The traditional model of plant-arbuscular mycorrhizal (AM) fungal coevolution, based solely on interactions between plants and AM fungi, became obsolete with the discovery of the critical roles that belowground microbiomes play in the function of mycorrhizal symbiosis. Based on insights into hyphosphere microbiota, we expand the plant-AM fungus-bacterium continuum into a multipartite AM fungal-orchestrated holobiont (H-AMF) framework, where AM fungi integrate plant roots with soil microbiota into a cross-kingdom ecological unit. A division of labor exists among plants, AM fungi, and hyphosphere microbes in the mycocentric H-AMF perspective. We summarize mechanisms by which AM fungi sustain cooperative relationships with plants and hyphosphere microbiota and propose holobiont-scale methodologies to advance understanding of plant-fungal-microbial interactions and their ecological functions.

Societal Impact Statement Sorghum bicolor is a globally important cereal crop with annual yields exceeding 50 million tons across more than 100 countries and can be grown on marginal lands where conventional agriculture is limited. We examined how eight genetically diverse sorghum genotypes shaped arbuscular mycorrhizal fungal (AMF) community assembly across two contrasting field environments. We found that sorghum genotype influences AMF community composition and that this showed a pattern over time. These findings suggest that crop genotype selection can be a useful practical tool to modulate root-microbial interactions in low-input and marginal agricultural systems, with implications for sustainable intensification strategies and microbiome-informed crop breeding programs.Summary Arbuscular mycorrhizal fungal (AMF) symbiosis can influence crop production but can be variable across environmental conditions, host-partner complementarity, and temporal dynamics. Understanding how these factors interact to shape AMF community assembly allows for the selection of crop genotypes that may maximally utilize AMF associations in agricultural systems. We assessed the development of AMF communities colonizing the roots of eight genetically diverse genotypes of Sorghum bicolor across a growing season. We used two field sites with contrasting environments and management histories. Sorghum cultivated in Georgia (GA) sorghum harbored 3.7-fold more species than Arizona (AZ). We observed evidence of host-filtering of AMF communities, with genotypes displaying more distinct associations in GA than AZ. AZ showed rapid shifts from early Funneliformis mosseae dominance to increasing dominance by either Entrophospora etunicata or Diversispora aurantia. In GA, we observed temporal variation associated with turnover of low-abundance taxa contributing to larger family-level patterns. Our findings demonstrate that there is potential for leveraging intra-species genetic variation in AMF community assembly as an extended plant phenotype.

Fungal connections among plants, popularly known as the "wood wide web," captured the interest of scientific and public audiences because these connections may facilitate increased growth, improved survival, nutrient transfer, and communication among plants. Research on these fungal networks has focused almost exclusively on known plant symbionts called mycorrhizal fungi. However, many non-mycorrhizal fungi also form ecologically important associations with plants. If non-mycorrhizal fungi such as Dark Septate Endophytes (DSEs) can form common networks among plants, then fungal connections among plants are likely more complex and prevalent than previously thought. In this study, we ask whether a common DSE can form hyphal connections between plants, improve plant biomass, and move water between them. Using a lab system with donor and receiver plants, we find that DSE hyphae crossed air gaps to physically connect plants. Receiver plants that were connected to a fungal network had higher biomass than those that were not. A water-soluble dye injected into donor plant leaves was detected in receiver leaves, but only when plants were connected via the fungal network. These results provide the first lab-based evidence that common non-mycorrhizal networks can occur and suggest that fungal networks among plants may extend beyond mycorrhizal fungi.

In situ manipulation of mesofauna communities is necessary to understand their functional importance in complex natural systems. Field mesocosms that control the recolonization of defaunated soil and litter by mesofauna are well suited to this purpose, but are infrequently used and can produce undesirable side effects on microclimate. Here, we present an inexpensive and easy to construct field mesocosm design that is intended to address some limitations of existing mesocosm methods. Our mesocosms were engineered to manipulate mesofauna communities over one or two years via mesh treatments (21 mu m, 41 mu m, and 1000 mu m mesh opening sizes) while minimizing mesh treatment side effects and allowing repeated access to mesocosm interiors for measurement of microclimate differences and mesofauna functions through time. They are also compatible with LICOR survey chambers, enabling measurement of gas flux from mesocosms. We tested these mesocosms in untreated and thinned/burned ponderosa pine (Pinus ponderosa) forests in Valles Caldera National Preserve, New Mexico, USA to compare their performance in differing abiotic and biotic contexts. The mesocosm treatments successfully manipulated microarthropods > 150 mu m for fifteen months but were only partially effective at manipulating microarthropods < 150 m. This mesocosm technique advances our ability to disentangle the functional contributions of mesofauna in complex natural systems because it enables manipulation experiments with repeated sampling in time and space.

Multicellular organisms are hosts to diverse communities of smaller organisms known as microbiomes. Plants have distinctive microbiomes that can provide important functions related to nutrition, defense, and stress tolerance. Empirical studies provide convincing evidence that in some-but not all-circumstances, belowground microbiomes help plants adapt to their local environment. The purpose of this review is to develop functional team selection (FTS) as a framework to help predict the conditions necessary for root microbiomes to generate local adaptation for their plant hosts. FTS envisions plants and their microbiomes as complex adaptive systems, and plant adaptations as emergent properties of these systems. If plants have the capacity to recognize and cultivate beneficial microbes and suppress pathogens, then it is possible for plants to evolve the capacity to gain adaptations by curating their microbiome. In resource-limited and stressful environments, the emergent functions of complex microbial systems may contribute to positive feedback linked to plant vigor, and ultimately, local adaptation. The key factors in this process are: (i) selective force, (ii) host constitution, (iii) microbial diversity, and (iv) time. There is increasing interest in harnessing beneficial microbial interactions in agriculture and many microbial growth-promoting products are commercially available, but their use is controversial because a large proportion of these products fail to consistently enhance plant growth. The FTS framework may help direct the development of durable plant-microbiome systems that enhance crop production and diminish pathogens. It may also provide valuable insights for understanding and managing other kinds of host-microbe systems.

Development interventions increasingly include women’s empowerment and gender equality among their objectives, but evaluating their impact has been stymied by the lack of measures that are comparable across interventions. This paper synthesizes the findings of 11 mixed-methods impact evaluations of agricultural development projects from South Asia and sub-Saharan Africa that were part of the Gender, Agriculture, and Assets Project, Phase 2 (GAAP2). As part of GAAP2, qualitative and quantitative data were used to develop and validate the multidimensional project-level Women’s Empowerment in Agriculture Index (pro-WEAI), which was used to assess the impact of GAAP2 projects on women’s empowerment. This paper assesses the extent to which: (1) a two- to three-year agricultural development project can contribute to women’s empowerment; and (2) a suite of methods comprising a standardized quantitative measure of women’s empowerment and a set of qualitative protocols, can evaluate such impacts. Our synthesis finds that the most common positive significant impacts were on the instrumental and collective agency indicators that comprise pro-WEAI, owing to the group-based approaches used. We found few projects significantly improved intrinsic agency, even among those with explicitly stated objectives to change gender norms. Unsurprisingly, we find mixed, and mostly null impacts on aggregate pro-WEAI, with positive impacts more likely in the South Asian, rather than African, cases. Our results highlight the need for projects to design their strategies specifically for empowerment, rather than assume that projects aiming to reach and benefit women automatically empower them. Our study also shows the value of a suite of methods containing a common metric to compare empowerment impacts and qualitative protocols to understand and contextualize these impacts.

Impacts of multiple environmental change factors on plant and soil microbial communities can have important ecological consequences, but have yet to be thoroughly elucidated. Improved understanding of bacterial community responses to environmental filters over long time periods is a fundamental step in developing mechanistic explanations of plant-bacterial interactions as environmental change progresses. This study examines responses of grassland root-associated bacterial communities to 15 years of experimental manipulation of plant species richness, plant functional group, and enrichment of atmospheric CO2 (eCO2 ) and soil nitrogen (+N). We used next-generation sequencing to characterize rhizobacterial communities and relative abundance of predicted functional genes to assess filtering on rhizobacterial community assemblages. Experimental treatments structured rhizobacterial communities. In plots with 16 plant species, +N altered rhizobacterial composition and increased the predicted abundance of nitrogenase-encoding genes, while the combination of eCO2 and N (eCO2 +N) increased predicted abundance of P-solubilizing genes. Regardless of resource additions, NO3- -reducing and P-solubilizing gene abundance had a significant positive linear relationship in 16-species plots. In plant monocultures, legumes had dissimilar rhizobacterial community composition than C3 grasses and C4 grasses. Both eCO2 and eCO2 +N altered rhizobacterial communities in monocultures of C3 and C4 grasses, and legumes. Under eCO2 , N2 -fixation genes increased on C3 grasses. Under eCO2 +N, NO3- -reducing genes increased on C3 and C4 grasses, but decreased on legumes. P-solubilizing genes increased for C3 grasses and decreased for legumes under eCO2 +N. Across the experiment, plant species richness was the strongest predictor of rhizobacterial community composition. In monocultures, plant functional group was most important in structuring rhizobacterial composition and predicted functional genes after 15 years of resource enrichment. Our findings suggest that grassland rhizobacterial community structure and function will be affected by environmental change, but such responses are strongly contingent on plant species richness and functional identity.

The presence of Arbuscular Mycorrhizal Fungi (AMF) in vascular land plant roots is one of the most ancient of symbioses supporting nitrogen and phosphorus exchange for photosynthetically derived carbon. Here we provide a multi-scale modeling approach to predict AMF colonization of a worldwide crop from a Recombinant Inbred Line (RIL) population derived from Sorghum bicolor and S. propinquum. The high-throughput phenotyping methods of fungal structures here rely on a Mask Region-based Convolutional Neural Network (Mask R-CNN) in computer vision for pixel-wise fungal structure segmentations and mixed linear models to explore the relations of AMF colonization, root niche, and fungal structure allocation. Models proposed capture over 95% of the variation in AMF colonization as a function of root niche and relative abundance of fungal structures in each plant. Arbuscule allocation is a significant predictor of AMF colonization among sibling plants. Arbuscules and extraradical hyphae implicated in nutrient exchange predict highest AMF colonization in the top root section. Our work demonstrates that deep learning can be used by the community for the high-throughput phenotyping of AMF in plant roots. Mixed linear modeling provides a framework for testing hypotheses about AMF colonization phenotypes as a function of root niche and fungal structure allocations.

Symbiotic mycorrhizal fungi strongly influence plant establishment and growth particularly in harsh environments, whereby sympatric, presumably co-adapted symbionts are considered particularly beneficial. However, the response of transferred sympatric mycorrhizal fungal communities to new environments remains largely ignored. We therefore studied the relative importance of initial inoculum, soil and climatic conditions on the composition, diversity and root colonization ability of arbuscular mycorrhizal fungal (AMF) communities. To do so, we analyzed the AMF communities in an extensive experiment with two ecotypes of Bouteloua gracilis planted in their sites of origin and in four new sites differing in climate and soil properties.After three seasons of growth, the sympatric AMF communities were little changed by the new abiotic conditions. The composition of the AMF communities in plant roots was most strongly determined by the initial inoculum, while the contribution of divergent soil and climatic conditions was an order of magnitude smaller. The levels of root colonization by AMF, in contrast, were significantly influenced by climatic and soil conditions and did not differ among communities of different origins. Their pattern indicates that mycorrhiza formation is facilitated in the plant's sympatric soil and climatic conditions, but also that transferred AMF communities adjust mycorrhiza formation to new abiotic conditions.

Summary It is well understood that agricultural management influences arbuscular mycorrhizal (AM) fungi, but there is controversy about whether farmers should manage for AM symbiosis. We assessed AM fungal communities colonizing wheat roots for three consecutive years in a long‐term (> 14 yr) tillage and fertilization experiment. Relationships among mycorrhizas, crop performance, and soil ecosystem functions were quantified. Tillage, fertilizers and continuous monoculture all reduced AM fungal richness and shifted community composition toward dominance of a few ruderal taxa. Rhizophagus and Dominikia were depressed by tillage and/or fertilization, and their abundances as well as AM fungal richness correlated positively with soil aggregate stability and nutrient cycling functions across all or no‐tilled samples. In the field, wheat yield was unrelated to AM fungal abundance and correlated negatively with AM fungal richness. In a complementary glasshouse study, wheat biomass was enhanced by soil inoculum from unfertilized, no‐till plots while neutral to depressed growth was observed in wheat inoculated with soils from fertilized and conventionally tilled plots. This study demonstrates contrasting impacts of low‐input and conventional agricultural practices on AM symbiosis and highlights the importance of considering both crop yield and soil ecosystem functions when managing mycorrhizas for more sustainable agroecosystems.

This article is a Commentary on Wang et al . (2023), 238 : 859–873 .

During the United Nation's Decade on Ecosystem Restoration, planting material shortages are constraining restoration, while climate change exacerbates the need for restoration and reduces recruitment. Concurrently, research shows that native mycorrhizal fungi (symbiotic with plant roots) appropriate to plant provenance and site conditions significantly accelerate restoration, support crucial ecosystem services, and provide natural climate solutions (sequestering carbon), and nature‐based solutions for climate change (climate adaptation). We reviewed 130 management plans for natural areas in the United States to evaluate whether restoring native mycorrhizal communities has translated into implementation. Although management plans frequently discussed the ecosystem services mycorrhizal fungi provide, nearly one half (46%) viewed fungi solely as pathogens or ignored them altogether. Only 8% of plans mentioned mycorrhizal fungi. Only one plan mentioned that mycorrhizae were potentially helpful to natural regeneration, while one other mentioned utilizing soil as a restoration tool. Our examination of publicly available data and case studies suggests that relatively meager protections for fungi, limited research funding and resulting data, research difficulty, and limited access to mycology experts and training contribute to this gap between science and implementation. A database of literature showcasing mycorrhizal ecosystem services and benefits is provided to highlight when and why mycorrhizae should be considered in management, regeneration, and restoration. Three action items are recommended to safeguard native mycorrhizal fungal communities and accelerate restoration and regeneration. Ten implementation tips based in scientific literature are provided to clarify the need and methods for mycorrhizal restoration.

Mechanized logging equipment causes considerable soil disturbance, but little information is available regarding thresholds for impacts on soil nematodes—critical members of soil foodwebs which perform important ecological functions. We examined responses of nematode communities and soil physical characteristics to the increasing number of passes (one, three, or nine) by a tracked feller buncher during thinning of a xeric mixed conifer forest in New Mexico, USA. Within and between the harvester tracks, we measured soil surface penetration resistance and shear strength, quantified bulk density at four depth increments up to a maximum depth of 27 cm, and characterized nematode assemblages in the upper 10 cm. Eight months after treatment, nematode communities were less impacted than soil physical properties by harvester passes. Total nematode abundance was unaffected by any level of feller buncher disturbance, and sensitive K-selected nematode groups were reduced only at nine passes. Conversely, soil compaction occurred with a single pass and extended deep into the soil profile to at least 23–27 cm. The first pass also decreased surface penetration resistance and shear strength, indicating disruption of soil surface structural integrity. Additional passes did not further increase bulk density or decrease surface structural integrity. Our results indicate that low levels of logging machinery traffic may have negligible effects on nematode communities, but nevertheless emphasize the importance of minimizing areas subjected to disturbance because of impacts on soil physical properties.

Climate change is altering temperature and precipitation, resulting in widespread plant mortality and shifts in plant distributions. Plants growing in soil types with low water holding capacity may experience intensified effects of reduced water availability as a result of climate change. Furthermore, complex biotic interactions between plants and soil organisms may mitigate or exacerbate the effects of climate change. This 3-year field experiment observed the performance of Bouteloua gracilis ecotypes that were transplanted across an environmental gradient with either sympatric soil from the seed source location or allopatric soil from the location that plants were transplanted into. We also inoculated plants with either sympatric or allopatric soil biotic communities to test: (1) how changes in climate alone influence plant growth, (2) how soil types interact with climate to influence plant growth, and (3) the role of soil biota in mitigating plant migration to novel environments. As expected, plants moved to cooler-wetter sites exhibited enhanced growth; however, plants moved to warmer-drier sites responded variably depending on the provenance of their soil and inoculum. Soil and inoculum provenance had little influence on the performance of plants moved to cooler-wetter sites, but at warmer-drier sites they were important predictors of plant biomass, seed set, and specific leaf area. Specifically, transplants inoculated with their sympatric soil biota and grown in their sympatric soil were as large as or larger than reference plants grown at the seed source locations; however, individuals inoculated with allopatric soil biota were smaller than reference site individuals at warmer, drier sites. These findings demonstrate complicated plant responses to various aspects of environmental novelty where communities of soil organisms may help ameliorate stress. The belowground microbiome of plants should be considered to predict the responses of vegetation more accurately to climate change.

Thinning, mastication, and prescribed fire are restoration treatments frequently employed in unnaturally dense second-growth Pinus ponderosa forests of the Western United States. Although a goal of these treatments is to restore ecosystem structure and function, little information is available regarding treatment effects on soil micro- and mesofauna, which comprise the overwhelming majority of metazoan forest inhabitants and occupy key positions in soil food webs. We quantified nematodes, mites, and collembolans in soil and litter habitats within untreated control, thinned (comprising thinning and masticating wood), and burned (comprising thinning and masticating, followed by broadcast burn) in P. ponderosa forest management units at Valles Caldera National Preserve in New Mexico, USA. We linked patterns in animal abundance to resource and habitat characteristics, hypothesizing that resources and available habitat for many taxa would increase with thinning and decrease with burning. Two years after thinning, densities of collembolans and nematodes in the thinned unit were higher than in the untreated control unit, but one year post-fire, their densities in the burned unit were similar to those of the untreated control unit. Mite abundance, however, was not elevated in the thinned unit and was lower in the burned unit. Although faunal communities were highly heterogeneous, a significant proportion of the variance in faunal abundances was explained by easily and inexpensively measured habitat and resource characteristics: bulk density, soil organic matter (SOM), pH, grass cover, and litter cover and depth. These findings demonstrate the abiotic and biotic factors that structure faunal habitats so that forest managers have a more complete understanding of the impacts of forest restoration treatments.

Soil has the ability to sequester carbon (C) and mitigate anthropogenic enrichment of carbon dioxide, however numerous variables influence its C storage potential. Climate, soil properties, plant species composition, and livestock management practices, may all influence C storage in rangeland soils. The purpose of this study was to examine the relative importance of these factors in predicting organic and inorganic soil C in a semi-arid rangeland in northern Arizona USA. Sampling sites at 60 locations within the 40,469 ha Diablo Trust Ranches were selected using a stratified random method to encompass five distinct soil series across a precipitation gradient (230 mm-623 mm mean annual precipitation) with fence-lines that separate actively grazed areas with adjacent areas that have excluded livestock for at least 20 years. A total of 240 soil samples were collected from two depths (0-5 cm and 20-25 cm) in grazed and adjacent ungrazed sides of fences. Soil texture, bulk density, plant community composition, root biomass, soil organic carbon (SOC) and soil inorganic carbon (SIC) were measured. Across the precipitation and soil gradient, SOC was highest (up to 28.6 Mg ha(-1)) in the surface layer of clay-rich soil derived from basalt and SIC was highest (up to 74.7 Mg ha(-1)) in subsurface soil derived from limestone. General linear models showed that grazing had no significant impact on total soil C, instead, soil depth and soil texture were the main predictors of SOC and SIC. Precipitation was positively correlated with SOC and negatively correlated with SIC. Soil texture and precipitation were highly autocorrelated, so only soil texture was included in structural equation models (SEMs). Separate SEMs for surface and subsurface soils showed that soil texture (and autocorrelated precipitation) was the strongest predictor of SOC, SIC and plant community composition at both soil depths. The relative abundance of C4 grasses was higher in grazed plots and was positively correlated with root biomass at the soil surface. Also, surface root biomass was weakly positively related to SOC while both surface and subsurface roots were negatively related to SIC. This study shows the importance of interactions among multiple factors in predicting soil C stocks and that SIC can be a substantial C reservoir in dryland soils, especially those derived from sedimentary parent material. We could not detect an influence of livestock grazing on either SOC or SIC in this landscape scale study. This suggests that in this semi-arid rangeland it may be difficult to increase total soil C storage through livestock management.

Improving policies-broadly defined-is at the heart of the structural transformation agenda. This paper describes the use of a new evaluation method-outcome trajectory evaluation (OTE), based on both evaluation and policy process theory-to explore the influence of HarvestPlus, a large and complex research for development program focused on improving nutrition, on a specific policy outcome, namely the establishment of biofortification crop breeding programs in national agricultural research institutes in Bangladesh, India, and Rwanda. The findings support claims of significant HarvestPlus contributions while also raising issues that need to be monitored to ensure sustainability. The paper also discusses the pros and cons of the OTE approach in terms of methodological rigor and the accumulation of learning from one evaluation to the next.

As one of the last remaining naturally grazed ecosystems on Earth, the Serengeti National Park is an ideal location to study the influence of migratory mammals on the structure of microbial communities and the factors that generate biogeography of soil microbes. Furthermore, volcanic inputs generate environmental gradients that may also structure microbial communities. We studied 16S rRNA amplicons in a 13-year herbivore removal experiment to examine the influence of grazing and environmental gradients on the natural distribution of soil microbes. Removal of mammalian herbivores shifted microbial community structure, with 31 taxa that were significant indicator taxa of the ungrazed treatment and three taxa that were indicators of the grazed treatment. The abundance of many taxa were correlated with soil texture, phosphorus, iron, calcium and rainfall, and the evenness of taxa within samples was also correlated with these variables. Bayesian general linear mixed effects models with single predictors of multiple, highly correlated variables of beta diversity were consistent with a significant, but weak (2%), effect of grazing, and stronger effects of phosphorus (14%). Beta diversity of microbial communities was greater in grazed than in ungrazed plots; suggesting that the impacts of grazing on community assembly of microbes results from deterministic environmental filtering caused by the influence of herbivores on plant communities and soil properties rather than stochastic dispersal via herds of large mammals. These herbivore effects are superimposed on deterministic environmental filtering by natural soil and precipitation gradients across the Serengeti.

There is evidence that the distribution of ecotypes of plants and their symbiotic arbuscular mycorrhizal (AM) fungi and other associated soil biota may be structured by the availability of essential soil nutrients; and that locally adapted partnerships most successfully acquire limiting nutrients. This study tests the hypotheses that plant genotypes are adapted to the water availability of their local environment, and this adaptation involves associations with local soil biota, including AM fungi. We grew semi‐arid Bouteloua gracilis ecotypes from relatively wet and dry sites, with either sympatric or allopatric soil inoculum under moderate and extreme soil drying treatments to examine (a) how varying degrees of water limitation influence grass responses to soil biota and (b) the relationship between AM fungal structures and the responses. Under extreme soil drying, the dry site ecotype tended to perform better than the wet site ecotype. Both ecotypes performed best in either drying treatment when inoculated with their sympatric soil biota. Sympatric pairings produced more AM fungal hyphae, arbuscules and dark septate fungi. Extreme soil drying tended to accentuate these apparent benefits of sympatry to both plants and fungal symbionts, relative to the moderate drying treatment. Our findings support the hypothesis that AM symbioses help Bouteloua gracilis ecotypes adapt to local water availability. This conclusion is based on the observations that as water became increasingly limited, sympatric partnerships produced more AM fungal hyphae and arbuscules and fewer vesicles. The abundances of hyphae and arbuscules were positively correlated with plant growth, suggesting that in sympatric pairs of plants and AM fungi, allocation to fungal structures is optimized to maximize benefits and minimize the costs of the symbioses. This provides strong evidence that co‐adaptation among plants and their associated AM fungi can ameliorate drought stress. Synthesis . Our study documents the role of locally adapted soil borne plant symbionts in ameliorating water stress. We found a relationship between AM fungal structures in roots and plant performance. Generally, plants and fungi from the same site resulted in more positive effects on plant growth.