Plastic pollution in the ocean is an emerging environmental concern in the Philippines. This study was conducted to investigate the prevalence of macroplastics, composition of plastic litter, and the clean-coast index (CCI) of urban and rural beaches in Sarangani Bay. Plastic litter was collected by delineating a 100-m transecting line with three 4 m × 4 m quadrats. The density of macroplastic litter in urban areas (0.66 items m−2) was significantly higher than in rural areas (0.29 items m−2). The plastics sampled were predominantly food packaging, such as polyethylene bags, which are locally known as sando bags. The accumulation rate of macroplastic litter ranged from 0.07 items d−1 m−2 to 0.40 items d−1 m−2, in which urban beaches (0.25 items d−1 m−2) have a significantly higher accumulation rate than rural beaches (0.11 items d−1 m−2). Overall, the calculated CCI of the beaches of Sarangani Bay was categorized as clean to moderately clean for rural beaches and moderately clean to extremely dirty for urban beaches.

Information is limited on the effects of commercial plant growth regulators (PGRs) on dragon fruit. Most studies on rooting effects on dragon fruit cuttings employed very high doses of plant growth regulators (PGRs), which are not deemed practical for greenhouse and field applications. This study was initiated to evaluate the responses of four genotypes of dragon fruit (‘Royal Red’, ‘Moroccan Red’, ‘Mexican White’, and ‘Hawaiian White’) during greenhouse acclimatization to diluted concentrations of commercial PGRs that are readily available in the market. A single factorial experiment on genotype effects on root and shoot responses, without PGR, was conducted. A second experiment with a 4x3x2 completely randomized design, with four genotypes, three diluted commercial PGR formulations and two exposure times as factors was also done. Root length, number of roots, number of days to first shoot emergence and number of new shoots were measured after 50 days of acclimatization in the greenhouse. In the single factorial experiment, only ‘genotype’ had an effect on number of new shoots (P<0.05). In the multifactorial experiment, all factors tested did not have significant interaction effects. However, the main effect of ‘genotype’ on number of new shoots and number of days to first shoot emergence was also significant (P<0.05). The lack of significant effect of other factors and their interactions on most growth responses suggest that it is difficult to resolve differences among the four genotypes using highly diluted commercial PGR formulations after a 50-day observation period. However, our data still suggest that the ‘Red’ genotypes are more superior than the ‘White’ genotypes in terms of shoot growth.

Demethylation inhibitors (DMIs) have been an important tool in the management of grapevine powdery mildew caused by Erysiphe necator. Long-term, intensive use of DMIs has resulted in reduced sensitivity in field populations. To further characterize DMI resistance and understand resistance mechanisms in this pathogen, we investigated the cyp51 sequence of 24 single-spored isolates from Virginia and surrounding states and analyzed gene expression in isolates representing a wide range of sensitivity. Two cyp51 alleles were found with respect to the 136th codon of the predicted EnCYP51 sequence: the wild-type (TAT) and the mutant (TTT), which results in the known Y136F amino acid change. Some isolates possessed both alleles, demonstrating gene duplication or increased gene copy number and possibly a requirement for at least one mutant copy of CYP51 for resistance. Cyp51 was over-expressed 1.4- to 19-fold in Y136F-mutant isolates. However, the Y136F mutation was absent in one isolate with moderate to high resistance factor. Two additional synonymous mutations were detected as well, one of which, A1119C was present only in isolates with high cyp51 expression. Overall, our results indicate that at least two mechanisms, cyp51 over-expression and the known target-site mutation in CYP51, contribute to resistance in E. necator, and may be working in conjunction with each other.

Management of grape powdery mildew (Erysiphe necator) using quinone outside inhibitors (QoIs) has eroded in an increasing number of regions due to resistance development. To determine persistence of resistance when QoIs are withdrawn, competition assays were conducted on unsprayed grape plants (Vitis vinifera 'Chardonnay') by cycling mixtures of resistant and sensitive isolates characterized as genetically diverse based on microsatellite analyses. Under laboratory conditions, %G143A, quantified by quantitative polymerase chain reaction (qPCR), increased significantly, indicating competitiveness of the resistant fraction. To confirm competitiveness in the field, trials using potted plants were conducted. Percent G143A tended to decrease in one growing season, probably due to spore migration and mixing of populations with natural background inoculum. In a second season, QoI resistance persisted at high frequency for 4 weeks. Resistant populations were also found to persist in one vineyard without QoI application for four consecutive years. The frequency was still about 25% in the fourth year, with higher frequency (36%) in a hotspot section. QoI-resistant populations with >5% G143A also harbored Y136F in the cyp51 gene that confers some resistance to sterol demethylation inhibitors, another fungicide class for powdery mildew control. Double resistance could have been partly responsible for persistence of QoI resistance at this location.

Grape powdery mildew (Erysiphe necator) isolates were collected from 2005 to 2007 from vineyards mostly in Virginia but also some in Maryland, North Carolina, and Pennsylvania. Using a leaf disc assay, the isolates were tested against five demethylation inhibitor (DMI) fungicides. Most isolates exhibited reduced sensitivity to the five DMIs when compared with a sensitive group (n = 12) and compared with unexposed populations reported from other areas. The median resistance factor (RF) was highest for tebuconazole (RF = 399) and myclobutanil (RF = 378), followed by triflumizole (RF = 70), triadimefon (RF = 62), and fenarimol (RF = 44). The sensitive group used as the basis for comparison appears to have been more sensitive than unexposed isolates in New York and California. Our finding that the greatest resistance shift occurred with tebuconazole and myclobutanil contrasts with earlier reports from New York and California, where the greatest resistance shift was observed with triadimefon or triadimenol. Sensitivities to all five DMI fungicides were strongly correlated (pairwise r values of 0.70 to 0.87) but our data suggest that some may retain greater utility than others.

A method was developed for enriching bacterial cells from soybean stems which was recalcitrant for a culture-independent analysis of bacterial community due to the interference with plant DNA. Stem homogenates were fractionated by a series of differential centrifugations followed by a Nycodenz density gradient centrifugation. The efficiency of bacterial cell enrichment was assessed by ribosomal intergenic spacer analysis (RISA). The intensity and the number of bacterial amplicons of RISA were markedly increased in the DNA extracted from the enriched bacterial cells compared to that in the DNA directly extracted from soybean stems. The phylogenetic diversity of the enriched bacterial cells was evaluated by analyzing a clone library of 16S rRNA gene in comparison with those of the culturable fractions of the enriched and non-enriched stem-associated bacteria, endophytic bacteria, and epiphytic bacteria. The results indicated that the method was able to enrich both endophytic and epiphytic bacteria from soybean stems, and was useful to assess the bacterial diversity based on a 16S rRNA gene clone library. When the sequence data from all clones (1,332 sequences) were combined, 72 operational taxonomic units were affiliated with Proteobacteria (Alpha-, Beta-, and Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteroidetes, which also provided the most comprehensive set of data on the bacterial diversity in the aerial parts of soybeans.

Diverse microorganisms are living as endophytes and epiphytes of plants in nature. Legumes have developed nodulation and autoregulation systems to attain mutual symbiosis with (brady)rhizobia during their evolution. Thus, we aimed to address whether the legume systems for (brady)rhizobia regulate the bacterial communities in field-grown soybeans. The diversity of microorganisms associated with the roots and stems of non-nodulated (Nod), wild-type nodulated (Nod), and hypernodulated (Nod) soybeans were evaluated by ribosomal intergenic transcribed spacer analysis (RISA) and clone library analysis of 16S rRNA gene. First, the roots of field-grown soybeans were washed with water, and subjected to culture-independent RISA. Differential RISA profiles were observed according to nodulation phenotypes. Principal component analysis revealed that bacterial communities were clustered into three groups corresponding to the nodulation phenotypes (Nod, Nod, or Nod). Interestingly, the microbial community in Nod soybeans was more similar to that of Nod than to Nod. Second, we developed a method of enriching bacterial cells by differential and density-gradient centrifugations to attain the community analysis of soybean stems. Third, soybeans were grown on the two neighboring fields dressed with standard heavy N-fertilizer. The abundance of Alphaproteobacteria in Nod soybeans (66%) was lower than those in Nod and Nod soybeans (75-76%) under standard N-fertilization, whereas the abundance of Gammaproteobacteria was vice versa (23% in Nod, and 12-16% in Nod and Nod soybeans). Principal coordinate analysis showed that the Nod and Nod soybeans under standard fertilization were tightly clustered together. Heavy N-fertilization increased Gammaproteobacteria (26-46%) and drove the communities to different dimensions on the plots. These results suggest that the size of subpopulation (Alphaproteobacteria) in soybean-associated bacteria is diminished by systemic factors induced by nodulation such as autoregulation beyond (brady)rhizobia. We want to discuss perspectives of microbial community analyses in crops including non-legumes in terms of the (meta)genomic era.

ABSTRACT Microorganisms associated with the stems and roots of nonnodulated (Nod − ), wild-type nodulated (Nod + ), and hypernodulated (Nod ++ ) soybeans [ Glycine max (L.) Merril] were analyzed by ribosomal intergenic transcribed spacer analysis (RISA) and automated RISA (ARISA). RISA of stem samples detected no bands specific to the nodulation phenotype, whereas RISA of root samples revealed differential bands for the nodulation phenotypes. Pseudomonas fluorescens was exclusively associated with Nod + soybean roots. Fusarium solani was stably associated with nodulated (Nod + and Nod ++ ) roots and less abundant in Nod − soybeans, whereas the abundance of basidiomycetes was just the opposite. The phylogenetic analyses suggested that these basidiomycetous fungi might represent a root-associated group in the Auriculariales . Principal-component analysis of the ARISA results showed that there was no clear relationship between nodulation phenotype and bacterial community structure in the stem. In contrast, both the bacterial and fungal community structures in the roots were related to nodulation phenotype. The principal-component analysis further suggested that bacterial community structure in roots could be classified into three groups according to the nodulation phenotype (Nod − , Nod + , or Nod ++ ). The analysis of root samples indicated that the microbial community in Nod − soybeans was more similar to that in Nod ++ soybeans than to that in Nod + soybeans.