A mosaic of environments comprises most volcanic ecosystems. Whether terrestrial or submarine, many of these environments contain large deposits of reduced minerals, or experience large fluxes of reduced substrates, especially sulfur-containing compounds. These systems, which also are typically characterized by temperature and pH extremes, have yielded a rich variety of chemolithotrophic bacteria, and contributed much to our understanding of chemolithotroph ecology and physiology. However, volcanic ecosystems also consist of environments where inorganic and organic substrates are limiting. In these cases, chemolithotrophs may still play important roles by scavenging carbon monoxide, hydrogen or both. These gases can support metabolism of facultative chemolithotrophs, a functional group that includes many nitrogen-fixing bacteria. Facultative chemolithotrophs may not only represent important early colonists on fresh volcanic substrates (e.g., basalts lacking sulfides), they may also contribute significantly to ecosystem succession through nitrogen fixation and interactions with vascular plants. Analyses of CO and hydrogen consumption by recent deposits on Kilauea volcano show that both substrates support significant activity, while molecular approaches show a high diversity of lithotrophs. Collectively, these and other observations indicate that chemolithotrophic metabolism is more widespread than generally acknowledged, and likely to play fundamental roles in shaping ecosystem dynamics.

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The effect of amino acids (glutamine, asparagine, and serine) and organic acids (citrate, malate, and pyruvate) on plasmid transfer was investigated on agar plates using Pseudomonas strains differing in physiological status. Counts by culture-dependent and culture-independent methods showed that the presence of organic compounds as the sole nutrient source increased the absolute number of transconjugants. Morevover, the presence of glutamine and pyruvate as the sole nutrient source resulted in a higher transfer frequency. This stimulatory effect of pyruvate was also investigated in short-term conjugation experiments under nutrient-amended conditions with glucose. Compared with glutamine, the presence of pyruvate resulted in a higher transfer frequency after 5 h of conjugation with active cells. The present study confirmed the importance of organic compounds and the physiological status of bacteria to plasmid transfer, and provided evidence that certain organic compounds (glutamine and pyruvate) can stimulate the growth of transconjugants and/or conjugal gene exchange between Pseudomonas spp.

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Fungal and bacterial communities were investigated by denaturing gradient gel electrophoresis (DGGE) and a pattern-based analysis after the application of two types of organic fertilizer (cattle manure and green manure). Crops were not cultivated in the experimental plots in order to minimize the effects of plants on the microbial communities. Unexpectedly, the microbial populations and DGGE profiles in the soils treated with cattle manure did not differ significantly from the controls. Although the microbial populations in the soils amended with green manure were significantly higher throughout the two-year experiment, differences in the DGGE band profiles were minor. A principal component analysis (PCA) demonstrated a succession of differences in the DGGE profiles, as the application of green manure slightly affected the fungal community. Principal component and sequence analyses for characteristic DGGE bands identified close relatives of Chaetomium globosum, Fusarium oxysporum, and Mortierella alpina which appeared to be involved with the decomposition of green manure. These results suggested that the application of green manure was more effective at increasing microbial populations than that of cattle manure, and activated several characteristic fungi which should be considered to play a significant role in the decomposition of green manure.

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The hypothesis that mercury-resistant bacteria exposed to polluted environments such as coastal areas can tolerate, detoxify, or biotransform a variety of other toxicants was examined. Several mercury-resistant marine bacteria from the coastal waters of India were evaluated for their ability to biotransform the heavy metals mercury, cadmium and lead as well as xenobiotics like polychlorinated biphenyls and tributyltin. These salt-tolerant bacteria removed mercury by means of volatilization and were successfully used to detoxify mercury-amended growth medium for the culturing of mercury-sensitive Phormidium sp. Over 70% cadmium and 95% of the lead from the growth medium were either cell-bound (cadmium) or precipitated (lead) by some of these bacteria. A pseudomonad strain, CH07, aerobically degraded fourteen toxic polychlorinated biphenyls including congeners with five or more chlorine atoms on the biphenyl ring and was also equally efficient in degrading more than 54% of the tributyltin. These bacteria offer great biotechnological opportunities in the bioremediation of toxic chemicals.

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In the present study, the abundance of Candidatus ‘Accumulibacter phosphatis’ and the accumulation of polyphosphate were investigated in five enhanced biological phosphorus removal (EBPR) activated sludge reactors operated with different carbon sources. Fluorescence in situ hybridization (FISH) in combination with 4',6-diamidino-2-phenylindole (DAPI) staining for polyphosphate granules confirmed the accumulation of polyphosphate by Candidatus ‘Accumulibacter phosphatis’ in all the reactors. The abundance of Candidatus ‘Accumulibacter phosphatis’ was determined from the FISH images. When EBPR activity was high and phosphorus content made up around 9% or more of mixed liquor volatile suspended solids (MLVSS), Candidatus ‘Accumulibacter phosphatis’ accounted for over 20% of the eubacteria in the reactors acclimatized with acetate, aspartate, or glucose. Whereas this value was as low as around 10% in the reactors acclimatized mainly with yeast extract, peptone, or glutamate. In these reactors, bacteria affiliated with Actinobacteria were found to accumulate polyphosphate and to contribute to phosphorus removal. Candidatus ‘Accumulibacter phosphatis’ takes part in the removal of phosphorus by using various carbon sources, but its abundance varies according to the type of carbon source.

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We found increased numbers of oxytetracycline (OTC)-resistant bacteria in sediment and seawater around a marine aquaculture site after OTC therapy. Samples were collected at an aquaculture site along the coast of the Seto Inland Sea, Japan in 2004. In April, the percentage of bacteria resistant to 60 μg mL^-1 OTC in the surface sediment was 6.8%-20.0%. The percentages increased during OTC therapy in the summer reaching 53.3%-60.7% in September. Ninety-two days after drug cessation, the percentages decreased to below 22.9%. Tet(M)-positive bacteria were detected in the sediment and seawater samples. Tet(M) was evident in both Gram-positive and Gram-negative bacteria from various genera, and was newly identified in Paenibacillus, Sporosarcina, Shewanella, and Pseudoalteromonas. The dominant tet(M)-positive isolates were strains of Vibrio suggesting that this genus is an important reservoir for tet(M) in the marine environment. Two different alleles were found, tet(M)-A and tet(M)-B, each in isolates from five genera. The data suggests drug therapy used in the aquaculture acted as a selective pressure promoting increased numbers of resistant bacteria.

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We investigated the quantities and phylogenies of amoA genes of ammonia-oxidizing archaea (AOA) belonging to Crenarchaeota and ammonia-oxidizing bacteria (AOB) belonging to Betaproteobacteria in water columns and deep-ocean cold seep sediment in the northeastern Japan Sea with a competitive PCR (cPCR) assay. Water samples were collected at depths of 2000 m and 2956 m. Sediment samples were collected where white bacterial mats had developed. The cPCR analysis revealed five to ten times more AOA than betaproteobacterial AOB in both the water columns and sediment. The abundance of the crenarchaeotal amoA gene was estimated at 6×10¹ and 3×10² copies ml^-1 in the water columns at depths of 2000 m and 2956 m, and 1×10⁸ and 1×10⁷ copies g^-1 in pelagic brown sediment and black sediment, respectively. Most archaeal amoA clones from water column at 2000 m fell into the Deep Marine Group. Most archaeal amoA clones from pelagic brown sediment were less closely related to known environmental clones. Moreover, incubation experiments revealed nitrite production at 4°C and 10°C. The results indicate that psychrophilic AOA and AOB may be responsible for nitrification in the deep-ocean region of the northeastern Japan Sea.

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We examined the genomic diversity of 29 representative Vibrio parahaemolyticus strains based on amplified fragment length polymorphism (AFLP) and multilocus sequence analysis (MLSA). Several strains had indistinguishable AFLP patterns, suggesting high genomic similarity. Recombination detection methods and phylogenetic reconstructions based on the gene sequences of recombination/repair protein (recA), DNA gyrase beta subunit (gyrB), and phosphoglucomutase (pgm) revealed that recombination has occurred within the species V. parahaemolyticus. We suggest that homologous recombination is an important force in the evolution of V. parahaemolyticus.

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The principle organization of microcystin biosynthesis (mcy) gene clusters is characterized in three genera among the microcystin-producing cyanobacteria. To examine the conservation of the mcy gene clusters among the genus Microcystis, internal non-coding regions of the cluster in 21 strains including M. aeruginosa, M. viridis, and M. wesenbergii, were amplified by PCR using specific primer sets and sequenced. PCR-based analysis revealed a completely conserved organization of the bidirectional cluster structure, mcyABC and mcyDEFGHIJ, among all toxic and some microcystin-negative strains. Furthermore, all mcy gene clusters were flanked by a gene with homology to dnaN adjacent to mcyJ and by uma1 with no-homology to any known genes at the 3'-end of mcyC. Transposase homolog genes were observed in a non-coding region between dnaN and mcyJ in three microcystin-producing Microcystis strains. Sequence analysis of a region adjacent to uma1 in mcy-negative strains revealed two types of gene constitution, dnaN-uma1 and the hypothetical protein gene-uma1. PCR-based analyses can be used to assess the identification of microcystin-producer strains in Microcystis spp.

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A soil column was percolated with Triton X-100 (octylphenol polyethoxylates; OPEO_n) under aerobic conditions for 300 days and OPEO_n-degrading bacteria were isolated and characterized phylogenetically. Populations of total culturable bacteria and OPEO_n (1000 mg L^-1)-resistant bacteria increased 10 times and 46 times, respectively, during the percolation. 16S rRNA gene sequencing of 128 OPEO_n-resistant isolates revealed an increase in the population level of Alphaproteobacteria and decreases in levels of Betaproteobacteria and Actinobacteria with the exposure to the compound. Four OPEO_n-degrading strains were isolated and characterized as being related to Bradyrhizobium liaoningense (3 strains) and Afipia sp. (1 strain).

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linA is a gene encoding γ-hexachlorocyclohexane dehydrochlorinase identified in a γ-HCH-degrading Sphingobium japonicum UT26 that had been isolated from soil of an experimental field treated with γ-HCH. The presence of linA-homologous nucleotide sequences and their sequence diversity was investigated by linA-targeted PCR amplification of DNA obtained from different soils in the field and in Japan. linA-homologous sequences were obtained from almost all the soils some of which had never been treated with γ-HCH. Deduced amino acid sequences suggested that they can be regarded as fragments of linA that encode LinA. Some common, natural function of LinA in soil was suggested.

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Chloroflexus and cyanobacterial mats developing at 50-65°C in Nakanoyu and Nakabusa hot springs, Japan, were collected and cultivated phototrophically at 50 and 37°C. Chloroflexus organisms grew when incubated at 50°C, whereas the incubation at 37°C resulted in the enrichment of pink- to brown-colored cultures, from which different species of phototrophic purple nonsulfur (PPNS) bacteria were isolated. The majority of the isolates grew at temperatures of up to 45°C and optimally at around 40°C. The high frequencies of the occurrence of PPNS bacteria in hot spring microbial mats suggest that these environments offer a favorable ecological niche for these bacteria.

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Seawater sampled from the Semarang port in Indonesia was streaked onto inorganic-medium plates coated with weathered crude oil, and 153 strains were isolated. Analyses of 16S rRNA gene sequences identified 67 different phylotypes affiliated with Alphaproteobacteria (111 strains/44 phylotypes), Gammaproteobacteria (8/8) and Actinobacteria (34/15). The organisms represented by 36 phylotypes could transform petroleum components in pure cultures. Many of them were affiliated with genera yet unrelated to hydrocarbon degradation. Strains unaffiliated with known genera were also obtained. Results suggest that many as-yet-unknown hydrocarbon-degrading bacteria are present in tropical marine environments.

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