Metagenomic analysis using 16S ribosomal RNA genes of a bacterial community in an urban stream,the Tama River,Tokyo

In an effort to determine genus- or species-level taxonomic profiles and diversity of bacterial consortia in the Tama River around urban Tokyo, next-generation sequencing technology targeting a 16S ribosomal RNA (rRNA) gene amplicon was employed. Metagenomic analysis performed by an Ion Personal Genome Machine after sequentially filtering samples through 5-, 0.8- and 0.2-μm filters yielded 1.48 Gb of 16S sequences (average 2.38 M reads/sample). The results indicated that half of the bacterial sequences belonged to Proteobacteria, followed by Bacteroidetes, Actinobacteria and Cyanobacteria. Flavobacterium (Bacteroidetes), possibly including a potential fish pathogen, was the most numerous genera in the Tama River metagenome, and accounted for?~?16% of assigned 16S reads, followed by Mycobacterium. Other dominant bacterial genera including Zoogloea, Sediminibacterium, Hyphomicrobium, Sphingopyxis, Thiothrix and Lysobacter, were thought to be associated with waste water and sludge. MiSeq metagenomic analysis revealed that environmental factors, particularly water temperature, influenced the bacterial composition throughout the year, with a strong negative correlation observed for Proteobacteria and a positive correlation for Bacteroidetes. In terms of bacterial genera, Flavobacterium was positively correlated with temperature, while Polaromonas, Pseudomonas and Bradyrhizobium were negatively correlated with this, suggesting dynamic change in the free-living bacterial population throughout the year and versatile adaptation strategies in relation to environmental factors.     

Element interconnections in Lotus japonicus: A systematic study of the effects of element additions on different natural variants

Lotus japonicus was used to study the distribution and interconnections of 15 elements in plant tissues, including essential and non-essential elements: boron (B), sodium (Na), magnesium (Mg), potassium (K), calcium (Ca), manganese (Mn), iron (Fe), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), strontium (Sr), molybdenum (Mo), cadmium (Cd) and cesium (Cs). Large amounts of B and Ca accumulated in plant leaves, while Fe, Na, Ni, As and Cd tended to mainly occur in the roots, and Mo was the only element to accumulate in the stems. The elemental compositions within plants were severely disturbed by treatment with toxic elements. Competition between element pairs in the same group (e.g. K and Cs; Ca and Sr) was not found. Iron, Cu and Zn accumulation were induced by Cd and Ni addition. When natural variants grew in a nutrition solution with subtoxic levels of As, Cd, Cs, Ni, Mo and Sr, intriguing relationships between the elements (such as Fe, As and K; Mg and Ni; Mn and Ca) were revealed using principal-component analysis. This study on the plant ionome offers detailed information of element interactions and indicates that chemically different elements might be closely linked in uptake or translocation systems.     

Phenolic constituents in the fruits of Cinnamomum zeylanicum and their antioxidant activity

Defatted cinnamon fruit powder was successively extracted with benzene ethyl acetate, acetone, MeOH, and water. The concentrated water extract contained the maximum amount of phenolics and showed the highest antioxidant activities. Hence, it was fractionated by Diaion HP-20SS, Diaion HP-20, and Sephadex LH-20 column chromatographies. It gave five purified compounds, the purities of which were analyzed by HPLC. Compounds 1-5 were identified as 3,4-dihydroxybenzoic acid (protocatechuic acid), epicatechin-(2beta-->O-7,4beta-->8)-epicatechin-(4beta-->8)-epicatechin (cinnamtannin B-1), 4-[2,3-dihydro-3-(hydroxymethyl)-5-(3-hydroxypropyl)-7-(methoxy)benzofuranyl]-2-methoxyphenyl beta-d-glucopyranoside (urolignoside), quercetin-3-O-(6-O-alpha-l-rhamnopyranosyl)-beta-d-glucopyranoside (rutin), and quercetin-3-O-alpha-l-rhamnopyranoside by using extensive spectral studies. The antioxidant activities of purified compounds were screened for their antioxidative potential using beta-carotene-linoleate and 1,1-diphenyl-2-picrylhydrazyl model systems. All of the compounds showed antioxidant and radical scavenging activities. This is the first report of the isolation and identification of nonvolatile constituents and as well as antioxidant activities from cinnamon fruits.     

The relationship between migration speed and release date for chum salmon Oncorhynchus keta fry exiting a 110-km northern Japanese river

The relationship between release date and migration speed was examined for hatchery chum salmon Oncorhynchus keta fry exiting the Nishibetsu River in eastern Hokkaido, northern Japan so that future releases might be scheduled so that fry arrive at the ocean during periods favoring high survival. Separate marked groups of chum salmon released in early April, mid-April, and early May in 2008, late March and mid-April in 2009, and mid-April in 2010 were recaptured with a rotary screw trap 12 km above the river mouth. Chum salmon in later release groups tended to migrate downstream faster than fish in earlier release groups. Those released after mid-April arrived in the lower river on average 9 days after release, while those released before mid-April arrived on average 26–28 days after release. Most marked fish arrived in the lower river during late April to mid-May. These results suggest that chum salmon are adapted to adjust their migratory speed so as to arrive at the ocean during a relatively discrete period, presumably during a time of high productivity favoring good survival.     

Benefits of live phytoplankton, <Emphasis Type="Italic">Chlorella vulgaris</Emphasis>, as a biocontrol agent against fish pathogen <Emphasis Type="Italic">Vibrio anguillarum</Emphasis>

The ability of the probiotic bacterium Sulfitobacter to inhibit the growth of two virulent strains (psh-9019 and ATCC 43306) of the fish pathogenic bacterium Vibrio anguillarum was tested. Probiotic and pathogenic bacteria were inoculated individually or together in three different types of media. Two of the phytoplankton media tested were filtrates of phytoplankton Chlorella vulgaris cultures, either the live phytoplankton (live-CV) or a condensed phytoplankton (condensed-CV). Phytoplankton culture medium, ESM, was used as a control medium without phytoplankton. In ESM, Sulfitobacter decreased the viable cell counts of both V. anguillarum strains by tenfold. In the live-CV filtrate, V. anguillarum was eradicated by Sulfitobacter within one week. Although colony counts of strain ATCC 43306 declined during the two-week co-incubation with Sulfitobacter, its growth was not fully inhibited; however, the counts were tenfold lower than that in control ESM medium. Neither of the pathogenic V. anguillarum strains were inhibited nor eradicated by Sulfitobacter in the condensed-CV filtrate medium. Our study indicates that commercially available condensed phytoplankton can enhance the growth of V. anguillarum. Thus, the addition of live phytoplankton, including the introduction of Roseobacter clade bacteria to fish larvae tanks, leads to better biocontrol of the fish pathogen V. anguillarum.     

Factors Affecting Small-Scale Farmers’ Land Allocation and Tree Density Decisions in an <Emphasis Type="Italic">Acacia decurrens</Emphasis>-Based <Emphasis Type="Italic">taungya</Emphasis> System in Fagita Lekoma District,North-Western Ethiopia

The development of woodlots as an additional source of livelihood and as a land management option for small-scale farmers is a challenging issue in the cereal-based subsistence farming systems of north-western Ethiopia. There is a need to understand why and which factors determine the decisions of small-scale farmers to grow short-rotation woodlots on their land. Data used in this study were collected from a survey of 200 randomly selected households in the region. A Tobit regression model was used to determine predictor variables for farmers’ decisions to allocate land to planting Acacia decurrens (J.C. Wendl.) Willd. and at what density trees are planted on the respective plots. The most important motivations for planting A. decurrens were income, soil fertility management, and soil and water conservation. Having a male head of household, long distance to markets and plots being on marginal land, among other factors, increased the allocation of land to A. decurrens woodlots. Having a male head of household, access to credit and plots being on marginal land, among other factors, increased tree planting density. Age had a negative effect on both allocation of land to woodlots and tree density, whereas farm size had an inverted U-shaped relationship with both decisions. These results suggest that wider expansion of A. decurrens-based plantation systems could be achieved through improving extension, credit access and road infrastructure to connect small-scale farmers to markets and finance.     

Attenuated mutants of Potato virus Y necrotic strain produced by nitrous acid treatment and mutagenesis-in-tissue culture methods

We produced attenuated mutants of Potato virus Y necrotic strain not only by nitrous acid treatment but also by a novel method, probably unique to plant viruses, which we call the “mutagenesis-in-tissue culture method”. This relies on the natural or experimental generation of virus sequence variants within an infected plant, and then isolating the mutants by serially cloning them in plants. A total of fifteen attenuated mutants were obtained and studied. Nucleotide and amino acid sequences of the genomes of the attenuated mutant populations were compared with those parental severe isolates, and the amino acid changes in relevant genomic regions for viral attenuation were inferred. Many of the mutations were located in the 5’ half of the genome; 65 % were located in the protein 1 (P1) and helper component proteinase protein (HC-Pro) encoding regions. Amino acid changes mostly involved simultaneous changes in two or more protein encoding regions, one of which was often in the HC-Pro encoding region. The attenuated mutants M-MY10 and N-NA10 were effective in cross-protection against the original severe isolate NTND6.     

Competence of <Emphasis Type="Italic">Frankliniella occidentalis</Emphasis> and <Emphasis Type="Italic">Frankliniella intonsa</Emphasis> strains as vectors for <Emphasis Type="Italic">Chrysanthemum stem necrosis virus</Emphasis>

The vector competence of Frankliniella occidentalis for Chrysanthemum stem necrosis virus (CSNV) was evaluated. Three vector strains with distinct competences for Tomato spotted wilt virus (TSWV) transmission were investigated, including an artificially selected strain (TsH) that has a particularly high competence (>90 %). Newly hatched larvae of F. occidentalis were given an acquisition access period of 5 days on CSNV-infected D. stramonium leaves, and reared to maturity. Their transmission efficiencies were examined using a leaf disk assay using Petunia x hybrida leaves. Following the leaf disk assay, the virus accumulation in the vectors was examined via a double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) of their bodies. The results showed that the CSNV acquisition and transmission efficiency of the TsH strain did not differ from those of the others, indicating that the competence of F. occidentalis as a vector for CSNV is not related to that for TSWV. The CSNV transmission and acquisition efficiencies of two F. intonsa strains (Hiroshima and Fukuoka) were also evaluated. In Hiroshima strain, 35 % of adults were viruliferous, but only two transmitters (3 %) were observed. In Fukuoka strain, 6 % were viruliferous, and no transmitters were observed. These results indicate that F. intonsa cannot be a major vector for CSNV. The accumulation of CSNV in the adults of F. occidentalis and F. intonsa evaluated using DAS-ELISA showed a significant difference in ELISA values among transmitter, viruliferous non-transmitter, and non-viruliferous individuals. These results clearly demonstrated that only transmitters that accumulated a threshold quantity of virus can transmit CSNV to plants.     

Reservoir sedimentation and its mitigating strategies: a case study of Angereb reservoir (NW Ethiopia)

Purpose  

The Angereb dam in northwestern Ethiopia was commissioned in 1997 to serve as a domestic water supply for 25 years. However, its sustainability is being threatened by rapid sedimentation. The overall objective of this study was to understand reservoir sedimentation in this tropical highland watershed and to propose its mitigating strategies that would contribute to the improved planning and management of reservoirs in similar regions.