Organomercurial-volatilizing bacteria in the mercury-polluted sediment of Minamata Bay, Japan.

A total of 4,604 bacterial strains isolated from the sediments of Minamata Bay and nearby low-level-mercury stations (control stations) were screened for the ability to volatilize mercury from inorganic and organic mercurial compounds. The strains that volatilize mercury from several kinds of organomercurials were found only in the sediments of Minamata Bay.     

The meroperon of a mercury-resistant Pseudoalteromonas haloplanktis strain isolated from Minamata Bay, Japan

A mer operon of mercury-resistant Pseudoalteromonas haloplanktis strain M1, isolated from sea water of Minamata Bay, was cloned and analyzed. The mer genes were located in the chromosome and organized as merR-merT-merP-merC-merA-merD, the same order as that in Tn21. However, the orientation of the merR gene is the same as that of other mer genes (opposite direction to Tn21), and merR was cotranscribed with other mer genes, a pattern that has not been previously seen with mer determinants from other Gram-negative bacteria. Furthermore, the amino acid similarities of the corresponding mer gene products between those from strain M1 and Tn21 were unusually low.     

Diversity of mercury resistance determinants among Bacillus strains isolated from sediment of Minamata Bay

Thirty mercury-resistant (Hg R) Bacillus strains were isolated from mercury-polluted sediment of Minamata Bay, Japan. Mercury resistance phenotypes were classified into broad-spectrum (resistant to inorganic Hg(2+) and organomercurials) and narrow-spectrum (resistant to inorganic Hg(2+) and sensitive to organomercurials) groups. Polymerase chain reaction (PCR) product sizes and the restriction nuclease site maps of mer operon regions from all broad-spectrum Hg R Bacillus were identical to that of Bacillus megaterium MB1. On the other hand, the PCR products of the targeted merP (extracellular mercury-binding protein gene) and merA (intracellular mercury reductase protein gene) regions from the narrow-spectrum Hg R Bacillus were generally smaller than those of the B. megaterium MB1 mer determinant. Diversity of gene structure configurations was also observed by restriction fragment length polymorphism (RFLP) profiles of the merA PCR products from the narrow-spectrum Hg R Bacillus. The genetic diversity of narrow-spectrum mer operons was greater than that of broad-spectrum ones.     

Characterization of microaerophilic bacteria isolated from the coastal waters of Tokyo Bay, Japan

Abstract A total of 84 strains of microaerophiles were isolated from the Edo River mouth, Tokyo Bay, Japan, and their morphological, physiological and biochemical properties and mole percent guanine-plus-cytosine contents (mol%) of DNAs extracted from them were examined. Eighty-eight to 100% of the strains, collected in summer, grew at 15–37°C but only 5% of the strains grew at 5°C. Seventy-seven to 100% of the strains, collected in winter, were able to grow at 10–25°C but 79% of the strains were unable to grow at 37°C. The shift in growth-range of bacteria strongly suggests that the microflora of estuarine microaerophiles changes seasonally. All the strains could grow at 50% seawater while 70 and 42% of the strains could not grow at 0 and 100% seawater, respectively.
On the other hand, 72 strains, out of the 84 strains, clustered into 9 phena using numerical taxonomy methods. The strains belonging to phena 1 through 9 were all Gram-negative, non-spore-forming rod-shaped organisms which were negative for susceptibility to vibrostatic agent O/129, H₂S production and acid from dulcitol, and the G + C contents of DNAs ranged from 29.8 to 56.6 mol%. However, almost all strains could not be identified and are suggested to be new species.     

Seasonal change of dinoflagellates cyst flux collected in a sediment trap in Omura Bay, West Japan

Sediment trap samples were harvested bimonthly from 1998 to2000 and examined to better understand the species compositionand seasonal variation of dinoflagellate cyst flux in OmuraBay in Japan. Samples’ living cyst flux clearly showedseasonal variation with the higher flux number between autumnand winter. In total, 43 different cyst taxa were recorded,and these were composed of two different ecological groups.The first group included Protoperidinium compressum and Protoperidiniumsubinerme, which increased every autumn to winter. The secondgroup included Gonyaulax spp. and Pheopolykrikos hartmanniiand was trapped throughout the year. These two groups manifestedthe different flux patterns and were, respectively, heterotrophicand autotrophic in nutrition. In the heterotrophic group, protoperidinioidcysts were dominant. Vegetative cells of protoperidinioid areknown to feed mainly diatoms. Sample diatom flux also increasedfrom autumn to winter. Therefore, the increase of protoperidinioidcysts in autumn to winter was observed to correlate with diatomblooms. In contrast, the autotrophic group mostly consistedof Gonyaulacoid cysts and were generally observed throughoutthe year, although occurrence varied between species most likelyresponding to favorable environmental conditions. The resultsindicate that cyst production is closely related to differentnutritional modes.     

Population structure of Alexandrium (Dinophyceae) cyst formation-promoting bacteria in Hiroshima Bay, Japan

A total of 31 bacterial isolates that have potential Alexandrium cyst formation-promoting activity (Alex-CFPB) were isolated from Hiroshima Bay (Japan), which is characterized by seasonal blooms of the toxic dinoflagellate Alexandrium tamarense. The population structure of Alex-CFPB was analyzed by means of restriction fragment length polymorphism analysis of the 16S rRNA genes (16S rDNA). Fourteen ribotypes, A to N, were observed among the 31 isolates of Alex-CFPB by using four restriction enzymes, MboI, HhaI, RsaI and BstUI. Among them, seven isolates, which were obtained from the seawater samples taken during the peak and termination periods of the A. tamarense bloom in 1998, belonged to ribotype A. This result suggests that bacterial strains of ribotype A may be dominant in the Alex-CFPB assemblages during these periods. The partial 16S rDNA-based phylogenetic tree of 10 ribotypes studied showed that nine of them fell into the Rhodobacter group of the alpha subclass of the Proteobacteria: Eight of nine ribotypes of the Rhodobacter group fell into the lineage of the Roseobacter subgroup, and one fell into the Rhodobacter subgroup. The non-Rhodobacter group type fell into the Marinobacterium-Neptunomonas-Pseudomonas group of the gamma-Proteobacteria: Isolates of Alex-CFPB ribotypes A and C do not have clear growth-promoting activities but have strong cyst formation-promoting activities (CFPAs) under our laboratory conditions. These results show that the Alex-CFPB assemblage may consist of various bacteria that belong mainly to the Roseobacter group and have strong CFPAs. These results suggest that not only the Alexandrium cyst formation-inhibiting bacteria (Alex-CFIB) reported previously but also Alex-CFPB, especially bacteria of ribotype A, may play significant roles in the process of encystment and bloom dynamics of Alexandrium in the natural environment.     

Antimicrobial potential of deep surface sediment associated bacteria from the Sea of Japan

The aim of this study was to survey microorganisms from the deep surface sediment samples collected from the Sea of Japan and to screen them for antimicrobial and antagonistic effects. Phylogenetic analysis revealed most isolates sharing 98–100 % sequence similarity to recognized species, including those recovered previously from marine or saline environments. Alteromonas, Halomonas, Marinobacter, Pseudoalteromonas, Salinicola, within the class Gammaproteobacteria, Sulfitobacter (Alphaproteobacteria), Bacillus, Paenibacillus and Paenisporosarcina (Firmicutes), Nocardiopsis and Streptomyces (Actinobacteria) occurred abundantly in all sediment samples. Antimicrobial screening revealed twenty three strains (13 %) capable to inhibit growth of one to eight test cultures and deep sediment isolates. Based on phylogenetic analysis mostly active strains belonged to the genera Bacillus, Brevibacillus, Nocardiopsis, Paenibacillus and Streptomyces. Antimicrobial substances (1–3) were isolated from strain Paenibacillus sp. Sl 79w showing a high inhibitory activity. On the basis of combined spectral analyses (IR, UV, ¹H and ¹³C NMR) the compounds 1, 2 and 3 with [M + H]⁺ at 409.1 and 409.2 m/z, and with [M + Na]⁺ at 822.5 m/z were found to have a carbon skeleton of isocoumarin and peptide antibiotics, respectively. Our findings demonstrated that the deep surface sediments of the Sea of Japan represent an untapped source of diverse microorganisms capable of antimicrobial metabolite production.     

Psychrotrophic amylolytic bacteria from deep sea sediment of Prydz Bay, Antarctic: diversity and characterization of amylases

Seventeen psychrotrophic bacteria with cold-adaptive amylolytic, lipolytic or proteolytic activity were isolated from deep sea sediment of Prydz Bay, Antarctic. They were affiliated with γ-Proteobacteria (12 strains) and gram-positive bacteria (5 strains) as determined by 16S rDNA sequencing. The amylase-producing strains belonged to genus Pseudomonas, Rhodococcus, and Nocardiopsis. Two Pseudomonas strains, 7193 and 7197, which showed highest amylolytic activity were chosen for further study. The optimal temperatures for their growth and amylase-producing were between 15 and 20°C. Both of the purified amylases showed highest activity at 40°C and pH 9.0, and retained 50% activity at 5°C. The SDS-PAGE and zymogram activity staining showed that the molecular mass of strain 7193 and 7197 amylases were about 60 and 50 kDa respectively. The Pseudomonas sp. 7193 amylase hydrolyzed soluble starch into glucose, maltose, maltotriose, and maltotetraose, indicating that it had both activities of α-amylase and glucoamylase. The product hydrolyzed by Pseudomonas sp. 7197 amylase was meltotetraose.     

Spread of bacteria of the genus Acinetobacter in the hydrobios of the Bay of Peter the Great, the Sea of Japan

The analysis of the spread of bacteria of the genus Acinetobacter among the invertebrate animals of the Bay of Peter the Great (the Sea of Japan): in bivalved mollusks, sea cucumbers and sea urchins Acinetobacter bacteria were detected more often than in cushion stars and crustaceous animals. The biological properties of 45 isolated bacteria were studied with the use of a wide variety of tests. The study revealed that 9% of Acinetobacter cultures isolated from marine animals had pronounced beta-hemolysis.     

Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): abundance and diversity related to geochemical zonation

In order to better understand the main factors that influence the distribution of sulfate-reducing bacteria (SRB), their population size and their metabolic activity in high- and low-sulfate zones, we studied the SRB diversity in 3- to 5-m-deep sediment cores, which comprised the entire sulfate reduction zone and the upper methanogenic zone. By combining EMA (ethidium monoazide that can only enter damaged/dead cells and may also bind to free DNA) treatment with real-time PCR, we determined the distributions of total intact bacteria (16S rDNA genes) and intact SRB ( dsrAB gene), their relative population sizes, and the proportion of dead cells or free DNA with depth. The abundance of SRB corresponded in average to 13% of the total bacterial community in the sulfate zone, 22% in the sulfate–methane transition zone and 8% in the methane zone. Compared with the total bacterial community, there were relatively less dead/damaged cells and free DNA present than among the SRB and this fraction did not change systematically with depth. By DGGE analysis, based on the amplification of the dsrA gene (400 bp), we found that the richness of SRB did not change with depth through the geochemical zones; but the clustering was related to the chemical zonation. A full-length clone library of the dsrAB gene (1900 bp) was constructed from four different depths (20, 110, 280 and 500 cm), and showed that the dsrAB genes in the near-surface sediment (20 cm) was mainly composed of sequences close to the Desulfobacteraceae , including marine complete and incomplete oxidizers such as Desulfosarcina , Desulfobacterium and Desulfococcus . The three other libraries were predominantly composed of Gram-positive SRB.     

Practical removal of radioactivity from sediment mud in a swimming pool in Fukushima, Japan by immobilized photosynthetic bacteria

About 90% of the radioactive Cs in the sediment mud of a school's swimming pool in Fukushima, Japan was removed by treatment for 3 d using the alginate immobilized photosynthetic bacterium Rhodobcater sphaeroides SSI. Even though batch treatment was carried out 3 times repeatedly, the activity of immobilized cells in removing Cs was maintained at levels of about 84% (second batch) and 78% (third batch). Cs was strongly attached to the sediment mud because, even with HNO(3) treatment at pH of 2.00-1.60 for 24 h, it was not eluted into the water. Furthermore, more than 75% of the Cs could be removed without solubilization with HNO(3). This suggests that the Cs attached to the sediment mud was transformed into immobilized cells via the Cs(+) ion by the negative charge of the immobilized cell surface and/or the potassium transport system of the photosynthetic bacterium.     

MIS 21 and the Mid-Pleistocene climate transition: Climate and sea-level variation from a sediment core in Osaka Bay,Japan

We report climate and sea-level variation for the marine oxygen isotope stage (MIS) 21, encompassing the end of the Mid-Pleistocene climate transition (MPT), based on pollen, diatom, and sulfur records from a 50-m thick sequence in a core from Osaka Bay. An extremely warm climate coincided with the sea level highstand of substage 21.5, when the warm-temperate element Quercus (Cyclobalanopsis) exceeds 40% of total arboreal pollen. This was followed by a warm-temperate to temperate and humid climate that continued until the end of MIS 21. A linear age model shows that climate was dominated by precessional cyclicity, with an inverse correlation between temperature and precipitation. The postglacial sea-level rise reached its highest peak in substage 21.5, when paleo-Osaka Bay reached its maximum extent including Kyoto and Nara Basins. At this time pelagic diatoms were dominant in the central part of the bay. Sea level dropped below the Osaka Bay sill (about ? 60 m at present) during substage 21.4, followed by a rise above the sill in substage 21.3, and a drop at 21.2. Sea level remained below the sill during substage 21.1. The thermal maximum and sea level peak occurred just after the rapid postglacial sea level rise, after which there was a gradual decline in temperature and sea level accompanied by precession-related oscillations; these features are typical of the post-MPT interglacials dominated by 100-ka cyclicity. These features may be a sign of termination of the MPT.     

Submarine groundwater discharge in Osaka Bay, Japan

Submarine groundwater discharge (SGD) rates in Osaka Bay were continuously measured and analyzed to evaluate seawater–groundwater interactions. Fast Fourier transfer and power spectrum density methods were applied to analyze the dominant periods of the SGD variations. Diurnal and semidiurnal periods of SGD variation were found, and they were caused by tidal effects. According to the separation of SGD into fresh and recirculated water components using automated seepage meter measurements and terrestrial groundwater flow analyses, the fresh groundwater component in SGD was evaluated to be in the range 4%–29% at Tannowa, Osaka. Therefore, SGD rates depend mainly on the volume of recirculated seawater. Correlation analyses between SGD and sea level show that SGD is delayed by 4h after sea level changes.     

Sulfate reduction and sediment metabolism in Tomales Bay,California

Sulfate reduction rates (SRR) in subtidal sediments of Tomales Bay, California, were variable by sediment type, season and depth. Higher rates were measured in near-surface muds during summer (up to 45 nmol cm^-3 h^-1), with lower rates in sandy sediments, in winter and deeper in the sediment. Calculations of annual, average SRR throughout the upper 20 cm of muddy subtidal sediments (about 30 mmol S m^-2 d^-1) were much larger than previously reported net estimates of SRR derived from both benthic alkalinity flux measurements and bay wide, budget stoichiometry (3.5 and 2.6 mmol m^-2 d^-1, respectively), indicating that most reduced sulfur in these upper, well-mixed sediments is re-oxidized. A portion of the net alkalinity flux across the sediment surface may be derived from sulfate reduction in deeper sediments, estimated from sulfate depletion profiles at 1.5 mmol m^-2 d^-1. A small net flux of CO₂ measured in benthic chambers despite a large SRR suggests that sediment sinks for CO₂ must also exist (e.g., benthic microalgae).     

Recreational Effects in Vostok Bay, Sea of Japan

The paper presents the results of three hydrochemical surveys performed in October 2000 and May and July 2001 and microbiological monitoring performed in June, July, and August 2001 in Vostok Bay (Sea of Japan), which is a favorite recreation area for the inhabitants of Primorye and the Russian Far East. It is shown that at the height of recreation occurs during late summer, as determined by the concentration of water-dissolved oxygen, the biochemical oxygen demand (BOD₅), the concentration of detergents, and the number of colony-forming enterobacteria in 1 ml of water. However, in autumn, especially by October, the anthropogenic pressure decreases and the quality of the water environment in the bay improves.     

Distribution and characteristics of Bacillus bacteria associated with hydrobionts and the waters of the Peter the Great Bay, Sea of Japan

Bacilli of the species Bacillus subtilis, B. pumilus, B. mycoides, B. marinus and B. licheniformis (a total of 53 strains) were isolated from 15 invertebrate species and the water of the Vostok Bay, Peter the Great Bay, Sea of Japan. Bacilli were most often isolated from bivalves (22.7%) and sea cucumbers (18.9%); they occurred less frequently in sea urchins and starfish (13.2 and 7.5%, respectively). Most of bacilli strains were isolated from invertebrates inhabiting silted sediments. No Bacillus spp. strains were isolated from invertebrates inhabiting stony and sandy environments. The species diversity of bacilli isolated from marine objects under study was low. Almost all bacterial isolates were resistant to lincomycin. Unlike B. pumilus, B. subtilis isolates were mostly resistant to benzylpenicillin and ampicillin. Antibiotic sensitivity of B. licheniformis strains was variable (two strains were resistant to benzylpenicillin and oxacillin, while one was sensitive). A significant fraction of isolated bacilli contained pigments. Pigmented strains were more often isolated from seawater samples, while colorless ones predominated within hydrobionts. B. subtilis colonies had the broadest range of colors. In the Bacillus strains obtained, DNase, RNase, phosphatase, elastolytic, chitinase, and agarolytic activity was detected. Bacilli strains with hydrolytic activity occurred in invertebrates more often than in seawater.     

The Meroplankton of Amurskii Bay (Peter the Great Bay,Sea of Japan)

Russian Journal of Marine Biology - The composition and seasonal dynamics of meroplankton in Amurskii Bay (Sea of Japan) were studied for the first time. The total survey period exceeded two years....     

Examining the relationship between bacteria and heterotrophic nanoflagellates in Funka Bay (Japan) using the size-fractionation method

The chemical and biological conditions, and the bacteria-heterotrophic nanoflagellate (HNF) relationship were investigated in the vicinity of Funka Bay, southwest of Hokkaido, Japan during early spring 1999. At the time of sampling, chlorophyll a concentration, bacteria, phycoerythrin rich-cyanobacteria, and HNF abundance were in the following ranges: 0.3–3.6 g l^–1, 2.5–5.6 × 10⁵ cells ml^–1, 0.6–1.2 × 10³ cells ml^–1, and 2.2–4.2 × 10³ cells ml^–1, respectively. Dissolved inorganic nitrogen, phosphate and silicate concentrations were in the ranges: 8.7–12.2 M, 0.9–2.0 M, and 21.6–25.5 M, respectively. Primary production ranged from 6.4 to 76.3 mg C m^–3 d^–1. Using water samples from regions of different productivity levels (in and outside bay), the bacteria - HNF relationship was uncoupled experimentally by the size-fractionation technique. Higher primary production (19.9 mg C m^–3 d^–1) in the bay supported higher bacterial growth rate (0.029 h^–1). However, outside the bay both primary production (6.4 mg C m^–3 d^–1) and bacterial growth rate (0.007 h^–1) were lower. The HNF growth rates and grazing rates were similar for both but by comparing both HNF grazing capacity and bacterial production, there was net decrease in bacterial abundance outside the bay and net increase inside the bay. The microbial parameters (rates and abundance) and the amount of carbon flow estimated through the phytoplankton – dissolved organic matter (DOM) – bacteria loop were different between the coastal station and the open ocean station. However HNF grazing and growth rates was similar for both stations.     

Dissolved oxygen concentration in river sediment of the Lake Biwa tributaries, Japan

The dissolved oxygen concentration in the sediment pore water downstream of rivers in the Lake Biwa basin was measured, and the factors affecting the dissolved oxygen concentration were analyzed. In August 2003, nine rivers (Sakai, Nakanoi, Hebisuna, Anziki, Yasu, Echi, Ane, Oh, and Ohura) were surveyed. The dissolved oxygen was depleted in the sediment pore water of the rivers with a high proportion of particles less than 250 μm in size. For these rivers, the difference between the dissolved oxygen concentrations of the river surface water and the pore water was large, ranging from −9.54 to −5.26 mg L⁻¹. It was found that the proportion of land turned to paddy fields has an effect on the percentage of the particles below 250 μm (standard partial regression coefficient = 0.807, p = 0.023). These results suggest that, in the Lake Biwa basin, the sedimentation of the fine particles released from paddy fields results in poor dissolved oxygen in the river sediment downstream. In addition, the water flow conditions in small- and medium-scale rivers without headwaters also affect the sedimentation of suspended particles.