Marine sediment in coastal zones is a habitat for various seaweeds, microalgae, invertebrates, and microorganisms. It is characterized by high biomass and diversity, and high rates of turnover of elements such as carbon, nitrogen and sulfur. One of the factors leading to this extensive biological activity is bioturbation, the process whereby benthic animals form local heterogeneous physical structures and topographic features. In this review, the basis of bioturbation and element cycles in marine sediment, and the relationship of bioturbation with microbial activity will be described.

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Over the last decade, taxonomic surveys have recovered sixteen strains of Halomonas-like marine heterotrophic bacteria from different ecological habitats. The sixteen strains were isolated from three N.W. Pacific Ocean habitats: seawater, the mussel Crenomytilus grayanus and the degraded thallus of brown alga Fucus evanescens. These strains were subjected to a taxonomic investigation of their phenotypic/physiological, genetic, and phylogenetic features. Analysis indicates these bacteria belong to Cobetia marina. The study found all strains tolerated CdCl₂ concentrations up to 875 mM. Taxonomically, the sixteen strains belong to the same species, nevertheless, their physiological features revealed distinguishing characteristics. For instance, strain KMM 296, recovered from the mussel Crenomytilus grayanus, was distinct from other C. marina strains by its ability to produce highly active alkaline phosphatase. The majority of C. marina strains that were isolated from degraded alga thallus appeared to have a particular metabolic specialisation by utilizing a range of easily assimilable monosaccharides. Notably, despite a high level of genetic similarity (80% of DNA relatedness), the phenotypic features of the strains isolated from degraded alga thallus differed with the type strain C. marina LMG 2217^T. These differences suggest an ecologically adapted population of C. marina at a subspecies level.

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A novel aerobic denitrifier, designated strain NH-14, was isolated from soil collected in Tsukuba, Japan. Strain NH-14 could reduce nitrite (NO₂^-) to nitrous oxide (N₂O) under aerobic and anaerobic conditions. The conversion of NO₂^- to N₂O occurred under extremely aerobic conditions (O₂ concentration: 4.2 mmol flask^-1), and was induced by NO₂^-, indicating aerobic denitrification. From the biochemical characterization and phylogenic analysis of the complete 16S rRNA gene, strain NH-14 was shown to belong to the genus Mesorhizobium with M. loti and M. amorphae as its closest relatives. The strain was designated Mesorhizobium sp. strain NH-14. It was concluded that Mesorhizobium sp. strain NH-14 is capable of denitrification under both aerobic and anaerobic conditions.

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Vertical profiles of polychlorinated dioxins and microbial biomass including "Dehalococcoides" populations in cores of sediment of Lake Suwa, Japan, were investigated. The core samples were analyzed in 3-cm intervals at 0-15 cm and 50 cm, where a sharp gradient of E_h from 5 to −110 mV with depth occurred. The concentration of polychlorinated dioxins was relatively constant at 0-15 cm, ranging from 7.6 to 8.3 ng (7.0-9.2 pg-TEQ [toxic equivalent]) g^-1 dry wt, but decreased sharply at 50 cm. The total bacterial count was in the order of 10⁸ to 10⁹ g^-1 dry wt, being highest at 3-6 cm and decreasing in the deeper sediment. A similar vertical profile was found for respiratory quinones with larger amounts of ubiquinones than menaquinones at 0-15 cm. Quantitative real-time PCR with a specific primer set showed that "Dehalococcoides" and its phylogenetic relatives occurred in the order of 10⁴ g ^-1 (dry wt) at 0-12 cm but were absent at 50 cm. The amplified clones showed 91-100% similarity (mostly <94%) in sequence to a well-known dioxin-dechlorinating organism, "Dehalococcoides" sp. strain CBDB1. These results suggested that the surface sediment up to a depth of 12 cm provided favorable conditions for the growth and activity of both aerobic and anaerobic microorganisms including "Dehalococcoides". It is likely that a wide variety of "Dehalococcoides" and phylogenetic relatives thereof are omnipresent even in sediment with low levels of dioxins and play the primary role in dechlorinating organohalorides over a relatively wide range of E_h.

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Semi-anaerobic microcosms containing different levels of polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) were constructed by seeding with different mass ratios of lake sediment and dioxin-contaminated soil and incubating with organic medium for 1 year. In all microcosms, PCDD/Fs were reduced as a first-order reaction with similar removal rate coefficients, and only trace amounts of less chlorinated congeners were produced as the intermediate and end products. This apparent complete dechlorination of PCDD/Fs seemed to be due to a combination of reductive dechlorination of PCDD/Fs and oxidative degradation of the dechlorinated products. Total cell counting, 16S rRNA gene clone library analyses and quinone profiling showed that the microcosms contained relatively constant total populations with members of the phyla Bacteroidetes, Firmicutes and Proteobacteria (especially "Deltaproteobacteria") as the major constituents, independent of pollution levels. Quantitative real-time PCR with a specific primer set showed that the population density of "Dehalococcoides" and its phylogenetic relatives was highly correlated with the concentration of PCDD/Fs present. Some "Dehalococcoides" strains were isolated from the microcosms by repeated enrichment with chloroaromatics as the terminal electron acceptor. However, these isolates did not match with the major "Dehalococcoides"-related clones directly PCR-amplified. The results of this study suggest that PCDD/Fs in natural environments under given conditions are transformed with similar half-reduction rates independent of their concentrations, and a wide variety of "Dehalococcoides"-related bacteria play the primary role in this process.

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Fungus-growing termites cultivate fungi of the genus Termitomyces in gardens inside their nests. Despite various reports of the presence of Termitomyces in these gardens, the entire fungal community structure of the gardens has not yet been described. To clarify whether the fungal crops in the gardens are monocultures of Termitomyces, we examined 18 fungus gardens derived from 5 species of fungus-growing termites covering 3 genera. Phylogenetic analysis of DNA sequences revealed that non-Termitomyces fungi might have inhabited the gardens. However, terminal restriction fragment length polymorphism (T-RFLP) analysis clearly demonstrated that non-Termitomyces fungi made up only a minor population within the gardens. This suggests that the fungus gardens were maintained as almost complete monocultures of Termitomyces.

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Twenty-six bacterial strains, which degrade nonylphenol (and octylphenol) polyethoxylates and accumulate mono-, di-, and/or tri-ethoxylated homologues, were isolated from coastal sea sediments of Japan. According to restriction-fragment polymorphisms of the PCR-amplified 16S rRNA gene, the strains were divided into 7 genotypes. Phylogenetic analyses of the16S rRNA gene indicated that the isolates were included in Gammaproteobacteria, and distinct from those of nonylphenol polyethoxylate-degrading bacteria isolated from active sludge and paddy fields.

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In the present study, we examined the feasibility of using a simplified ribosomal intergenic spacer analysis (RISA) technique to investigate the impact of chrysanthemum genotypes, including Bt transgenic lines, the control parental line and a wild species, on microbial communities in their rhizospheric soils. Differential bands among the plant genotypes were identified from RISA profiles. Sequence data revealed that some bands showed high levels of similarity to known species, such as a fungal group of Exidiopsis and Exidia and a protozoan, Tetrahymena tropicalis. None, however, shared homology to either pathogenic or beneficial microbes that have previously been identified in association with both animals and plants.

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A number of gram-negative fish pathogens have a quorum-sensing system. These bacteria produce N-acyl-L-homoserine lactone (AHL) as a quorum-sensing signal molecule. We isolated AHL-producing and degrading bacteria from the intestinal microbial flora of Ayu fish (Plecoglossus altivelis). AHL-producing and degrading isolates were identified as members of the genus Aeromonas and Shewanella, respectively. Aeromonas sp. strain MIB010 produced at least three kinds of AHLs and it was predicted that the production of extracellular protease in strain MIB010 was regulated through quorum sensing. Shewanella sp. strain MIB015 showed obvious AHL-degrading activity and interrupted the AHL-mediated production of protease by the Aeromonas sp. Intestinal Shewanella strains might be useful as probiotic bacteria effective in the prevention of bacterial infectious diseases controlled by quorum sensing.

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