Nitrosopumilus zosterae sp. nov., an autotrophic ammonia-oxidizing archaeon of phylum Thaumarchaeota isolated from coastal eelgrass sediments of Japan.

A novel mesophilic and aerobic ammonia-oxidizing archaeon of the phylum Thaumarchaeota, strain NM25T, was isolated from coastal eelgrass zone sediment sampled in Shimoda (Japan). The cells were rod-shaped with an S-layer cell wall. The temperature range for growth was 20-37 °C, with an optimum at 30 °C. The pH range for growth was pH 6.1-7.7, with an optimum at pH 7.1. The salinity range for growth was 5-40 %, with an optimum range of 15-32 %. Cells obtained energy from ammonia oxidation and used bicarbonate as a carbon source. Utilization of urea was not observed for energy generation and growth. Strain NM25T required a hydrogen peroxide scavenger, such as α-ketoglutarate, pyruvate or catalase, for sustained growth on ammonia. Growth of strain NM25T was inhibited by addition of low concentrations of some organic compounds and organic mixtures, including complete inhibition by glycerol, peptone and yeast extract. Phylogenetic analysis of four concatenated housekeeping genes (16S rRNA, rpoB, rpsI and atpD) and concatenated AmoA, AmoB, AmoC amino acid sequences indicated that the isolate is similar to members of the genus Nitrosopumilus. The closest relative is Nitrosopumilus ureiphilus PS0T with sequence similarities of 99.5 % for the 16S rRNA gene and 97.2 % for the amoA gene. Genome relatedness between strain NM25T and N. ureiphilus PS0T was assessed by average nucleotide identity and digital DNA-DNA hybridization, giving results of 85.4 and 40.2 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain NM25T represents a novel species of the genus Nitrosopumilus, for which the name sp. nov, is proposed. The type strain is NM25T (=NBRC 111181T=ATCC TSD-147T).

Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan.

Nitrous oxide (N2O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N2O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N2O-reducing microbiome in the in situ sediments of eelgrass zones. Sulfur-oxidizing Gammaproteobacteria within nosZ gene clade II dominated in the lineage Dechloromonas-Magnetospirillum-Thiocapsa. Alphaproteobacteria within nosZ gene clade I were predominant in both zones. The proportions of Epsilonproteobacteria within nosZ gene clade II increased after incubations in the eelgrass zone microcosm supplemented with N2O only. Collectively, these results suggest that the N2O-reducing microbiome in eelgrass meadows is largely responsible for coastal N2O mitigation.

Sedimentary records of metal deposition in Japanese alpine lakes for the last 250 years: recent enrichment of airborne Sb and In in East Asia.

Concentrations of 18 elements, including Sb, In, Sn, and Bi, were measured in sediment cores from two pristine alpine lakes on Mount Hachimantai, northern Japan, representing the past 250 years. Vertical variations in concentrations are better explained by atmospheric metal deposition than by diagenetic redistribution of Fe and Mn hydroxide and organic matter. Anthropogenic metal fluxes were estimated from (210)Pb-derived accumulation rates and metal concentrations in excess of the Al-normalized mean background concentration before 1850. Anthropogenic fluxes of Sb and In showed gradual increases starting around 1900 in both lakes, and marked increases after 1980. Comparison of Sb/Pb and Pb stable isotope ratios in sediments with those in aerosols of China or northern Japan and Japanese source materials (recent traffic- and incinerator-derived dust) suggest that the markedly elevated Sb flux after 1980 resulted primarily from enhanced long-range transport in aerosols containing Sb and Pb from coal combustion on the Asian continent. The fluxes of In, Sn, and Bi which are present in Chinese coal showed increasing trends similar to Sb for both study lakes. This suggests that the same source although incinerators in Japan may not be ruled out as sources of In. The sedimentary records for the last 250 years indicate that atmospheric pollution of Sb and In in East Asia have intensified during recent decades.

Distribution and diversity of anaerobic ammonium oxidation (anammox) bacteria in the sediment of a eutrophic freshwater lake, Lake Kitaura, Japan.

Although the emission of N(2) via anaerobic ammonium oxidation (anammox) is a key process in the elimination of nitrogenous compounds from aquatic environments, little information is available regarding its significance and the relevant microorganisms (anammox bacteria) in eutrophic freshwater lakes. In the present study, the anammox bacteria in the sediment of a eutrophic lake in Japan, Lake Kitaura, were examined using a (15)N-tracer technique to measure their potential anammox activity. Potential anammox activity was localized to the northern region of the lake where a stable supply of both NH(4)(+) and NO(3)(-) existed in the sediment. These results suggest the contribution of anammox bacteria to the total emission of N(2) from sediment in this eutrophic lake to not be negligible. Moreover, selective PCR successfully amplified anammox bacteria-related (Brocadiales-related) 16S rRNA genes from sediment samples in which potential anammox activity was observed. The clone libraries consisted of diverse phylotypes except the genus "Scalindua"-lineages, and the lineages of genus "Brocadia" were dominantly recovered, followed by the genus "Kuenenia"-lineages. Most of them, however, were novel and phylogenetically distinguishable from known Brocadiales species. A unique population of anammox bacteria inhabits and potentially contributes to the emission of N(2) from Lake Kitaura.

Contribution of anammox bacteria to benthic nitrogen cycling in a mangrove forest and shrimp ponds, Haiphong, Vietnam.

Mangrove forests are common in subtropical regions, and have received considerable attention as vegetative buffers against anthropogenic N-loading. In this study, we investigated anaerobic ammonium oxidation (anammox) as one of potentially important microbial N-removing pathways in mangrove and shrimp pond sediment in Haiphong, Vietnam. Measurements with (15)N-labeled compounds demonstrated the occurrence of anammox in sediment of mangrove forest and a water channel connecting shrimp ponds to the sea in both 2005 and 2007, and of a semi-intensive shrimp pond in 2005. The rate of potential anammox activity reached to 0.7 nmol-N(2) cm(-3) h(-1), although the contribution of anammox was less significant than denitrification. Anammox-type 16S rRNA gene fragments phylogenetically related to 'Scalindua' species were predominantly recovered from mangrove forest and water channel sediment in a PCR-clone library analysis targeting anammox bacteria. 'Kuenenia'-like gene fragments were also recovered from shrimp pond sediment as the major component. We demonstrated the occurrence of potential anammox activity, and suggested the possibility that diverse species of uncultured anammox bacteria contribute to the nitrogen cycle in subtropical mangrove-aquaculture ecosystems. Furthermore, this study provides new insight into the biogeography of anammox bacteria: 'Scalindua' and 'Kuenenia'-like species coexisted in the blackish sediment as in some temperate estuarine sediment.

A simple and rapid GC/MS method for the simultaneous determination of gaseous metabolites.

We modified and tuned a commercial model of a gas chromatography/mass spectrometry (GC/MS) instrument to develop a simple and rapid method for the simultaneous quantification of a variety of gas species. Using the developed method with the newly modified instrument, gas species such as H(2), N(2), O(2), CO, NO, CH(4), CO(2), and N(2)O, which are common components of microbial metabolism, were accurately identified based on their retention times and/or mass-to-charge ratios (m/z) in less than 2.5 min. By examining the sensitivities and dynamic ranges for the detection of H(2), N(2), O(2), CH(4), CO(2), and N(2)O, it was demonstrated that the method developed in this study was sufficient for accurately monitoring the production and the consumption of these gaseous species during microbial metabolism. The utility of the new method was demonstrated by a denitrification study with Pseudomonas aureofaciens ATCC 13985(T). This method will be suitable for a variety of applications requiring the identification of gaseous metabolites in microorganisms, microbial communities, and natural ecosystems.

Rate determination and distribution of anammox activity in activated sludge treating swine wastewater.

This paper presents a quantitative investigation and analysis of anammox activity in sludge taken from biological swine wastewater treatment plants. An incubation experiment using a (15)N tracer technique showed anammox activity in sludge taken from 6 out of 13 plants with the rate ranging from 0.0036 micromol-N(2)/g-VSS/h to 3.1 micromol-N(2)/g-VSS/h, and in a biofilm with the highest activity at 25.8 micromol-N(2)/g-VSS/h. It is notable that 9 out of 11 sludges in which the pH was maintained between 6.6 and 8.1 retained anammox activity, while those with either a lower or higher pH did not. Moreover, anammox-positive sludge had a significantly higher concentration of NO(2)(-)-N plus NO(3)(-)-N than did anammox-negative sludge. A significant difference was not observed between anammox-positive and -negative sludge regarding BOD/NH(4)(+)-N in the influent, DO concentration in aeration tanks, and the concentrations of NH(4)(+)-N, free nitric acid, and free ammonia.

Estimation of pathways of the production of greenhouse gases in the tropical swamp forest in Thailand by stable isotope investigation.

Dynamics of greenhouse gases (N(2)O and CH(4)) with the dry-wet cycle along with the variation of oxidation-reduction boundaries were investigated in the tropical wetland in monsoon Asia. It was clarified that the production of N(2)O and CH(4) was closely related to the development of a redox boundary in the Bang Nara River systems. An intermittent increase in N(2)O was observed at the beginning of the rainy season, when a large amount of easily decomposable organic matter was introduced into the river. After 10 days, when dissolved oxygen was consumed completely at the middle reaches, the emission of CH(4) became maximal due to the possible occurrence of denitrification. The distribution of stable isotope ratios in N(2)O clearly demonstrated that nitrification is the major process for its production. Furthermore, the production of N(2)O in this study area was found to vary in time and space with changes in the redox boundary along the water flow.

The chloroplast avoidance response decreases internal conductance to CO2 diffusion in Arabidopsis thaliana leaves.

The relationship between chloroplast arrangement and diffusion of CO(2) from substomatal cavities to the chloroplast stroma was investigated in Arabidopsis thaliana. Chloroplast position was manipulated by varying the amount of blue light and by cytochalasin D (CytD) treatment. We also investigated two chloroplast positioning mutants. Chloroplast arrangement was assessed by the surface area of chloroplasts adjacent to intercellular airspaces (S(c)). Although it has been previously shown that long-term acclimation to high light is linked with a large S(c), we found that the short-term chloroplast avoidance response reduces S(c). This effect was not apparent in the blue-light-insensitive phot2 mutant, which did not show the avoidance response. As expected, the smaller S(c) induced by the avoidance response was coupled to a similar decrease in internal conductance. This reduction in internal conductance resulted in an increased limitation of the rate of photosynthesis. The limiting effect of S(c) on internal conductance and photosynthesis was also shown in chup1, a mutant with a constant small S(c) as the result of an unusual chloroplast arrangement. We conclude that chloroplast movements in A. thaliana can rapidly alter leaf morphological parameters, and this has significant consequences for the diffusion of CO(2) through the mesophyll.