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Oil palm (Elaeis guineensis) is among the fastest expanding crops, due to high global demand for vegetable oils. Large areas of forest are converted into oil palm plantation to meet the market demand in producing countries which causes rapid decline in tropical biodiversity, including arthropods. The alley-cropping system has the potential to promote faunal biodiversity, related ecosystem services and food security in agricultural landscapes. In alley-cropping, a main crop is intercropped with a secondary crop (often a food crop), secondary crops are cultivated in the alleys in between the main crop. We compared arthropod taxonomic richness, arthropod predators and decomposers between five alley-cropping treatments (pineapple, bamboo, black pepper, cacao, bactris), where oil palm is intercropped with another species. In addition, we sampled two control treatments: monoculture oil palm, aged seven and 15 years old. A total of 50,155 arthropod individuals were recorded using pitfall trap sampling, representing 19 orders and 28 families. Fourteen orders belonging to sub-phylum Insecta, three orders from Arachnida (Araneae; Acarinae; Scorpiones) and two orders from Myriapoda (Chordeumatida; Geophilomorpha). We detected an increase in beta-diversity of oil palm production landscape. Specifically, we found that the number of arthropod orders, families and abundance were significantly greater in alley-cropping farming plots than those in monoculture plots. In addition, alley-cropping treatments contained larger numbers of predators and decomposers. Our findings suggest that the alley-cropping system can become a key management strategy to improve biodiversity and ecosystem functions within oil palm production landscapes.

Eucalyptus is a diverse genus from which several species are often deployed for commercial industrial tree plantation due to their desirable wood properties for utilization in both solid wood and fiber products, as well as their growth and productivity in many environments. In this study, a method for monitoring the health status of a 22.78 ha Eucalyptus pellita plantation stand was developed using the red-green-blue channels captured using an unmanned aerial vehicle. The ortho-image was generated, and visual atmospheric resistance index (VARI) indices were developed. Herein, four classification levels of pest and disease were generated using the VARI-green algorithm. The range of normalized VARI-green indices was between −2.0 and 2.0. The results identified seven dead trees (VARI-green index −2 to 0), five trees that were severely infected (VARI-green index 0 to 0.05), 967 trees that were mildly infected (VARI-green index 0.06 to 0.16), and 10,090 trees that were considered healthy (VARI-green index 0.17 to 2.00). The VARI-green indices were verified by manual ground-truthing and by comparison with normalized difference vegetation index which showed a mean correlation of 0.73. This study has shown practical application of aerial survey of a large-scale operational area of industrial tree plantation via low-cost UAV and RGB camera, to analyze VARI-green images in the detection of pest and disease.

Rhizophora mucronata is an important ecosystem entity of the Malaysian mangrove forest. Since the species grows in a harsh environment, any organism that is isolated from this species would be of huge interest due to its potential in having novel bioactive compounds. In the present work, we isolated, identified and characterized, a total of 78 fungal isolates harboring inside the leaf tissues of R. mucronata. Molecular identification using the nuclear ribosomal DNA internal transcribe spacer (ITS) sequences returned with high similarity matches to known sequences in the GenBank. Maximum likelihood analysis revealed the phylogenetic relationship of all isolates from this study. Most of the dominating fungal endophytes were from the genera Pestalotiopsis, followed by Alternaria and Cladosporium. Six isolates representing the genera Alternaria, Fusarium, Nigrospora, Pestalotiopsis, Phoma, and Xylaria, were further screened for their antagonism activities. Dual culture test assay revealed their inhibition percentages against the phytopathogenic fungus Fusarium solani between 45–66%, and 0.8–23% when using non-volatile test assay. Of the six isolates, only Fusarium lateritium and Xylaria sp. showed antibacterial activities against the pathogenic bacteria, Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus, with the Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC) ranging from 0.5 to 2 mg/mL. The DPPH radical scavenging assay recorded a high level of antioxidant activity in Xylaria sp., 3-fold above that of F. lateritium. We demonstrate for the first time, two members belonging to the endophytic fungal community in the tropical mangrove species that have potential use as antagonists and antibacterial agents for future biotechnological applications.

Known for its valuable agarwood, Aquilaria malaccensis Lam. is an evergreen tropical forest tree species endemic to the Indo-malesian region. Indiscriminate damaging and harvesting of the trees in the wild have resulted in it being listed in the CITES Appendix II for controlled trade and in the IUCN Red List as ‘Vulnerable (VU)’. In this study, the complete chloroplast genome of A. malaccensis was assembled using data from high-throughput Illumina sequencing. The chloroplast genome was 174,832 bp in size, which included two inverted repeat regions of 42,091 bp each, separated by a large single copy region of 87,302 bp and a small single copy region of 3,348 bp. A total of 139 genes were predicted, including 39 tRNA, 8 rRNA, and 92 protein-coding genes. Phylogenetic analysis placed A. malaccensis within the family Thymelaeaceae. The chloroplast genome sequence of A. malaccensis offers a useful resource for future studies on the taxonomy and conservation of the threatened Aquilaria trees.

Hydrophobins are small secreted fungal proteins that play roles in growth and development of filamentous fungi, i.e. in the formation of aerial structures and the attachment of hyphae to hydrophobic surfaces. In Botrytis cinerea, three hydrophobin genes have been identified. Studies by Mosbach et al. (2011) showed that hydrophobins are neither involved in conferring surface hydrophobicity to conidia and aerial hyphae of B. cinerea, nor are they required for virulence. The present study investigated the role of hydrophobins in sclerotium and apothecium development. Expression analysis revealed high expression of the Bhp1 gene during different stages of apothecium development. Two Bhp1 splice variants were detected that differ by an internal stretch of 13 amino acid residues. Seven different mutants in which either a single, two or three hydrophobin genes were knocked out, as well as two wild type strains of opposite mating types, were characterized for sclerotium and apothecium development. No aberrant morphology was observed in sclerotium development when single deletion mutants in hydrophobin genes were analyzed. Sclerotia of double knock out mutant ¿Bhp1/¿Bhp3 and the triple knock out mutant, however, showed easily wettable phenotypes. For analyzing apothecium development, a reciprocal crossing scheme was setup. Morphological aberrations were observed in crosses with two hydrophobin mutants. When the double knock out mutant ¿Bhp1/¿Bhp2 and the triple knock out mutant were used as the maternal parent (sclerotia), and fertilized with wild type microconidia, the resulting apothecia were swollen, dark brown in color and had a blotched surface. After initially growing upwards toward the light source, the apothecia in many cases collapsed due to loss of structural integrity. Aberrant apothecium development was not observed in the reciprocal cross, when these same mutants were used as the paternal parent (microconidia). These results indicate that the presence of hydrophobins in maternal tissue is important for normal development of apothecia of B. cinerea.

Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry. They are also part of the natural ecosystem and may play a role in regulating plant numbers/density. Morphological identification and analysis of plant pathogenic fungi, while important, is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi. Molecular (DNA sequence) data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies, although hampered in part by non-standard laboratory practices and analytical methods. To facilitate current and future research, this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, Basidiomycota, Mucormycotina (Fungi), and Oomycota, using recent molecular data, up-to-date names, and the latest taxonomic insights. Lineage-specific laboratory protocols together with advice on their application, as well as general observations, are also provided. We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge. Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort. Bipolaris, Botryosphaeriaceae, Botryosphaeria, Botrytis, Choanephora, Colletotrichum, Curvularia, Diaporthe, Diplodia, Dothiorella, Fusarium, Gilbertella, Lasiodiplodia, Mucor, Neofusicoccum, Pestalotiopsis, Phyllosticta, Phytophthora, Puccinia, Pyrenophora, Pythium, Rhizopus, Stagonosporopsis, Ustilago and Verticillium are dealt with in this paper.