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In Asia, large swathes of rainforest have been converted to rubber plantations, with major consequences for biodiversity and ecosystem services. However, the impact of this land use conversion on rhizosphere soil mycobiome has not yet been addressed. This study aims to investigate how rhizosphere soil fungal communities and their associated biological activity (soil respiration, soil methane (CH4) and potential soil enzyme production) are impacted by the conversion of rainforest to rubber plantations. Fungal richness and community composition in rhizosphere soils collected from natural rainforests, immature rubber, and mature rubber plantations were analyzed using paired-end Illumina sequencing. The conversion of natural rainforest to rubber plantations significantly altered fungal community composition of specific functional groups (saprotrophs, pathogens and mycorrhiza). We observed significant loss of saprotrophic and ectomycorrhizal fungi in natural rainforests, but enrichment of plant pathogenic fungi in immature rubber plantations. The mechanism underlying the effects of forest conversion on changes of fungal communities is related to reductions in soil pH, total nitrogen (N) and ammonium (NH4) in rubber plantations. Conversion to rubber plantation also resulted in decline of soil respiration rates and less potential for cellulase and chitinase productions. The significant negative correlations between fungal richness and soil respiration in mature rubber plantations indicated high competition among fungi and low nutrient availability in this system. We demonstrate the negative consequences of the conversion of rainforest to rubber plantations on soil biological activity and significant changes in fungal community composition that could threaten long-term ecosystem functions.

Recent studies have indicated that arbuscular mycorrhizal fungi (AMF) are able to influence litter decomposition by interacting with the soil fungal community. However, it remains unclear exactly which constituent groups of the soil fungal community respond to AMF during litter decomposition, and in what ways. To better understand this relationship, we investigated the effect of AMF on soil fungal communities in a greenhouse experiment. Our study found that the composition and richness of the fungal community, at higher taxonomical levels (e.g. phyla, order), remained stable across treatments. However, the relative abundance of some key genera including Mycena, Glomerella, Pholiotina, and Sistotrema were significantly affected by AMF inoculation. Soil fungal community structure was also altered by AMF inoculation during the later stages of litter decomposition. Our study provides new insights into understanding the interaction between AMF and soil fungal communities and reinforces the importance of AMF in soil nutrient cycling.

Bacterial communities and arbuscular mycorrhizal fungi (AMF) co-occur in the soil, however, the interaction between these two groups during litter decomposition remains largely unexplored. In order to investigate the effect of AMF on soil bacterial communities, we designed dual compartment microcosms, where AMF (Funneliformis mosseae) was allowed access (AM) to, or excluded (NM) from, a compartment containing forest soil and litterbags. Soil samples from this compartment were analyzed at 0, 90, 120, 150, and 180 days. For each sample, Illumina sequencing was used to assess any changes in the soil bacterial communities. We found that most of the obtained operational taxonomic units (OTUs) from both treatments belonged to the phylum of Proteobacteria, Acidobacteria, and Actinobacteria. The community composition of bacteria at phylum and class levels was slightly influenced by both time and AMF. In addition, time and AMF significantly affected bacterial genera (e.g., Candidatus Solibacter, Dyella, Phenylobacterium) involved in litter decomposition. Opposite to the bacterial community composition, we found that overall soil bacterial OTU richness and diversity are relatively stable and were not significantly influenced by either time or AMF inoculation. OTU richness at phylum and class levels also showed consistent results with overall bacterial OTU richness. Our study provides new insight into the influence of AMF on soil bacterial communities at the genus level.

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.