Crop harvest followed by a fallow period can act as a disturbance on soil microbial communities. Cropping systems intended to improve alpha-diversity of communities may also confer increased compositional stability during succeeding growing seasons. Over a single growing season in a long-term (18 year) agricultural field experiment incorporating conventional (CON), conservation (CA), organic (ORG) and integrated (INT) cropping systems, temporal changes in prokaryote, fungal and arbuscular mycorrhizal fungi (AMF) communities were investigated overwinter, during crop growth and at harvest. While certain prokaryote phyla were influenced by cropping system (e.g. Acidobacteria), the community as a whole was primarily driven by temporal changes over the growing season as distinct overwinter and crop-associated communities, with the same trend observed regardless of cropping system. Species-rich prokaryote communities were most stable over the growing season. Cropping system exerted a greater effect on fungal communities, with alpha-diversity highest and temporal changes most stable under CA. CON was particularly detrimental for alpha-diversity in AMF communities, with AMF alpha-diversity and stability improved under all other cropping systems. Practices that promoted alpha-diversity tended to also increase the similarity and temporal stability of soil fungal (and AMF) communities during a growing season, while prokaryote communities were largely insensitive to management.

The recycling of biogas residues resulting from the anaerobic digestion of organic waste on agricultural land is among the means to reduce chemical fertilizer use and combat climate change. This in sacco decomposition study investigates (1) the potential of the granulated biogas residue fraction to provide nutrients and enhance soil carbon sequestration when utilized as exogenous organic matter in grassland soils, and (2) the impact of different nitrogen fertilizers on the organic matter decomposition and nutrient release processes. The experiment was conducted in two permanent grasslands of the Greater Region over one management period using rooibos tea as a comparator material. The decomposition and chemical changes of the two materials after incubation in the soil were assessed by measuring the mass loss, total carbon and nitrogen status, and fibre composition in cellulose, hemicellulose and lignin. Overall, after the incubation period, granulated biogas residue maintained up to 68% of its total mass, organic matter and total carbon; increased its content in recalcitrant organic matter by up to 45% and released 45% of its total nitrogen. Granulated biogas residue demonstrated resilience and a higher response uniformity when exposed to different nitrogen fertilizers, as opposed to the comparator material of rooibos tea. However, the magnitude of fertilizer-type effect varied, with ammonium nitrate and the combinatorial treatment of raw biogas residue mixed with urea leading to the highest organic matter loss from the bags. Our findings suggest that granulated biogas residue is a biofertilizer with the potential to supply nutrients to soil biota over time, and promote carbon sequestration in grassland soils, and thereby advance agricultural sustainability while contributing to climate change mitigation.

Isotope labeling enables the detection and quantification of nutrient fluxes between soil and plants through arbuscular mycorrhizal (AM) fungi. Here we describe the use of radioactive isotopes, 33P and 32P, to study the uptake of P from soil by AM fungal mycelium and its transfer to the host plant through the mycorrhizal pathway.

An in vivo whole-plant bi-dimensional experimental system has been devised and tested with different host plants, in order to obtain extraradical mycelium (ERM) produced by different arbuscular mycorrhizal fungi (AMF). In this system, a host plant germling is inoculated with AMF to establish mycorrhizal symbiosis, and, after colonization, newly formed extraradical hyphae and spores are removed. Then the mycorrhizal root system is wrapped in a nylon net and placed between membranes in a Petri dish, allowing ERM to grow on the membrane surface. Such extraradical hyphae may be used for in situ morphometric analyses or collected for molecular or biochemical assays: in the latter case, the plant with its root sandwich may be reassembled to renew mycelium production. In this experimental system, which was tested with diverse host plant species and lines, values of explored membrane surface areas and densities of ERM showed wide ranges of variation, and its length ranged from 9.7 ± 2.0 to 48.8 ± 9.9 m per plant, depending on host and AMF identity. Across the different plant-AMF combinations tested, the whole-plant system produced 2.0 ± 0.6 to 5.3 ± 0.3 mg of ERM fresh biomass per plant per harvest. This experimental system can be used for a wide range of AMF and host plants species, either establishing arbuscular mycorrhizas or other mycorrhizal interactions. ERM produced and collected in the whole-plant system is suitable for morphological, physiological, and molecular analyses, facilitating studies on the different aspects of mycorrhizal symbiotic interactions.

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BACKGROUND: Rice, which serves as a staple food for more than half of the world\'s population, is very susceptible to the pathogenic fungus, Magnaporthe oryzae. However, common wild rice (Oryza rufipogon), which is the ancestor of Asian cultivated rice (O. sativa), has significant potential as a genetic source of resistance to M. oryzae. Recent studies have shown that the domestication of rice has altered its relationship to symbiotic arbuscular mycorrhizae. A comparative response of wild and domestic rice inhabited by mycorrhizae to infection by M. oryzae has not been documented.
RESULTS: In the current study, roots of wild and cultivated rice colonized with the arbuscular mycorrhizal (AM) fungus (AMF) Rhizoglomus intraradices were used to compare the transcriptomic responses of the two species to infection by M. oryzae. Phenotypic analysis indicated that the colonization of wild and cultivated rice with R. intraradices improved the resistance of both genotypes to M. oryzae. Wild AM rice, however, was more resistant to M. oryzae than the cultivated AM rice, as well as nonmycorrhizal roots of wild rice. Transcriptome analysis indicated that the mechanisms regulating the responses of wild and cultivated AM rice to M. oryzae invasion were significantly different. The expression of a greater number of genes was changed in wild AM rice than in cultivated AM rice in response to the pathogen. Both wild and cultivated AM rice exhibited a shared response to M. oryzae which included genes related to the auxin and salicylic acid pathways; all of these play important roles in pathogenesis-related protein synthesis. In wild AM rice, secondary metabolic and biotic stress-related analyses indicated that the jasmonic acid synthesis-related α-linolenic acid pathway, the phenolic and terpenoid pathways, as well as the phenolic and terpenoid syntheses-related mevalonate (MVA) pathway were more affected by the pathogen. Genes related to these pathways were more significantly enriched in wild AM rice than in cultivated AM rice in response to M. oryzae. On the other hand, genes associated with the \'brassinosteroid biosynthesis\' were more enriched in cultivated AM rice.
CONCLUSIONS: The AMF R. intraradices-colonized rice plants exhibited greater resistance to M. oryzae than non-AMF-colonized plants. The findings of the current study demonstrate the potential effects of crop domestication on the benefits received by the host via root colonization with AMF(s), and provide new information on the underlying molecular mechanisms. In addition, results of this study can also help develop guidelines for the applications of AMF(s) when planting rice.

Arbuscular mycorrhizal fungi (AMF) are obligate plant root symbionts delivering a range of benefits to the host plant such as improved nutrient acquisition and resistance to pathogens and abiotic stress. However, whether they can enhance the function of plant root systems damaged due to subsidence caused by excessive coal mining has not been well explored. In the present study, we investigated the effects of AMF using Funneliformis mosseae (FM) as the test fungus on maize (Zea mays L.) growth and hormone levels under different levels of root damage stress by simulating mining subsidence. The results show that plants treated with FM had more shoots, roots, mycorrhizal colonization and higher hyphal density than those without FM under the same simulated mining-induced subsidence conditions. In addition, plants treated with FM also possessed higher N, P, K, Ca, and Mg contents in the shoots and the roots and higher indole-3-acetic acid, gibberellin (GA), and cytokinin (CTK) contents in the roots, indicating that the mycorrhizal association promoted plant biomass and nutrient uptake. FM treatment was no longer beneficial when root damage due to mining-induced subsidence affected more than half of the roots. Soil SOC, AK, and TG were identified as key factors affecting GA, CTK, IAA, and ABA, and AMF can alter plant hormones directly via the hyphae and indirectly by altering soil physicochemical properties under root damage stress. Overall, our results provide baseline data for assessing the biological reclamation effects of AMF on coal mining-induced subsidence.

In forests, negative density/distance-dependent seedling mortality (NDD) caused by natural enemies plays a key role in maintaining species diversity [Janzen-Connell (J-C) model]. However, the relative importance of natural enemies in mediating NDD under heterogeneous light conditions has remained unclear. We examined the relative importance of pathogens (i.e., soil pathogens, leaf diseases) on seedling performance in forest understories (FUs) and gaps (gaps) during a 3-year period (results of first year of our study have been previously reported). For the hardwood, Prunus grayana, we investigated seedling mortality, morbidity agents, growth, and root infection by arbuscular mycorrhizal fungi (AMF) beneath conspecific and heterospecific adults in FUs and gaps. Seedling mortality was higher beneath conspecific than heterospecific adults throughout 3 years at both sites, mainly due to continuous leaf disease (i.e., angular leaf spot), whereas damping-off diseases caused mortality only in the first year. Beneath each adult, seedling mortality was higher in FUs than in gaps until second year, but it did not differ between two habitat types in the third year, because leaf diseases caused severe damage even in gaps. Seedling mass was significantly lower beneath conspecific adults. AMF infection of seedlings was also lower beneath conspecific adults, while it was higher in gaps than in FUs beneath both adults. This study demonstrates that the J-C model in a hardwood tree, P. grayana is mainly driven by high NDD seedling mortality caused by airborne leaf diseases, which continuously attack seedlings in a NDD manner regardless of environmental light conditions.

Molecular tools have progressively replaced morphological approaches to characterize microbial communities in nature. Arbuscular mycorrhizal (AM) fungi are no exception to this rule. Yet, one challenge posed by these symbionts is that they colonize simultaneously both plant roots and soil, which complicates their detection and quantification. In most studies conducted to date, AM fungal communities have been characterized from roots only, soil only or spores only. Here, we discuss the pitfalls associated to drawing ecological inferences using such datasets. We also conclude by arguing that molecular biology will contribute most to advance knowledge in AM fungal ecology if it is integrated into broader perspectives taking into account the natural history of these organisms. This calls for a better merging of molecular and morphological approaches, and the establishment of intensive, long-term research programs.

Controlled experiments show that arbuscular mycorrhizal fungi (AMF) can increase competitiveness of exotic plants, potentially increasing invasion success. We surveyed AMF abundance and community composition in Centaurea stoebe and Potentilla recta invasions in the western USA to assess whether patterns were consistent with mycorrhizal-mediated invasions. We asked whether (1) AMF abundance and community composition differ between native and exotic forbs, (2) associations between native plants and AMF shift with invading exotic plants, and (3) AMF abundance and/or community composition differ in areas where exotic plants are highly invasive and in areas where they are not. We collected soil and roots from invaded and native forb communities along invasion gradients and in regions with different invasion densities. We used AMF root colonization as a measure of AMF abundance and characterized AMF communities in roots using 454-sequencing of the LSU-rDNA region. All plants were highly colonized (>60%), but exotic forbs tended to be more colonized than natives (P < 0.001). We identified 30 AMF operational taxonomic units (OTUs) across sites, and community composition was best predicted by abiotic factors (soil texture, pH). Two OTUs in the genera Glomus and Rhizophagus dominated in most communities, and their dominance increased with invasion density (r = 0.57, P = 0.010), while overall OTU richness decreased with invasion density (r = -0.61, P = 0.006). Samples along P. recta invasion gradients revealed small and reciprocal shifts in AMF communities with >45% fungal OTUs shared between neighboring native and P. recta plants. Overall, we observed significant, but modest, differences in AMF colonization and communities between co-occurring exotic and native forbs and among exotic forbs across regions that differ in invasion pressure. While experimental manipulations are required to assess functional consequences, the observed patterns are not consistent with those expected from strong mycorrhizal-mediated invasions.