Conservation tillage decreases selection pressure on community assembly in the rhizosphere of arbuscular mycorrhizal fungi

Distinct biogeographic patterns in Glomeromycotinian and Mucoromycotinian arbuscular mycorrhizal fungi across China: A meta-analysis

Fine root endophytes, recently reclassified as Mucoromycotinian arbuscular mycorrhizal fungi (M-AMF), are now recognized as functionally important as Glomeromycotinian AMF (G-AMF). However, little is known about the biogeography and ecology of M-AMF and G-AMF communities, particularly on a large scale, preventing a systematic assessment of ecosystem diversity and functioning. Here, we investigated the biogeographic assemblies and ecological diversity patterns of both G-AMF and M-AMF, using published 18S rDNA amplicon datasets and associated metadata from 575 soil samples in six ecosystems across China. Contrasting with G-AMF, putative M-AMF were rare in natural/semi-natural sites, where their communities were a subset of those in agricultural sites characterized by intensive disturbances, suggesting different ecological niches that they could occupy. Spatial and environmental factors (e.g., vegetation type) significantly influenced both fungal communities, with soil total‑nitrogen and mean-annual-precipitation being the strongest predictors for G-AMF and M-AMF richness, respectively. Both groups exhibited a strong spatial distance-decay relationship, shaped more by environmental filtering than spatial effects for M-AMF, and the opposite for G-AMF, presumably because stochasticity (e.g., drift) dominantly structured G-AMF communities; while the narrower niche breadth (at community-level) of M-AMF compared to G-AMF suggested its more susceptibility to environmental differences. Furthermore, co-occurrence network links between G-AMF and M-AMF were prevalent across ecosystems, and were predicted to play a key role in stabilizing overall communities harboring both fungi. Based on the macroecological spatial scale datasets, this study provides solid evidence that the two AMF groups have distinct ecological preferences at the continental scale in China, and also highlights the potential impacts of anthropogenic activities on distributions of AMF. These results advance our knowledge of the ecological differences between the two fungal groups in terrestrial ecosystems, suggesting the need for further field-based investigation that may lead to a more sophisticated understanding of ecosystem function and sustainable management.

Biogeographic Patterns of Fungal Sub-Communities under Different Land-Use Types in Subtropical China

Revealing the regional distribution and diversity of fungal sub-communities under different land management practices is essential to conserve biodiversity and predict microbial change trends. In this study, a total of 19 tilled and 25 untilled soil samples across different land-use types were collected from subtropical China to investigate the differences between the spatial distribution patterns, diversity, and community assembly of fungal sub-communities using high-throughput sequencing technology. Our results found that anthropogenic disturbances significantly reduced the diversity of abundant taxa but significantly increased the diversity of rare taxa, suggesting that the small-scale intensive management of land by individual farmers is beneficial for fungal diversity, especially for the conservation of rare taxa. Abundant, intermediate, and rare fungal sub-communities were significantly different in tilled and untilled soils. Anthropogenic disturbances both enhanced the homogenization of fungal communities and decreased the spatial-distance-decay relationship of fungal sub-communities in tilled soils. Based on the null model approach, the changes in the assembly processes of the fungal sub-communities in tilled soils were found to shift consistently to stochastic processes, possibly as a result of the significant changes in the diversity of those fungal sub-communities and associated ecological niches in different land-use types. Our results provide support for the theoretical contention that fungal sub-communities are changed by different land management practices and open the way to the possibility of predicting those changes.

Disentangling the impact of straw incorporation on soil microbial communities: Enhanced network complexity and ecological stochasticity

Straw incorporation is typically employed to enhance the nutrient content of soil and promote crop growth in intensive agricultural systems. Despite studies regarding the effects of straw incorporation on soil microbial communities, the underlying mechanisms of its effect on community co-occurrence interactions and assembly processes remain poorly understood. Herein, soil samples with or without straw incorporation were collected across a latitudinal gradient from north to central China. We found that straw incorporation considerably altered the structure of soil microbial community. The relative abundance of bacterial Latescibacterota and fungal Mortierellomycota were higher in straw-amended soils owing to their ability to decompose straw residues. The co-occurrence network in straw-amended soil exhibited greater complexity, including more network connectivity and keystone species, and higher average degrees and clustering coefficients compared with the control sample network. The network robustness and vulnerability indices suggested that straw incorporation increased the microbial network stability. Normalized stochastic ratios demonstrated that the stochastic process was the dominant mechanisms shaping the assembly of microbial communities in straw-amended soils. Concurrently, null model analysis revealed that straw increased the contribution of dispersal limitation to the assembly of bacterial and fungal communities. The migration rate of the microbial community, obtained from Sloan neutral community model, was relatively low in straw-amended soil at all the sample sites, potentially indicating the great importance of dispersal limitation. These findings would enhance our understanding of the ecological patterns and interactions of soil microbial communities in response to straw incorporation.

Stochastic processes dominate soil arbuscular mycorrhizal fungal community assembly along an elevation gradient in central Japan

Arbuscular mycorrhizal (AM) fungi play an important role in facilitating ecosystem function and stability. Yet, their community response patterns and ecological assembly processes along elevational gradients which cross a range of climates and soil conditions remain elusive. We used Illumina MiSeq sequencing to examine trends in soil AM fungal community along an elevational gradient from 100 m to 2300 m in central Japan. A total of 750 operational taxonomic units (OTUs) affiliated to 12 AM fungal genera were identified from soil samples, and the AM fungal community composition differed strongly with elevation, with variance explained more by climate, followed by soil and plant factors. The AM fungal α-diversity, network connectivity and complexity between AM fungal taxa and also with plant communities all exhibited a maximum at the mid-elevation of 800 m and then declined, principally influenced by soil pH and precipitation. Stochastic processes dominated AM fungal community assembly across the whole elevation gradient, with homogenizing dispersal being the main process. Only when AM fungal communities were contrasted across a relatively broad range of elevations, did variable selection (deterministic process) became significant, and even then in a mixed role with stochasticity. While OTUs of AM fungi are clearly adapted to particular environmental ranges, stochasticity due to rapid dispersal has a major role in determining their occurrence, suggesting that AM fungi may possess generalized and interchangeable niches, and can adjust their distribution rapidly - at least on the scale of a single mountain. This finding emphasizes that the roles of AM fungi in plant ecology may be non-specific and easily substituted, and furthermore that there is rapid local scale dispersal, which may allow plants to maintain effective AM associations under environmental change.

Response of Fungal Sub-Communities in a Maize-Wheat Rotation Field Subjected to Long-Term Conservation Tillage Management

Conservation tillage is an advanced agricultural technology that seeks to minimize soil disturbance by reducing, or even eliminating tillage. Straw or stubble mulching in conservation tillage systems help to increase crop yield, maintain biodiversity and increase levels of exogenous nutrients, all of which may influence the structure of fungal communities in the soil. Currently, however, the assembly processes and co-occurrence patterns of fungal sub-communities remain unknown. In this paper, we investigated the effects of no-tillage and straw mulching on the composition, assembly process, and co-occurrence patterns of soil fungal sub-communities in a long-term experimental plot (15 years). The results revealed that combine straw mulching with no-tillage significantly increased the richness of fungi but not their diversity. Differential abundance analysis and principal component analysis (PCA) indicated that tillage management had a greater effect on the fungal communities of abundant and intermediate taxa than on the rare taxa. Available phosphorus (AP) and total nitrogen (TN) were the major determinants of fungal sub-communities in NT treatment. The abundant fungal sub-communities were assembled by deterministic processes under medium strength selection, while strong conservation tillage strength shifts the abundant sub-community assembly process from deterministic to stochastic. Overall, the investigation of the ecological network indicated that no-tillage and straw mulching practices decreased the complexity of the abundant and intermediate fungal networks, while not significantly influencing rare fungal networks. These findings refine our knowledge of the response of fungal sub-communities to conservation tillage management techniques and provide new insights into understanding fungal sub-community assembly.

Roles of Arbuscular Mycorrhizal Fungi on Soil Fertility: Contribution in the Improvement of Physical, Chemical, and Biological Properties of the Soil

Many of the world's soils are experiencing degradation at an alarming rate. Climate change and some agricultural management practices, such as tillage and excessive use of chemicals, have all contributed to the degradation of soil fertility. Arbuscular Mycorrhizal Fungi (AMFs) contribute to the improvement of soil fertility. Here, a short review focusing on the role of AMF in improving soil fertility is presented. The aim of this review was to explore the role of AMF in improving the chemical, physical, and biological properties of the soil. We highlight some beneficial effects of AMF on soil carbon sequestration, nutrient contents, microbial activities, and soil structure. AMF has a positive impact on the soil by producing organic acids and glomalin, which protect from soil erosion, chelate heavy metals, improve carbon sequestration, and stabilize soil macro-aggregation. AMF also recruits bacteria that produce alkaline phosphatase, a mineralization soil enzyme associated with organic phosphorus availability. Moreover, AMFs influence the composition, diversity, and activity of microbial communities in the soil through mechanisms of antagonism or cooperation. All of these AMF activities contribute to improve soil fertility. Knowledge gaps are identified and discussed in the context of future research in this review. This will help us better understand AMF, stimulate further research, and help in sustaining the soil fertility.

Soil acidification mediates changes in soil bacterial community assembly processes in response to agricultural intensification

Agricultural intensification is known to alter the assembly of soil microbial communities, which regulate several critical ecosystem processes. However, the underlying ecological processes driving changes in microbial community assembly, particularly at the regional scale, remain poorly understood. Using 16S rDNA sequencing, we characterized soil bacterial community assembly in three land‐use types with increasing land‐use intensity: open fields cultivated with main crops (CF) or vegetables (VF), and greenhouses cultivated with vegetables (VG). Compared with CF, VF and VG altered bacterial community composition and decreased spatial turnover rates of edaphic variables and bacterial communities. Bacterial community assembly was primarily governed by deterministic processes; however, bacterial communities in VF and VG were phylogenetically less clustered and more influenced by variable selection and less by dispersal limitation. Soil pH was the most important edaphic variable mediating the changes in bacterial community assembly processes induced by agricultural intensification. Specifically, decreasing soil pH led to stochastic assembly of bacterial community. Soil pH was lower in more intensively managed lands, especially in case of VG (pH range: 5.86–7.42). Overall, agricultural intensification altered soil bacterial community assembly processes, which was associated with soil acidification. These findings may have implications for improving soil quality and agroecosystem sustainability.

Different tillage practices change assembly, composition, and co-occurrence patterns of wheat rhizosphere diazotrophs

Tillage has a considerable effect on the soil ecosystem and its services, including microbial communities. Harnessing beneficial microbes is a sustainable way to optimizing crop management and agricultural production. Although diazotrophs play a major role in global biological nitrogen fixation, the effects of tillage on diazotrophic communities in the rhizosphere are not fully understood. In the present study, we investigated the diazotrophic community in wheat rhizosphere soil under different tillage treatments in a long-term experiment, i.e., plow tillage (considered as conventional tillage), chisel plow tillage (considered as conservation tillage), and zero tillage (considered as conservation tillage). Tillage led to a divergent distribution in the rhizosphere diazotrophic community and significant changes in community structure. Tillage caused specific responses from members/modules of the rhizosphere diazotrophic community co-occurrence network, and the relative abundance of keystone taxa was higher under conservation tillage than under conventional tillage. The increased abundance of tillage-sensitive modules under conservation tillage had a broad and significant positive correlation with rhizosphere nutrient availability, whereas the opposite was true for conventional tillage. Differences in nutrients under different tillage practices may lead to different assembly processes of diazotrophs. Overall, our findings indicate that tillage significantly affects the assembly and composition of the rhizosphere diazotrophic community, emphasizing the importance of improved substrate availability for rhizosphere diazotrophic modules under conservation tillage. This knowledge could deepen our understanding of the rhizosphere functional microbial community (e.g., biological nitrogen fixation).

Social networking in crop plants: Wired and wireless cross-plant communications

The plant-associated microbial community (microbiome) has an important role in plant-plant communications. Plants decipher their complex habitat situations by sensing the environmental stimuli and molecular patterns and associated with microbes, herbivores and dangers. Perception of these cues generates inter/intracellular signals that induce modifications of plant metabolism and physiology. Signals can also be transferred between plants via different mechanisms, which we classify as wired- and wireless communications. Wired communications involve direct signal transfers between plants mediated by mycorrhizal hyphae and parasitic plant stems. Wireless communications involve plant volatile emissions and root exudates elicited by microbes/insects, which enable inter-plant signalling without physical contact. These producer-plant signals induce microbiome adaptation in receiver plants via facilitative or competitive mechanisms. Receiver plants eavesdrop to anticipate responses to improve fitness against stresses. An emerging body of information in plant-plant communication can be leveraged to improve integrated crop management under field conditions.

Emerging strategies for precision microbiome management in diverse agroecosystems

Substantial efforts to characterize the structural and functional diversity of soil, plant and insect-associated microbial communities have illuminated the complex interacting domains of crop-associated microbiomes that contribute to agroecosystem health. As a result, plant-associated microorganisms have emerged as an untapped resource for combating challenges to agricultural sustainability. However, despite growing interest in maximizing microbial functions for crop production, resource efficiency and stress resistance, research has struggled to harness the beneficial properties of agricultural microbiomes to improve crop performance. Here, we introduce the historical arc of agricultural microbiome research, highlighting current progress and emerging strategies for intentional microbiome manipulation to enhance crop performance and sustainability. We synthesize current practices and limitations to managing agricultural microbiomes and identify key knowledge gaps in our understanding of microbe-assisted crop production. Finally, we propose research priorities that embrace a holistic view of crop microbiomes for achieving precision microbiome management that is tailored, predictive and integrative in diverse agricultural systems.

Mycorrhizal Interventions for Sustainable Potato Production in Africa

The potato (Solanum tuberosum L.) is an important tuber crop with high dietary value that could potentially help to alleviate malnutrition and hunger in Africa. However, production is expensive, with high fertilizer and pesticide demands that lead to environmental pollution, and tillage practices that negatively affect soil structure. Microorganisms of different types have increasingly been found to be useful as biofertilizers, and arbuscular mycorrhizal (AM) fungi are an important crop symbiont. AM fungi have been shown to increase tolerance of crop plants to drought, salinity and disease by facilitating water and nutrient acquisition and by improving overall soil structure. However, the establishment and maintenance of the symbioses are greatly affected by agricultural practices. Here, we review the benefits that AM fungi confer in potato production, discuss the role and importance of mycorrhiza helper bacteria, and focus on how AM fungal diversity and abundance can be affected by conventional agricultural practices, such as those used in potato production. We suggest approaches for maintaining AM fungal abundance in potato production by highlighting the potential of conservation tillage practices augmented with cover crops and crop rotations. An approach that balances weed control, nutrient provision, and AM fungal helper bacterial populations, whilst promoting functional AM fungal populations for varying potato genotypes, will stimulate efficient mycorrhizal interventions.