radiation X-ray microbeam to analyze the tissue samples directly with minimal sample preparation. By this method, many accumulation points for Hg and Se on a micron scale were found in thin sections of the spleen and liver tissue and consequently, the XRF spectra and the XRD pattern of the hot spots confirmed the presence of tiemannite, HgSe. On the other hand, the insoluble fractions after enzyme digestion of the nuclear and mitochondrial fractions of all tissues were subjected to X-ray absorption fine structure (XAFS) analysis. XAFS analysis confirmed the presence of HgSe in all the tissues examined (liver, kidney, lung, spleen, pancreas, muscle and brain) of the striped dolphin. The presence of HgSe in all the tissues examined suggests that Se would be involved in the detoxification process of Hg in various tissues other than the liver. This contribution seems to be large especially in the liver and spleen but relatively small in the kidney, pancreas and brain, because the proportion of insoluble fraction containing HgSe was lower in these tissues (25 to 46%). This is the first report on the presence of tiemannite HgSe in various tissues of marine mammals.

Accumulation of trace elements in harp seals (Phoca groenlandica) from Pangnirtung in the Baffin Island, Canada.

Nineteen trace elements were determined in liver, muscle, kidney, gonads, and hair of 18 harp seals (Phoca groenlandica) from Pangnirtung in the Baffin Island, Canada. Concentrations of V, Mn, Fe, Cu, Mo, Ag, and Hg in the liver, Co, Cd, and Tl in the kidney, and Ba and Pb in the hair were significantly higher than those in other tissues. Significant positive correlations between Hg concentrations in the hair, and liver, kidney and testis imply usefulness of the hair sample for non-destructive monitoring of Hg in the harp seals. It is suggested that whereas Hg preferentially accumulates in the liver, the accumulation in other tissues is induced at higher hepatic Hg levels. In contrast, Se may not be accumulated in other tissues compared with the liver even at higher hepatic Hg levels because of the presence of excess Se for Hg detoxification in other tissues.

Genetic variants associated with arsenic metabolism within human arsenic (+3 oxidation state) methyltransferase show wide variation across multiple populations.

Human arsenic (+3 oxidation state) methyltransferase (AS3MT) is known to catalyze the methylation of arsenite. The objective of this study was to investigate the diversity of the AS3MT gene in Mexican and German populations. The distribution of 18 single nucleotide polymorphisms (SNPs) in AS3MT was assessed on healthy individuals: 38 Mestizo, 69 Nahuas, 50 Huicholes, and 32 Germans. All 18 SNPs were polymorphic in the German and Mexican populations. Of the three Mexican populations, a minor allele frequency was the highest in the Mestizo, followed by the Nahuas and Huicholes. In the German and three Mexican groups, haplotype #1(TATAGAAGTCTTCATGAC) was the most predominant. Seven haplotypes were newly found in the German and three Mexican populations. The D' values between SNP pairs were high in the German and Nahua populations; they had a similar pattern. The pattern of the Mestizo was more similar to the African than to the other Mexican populations. Huicholes had a moderate pattern of the African and German/Nahua populations. The network had three clusters. One originated in the African population and another may have originated in an Asian (Chinese and/or Japanese) population. The third one may have originated among Caucasians. This study is the first to demonstrate the existence of genetic heterogeneity in the distribution of 18 SNPs in AS3MT of German and Mexican populations.

Exposure, metabolism, and health effects of arsenic in residents from arsenic-contaminated groundwater areas of Vietnam and Cambodia: a review.

In this review, we summarize the current knowledge on exposure, metabolism, and health effects of arsenic (As) in residents from As-contaminated groundwater areas of Vietnam and Cambodia based on our findings from 2000 and other studies. The health effects of As in humans include severe gastrointestinal disorders, hepatic and renal failure, cardiovascular disturbances, skin pigmentation, hyperkeratosis, and cancers in the lung, bladder, liver, kidney, and skin. Arsenic contamination in groundwater is widely present at Vietnam and Cambodia and the highest As levels are frequently found in groundwater from Cambodia. Sand filter system can reduce As concentration in raw groundwater. The results of hair and urine analyses indicate that residents from these As-contaminated areas are exposed to As. In general, sex, age, body mass index, and As exposure level are significantly associated with As metabolism. Genetic polymorphisms in arsenic (+III) methyltransferase and glutathione-S-transferase isoforms may be influenced As metabolism and accumulation in a Vietnamese population. It is suggested oxidative DNA damage is caused by exposure to As in groundwater from residents in Cambodia. An epidemiologic study on an association of As exposure with human health effects is required in these areas.

Global analysis of genetic variation in human arsenic (+3 oxidation state) methyltransferase (AS3MT).

Human arsenic (+3 oxidation state) methyltransferase (AS3MT) is known to catalyze the methylation of arsenite. The objective of this study was to investigate the diversity of the AS3MT gene at the global level. The distribution of 18 single nucleotide polymorphisms (SNPs) in AS3MT was performed in 827 individuals from 10 populations (Japanese, Korean, Chinese, Mongolian, Tibetans, Sri Lankan Tamils, Sri Lankan Sinhalese, Nepal Tamangs, Ovambo, and Ghanaian). In the African populations, the A allele in A6144T was not observed; the allele frequencies of C35587 were much lower than those in other populations; the allele frequencies of A37616 and C37950 were relatively higher than those in other populations. Among Asian populations, Mongolians showed a different genotype distribution pattern. A lower C3963 and T6144 frequencies were observed, and, in the C37616A and T37950C polymorphism, the Mongolian population showed higher A37616 and C37950 allele frequencies than other Asian populations, similarly to the African populations. A total of 66 haplotypes were observed in the Ovambo, 48, in the Ghanaian, 99, in the Japanese, 103, in the Korean, 103, in the South Chinese, 20, in the Sri Lankan Tamil, 12, in the Sri Lankan Sinhalese, 21, in the Nepal Tamang, 50, in the Tibetan, and 45, in the Mongolian populations. The D' values between the SNP pairs were extremely high in the Sri Lankan Sinhalese population. Relatively higher D' values were observed in Mongolian and Sri Lankan Tamil populations. Network analysis showed two clusters that may have different origins, African and Asians (Chinese and/or Japanese). The present study is the first to demonstrate the existence of genetic heterogeneity in a world wide distribution of 18 SNPs in AS3MT.

Genetic polymorphisms in glutathione S-transferase (GST) superfamily and arsenic metabolism in residents of the Red River Delta, Vietnam.

To elucidate the role of genetic factors in arsenic metabolism, we investigated associations of genetic polymorphisms in the members of glutathione S-transferase (GST) superfamily with the arsenic concentrations in hair and urine, and urinary arsenic profile in residents in the Red River Delta, Vietnam. Genotyping was conducted for GST omega1 (GSTO1) Ala140Asp, Glu155del, Glu208Lys, Thr217Asn, and Ala236Val, GST omega2 (GSTO2) Asn142Asp, GST pi1 (GSTP1) Ile105Val, GST mu1 (GSTM1) wild/null, and GST theta1 (GSTT1) wild/null. There were no mutation alleles for GSTO1 Glu208Lys, Thr217Asn, and Ala236Val in this population. GSTO1 Glu155del hetero type showed higher urinary concentration of As(V) than the wild homo type. Higher percentage of DMA(V) in urine of GSTM1 wild type was observed compared with that of the null type. Strong correlations between GSTP1 Ile105Val and arsenic exposure level and profile were observed in this study. Especially, heterozygote of GSTP1 Ile105Val had a higher metabolic capacity from inorganic arsenic to monomethyl arsenic, while the opposite trend was observed for ability of metabolism from As(V) to As(III). Furthermore, other factors including sex, age, body mass index, arsenic level in drinking water, and genotypes of As (+3 oxidation state) methyltransferase (AS3MT) were also significantly co-associated with arsenic level and profile in the Vietnamese. To our knowledge, this is the first study indicating the associations of genetic factors of GST superfamily with arsenic metabolism in a Vietnamese population.

Genetic polymorphisms in AS3MT and arsenic metabolism in residents of the Red River Delta, Vietnam.

To elucidate the role of genetic factors in arsenic (As) metabolism, we studied associations of single nucleotide polymorphisms (SNPs) in As (+3 oxidation state) methyltransferase (AS3MT) with the As concentrations in hair and urine, and urinary As profile in residents in the Red River Delta, Vietnam. Concentrations of total As in groundwater were 0.7-502 mug/l. Total As levels in groundwater drastically decreased by using sand filter, indicating that the filter could be effective to remove As from raw groundwater. Concentrations of inorganic As (IAs) in urine and total As in hair of males were higher than those of females. A significant positive correlation between monomethylarsonic acid (MMA)/IAs and age in females indicates that older females have higher methylation capacity from IAs to MMA. Body mass index negatively correlated with urinary As concentrations in males. Homozygote for SNPs 4602AA, 35991GG, and 37853GG, which showed strong linkage disequilibrium (LD), had higher percentage (%) of dimethylarsinic acid (DMA) in urine. SNPs 4740 and 12590 had strong LD and associated with urinary %DMA. Although SNPs 6144, 12390, 14215, and 35587 comprised LD cluster, homozygotes in SNPs 12390GG and 35587CC had lower DMA/MMA in urine, suggesting low methylation capacity from MMA to DMA in homo types for these SNPs. SNPs 5913 and 8973 correlated with %MMA and %DMA, respectively. Heterozygote for SNP 14458TC had higher MMA/IAs in urine than TT homozygote, indicating that the heterozygote may have stronger methylation ability of IAs. To our knowledge, this is the first study on the association of genetic factors with As metabolism in Vietnamese.

Relationship of urinary arsenic metabolites to intake estimates in residents of the Red River Delta, Vietnam.

This study investigated the status of arsenic (As) exposure from groundwater and rice, and its methylation capacity in residents from the Red River Delta, Vietnam. Arsenic levels in groundwater ranged from <1.8 to 486 microg/L. Remarkably, 86% of groundwater samples exceeded WHO drinking water guideline of 10 microg/L. Also, estimated inorganic As intake from groundwater and rice were over Provisional Tolerable Weekly Intake (15 microg/week/kg body wt.) by FAO/WHO for 92% of the residents examined. Inorganic As and its metabolite (monomethylarsonic acid and dimethylarsinic acid) concentrations in human urine were positively correlated with estimated inorganic As intake. These results suggest that residents in these areas are exposed to As through consumption of groundwater and rice, and potential health risk of As is of great concern for these people. Urinary concentration ratios of dimethylarsinic acid to monomethylarsonic acid in children were higher than those in adults, especially among men, indicating greater As methylation capacity in children.