Tokyo Bay, a eutrophic bay in Japan, receives nutrients from wastewater plants and other urban diffuse sources via river input. A transect was conducted along a line from the Arakawa River into Tokyo Bay to investigate the ecological relationship between the river outflow and the distribution, abundance and population structure of ammonia-oxidizing bacteria (AOB). Five surficial marine sediments were collected and analysed with polyphasic approaches. Heterogeneity and genetic diversity of beta-AOB populations were examined using restriction fragment length polymorphism (RFLP) analysis of 16S rRNA and amoA genes. A shift of the microbial community was detected in samples along the transect. Both 16S rRNA and amoA genes generated polymorphisms in the restriction profiles that were distinguishable at each sampling site. Two 16S rRNA gene libraries were constructed using the reverse transcription polymerase chain reaction (RT-PCR) method to determine the major ammonia oxidizers maintaining high cellular rRNA content. Two major groups were observed in the Nitrosomonas lineage; no Nitrosospira were detected. The effort to isolate novel AOB was successful; the isolate dominated in the gene libraries. For quantitative analysis, a real-time PCR assay targeting the 16S rRNA gene was developed. The population sizes of beta-AOB ranged from 1.6 x 10(7) to 3.0 x 10(8) cells g(-1) in dry sediments, which corresponded to 0.1-1.1% of the total bacterial population. An immunofluorescence staining using anti-hydroxylamine oxidoreductase (HAO) antibody was also tested to obtain complementary data. The population sizes of ammonia oxidizers ranged between 2.4 x 10(8) and 1.2 x 10(9) cells g(-1) of dry sediments, which corresponded to 1.2-4.3% of the total bacterial fraction. Ammonia-oxidizing bacteria cell numbers deduced by the two methods were correlated (R = 0.79, P < 0.01). In both methods, the number of AOB increased with the distance from the river mouth; ammonia-oxidizing bacteria were most numerous at B30, where the ammonium concentration in the porewater was markedly lower and the nitrite concentration was slightly higher than nearby sites. These results reveal spatial distribution and shifts in the population structure of AOB corresponding to nutrients and organic inputs from the river run-off and phytoplankton bloom.

A polyphasic, culture-independent study was conducted to investigate the abundance and population structure of ammonia-oxidizing bacteria (AOB) in canal sediments receiving wastewater discharge. The abundance of AOB ranged from 0.2 to 1.9% and 1.6 to 5.7% of the total bacterial fraction by real-time PCR and immunofluorescence staining, respectively. Clone analysis and restriction endonuclease analysis revealed that the AOB communities influenced by the wastewater discharge were dominated by Nitrosomonas, were similar to each other, and were less diverse than the communities outside of the immediate discharge zone.Tokyo Bay is a representative enclosed eutrophic bay in the southern Kanto region of Japan. More than 86% of the shoreline is reclaimed, and artificial structures, such as canals and landfill islands, occupy the inner bay area (29). These artificial structures often hamper water exchange and accelerate precipitation of sludge containing excess organic matter, heavy metals, and toxic compounds (16,17,29). These human activities negatively affect the sea-bottom environment and limit natural remediation in the coastal ecosystem (19).Nitrification is essential to the nitrogen cycle in aquatic environments. When coupled with denitrification and/or anaerobic ammonium oxidation, it relieves the negative impacts of eutrophication through removal of nitrogen to the atmosphere as nitrous oxide or molecular nitrogen (5, 9, 38). However, nitrification is sensitive to environmental stress and contaminants (18, 23, 37). Ammonia-oxidizing bacteria (AOB) carry out the first, rate-limiting step of nitrification: conversion of ammonia to nitrite. The ecology and physiology of AOB are particularly difficult to study by conventional cultivation techniques because of their long generation times and low growth rates, which can result in underestimations of their numbers in the environment (21). Compared to the studies of AOB diversity in nature (1,4,6,12,13,22), quantitative studies have been limited, especially for marine environments (11). Therefore, a rapid, culture-independent detection technique for AOB would be useful for the study of marine AOB. Through this study, we developed and combined molecular and novel immunofluorescence staining approaches to investigate the spatial distribution, abundance, and population structure of AOB in a canal area of Tokyo Bay that is heavily polluted by excess organic and nutrient loading from wastewater treatment plant discharges. Particularly important for this study was quantification of AOB because of the deficiency of quantitative studies of AOB populations in marine environments

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A new cohort of the Manila clam Ruditapes philippinarum was established in Sanbanse (the shallow coastal area of Tokyo Bay) during October–November 1998. Growth of clams within this cohort was monitored monthly or bimonthly at five stations along an inshore‐offshore transect in Sanbanse through November 1999. Mean shell length was about 0.4 mm in November 1998 and increased gradually to about 1 mm in March 1999. The clams then grew rapidly during the warm season and mean shell length reached 25–29 mm in November 1999 at each station. Comparisons of growth among stations in terms of shell length and soft‐body dry weight suggest that the growth of R. philippinarum was faster at offshore than inshore stations during warm periods.

Material from the genus Hyale, family Hyalidae, collected from the coast of Japan and adjacent waters was examined for the present work. This study revealed seven species, among which five were new to science, two were new to Japan. Herewith new species: H. kajiharai sp. nov., H. nuda sp. nov., H. triangulata sp. nov., H. misakiensis sp. nov., and H. latimana sp. nov. were described, and H. aftinis Chevreux and H. honoluluensis Schellenberg were re-diagnosed. Hyale bassargini Derzhavin was redescribed based on the type material. In total the number of Hyale species of Japanese waters is 15. A key to the species of Hyale from Japanese waters is presented.

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