Abundance Of Plant Pathogens Research Articles

Alfalfa Cover Crops Influence the Soil Fungal Community and Function in Apple Orchards in Arid Desert Oases in Northwest China

The present study investigated the effects of alfalfa cover crops on soil fungal communities and function in apple orchards in arid desert oases. A five-year apple orchard was subjected to two treatments: Intercropping with an alfalfa cover crop (A) and clean tillage (QG). The soil fungal ITS (internal transcribed spacer) region was analyzed using Illumina MiSeq high-throughput sequencing technology, and fungal function was determined using FUNGuild. Changes in the fungal community structure, diversity, and metabolic function in the 0–60 cm soil layer of the apple orchard were compared. The results showed that the alfalfa cover crops enhanced fungal richness but reduced diversity. The alfalfa cover crops improved fungal copy numbers but reduced the relative abundance of the dominant phylum, Ascomycota. Correlations between soil fungi and soil factors revealed that total nitrogen and total carbon were the most important nutrient factors in positively regulating the fungal community. The main negative factors were soil total salts and pH. The FUNGuild functional prediction showed that Ectomycorrhizal-Wood Saprotroph and Endophyte-Undefined Saprotroph only appeared in the alfalfa cover crops. The abundance of endophytes was enhanced (p < 0.05), but the abundance of plant pathogens and wood saprotrophs decreased (p < 0.01). Alfalfa cover crops could increase the copy numbers and richness in arid oasis apple orchards.

Microalgae as a potential conditioner for continuous cropping obstacles for taro (Colocasia esculenta L. Schott) production

Continuous cropping of Fenghua taro leads to poor quality. In this research, two pollution tolerant algae, Spirulina platensis and Chlorella vulgaris, were selected as conditioners for continuous cropping obstacles of taro production. The composition, abundance, and biodiversity of the bacteria and fungi communities in soil rhizosphere of continuous cropping were compared to non-continuous cropping, and studied in-depth. These results showed that the growth of taro during continuous cropping, when irrigated with Chlorella vulgaris and Spirulina platensis, was significantly better than the control group without algal cell irrigation. Accordingly, the plant height, leaf length, leaf area, moisture, carbohydrate, and protein in continuous cropping were 128 cm, 69 cm, 56 cm, 72 g/100 g, 10.8 g/100 g and 2.4 g/100 g, respectively, when watered with Chlorella vulgaris. Furthermore, compared with continuous cropping, the abundance of plant pathogens in the taro rhizosphere, fertilized with Spirulina platensis, were significantly reduced, while the corresponding abundance of soil beneficial bacteria was significantly increased. Specifically, the abundance of beneficial bacteria Ceratobasidium and Pulveroboletus increased, and the pathogens such as Curvularia, Erysiphe, and Clonostachys decreased, during continuous cropping when irrigated with Spirulina platensis. Live microalgae, after wastewater treatment, could be used as potential conditioners to avoid obstacles during continuous cropping of taro production.

Seed quantity affects the fungal community composition detected using metabarcoding

Pest introductions via trade in tree seed may result from a lack of adequate survey and validation protocols. Developing better diagnostic protocols to identify potentially harmful pests and pathogens in forest tree seed is of critical importance. High-throughput sequencing-based barcoding and metabarcoding provide effective tools for screening potentially harmful organisms in various plant materials, including seeds. However, the sample size needed to detect the total microorganism diversity of a community is a major challenge in microbiome studies. In this work, we examined how increasing sample size (ranging between 100 and 1000 seeds) influences diversity of fungal communities detected by high throughput sequencing in Pinus sylvestris seeds. Our results showed that as sample size increased, fungal alpha diversity also increased. Beta-diversity estimators detected significant differences between the mycobiota from different samples. However, taxonomic and functional diversity were not correlated with sample size. In addition, we found that increasing the number of PCR replicates resulted in a higher abundance of plant pathogens. We concluded that for the purpose of screening for potentially harmful pathogens using HTS, greater efforts should be made to increase the sample size and replicates when testing tree seed.

Soil Fungal Communities under Pinus patula Schiede ex Schltdl. & Cham. Plantation Forests of Different Ages in Ethiopia

The cultivation of plantation forests is likely to change the diversity and composition of soil fungal communities. At present, there is scant information about these communities in Ethiopian plantation forest systems. We assessed the soil fungal communities in Pinus patula Schiede ex Schltdl. & Cham. stands aged 5, 11, or 36-years-old using DNA metabarcoding of ITS2 amplicons. The ecological conditions of each plot, such as climate, altitude, and soil, were similar. Stand age and soil fertility influenced soil fungal species diversity and ecological guilds. In total, 2262 fungal operational taxonomic units were identified, of which 2% were ectomycorrhizal (ECM). The diversity of ECM fungi was higher in the 5 and 36-year-old stands than in the 11-year-old P. patula stands. Contrary to our expectations, a high level of ECM species diversity was observed in young stands, suggesting that these ECM species could compensate for the effects of nutrient stress in these stands. Our results also suggested that the abundance of plant pathogens and saprotrophs was not affected by stand age. This study provides baseline information about fungal community changes across tree stands of different ages in P. patula plantations in Ethiopia that are likely related to ECM fungi in young stands where relatively low soil fertility prevails. However, given that the plots were established in a single stand for each age class for each treatment, this study should be considered as a case study and, therefore, caution should be exercised when applying the conclusions to other stands.

Functional groups of soil fungi decline under grazing

Fungi play vital roles in organic matter decomposition, and mineralisation of phosphorus and nitrogen, are significant plant and animal pathogens, and major mutualistic symbionts with the roots of higher plants. Despite their importance, relatively little is known about the effects of livestock grazing on different functional groups of fungi. We used structural equation modelling to examine how grazing by domestic livestock and native herbivores, and aridity, plant cover and soil carbon influenced four functional groups of soil fungi (ectomycorrhizal fungi, arbuscular mycorrhizal fungi, dung saprobes, plant pathogens) from three microsites (tree, shrub, grass) at 54 woodland sites across 0.4 million km2 of dryland in eastern Australia. Structural equation modelling showed that aridity influenced fungi indirectly by affecting different herbivores and by changing plant cover, which had different effects on different fungal groups. Rabbit grazing had a direct negative effect on ectomycorrhizal and arbuscular mycorrhizal fungi, most likely by disrupting hyphal networks through soil disturbance. Increased cattle grazing was directly positively associated with fungal dung saprobe abundance, and indirectly, negatively associated with dung saprobes by suppressing the positive effects of soil carbon. Sheep had direct and indirect negative effects on the abundance of plant pathogens. Grazing was always an important predictor of the relative abundance of all fungal groups, either directly or indirectly. Thus, overgrazing is likely to have substantial effects on a range of important soil processes controlled by these microorganisms. Overall, our work indicates that increasing grazing, linked to on-going land use intensification to support a growing global population, will have major impacts on fungal functional groups.

Plant pathogens but not antagonists change in soil fungal communities across a land abandonment gradient in a Mediterranean landscape

We assessed whether the presence and abundance of plant pathogens and antagonists change in soil fungal communities along a land abandonment gradient. The study was carried out in the Cilento area (Southern Italy) at a site with three different habitats found along a land abandonment gradient: agricultural land, Mediterranean shrubland and woodland. For all microbiological substrates the colony forming units were about 3.1 × 106 g−1 soil for agricultural land and about 1.1 × 106 g−1 soil for Mediterranean shrubland and woodland. We found the following genera in all habitats: Cladosporium, Mortierella, Penicillium and Trichoderma. In agricultural land, the significantly most abundant fungus genera were Aspergillus, Fusarium, Cylindrocarpon and Nectria; in Mediterranean shrubland, Rhizopus and Trichoderma; and in woodland, Bionectria, Mortierella, Cladosporium, Diplodia, Paecilomyces, Penicillium and Trichoderma. We found a total of 8, 8 and 9 species of fungal antagonist, and 16, 6 and 6 species of fungal plant pathogens in agricultural land, Mediterranean shrubland and woodland respectively. Fungal plant pathogens decreased significantly over a land abandonment gradient, while we no found significant differences among fungal antagonists in the three habitats. We conclude that a decrease in the number of fungal pathogen species occurs when formerly cultivated areas are abandoned. On the other hand, fungal antagonists seem not to be affected by this process.

Multi‐scale patterns of human activity and the incidence of an exotic forest pathogen

Summary Plant pathogens can have major impacts on diverse taxa and ecological systems world‐wide, and some of the most conspicuous of these are invasive non‐native species. Although many factors are known to influence the distribution and abundance of plant pathogens, the extent to which humans play a role is less well‐known but still critical for understanding the dynamics of invasive pathogens in natural systems. One invasive pathogen of great concern world‐wide is Phytophthora ramorum, which causes Sudden Oak Death, an emerging forest disease. Here, we examined the influence of humans and a range of environmental factors on the distribution of P. ramorum at three distinct spatial scales in northern and central California. At the local scale, P. ramorum more commonly occurred in soil on hiking trails used heavily by humans than in soil from adjacent areas off trails. These results support the hypothesis that humans dispersed the pathogen within already infected areas and into areas lacking local sources of inoculum. At the landscape scale, using a network of 202 randomly located plots across a 275 km2 area, we found that forests on public land open to recreation exhibited higher prevalence of disease in a critical infectious host tree (bay laurel, Umbellularia californica), than forests on private lands. Infection levels were also higher in plots surrounded by large amounts of forest with warm climatic conditions and greater potential soil moisture. Although prevalence of diseased canker hosts (Quercus agrifolia, Q. kelloggii and Lithocarpus densiflora) was positively associated with dominance of bay laurel and rainy season temperatures, it was not significantly related to public access, and we hypothesize that this occurred because our study area was in the early stages of infection. At the regional scale, the probability of disease occurrence at 165 sites distributed across the geographic range of P. ramorum in California increased significantly as human population density increased in the surrounding area. Chances of infection also increased significantly with precipitation and presence of bay laurel. Synthesis. Our results suggest that human activity – along with temperature, moisture and host composition – is associated with increased prevalence of an influential exotic forest pathogen. These results indicate that there may be conflicts between humans and disease, and that efforts to address this issue may require aggressive management of human activity.