Although fungal endophytes are commonly investigated for their ability to deter microbial plant pathogens, few studies have examined the activity of fungal root endophytes against nematodes. The soybean cyst nematode (SCN; Heterodera glycines), the most severe yield-limiting pathogen of soybean (Glycine max), is commonly managed through rotation of soybean with corn (Zea mays), a nonhost of the SCN. A total of 626 fungal endophytes were isolated from surface-sterilized corn and soybean roots from experimental plots in which soybean and corn had been grown under annual rotation and under 1, 3, 5, and 35 years of continuous monoculture. Fungal isolates were grouped into 401 morphotypes, which were clustered into 108 operational taxonomic units (OTUs) based on 99% sequence similarity of the full internal transcribed spacer region. Morphotype representatives within each OTU were grown in malt extract broth and in a secondary metabolite-inducing medium buffered with ammonium tartrate, and their culture filtrates were tested for nematicidal activity against SCN juveniles. A majority of OTUs containing isolates with nematicidal culture filtrates were in the order Hypocreales, with the genus Fusarium being the most commonly isolated nematicidal genus from corn and soybean roots. Less commonly isolated taxa from soybean roots included the nematophagous fungi Hirsutella rhossiliensis, Metacordyceps chlamydosporia, and Arthrobotrys iridis. Root endophytic fungal diversity in soybean was positively correlated with SCN density, suggesting that the SCN plays a role in shaping the soybean root endophytic community.

Genetic resistance remains a key component in integrated pest management systems. The cosmopolitan root-knot nematode (RKN; Meloidogyne spp.) proves a significant management challenge as virulence and pathogenicity vary among and within species. RKN greatly reduces commercial bell pepper yield, and breeding programs continuously develop cultivars to emerging nematode threats. However, there is a lack of knowledge concerning the nature and forms of nematode resistance. Defining how resistant and susceptible pepper cultivars mount defenses against RKN attacks can help inform breeding programs. Here, we characterized the transcriptional responses of the highly related resistant (Charleston Belle) and susceptible (Keystone Resistance Giant) pepper cultivars throughout early nematode infection stages. Comprehensive transcriptomic sequencing of resistant and susceptible cultivar roots with or without Meloidogyneincognita infection over three-time points; covering early penetration (1-day), through feeding site maintenance (7-days post-inoculation), produced > 300 million high quality reads. Close examination of chromosome P9, on which nematode resistance hotspots are located, showed more differentially expressed genes were upregulated in resistant cultivar at day 1 when compared to the susceptible cultivar. Our comprehensive approach to transcriptomic profiling of pepper resistance revealed novel insights into how RKN causes disease and the plant responses mounted to counter nematode attack. This work broadens the definition of resistance from a single loci concept to a more complex array of interrelated pathways. Focus on these pathways in breeding programs may provide more sustainable and enduring forms of resistance.

Corn ( Zea mays ) and soybean ( Glycine max ) production forms an integral part of economies worldwide, but yields are limited by biotic and abiotic factors associated with short rotations and long-term monocultures. In this study, a long-term rotation study site with corn and soybean planted in annual rotation, five-year rotation, and long-term monoculture was utilized to examine the relationships between crop sequences, soil fungal communities, soybean cyst nematode (SCN, Heterodera glycines ) densities, soil properties, and crop yields. High throughput sequencing of the ITS1 region of fungal rDNA revealed that soil fungal community structure varied significantly by crop sequence, with fungal communities under five consecutive years of monoculture becoming progressively similar to communities in long-term monoculture plots associated with their respective crop hosts. Total alpha diversity was greater under corn, but patterns of diversity and relative abundance of specific functional groups differed by crop host, with more pathotrophs proliferating under soybean and more saprotrophs and symbiotrophs proliferating under corn. Soil phosphorus (P) varied significantly by crop sequence, with lower levels of P corresponding with relative abundance of Glomerales, Paraglomerales, and Sebacinales and higher levels of P corresponding with relative abundance of Mortierellales. Soil density of the SCN was positively correlated with relative abundance and diversity of nematode-trapping fungi and with relative abundance of many potential nematode egg parasites. These results suggest several possible explanations for the improved yields associated with crop rotation, including decreased pathogen pressure, modification of soil properties, and increased diversity of soil fungal communities. Future research should investigate the potential of nematode-trapping fungi to regulate SCN densities and examine the relationships between soil P and specific arbuscular mycorrhizal and mortierellalean fungi associated with corn and soybean hosts.

Background: Fungi are essential agents in decomposing woody debris (WD), an important carbon pool in forests. However, the ecology and dynamics of these fungal communities are poorly understood, especially in tropical forests. A better understanding of anthropogenic impacts, such as forest disturbances, on WD decomposition is also needed to appreciate their consequences on ecosystem functioning. Here, we examined the impacts of forest degradation and roles of fungal diversity and composition on WD decomposition rates across a disturbance gradient in a tropical montane rain forest in Xishuangbanna, SW China over three years. We measured wood specific gravity (WSG) loss from 280 logs from Litsea cubeba (low-WSG) and Castanopsis mekongensis (high-WSG). We concomitantly monitored fungal communities from 418 samples using next-generation sequencing after 0, 18 and 36 months field exposure. Results: Incubation time, habitat and termite presence were key drivers of fungal community composition. Fungal community succession showed a priority effect of precedent communities. C. mekongensis WD consistently harbored ~1.4 times less fungal species than L. cubeba , but had ~1.4 times more unique operational taxonomic unit (OTU) at 18 mo. Shared OTUs between wood species increased with time up to ~63 % at 36 mo. Regardless of wood species, fungal diversity and both saprotrophs and white-rot abundances peaked at 18 months. However, fungal diversity was not a significant predictor of WSG loss. WSG loss did not vary among habitats. This may result from compensatory changes in dominant functional traits, such as decay mechanisms (e.g., proportion of white rot-fungi, soft-rot fungi). For example white- rot fungal proportions were double in open land compared to mature forest. Likewise, more saprothrophs colonized high-WSG wood. Finally, ascomycetes (mainly Sordariomycetes and Dothiodeomycetes) and basidiomycetes (mostly Agaricomycetes) were dominant fungal groups. Open land was dominated by Trichoderma, regenerating forest by Herpothrichiellaceae and mature forest by Penicillium . Conclusions: White- and soft-rot fungi co-dominated decomposition, with the later increasing through time. A succession of different fungal functional groups yielded similar decomposition rates across the disturbance gradient. Incorporating dominant fungal functional trait dynamics into biogeochemical models may improve predictions of carbon dynamics.