THE SAVE SANRIKU OYSTERS PROJECT

Oyster business reconstruction project from the Great East Japan Earthquake.

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It was also featured on NHK radio 7: Read the article April 4th, The project was featured in Sankei Shinbun 's newspaper. Read the article April 3th, The project was featured in Sankei news. Read the article March 30th, The project was featured in in Yahoo! Read the article March 29th, The project was featured in IT media. June 4th, We bought oyster seeds for Akasaki, Oofunato. We bought oyster seeds of crassostrea nippona for a producer group in Akasaki. May 27th, We made PDF flyers.

The flyers include an overview of the project, please print them out and distribute! We also bought them from the local area, Higashimatsushima, Miyagi. May 19th, We sincerely apologize for the delay in sending them out. We are going to ship them from May 20th for those who applied between March 26th and April.

We appreciate your patience. May 17th, We donated 1,, yen approx. Reports April 13th, We have been visiting producers in various areas since last week. Encouragement we received from oyster owners.

March 30th, We posted the map of oyster-producing areas affected by the Great East Japan Earthquake. Donation boxes will be placed on that day.

The project was featured in Nikkei Shinbun newspaper Northern Japan ver. The nucleic acids were finally treated with RNase The PCR conditions used were as follows: Amplified fragments were purified by electrophoresis, ligated into the pGEM-T vector Promega, Madison, WI , and cloned into Escherichia coli as described previously Clones containing appropriate insert sizes were selected by an electrophoretic analysis, and their nucleotide sequences were determined as described previously The profile alignment technique of ClustalW, version 1.

Each alignment was refined by visual inspection, and secondary structures were considered for the refinement analysis A phylogenetic tree was constructed by the neighbor-joining method 36 and the maximum-likelihood method Nucleotide positions at which any sequence had a gap or an ambiguous base were not included in the phylogenetic calculations.

Checks for chimeric sequences were conducted by the chimera check program in the Ribosomal Database Project database 25 , and possible chimeras were excluded from further analyses. The composition of PCR was as described above, except for the competitor fragment being added at a known copy number. Two microliters of the PCR product was analyzed by electrophoresis through 1. The band intensities of the target and competitor fragments were quantified by using the Multianalyst program supplied with Gel Doc Bio-Rad, Hercules, CA.

At least three PCR assays with different concentrations of a competitor generally, decimal dilutions were conducted for estimating a copy number of a target fragment.

A relative amplification efficiency of a target to a competitor was estimated by PCR with known numbers of target and competitor fragments. The copy number of the target was estimated by considering the band intensities, length of the fragment, relative amplification efficiency of the target to the competitor, and copy number of the competitor as described by Lee et al. Incubation for determining SRR was initiated within 3 h after sampling. A sediment sample 20 g [wet wt] was suspended in an equal weight of deaerated natural seawater in a bottle mlcapacity under a nitrogen atmosphere, and the bottle was sealed with a butyl rubber septum and aluminum crimp cap.

The sediment was washed two times with natural seawater, and the three seawater fractions were mixed. An appropriate amount of the seawater mixture or zinc-acetate solution was added to 10 ml of a ScintiVerse liquid scintillation cocktail Fisher Scientific, Tokyo, Japan , and radioactivity was measured using a model CA Tri-Carb liquid scintillation analyzer Perkin-Elmer, Boston, MA.

SRR was estimated from the radioactivities, sulfate concentration, sediment weight, incubation time 24 h , and isotope-fractionation ratio according to an equation described previously Incubation for determining SOR was initiated within 3 h after sampling. The sediment sample 20 g was suspended in an equal weight of sulfate-depleted artificial seawater composed per liter of NaCl, This slurry was transferred to a bottle ml under air and supplemented with 0. Autoclaved sediment was incubated under the same conditions, which served as the abiotic control for estimating rates for chemical oxidation.

The SOR was estimated by subtracting the chemical oxidation rate from the total oxidation rate. The values for COD and sulfate concentrations of Y-mean weare also significantly different from the values for the Y-D sediment. Since sampling point Y-D was situated at the mouth of the Orikasa river and out of the aquaculture zone, it is likely that this sediment was mostly affected by organic loads from the river but not by the aquaculture activity.

The phylogenetic relations appearing in Fig. In addition, the Kamaishi library contained many phylotypes affiliated with candidate divisions OP8 and OP9.

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The bold vertical bar to the right of the tree in panel A represents the range of Thiotrichales , while the one to the right of the tree in panel B represents Desulfobulbaceae. Accession numbers for the reference sequences are shown in parentheses. Phylogenetic distribution of clones in each library.

Another phylotype found abundantly in the libraries was K82 containing nine clones in the KM library ; this phylotype and three other phylotypes Y67, Y, and Y were affiliated with Crenarchaeota and related to 16S rRNA gene clones in marine benthic group C i. The utility and limitation of qcPCR assays for quantifying microbial populations in natural ecosystems have been described previously 22 , This method can prevent a possible incorrect estimate of the copy number resulting from variation in the DNA extraction efficiency. Comparison of the K-mean with the Y-mean in Fig.

Similar trends in qcPCR were observed for sediments obtained in data not shown. This study investigated prokaryotes in coastal marine sediments in the Sanriku region. Although the Yamada and Kamaishi bays are close to each other and have similar hydrogeological characteristics and water qualities, the bacterial community structure in the sediment of these two bays was substantially different.

These results indicate that the sulfur cycle has become active in the Yamada sediment beneath the shellfish bed. Similar levels of prokaryotic diversity in the marine sediment have been reported previously 4 , Bowman and McCuaig found that phylotypes were present in a subsample of clones 1, clones in a 16S rRNA gene library constructed from Antarctic marine sediments 4. A rarefraction analysis conducted for the Arctic sediment library 31 has, however, suggested that the prokaryotic diversity in the marine sediment can only be partially assessed at this scale of analysis with several hundred clones.

Nevertheless, when the results of clone library analyses are compared with those of quantitative community analyses, e.

It is therefore possible to obtain a fundamental insight into the major prokaryotic populations by clone-library analysis on a similar scale. This phylotype was closely related to the genus Desulfotalea that had been isolated from permanently cold Arctic marine sediments off the coast of Svalbard 21 and has been identified as psychrophilic SRB capable of incomplete oxidization of fatty acids Related sequences have also been cloned from the Svalbard sediments 31 , Antarctic shelf sediment 4 , deep-sea sediments 23 , and coastal sediments off Japan 42 , indicating that this group of SRB is widely distributed in marine sediment.

A previous study has used the rRNA blot analysis for estimating this group of SRB in the Svalbard sediments 35 , showing that they made up from 1. In the present study, it was also shown that the relative abundance of the SVA group Fig. Based on these data, we concluded that SVA group SRB are the important sulfate-reducing population in the Sanriku coast sediment and suggest that their importance is not restricted to permanently cold marine sediments. Further studies are thus needed to understand the total population structure of SOB in marine sediments. A previous study showed that mussel aquaculture affected the macrobenthic community 40 , demonstrating that dominant species were shifted from suspension feeders to deposit feeders.

Such a difference in macrobenthos populations has not been observed in the Kamaishi and Yamada bays; the major benthos in these bays have been reported to be lugworms affiliated with Polychaeta http: Other studies analyzed changes in compositions of biological molecules, e. The results suggested that these biological signatures can be used as indices for the trophic states of the coastal environment. In the present study, we detected differences in the number and activity of sulfate reducers and sulfur oxidizers in marine sediments taken from two different bays, suggesting that these bacteria can serve as indices for assessing the organic load to the marine sediment.

MATERIALS AND METHODS

To further support this idea, comparative ecological surveys should be done, in which sediment samples will be taken from several different Sanriku bays with different levels of aquaculture and analyzed by the methods employed in the present study. In addition, it will also be necessary to examine contribution of other types of terminal electron-accepting processes e. If this idea is fully supported by these analyses, sediment bacteria involved in the sulfur cycle e.

National Center for Biotechnology Information , U. Journal List Appl Environ Microbiol v. Author information Article notes Copyright and License information Disclaimer. Received Oct 3; Accepted Dec This article has been cited by other articles in PMC. Abstract Prokaryotes in marine sediments taken from two neighboring semienclosed bays the Yamada and Kamaishi bays at the Sanriku coast in Japan were investigated by the culture-independent molecular phylogenetic approach coupled with chemical and activity analyses.

Open in a separate window. Sampling and characterization of sediment. DNA extraction and purification. PCR primers used in this study. Summary of qcPCR assays. Potential sulfate reduction rate SRR. Potential sulfur oxidation rate SOR. Nucleotide sequence accession numbers. Phylotypes obtained in this study.

Acknowledgments We thank Ikuko Hiramatsu for technical assistance.

Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms. Prokaryotic metabolic activity and community structure in Antarctic continental shelf sediment. Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment. A polyphasic approach to study the diversity and vertical distribution of sulfur-oxidizing Thiomicrospira species in coastal sediments of the German Wadden Sea.

Characterization of Thiomicrospira kuenenii sp.