DNA metabarcoding focusing on the plankton community: an effective approach to reconstruct the paleo-environment.

DNA metabarcoding (DNA-MB) targeting the whole plankton community is a promising approach in studies of sediment samples from water bodies, but its effectiveness in ancient material is not well demonstrated. We applied DNA-MB of plankton in a sediment core to reconstruct the paleo-environment of Lake Shinji, Japan, through a marine lagoon/freshwater lake transition during the past 2300 years. We interpreted core-sample plankton taxonomy and habitat by reference to the modern plankton community in water samples. OTUs (operational taxonomic units) belonging to Dictyochophyceae were 81.05% of the total reads in sediments. However, Ciliophora, Copepoda and Labyrinthulea formed the majority of plankton taxa in the water samples, suggesting that they are under-represented in sediment. A drastic change in plankton composition correlated with a large decrease in sediment sulfur concentration, implying the change of aquatic environment from marine lagoon to freshwater lake. This event took place ca. 1200 CE in Lake Shinji. A 250 year-long transitional period followed, during which the total DNA sequence reads were very low. This suggests that salinity fluctuations created a hostile environment for both marine and freshwater plankton species. Our results show that DNA-MB of the whole plankton community is effective in reconstructing paleo-environments.

The variations in the East Asian summer monsoon over the past 3 kyrs and the controlling factors.

The mechanisms driving the variations in the centennial-scale East Asian summer monsoon (EASM) remain unclear. Here, we use the δ18O records from adult ostracode shells to reconstruct the EASM variations over the last 3 kyrs in southwestern Japan. A common variation with a 200 yr periodicity among the Asian monsoonal regions was recognized between BC 800 and BC 100. Since then, neither a correlation between the EASM variation and solar activity or a common EASM variation through EASM regions has been identified. The evidence reveals that solar activity dominantly affected the centennial-scale EASM variations throughout Asian monsoonal regions until BC 100. Furthermore, factors other than solar activity that varied and differed in specific regions controlled the EASM intensity due to decreasing summer solar insolation in the Northern Hemisphere after BC 100. These relations indicate that the dominant factor that affects the EASM variations shifts according to the solar insolation intensity.

Ecological shifts due to anthropogenic activities in the coastal seas of the Seto Inland Sea, Japan, since the 20th century.

Multiproxy analyses were conducted using sediment cores in a low-polluted coastal site (Hiuchi-nada) in the Seto Inland Sea (SIS), Japan. Heavy metal and organic pollution peaked in the 1960s and the bottom environments have ameliorated since the 1980s due to several environmental regulations. First ecological shifts in meiobenthic ostracodes and diatoms occurred in the 1960s due to the initiation of eutrophication. Then, a second ecological shift occurred in the 1980s due to the amelioration of the water and the bottom quality. A compilation of similar analytical results in the coastal seas of the SIS reveals three types of ecological and environmental history since the 20th century. The environmental improvement since the 1980s affects the ecosystems, in particular, in a low-polluted bay. However, ecological compositions are different from those prior to the 1960s, suggesting that the ecosystem was not recovered but changed into the next stage in the SIS.

Opening of the closed water area and consequent changes of ²²8Ra/²²6Ra activity ratios in coastal lagoon Nakaumi, southwest Japan.

In Lake Nakaumi, the second largest coastal lagoon in Japan, artificially closed (Honjyo) area, which was left untouched for 28 years, was partly opened in May, 2009. (228)Ra/(226)Ra ratio of waters in Honjyo area and Lake Nakaumi showed a well-tuned seasonal variation exhibiting high value in summer. After the opening event, however, the (228)Ra/(226)Ra ratios in the Honjyo water showed an unclear seasonal variation in both surface and deep water. This opening event caused the change of active movement of lake and marine water.

The ecological roles of bacterial populations in the surface sediments of coastal lagoon environments in Japan as revealed by quantification and qualification of 16S rDNA.

Based on quantification and qualification of bacterial 16S rDNA, we verified the bacterial ecological characteristics of surface sediments of Lakes Shinji and Nakaumi, which are representative of coastal lagoons in Japan. Quantification and qualification of the 16S rDNA sequences was carried out using real time polymerase chain reaction and polymerase chain reaction denaturing gradient gel electrophoresis and non-metric multidimensional scaling, respectively. The results revealed that the copy number per gram of sediment ranged from 8.33 × 10(8) (Lake Nakaumi) to 1.69 × 10(11) (Honjo area), suggesting that bacterial carbon contributed only 0.05-9.64 % of the total carbon content in the samples. Compared with other aquatic environments, these results indicate that sedimentary bacteria are not likely to be important transporters of nutrients to higher trophic levels, or to act as carbon sinks in the lagoons. The bacterial compositions of Lake Shinji and Lake Nakaumi and the Honjo area were primarily influenced by sediment grain sizes and salinity, respectively. Statistical comparisons of the environmental properties suggested that the areas that were oxygen-abundant (Lake Shinji) and at a higher temperature (Honjo area) presented efficient organic matter degradation. The 16S rDNA copy number per gram of carbon and nitrogen showed the same tendency. Consequently, the primary roles of bacteria were degradation and preservation of organic materials, and this was affected by oxygen and temperature. These roles were supported by the bacterial diversity rather than the differences in the community compositions of the sedimentary bacteria in these coastal lagoons.

Effects of regional climate changes on the planktonic ecosystem and water environment in the frozen Notoro Lagoon, northern Japan.

Diatom fossils from core sediments and living diatoms from water samples of Notoro Lagoon in northern Japan were examined to evaluate natural climate effects on lagoon environmental changes. In 1974, the artificial inlet was excavated. Immediately after, the anoxic bottom water in Notoro Lagoon began to disappear due to an increasing water exchange rate. However, chemical oxygen demand (COD) in the bottom water of Notoro Lagoon gradually increased, with fluctuations, during the last 30 years. In addition, the dominant diatom assemblages in Notoro Lagoon shifted to ice-related and spring bloom taxa after the excavation. The dominant taxa of each year in the sediment core were also strongly related to the timing of lagoon ice melting. This is because the COD in Notoro Lagoon was affected by the deposited volume of blooming diatoms, which was controlled by the duration of ice cover and the timing of ice discharge to the Okhotsk Sea likely due to an air pressure pattern change over the northern North Pacific like the Pacific Decadal Oscillation (PDO).

Recent sedimentary environment of coastal lagoon in southwestern Japan: evidence from major and trace elements.

A geochemical study of the bottom sediments of Lake Shinji and the River Ohashi in southwestern Japan was carried out to determine their elemental compositions and to evaluate the pollution status of lake sediments by employing enrichment factor (EF), pollution load index (PLI), and geoaccumulation index (Igeo). Present-day water quality was also assessed. Results showed that the water quality of Lake Shinji contrasts slightly between the upper and lower parts. The chemical composition of the sediments, as measured by X-ray fluorescence, included major and trace elements and total sulfur (TS). Average abundances of As, Pb, Zn, Cu, Ni, and Cr in the Shinji sediments were 10, 29, 143, 27, 19, and 54 ppm, respectively, compared to 6, 18, 57, 16, 10, and 37 ppm in the river sediments. Based on the EF, PLI, and Igeo, the lake sediments are moderately to strongly polluted with respect to As, moderately polluted with Pb, Zn, and Cr, and unpolluted with Cu and Ni. The high EF and Igeo for As, Pb, and Zn in the lake sediments indicate that metal concentration has occurred in Shinji. Increases in the abundances of these metals are likely related to the fine-grained nature of the sediments, reducing conditions of the bottom sediments, enrichment in organic matter, and possibly a minor contribution from non-point anthropogenic sources. Trace metal contents are strongly correlated with Fe2O3 and TS, suggesting that Fe oxides and sulfides play a role in controlling abundances in the investigated areas.

Abundances, distribution, and sources of trace metals in Nakaumi-Honjo coastal lagoon sediments, Japan.

Bottom sediments from Nakaumi Lagoon and the Honjo Area in southwest Japan were analyzed to determine their geochemical compositions and to assess potential impacts by comparison with sediment quality guidelines. Present-day water quality was also assessed. Results showed that the water quality of Nakaumi Lagoon and the Honjo area contrasts between their upper and lower parts. Average abundances of As, Pb, Zn, Cu, Ni, and Cr in the Nakaumi sediments were 12, 25, 135, 32, 21, and 46 ppm, respectively, compared to 10, 24, 110, 26, 20, and 38 ppm in the Honjo area. All averages are greater than those of the upper continental crust. The elevated metal concentrations are probably related to the fine-grained nature of the sediments, reducing bottom conditions produced by abundant organic matter and possibly minor non-point anthropogenic sources. Trace metal contents are strongly correlated with Fe2O3, suggesting that Fe oxides play a role in controlling abundances. Metal concentrations exceed the NYSDEC lowest effect level and CCME interim sediment quality guidelines that indicate moderate impact on aquatic organisms. Average abundances of As and Zn are comparable to the Coastal Ocean Sediment Database threshold, whereas maximum concentrations exceed that value, indicating that the concentrations of these metals are potentially toxic. These enrichments suggest that regular monitoring may be desirable even where no point sources of metal pollution exist.