Evolutionary ecology of mycorrhizal functional diversity in agricultural systems

Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes

Cyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics and agricultural practices: more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes or those uninfected by nematodes. Based on a network analysis of potential microbe-microbe associations, we further found that several fungal taxa potentially preying on nematodes (Dactylellina (Orbiliales), Rhizophydium (Rhizophydiales), Clonostachys (Hypocreales), Pochonia (Hypocreales) and Purpureocillium (Hypocreales)) co-occurred in the soybean rhizosphere at a small spatial scale. This study suggests how 'consortia' of anti-nematode microbes can derive from indigenous (resident) microbiomes, providing basic information for managing anti-nematode microbial communities in agroecosystems.

Abiotic contexts consistently influence mycorrhiza functioning independently of the composition of synthetic arbuscular mycorrhizal fungal communities

The relationship between mycorrhiza functioning and composition of arbuscular mycorrhizal (AM) fungal communities is an important but experimentally still rather little explored topic. The main aim of this study was thus to link magnitude of plant benefits from AM symbiosis in different abiotic contexts with quantitative changes in AM fungal community composition. A synthetic AM fungal community inoculated to the model host plant Medicago truncatula was exposed to four different abiotic contexts, namely drought, elevated phosphorus availability, and shading, as compared to standard cultivation conditions, for two cultivation cycles. Growth and phosphorus uptake of the host plants was evaluated along with the quantitative composition of the synthetic AM fungal community. Abiotic context consistently influenced mycorrhiza functioning in terms of plant benefits, and the effects were clearly linked to the P requirement of non-inoculated control plants. In contrast, the abiotic context only had a small and transient effect on the quantitative AM fungal community composition. Our findings suggest no relationship between the degree of mutualism in AM symbiosis and the relative abundances of AM fungal species in communities in our simplified model system. The observed progressive dominance of one AM fungal species indicates an important role of different growth rates of AM fungal species for the establishment of AM fungal communities in simplified systems such as agroecosystems.

Dynamics of arbuscular mycorrhizal fungal community structure and functioning along a nitrogen enrichment gradient in an alpine meadow ecosystem

Nitrogen (N) availability is increasing dramatically in many ecosystems, but the influence of elevated N on the functioning of arbuscular mycorrhizal (AM) fungi in natural ecosystems is not well understood. We measured AM fungal community structure and mycorrhizal function simultaneously across an experimental N addition gradient in an alpine meadow that is limited by N but not by phosphorus (P). AM fungal communities at both whole-plant-community (mixed roots) and single-plant-species (Elymus nutans roots) scales were described using pyro-sequencing, and the mycorrhizal functioning was quantified using a mycorrhizal-suppression treatment in the field (whole-plant-community scale) and a glasshouse inoculation experiment (single-plant-species scale). Nitrogen enrichment progressively reduced AM fungal abundance, changed AM fungal community composition, and shifted mycorrhizal functioning towards parasitism at both whole-plant-community and E. nutans scales. N-induced shifts in AM fungal community composition were tightly linked to soil N availability and/or plant species richness, whereas the shifts in mycorrhizal function were associated with the communities of specific AM fungal lineages. The observed changes in both AM fungal community structure and functioning across an N enrichment gradient highlight that N enrichment of ecosystems that are not P-limited can induce parasitic mycorrhizal functioning and influence plant community structure and ecosystem sustainability.

Little evidence that farmers should consider abundance or diversity of arbuscular mycorrhizal fungi when managing crops

Contents Summary 1092 I. Introduction 1093 II. Investigating activity of AMF in agroecosystems 1093 III. Crop benefit from AMF: agronomic and mycorrhizal literature differ 1094 IV. Flawed methodology leads to benefits of mycorrhizas being overstated 1094 V. Rigorous methodology suggests low colonisation by AMF can sometimes reduce crop yield 1095 VI. Predicting when mycorrhizas matter for crop yield 1096 VII. Crop genotype 1099 VIII. Fungal genotype 1100 IX. Complex interactions between the mycorrhizal fungal and soil microbial communities 1102 X. Phosphorus-efficient agroecosystems 1102 XI. Conclusions 1103 Acknowledgements 1104 References 1104 SUMMARY: Arbuscular mycorrhizal fungi (AMF) are ubiquitous in agroecosystems and often stated to be critical for crop yield and agroecosystem sustainability. However, should farmers modify management to enhance the abundance and diversity of AMF? We address this question with a focus on field experiments that manipulated colonisation by indigenous AMF and report crop yield, or investigated community structure and diversity of AMF. We find that the literature presents an overly optimistic view of the importance of AMF in crop yield due, in part, to flawed methodology in field experiments. A small body of rigorous research only sometimes reports a positive impact of high colonisation on crop yield, even under phosphorus limitation. We suggest that studies vary due to the interaction of environment and genotype (crop and mycorrhizal fungal). We also find that the literature can be overly pessimistic about the impact of some common agricultural practices on mycorrhizal fungal communities and that interactions between AMF and soil microbes are complex and poorly understood. We provide a template for future field experiments and a list of research priorities, including phosphorus-efficient agroecosystems. However, we conclude that management of AMF by farmers will not be warranted until benefits are demonstrated at the field scale under prescribed agronomic management.

Structural diversity across arbuscular mycorrhizal, ectomycorrhizal, and endophytic plant-fungus networks

BACKGROUND

Below-ground linkage between plant and fungal communities is one of the major drivers of terrestrial ecosystem dynamics. However, we still have limited knowledge of how such plant-fungus associations vary in their community-scale properties depending on fungal functional groups and geographic locations.

METHODS

By compiling a high-throughput sequencing dataset of root-associated fungi in eight forests along the Japanese Archipelago, we performed a comparative analysis of arbuscular mycorrhizal, ectomycorrhizal, and saprotrophic/endophytic associations across a latitudinal gradient from cool-temperate to subtropical regions.

RESULTS

In most of the plant-fungus networks analyzed, host-symbiont associations were significantly specialized but lacked "nested" architecture, which has been commonly reported in plant-pollinator and plant-seed disperser networks. In particular, the entire networks involving all functional groups of plants and fungi and partial networks consisting of ectomycorrhizal plant and fungal species/taxa displayed "anti-nested" architecture (i.e., negative nestedness scores) in many of the forests examined. Our data also suggested that geographic factors affected the organization of plant-fungus network structure. For example, the southernmost subtropical site analyzed in this study displayed lower network-level specificity of host-symbiont associations and higher (but still low) nestedness than northern localities.

CONCLUSIONS

Our comparative analyses suggest that arbuscular mycorrhizal, ectomycorrhizal, and saprotrophic/endophytic plant-fungus associations often lack nested network architecture, while those associations can vary, to some extent, in their community-scale properties along a latitudinal gradient. Overall, this study provides a basis for future studies that will examine how different types of plant-fungus associations collectively structure terrestrial ecosystems.

Precrop Functional Group Identity Affects Yield of Winter Barley but Less so High Carbon Amendments in a Mesocosm Experiment

Nitrate leaching is a pressing environmental problem in intensive agriculture. Especially after the crop harvest, leaching risk is greatest due to decomposing plant residues, and low plant nutrient uptake and evapotranspiration. The specific crop also matters: grain legumes and canola commonly result in more leftover N than the following winter crop can take up before spring. Addition of a high carbon amendment (HCA) could potentially immobilize N after harvest. We set up a 2-year mesocosm experiment to test the effects of N fertilization (40 or 160 kg N/ha), HCA addition (no HCA, wheat straw, or sawdust), and precrop plant functional group identity on winter barley yield and soil C/N ratio. Four spring precrops were sown before winter barley (white lupine, faba bean, spring canola, spring barley), which were selected based on a functional group approach (colonization by arbuscular mycorrhizal fungi [AMF] and/or N2-fixing bacteria). We also measured a subset of faba bean and spring barley for leaching over winter after harvest. As expected, N fertilization had the largest effect on winter barley yield, but precrop functional identity also significantly affected the outcome. The non-AMF precrops white lupine and canola had on average a positive effect on yield compared to the AMF precrops spring barley and faba bean under high N (23% increase). Under low N, we found only a small precrop effect. Sawdust significantly reduced the yield compared to the control or wheat straw under either N level. HCAs reduced nitrate leaching over winter, but only when faba bean was sown as a precrop. In our setup, short-term immobilization of N by HCA addition after harvest seems difficult to achieve. However, other effects such as an increase in SOM or nutrient retention could play a positive role in the long term. Contrary to the commonly found positive effect of AMF colonization, winter barley showed a greater yield when it followed a non-AMF precrop under high fertilization. This could be due to shifts of the agricultural AMF community toward parasitism.

Dark septate endophytes isolated from a xerophyte plant promote the growth of Ammopiptanthus mongolicus under drought condition

Dark septate endophytes (DSE) may facilitate plant growth and stress tolerance in stressful ecosystems. However, little is known about the response of plants to non-host DSE fungi isolated from other plants, especially under drought condition. This study aimed to seek and apply non-host DSE to evaluate their growth promoting effects in a desert species, Ammopiptanthus mongolicus, under drought condition. Nine DSE strains isolated from a super-xerophytic shrub, Gymnocarpos przewalskii, were identified and used as the non-host DSE. And DSE colonization rate (30–35%) and species composition in the roots of G. przewalskii were first reported. The inoculation results showed that all DSE strains were effective colonizers and formed a strain-dependent symbiosis with A. mongolicus. Specifically, one Darksidea strain, Knufia sp., and Leptosphaeria sp. increased the total biomass of A. mongolicus compared to non-inoculated plants. Two Paraconiothyrium strains, Phialophora sp., and Embellisia chlamydospora exhibited significantly positive effects on plant branch number, potassium and calcium content. Two Paraconiothyrium and Darksidea strains particularly decreased plant biomass or element content. As A. mongolicus plays important roles in fixing moving sand and delay desertification, the ability of certain DSE strains to promote desert plant growth indicates their potential use for vegetation recovery in arid environments.

Can phosphorus application and cover cropping alter arbuscular mycorrhizal fungal communities and soybean performance after a five-year phosphorus-unfertilized crop rotational system?

Background

Understanding diversity of arbuscular mycorrhizal fungi (AMF) is important for optimizing their role for phosphorus (P) nutrition of soybeans (Glycine max (L.) Merr.) in P-limited soils. However, it is not clear how soybean growth and P nutrition is related to AMF colonization and diversity of AMF communities in a continuous P-unfertilized cover cropping system. Thus, we investigated the impact of P-application and cover cropping on the interaction among AMF colonization, AMF diversity in soybean roots, soybean growth and P nutrition under a five-year P-unfertilized crop rotation.

Methods

In this study, we established three cover crop systems (wheat, red clover and oilseed rape) or bare fallow in rotation with soybean. The P-application rates before the seeding of soybeans were 52.5 and 157.5 kg ha^-1 in 2014 and 2015, respectively. We measured AMF colonization in soybean roots, soybean growth parameters such as aboveground plant biomass, P uptake at the flowering stage and grain yields at the maturity stage in both years. AMF community structure in soybean roots was characterized by specific amplification of small subunit rDNA.

Results

The increase in the root colonization at the flowering stage was small as a result of P-application. Cover cropping did not affect the aboveground biomass and P uptake of soybean in both years, but the P-application had positive effects on the soybean performance such as plant P uptake, biomass and grain yield in 2015. AMF communities colonizing soybean roots were also significantly influenced by P-application throughout the two years. Moreover, the diversity of AMF communities in roots was significantly influenced by P-application and cover cropping in both years, and was positively correlated with the soybean biomass, P uptake and grain yield throughout the two years.

Discussion

Our results indicated that P-application rather than cover cropping may be a key factor for improving soybean growth performance with respect to AMF diversity in P-limited cover cropping systems. Additionally, AMF diversity in roots can potentially contribute to soybean P nutrition even in the P-fertilized cover crop rotational system. Therefore, further investigation into the interaction of AMF diversity, P-application and cover cropping is required for the development of more effective P management practices on soybean growth performance.

Chronic fertilization of 37 years alters the phylogenetic structure of soil arbuscular mycorrhizal fungi in Chinese Mollisols

Arbuscular mycorrhizal fungi (AMF) play vital roles in sustaining soil productivity and plant communities. However, adaption and differentiation of AMF in response to commonly used fertilization remain poorly understood. In this study, we showed that the AMF community composition was primarily driven by soil physiochemical changes associated with chronic inorganic and organic fertilization of 37 years in Mollisols. High-throughput sequencing indicated that inorganic fertilizer negatively affected AMF diversity and richness, implying a reduction of mutualism in plant-AMF symbiosis; however, a reverse trend was observed for the application of inorganic fertilizer combined with manure. With regards to AMF community composition, order Glomerales was dominant, but varied significantly among different fertilization treatments. All fertilization treatments decreased family Glomeraceae and genus Funneliformis, while Rhizophagus abundance increased. Plant-growth-promoting-microorganisms of family Claroideoglomeraceae and genus Claroideoglomus were stimulated by manure application, and likely benefited pathogen suppression and phosphorus (P) acquisition. Family Gigasporaceae and genus Gigaspora were negatively correlated with available P in soil. Additionally, redundancy analysis further suggested that soil available P, organic matter and pH were the most important factors in shaping AMF community composition. These results provide strong evidence for niche differentiation of phylogenetically distinct AMF populations under different fertilization regimes. Manure likely contributes to restoration and maintenance of plant-AMF symbiosis, and the balanced fertilization would favor the growth of beneficial AMF communities as one optimized management in support of sustainable agriculture in Mollisols.

Impacts of domestication on the arbuscular mycorrhizal symbiosis of 27 crop species

The arbuscular mycorrhizal (AM) symbiosis is key to plant nutrition, and hence is potentially key in sustainable agriculture. Fertilization and other agricultural practices reduce soil AM fungi and root colonization. Such conditions might promote the evolution of low mycorrhizal responsive crops. Therefore, we ask if and how evolution under domestication has altered AM symbioses of crops. We measured the effect of domestication on mycorrhizal responsiveness across 27 crop species and their wild progenitors. Additionally, in a subset of 14 crops, we tested if domestication effects differed under contrasting phosphorus (P) availabilities. The response of AM symbiosis to domestication varied with P availability. On average, wild progenitors benefited from the AM symbiosis irrespective of P availability, while domesticated crops only profited under P-limited conditions. Magnitudes and directions of response were diverse among the 27 crops, and were unrelated to phylogenetic affinities or to the coordinated evolution with fine root traits. Our results indicate disruptions in the efficiency of the AM symbiosis linked to domestication. Under high fertilization, domestication could have altered the regulation of resource trafficking between AM fungi and associated plant hosts. Provided that crops are commonly raised under high fertilization, this result has important implications for sustainable agriculture.

Herbivore removal reduces influence of arbuscular mycorrhizal fungi on plant growth and tolerance in an East African savanna

The functional relationship between arbuscular mycorrhizal fungi (AMF) and their hosts is variable on small spatial scales. Here, we hypothesized that herbivore exclusion changes the AMF community and alters the ability of AMF to enhance plant tolerance to grazing. We grew the perennial bunchgrass, Themeda triandra Forssk in inoculum from soils collected in the Kenya Long-term Exclosure Experiment where treatments representing different levels of herbivory have been in place since 1995. We assessed AMF diversity in the field, using terminal restriction fragment length polymorphism and compared fungal diversity among treatments. We conducted clipping experiments in the greenhouse and field and assessed regrowth. Plants inoculated with AMF from areas accessed by wild herbivores and cattle had greater biomass than non-inoculated controls, while plants inoculated with AMF from where large herbivores were excluded did not benefit from AMF in terms of biomass production. However, only the inoculation with AMF from areas with wild herbivores and no cattle had a positive effect on regrowth, relative to clipped plants grown without AMF. Similarly, in the field, regrowth of plants after clipping in areas with only native herbivores was higher than other treatments. Functional differences in AMF were evident despite little difference in AMF species richness or community composition. Our findings suggest that differences in large herbivore communities over nearly two decades has resulted in localized, functional changes in AMF communities. Our results add to the accumulating evidence that mycorrhizae are locally adapted and that functional differences can evolve within small geographical areas.

Effects of vegetation management intensity on biodiversity and ecosystem services in vineyards: A meta-analysis

At the global scale, vineyards are usually managed intensively to optimize wine production without considering possible negative impacts on biodiversity and ecosystem services (ES) such as high soil erosion rates, degradation of soil fertility or contamination of groundwater. Winegrowers regulate competition for water and nutrients between the vines and inter‐row vegetation by tilling, mulching and/or herbicide application. Strategies for more sustainable viticulture recommend maintaining vegetation cover in inter‐rows, however, there is a lack of knowledge as to what extent this less intensive inter‐row management affects biodiversity and associated ES.

We performed a hierarchical meta‐analysis to quantify the effects of extensive vineyard inter‐row vegetation management in comparison to more intensive management (like soil tillage or herbicide use) on biodiversity and ES from 74 studies covering four continents and 13 wine‐producing countries.

Overall, extensive vegetation management increased above‐ and below‐ground biodiversity and ecosystem service provision by 20% in comparison to intensive management. Organic management together with management without herbicides showed a stronger positive effect on ES and biodiversity provision than inter‐row soil tillage.

Soil loss parameters showed the largest positive response to inter‐row vegetation cover. The second highest positive response was observed for biodiversity variables, followed by carbon sequestration, pest control and soil fertility. We found no trade‐off between grape yield and quality vs. biodiversity or other ES.

Synthesis and applications. Our meta‐analysis concludes that vegetation cover in inter‐rows contributes to biodiversity conservation and provides multiple ecosystem services. However, in drier climates grape yield might decrease without irrigation and careful vegetation management. Agri‐environmental policies should therefore focus on granting subsidies for the establishment of locally adapted diverse vegetation cover in vineyard inter‐rows. Future studies should focus on analysing the combined effects of local vineyard management and landscape composition and advance research in wine‐growing regions in Asia and in the southern hemisphere.

Our meta‐analysis concludes that vegetation cover in inter‐rows contributes to biodiversity conservation and provides multiple ecosystem services. However, in drier climates grape yield might decrease without irrigation and careful vegetation management. Agri‐environmental policies should therefore focus on granting subsidies for the establishment of locally adapted diverse vegetation cover in vineyard inter‐rows. Future studies should focus on analysing the combined effects of local vineyard management and landscape composition and advance research in wine‐growing regions in Asia and in the southern hemisphere.

Species diversity and drivers of arbuscular mycorrhizal fungal communities in a semi-arid mountain in China

Arbuscular mycorrhizal fungi (AMF) play an essential role in complex ecosystems. However, the species diversity and composition of AMF communities remain unclear in semi-arid mountains. Further, it is not well understood if the characteristics of AMF community assemblies differ for different habitat types, e.g., agricultural arable land, artificial forest land, natural grassland, and bush/wood land. Here, using the high-throughput technology by Illumina sequencing on the MiSeq platform, we explored the species diversity and composition of soil AMF communities among different habitat types in a semi-arid mountain (Taihang Mountain, Mid-western region of China). Then, we analyzed the effect of nutrient composition and soil texture on AMF community assembly. Our results showed that members of the Glomus genera were predominated in all soil types. The distance-based redundancy analysis indicated that the content of water, available phosphorus, and available potassium were the most crucial geochemical factors that significantly affected AMF communities (p < 0.05). The analysis of the soil texture confirmed that AMF diversity was negatively correlated with soil clay content. The comparison of AMF diversity among the various habitat types revealed that the artificial forest land had the lowest AMF diversity in comparison with other land types. Our findings suggest that there were differences in species diversity and composition of soil AMF communities among different habitat types. These findings shed new light on the characteristics of community structure and drivers of community assembly in AMF in semi-arid mountains, and point to the potential importance of different habitat types on AMF communities.

Agricultural practices to improve nitrogen use efficiency through the use of arbuscular mycorrhizae: Basic and agronomic aspects

Nitrogen cycling in agroecosystems is heavily dependent upon arbuscular mycorrhizal fungi (AMF) present in the soil microbiome. These fungi develop obligate symbioses with various host plant species, thus increasing their ability to acquire nutrients. However, AMF are particularly sensitive to physical, chemical and biological disturbances caused by human actions that limit their establishment. For a more sustainable agriculture, it will be necessary to further investigate which agricultural practices could be favorable to maximize the benefits of AMF to improve crop nitrogen use efficiency (NUE), thus reducing nitrogen (N) fertilizer usage. Direct seeding, mulch-based cropping systems prevent soil mycelium disruption and increase AMF propagule abundance. Such cropping systems lead to more efficient root colonization by AMF and thus a better establishment of the plant/fungal symbiosis. In addition, the use of continuous cover cropping systems can also enhance the formation of more efficient interconnected hyphal networks between mycorrhizae colonized plants. Taking into account both fundamental and agronomic aspects of mineral nutrition by plant/AMF symbioses, we have critically described, how improving fungal colonization through the reduction of soil perturbation and maintenance of an ecological balance could be helpful for increasing crop NUE.

High effectiveness of Rhizophagus irregularis is linked to superior modulation of antioxidant defence mechanisms in Cajanus cajan (L.) Millsp. genotypes grown under salinity stress

Salinity stress leads to the production of reactive oxygen species (ROS) which can cause oxidative damage in plants. A correlation between antioxidant capacity and salt tolerance has been demonstrated in several plant species, which may be enhanced by inoculation with arbuscular mycorrhizal fungi (AMF). However, plant responses to mycorrhization may differ depending on the host plant as well as AMF isolate. It has been proposed that AMF sourced from stressed environments may be better suited as stress ameliorators than non-native/exotic ones. The present study compared the effectiveness of a native inoculum from saline soil and two exotic single isolates, Funneliformis mossseae and Rhizophagus irregularis (single or dual mix), and associated their effectiveness with modulation of antioxidant defence, in two Cajanus cajan (pigeonpea) genotypes (salt sensitive-Paras, salt tolerant-Pusa 2002) under NaCl stress. Plants subjected to NaCl (0-100 mM) recorded a substantial build-up of ROS, more in Paras than Pusa 2002. Although mycorrhization with all AMF improved plant biomass and reduced oxidative burst by strengthening antioxidant enzymatic activities, inoculation with R. irregularis (alone or in combination with F. mosseae) resulted in higher biomass accumulation which correlated with its higher root colonization and improved redox stability through rapid recycling of reduced ascorbate and glutathione. The study thus suggested that mitigation of salt-induced oxidative burden by increased activation of scavenging antioxidants is an important mechanism that determined the higher effectiveness of R. irregularis over the native saline mix in pigeonpea plants.

Host-specific effects of soil microbial filtrates prevail over those of arbuscular mycorrhizae in a fragmented landscape

Plant-soil interactions have been shown to determine plant community composition in a wide range of environments. However, how plants distinctly interact with beneficial and detrimental organisms across mosaic landscapes containing fragmented habitats is still poorly understood. We experimentally tested feedback responses between plants and soil microbial communities from adjacent habitats across a disturbance gradient within a human-modified tropical montane landscape. In a greenhouse experiment, two components of soil microbial communities were amplified; arbuscular mycorrhizal fungi (AMF) and a filtrate excluding AMF spores from the soils of pastures (high disturbance), coffee plantations (intermediate disturbance), and forest fragments (low disturbance), using potted seedlings of 11 plant species common in these habitats (pasture grass, coffee, and nine native species). We then examined their effects on growth of these same 11 host species with reciprocal habitat inoculation. Most plant species received a similar benefit from AMF, but differed in their response to the filtrates from the three habitats. Soil filtrate from pastures had a net negative effect on plant growth, while filtrates from coffee plantations and forests had a net positive effect on plant growth. Pasture grass, coffee, and five pioneer tree species performed better with the filtrate from "away" (where these species rarely occur) compared to "home" (where these species typically occur) habitat soils, while four shade-tolerant tree species grew similarly with filtrates from different habitats. These results suggest that pastures accumulate species-specific soil enemies, while coffee plantations and forests accumulate beneficial soil microbes that benefit pioneer native plants and coffee, respectively. Thus, compared to AMF, soil filtrates exerted stronger habitat and host-specific effects on plants, being more important mediators of plant-soil feedbacks across contrasting habitats.

Long-term agricultural fertilization alters arbuscular mycorrhizal fungal community composition and barley (Hordeum vulgare) mycorrhizal carbon and phosphorus exchange

Agricultural fertilization significantly affects arbuscular mycorrhizal fungal (AMF) community composition. However, the functional implications of community shifts are unknown, limiting understanding of the role of AMF in agriculture. We assessed AMF community composition at four sites managed under the same nitrogen (N) and phosphorus (P) fertilizer regimes for 55 yr. We also established a glasshouse experiment with the same soils to investigate AMF-barley (Hordeum vulgare) nutrient exchange, using carbon (¹³ C) and ³³ P isotopic labelling. N fertilization affected AMF community composition, reducing diversity; P had no effect. In the glasshouse, AMF contribution to plant P declined with P fertilization, but was unaffected by N. Barley C allocation to AMF also declined with P fertilization. As N fertilization increased, C allocation to AMF per unit of P exchanged increased. This occurred with and without P fertilization, and was concomitant with reduced barley biomass. AMF community composition showed no relationship with glasshouse experiment results. The results indicate that plants can reduce C allocation to AMF in response to P fertilization. Under N fertilization, plants allocate an increasing amount of C to AMF and receive relatively less P. This suggests an alteration in the terms of P-C exchange under N fertilization regardless of soil P status.

Probiotic Diversity Enhances Rhizosphere Microbiome Function and Plant Disease Suppression

Bacterial communities associated with plant roots play an important role in the suppression of soil-borne pathogens, and multispecies probiotic consortia may enhance disease suppression efficacy. Here we introduced defined Pseudomonas species consortia into naturally complex microbial communities and measured the importance of Pseudomonas community diversity for their survival and the suppression of the bacterial plant pathogen Ralstonia solanacearum in the tomato rhizosphere microbiome. The survival of introduced Pseudomonas consortia increased with increasing diversity. Further, high Pseudomonas diversity reduced pathogen density in the rhizosphere and decreased the disease incidence due to both intensified resource competition and interference with the pathogen. These results provide novel mechanistic insights into elevated pathogen suppression by diverse probiotic consortia in naturally diverse plant rhizospheres. Ecologically based community assembly rules could thus play a key role in engineering functionally reliable microbiome applications.

The increasing demand for food supply requires more-efficient control of plant diseases. The use of probiotics, i.e., naturally occurring bacterial antagonists and competitors that suppress pathogens, has recently reemerged as a promising alternative to agrochemical use. It is, however, still unclear how many and which strains we should choose for constructing effective probiotic consortia. Here we present a general ecological framework for assembling effective probiotic communities based on in vitro characterization of community functioning. Specifically, we show that increasing the diversity of probiotic consortia enhances community survival in the naturally diverse rhizosphere microbiome, leading to increased pathogen suppression via intensified resource competition and interference with the pathogen. We propose that these ecological guidelines can be put to the test in microbiome engineering more widely in the future.

Field Trials Reveal Ecotype-Specific Responses to Mycorrhizal Inoculation in Rice

The overuse of agricultural chemicals such as fertilizer and pesticides aimed at increasing crop yield results in environmental damage, particularly in the Sahelian zone where soils are fragile. Crop inoculation with beneficial soil microbes appears as a good alternative for reducing agricultural chemical needs, especially for small farmers. This, however, requires selecting optimal combinations of crop varieties and beneficial microbes tested in field conditions. In this study, we investigated the response of rice plants to inoculation with arbuscular mycorrhizal fungi (AMF) and plant growth promoting bacteria (PGPB) under screenhouse and field conditions in two consecutive seasons in Senegal. Evaluation of single and mixed inoculations with AMF and PGPB was conducted on rice (Oryza sativa) variety Sahel 202, on sterile soil under screenhouse conditions. We observed that inoculated plants, especially plants treated with AMF, grew taller, matured earlier and had higher grain yield than the non-inoculated plants. Mixed inoculation trials with two AMF strains were then conducted under irrigated field conditions with four O. sativa varieties, two O. glaberrima varieties and two interspecific NERICA varieties, belonging to 3 ecotypes (upland, irrigated, and rainfed lowland). We observed that the upland varieties had the best responses to inoculation, especially with regards to grain yield, harvest index and spikelet fertility. These results show the potential of using AMF to improve rice production with less chemical fertilizers and present new opportunities for the genetic improvement in rice to transfer the ability of forming beneficial rice-microbe associations into high yielding varieties in order to increase further rice yield potentials.

Diversity of root-associated arbuscular mycorrhizal fungal communities in a rubber tree plantation chronosequence in Northeast Thailand

Rubber tree (Hevea brasiliensis) is of major economic importance in Southeast Asia and for small land holders in Thailand in particular. Due to the high value of latex, plantations are expanding into unsuitable areas, such as the northeast province of Thailand where soil fertility is very low and therefore appropriate management practices are of primary importance. Arbuscular mycorrhizal fungi (AMF) contribute to plant growth through a range of mechanisms and could play a key role in a more sustainable management of the rubber plantations. We described the diversity of AMF associated with rubber tree roots in Northeast Thailand in relation to tree age and soil parameters along a chronosequence of rubber tree plantations. Cassava fields were included for comparison. Rubber tree and cassava roots harbored high diversity of AMF (111 Virtual Taxa, VT), including 20 novel VT. AMF VT richness per sample was consistently high (per site mean 16 to 21 VT per sample) along the chronosequence and was not related to soil properties. The composition of AMF communities differed between cassava and rubber tree plantations and was influenced by soil texture and nutrient content (sand, K, P, Ca). AMF community composition gradually shifted with the age of the trees. Our results suggest that the high diversity of AMF in this region is potentially significant for maintaining high functionality of AMF communities.

Stressed out symbiotes: hypotheses for the influence of abiotic stress on arbuscular mycorrhizal fungi

Abiotic stress is a widespread threat to both plant and soil communities. Arbuscular mycorrhizal (AM) fungi can alleviate effects of abiotic stress by improving host plant stress tolerance, but the direct effects of abiotic stress on AM fungi are less well understood. We propose two hypotheses predicting how AM fungi will respond to abiotic stress. The stress exclusion hypothesis predicts that AM fungal abundance and diversity will decrease with persistent abiotic stress. The mycorrhizal stress adaptation hypothesis predicts that AM fungi will evolve in response to abiotic stress to maintain their fitness. We conclude that abiotic stress can have effects on AM fungi independent of the effects on the host plant. AM fungal communities will change in composition in response to abiotic stress, which may mean the loss of important individual species. This could alter feedbacks to the plant community and beyond. AM fungi will adapt to abiotic stress independent of their host plant. The adaptation of AM fungi to abiotic stress should allow the maintenance of the plant-AM fungal mutualism in the face of changing climates.

Roles of Arbuscular Mycorrhizal Fungi and Soil Abiotic Conditions in the Establishment of a Dry Grassland Community

BACKGROUND

The importance of soil biota in the composition of mature plant communities is commonly acknowledged. In contrast, the role of soil biota in the early establishment of new plant communities and their relative importance for soil abiotic conditions are still poorly understood.

AIMS AND METHODS

The aim of this study was to understand the effects of soil origin and soil fungal communities on the composition of a newly established dry grassland plant community. We used soil from two different origins (dry grassland and abandoned field) with different pH and nutrient and mineral content. Grassland microcosms were established by sowing seeds of 54 species of dry grassland plants into the studied soils. To suppress soil fungi, half of the pots were regularly treated with fungicide. In this way, we studied the independent and combined effects of soil origin and soil community on the establishment of dry grassland communities.

KEY RESULTS

The effect of suppressing the soil fungal community on the richness and composition of the plant communities was much stronger than the effect of soil origin. Contrary to our expectations, the effects of these two factors were largely additive, indicating the same degree of importance of soil fungal communities in the establishment of species-rich plant communities in the soils from both origins. The negative effect of suppressing soil fungi on species richness, however, occurred later in the soil from the abandoned field than in the soil from the grassland. This result likely occurred because the negative effects of the suppression of fungi in the field soil were caused mainly by changes in plant community composition and increased competition. In contrast, in the grassland soil, the absence of soil fungi was limiting for plants already at the early stages of their establishment, i.e., in the phases of germination and early recruitment. While fungicide affects not only arbuscular mycorrhizal fungi but also other biota, our data indicate that changes in the AMF communities are the most likely drivers of the observed changes. The effects of other soil biota, however, cannot be fully excluded.

CONCLUSIONS

These results suggest that the availability of soil fungi may not be the most important limiting factor for the establishment of grassland species in abandoned fields if we manage to reduce the intensity of competition at these sites e.g., by mowing or grazing.

Soil Functional Zone Management: A Vehicle for Enhancing Production and Soil Ecosystem Services in Row-Crop Agroecosystems

There is increasing global demand for food, bioenergy feedstocks and a wide variety of bio-based products. In response, agriculture has advanced production, but is increasingly depleting soil regulating and supporting ecosystem services. New production systems have emerged, such as no-tillage, that can enhance soil services but may limit yields. Moving forward, agricultural systems must reduce trade-offs between production and soil services. Soil functional zone management (SFZM) is a novel strategy for developing sustainable production systems that attempts to integrate the benefits of conventional, intensive agriculture, and no-tillage. SFZM creates distinct functional zones within crop row and inter-row spaces. By incorporating decimeter-scale spatial and temporal heterogeneity, SFZM attempts to foster greater soil biodiversity and integrate complementary soil processes at the sub-field level. Such integration maximizes soil services by creating zones of 'active turnover', optimized for crop growth and yield (provisioning services); and adjacent zones of 'soil building', that promote soil structure development, carbon storage, and moisture regulation (regulating and supporting services). These zones allow SFZM to secure existing agricultural productivity while avoiding or minimizing trade-offs with soil ecosystem services. Moreover, the specific properties of SFZM may enable sustainable increases in provisioning services via temporal intensification (expanding the portion of the year during which harvestable crops are grown). We present a conceptual model of 'virtuous cycles', illustrating how increases in crop yields within SFZM systems could create self-reinforcing feedback processes with desirable effects, including mitigation of trade-offs between yield maximization and soil ecosystem services. Through the creation of functionally distinct but interacting zones, SFZM may provide a vehicle for optimizing the delivery of multiple goods and services in agricultural systems, allowing sustainable temporal intensification while protecting and enhancing soil functioning.

Evidence for functional redundancy in arbuscular mycorrhizal fungi and implications for agroecosystem management

Arbuscular mycorrhizal (AM) fungi provide benefits to host plants and show functional diversity, with evidence of functional trait conservation at the family level. Diverse communities of AM fungi ought therefore to provide increased benefits to the host, with implications for the management of sustainable agroecosystems. However, this is often not evident in the literature, with diversity saturation at low species number. Growth and nutrient uptake were measured in onions in the glasshouse on AM-free phosphorus (P)-poor soil, inoculated with between one and seven species of AM fungi in all possible combinations. Inoculation with AM fungi increased shoot dry weight as well as P and copper concentrations in shoots but reduced the concentration of potassium and sulphur. There was little evidence of increased benefit from high AM fungal diversity, and increasing diversity beyond three species did not result in significantly higher shoot weight or P or Cu concentrations. Species of Glomeraceae had the greatest impact on growth and nutrient uptake, while species of Acaulospora and Racocetra did not have a significant impact. Failure to show a benefit from high AM fungal diversity in this and other studies may be the result of experimental conditions, with the benefits of AM fungal diversity only becoming apparent when the host plant is faced with multiple stress factors. Replicating the complex interactions between AM fungi, the host plant and their environment in the laboratory in order to fully understand these interactions is a major challenge to AM research.

Cooperation through Competition-Dynamics and Microeconomics of a Minimal Nutrient Trade System in Arbuscular Mycorrhizal Symbiosis

In arbuscular mycorrhizal (AM) symbiosis, fungi and plants exchange nutrients (sugars and phosphate, for instance) for reciprocal benefit. Until now it is not clear how this nutrient exchange system works. Here, we used computational cell biology to simulate the dynamics of a network of proton pumps and proton-coupled transporters that are upregulated during AM formation. We show that this minimal network is sufficient to describe accurately and realistically the nutrient trade system. By applying basic principles of microeconomics, we link the biophysics of transmembrane nutrient transport with the ecology of organismic interactions and straightforwardly explain macroscopic scenarios of the relations between plant and AM fungus. This computational cell biology study allows drawing far reaching hypotheses about the mechanism and the regulation of nutrient exchange and proposes that the "cooperation" between plant and fungus can be in fact the result of a competition between both for the same resources in the tiny periarbuscular space. The minimal model presented here may serve as benchmark to evaluate in future the performance of more complex models of AM nutrient exchange. As a first step toward this goal, we included SWEET sugar transporters in the model and show that their co-occurrence with proton-coupled sugar transporters results in a futile carbon cycle at the plant plasma membrane proposing that two different pathways for the same substrate should not be active at the same time.

Arbuscular mycorrhizal fungal communities and Rhizophagus irregularis populations shift in response to short-term ploughing and fertilisation in a buffer strip

Short-term effects of soil physical disturbance by ploughing and nitrogen and phosphate fertilisation on arbuscular mycorrhizal fungal (AMF) communities and on intraspecific populations of Rhizophagus irregularis in a buffer strip surrounded by arable fields were studied. Pre-grown Plantago lanceolata plantlets were transplanted into fertilised and/or ploughed experimental plots. After 3 months, the glomeromycotan communities in the roots of these trap plants were analysed using 454 pyrosequencing of a fragment of the RNA polymerase II gene (RPB1). Intraspecific populations of R. irregularis were studied by restriction fragment length polymorphism (RFLP) analysis of the mitochondrial large ribosomal subunit (mtLSU) gene. Soil disturbance significantly increased the diversity of species-level molecular taxa (MTs) and altered community structure, whilst fertilisation alone had no significant effect, unless coupled with ploughing. At the population level, the expected shift from genotypes of R. irregularis typically found in grasslands to those usually found in arable sites was only partially observed. In conclusion, in the short-term, physical soil disturbance, as well as nitrogen fertilisation when coupled with physical soil disturbance, affected AMF community and to a smaller extent population composition.

Spatial soil heterogeneity has a greater effect on symbiotic arbuscular mycorrhizal fungal communities and plant growth than genetic modification with Bacillus thuringiensis toxin genes

Maize, genetically modified with the insect toxin genes of Bacillus thuringiensis (Bt), is widely cultivated, yet its impacts on soil organisms are poorly understood. Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with plant roots and may be uniquely sensitive to genetic changes within a plant host. In this field study, the effects of nine different lines of Bt maize and their corresponding non-Bt parental isolines were evaluated on AMF colonization and community diversity in plant roots. Plants were harvested 60 days after sowing, and data were collected on plant growth and per cent AMF colonization of roots. AMF community composition in roots was assessed using 454 pyrosequencing of the 28S rRNA genes, and spatial variation in mycorrhizal communities within replicated experimental field plots was examined. Growth responses, per cent AMF colonization of roots and AMF community diversity in roots did not differ between Bt and non-Bt maize, but root and shoot biomass and per cent colonization by arbuscules varied by maize cultivar. Plot identity had the most significant effect on plant growth, AMF colonization and AMF community composition in roots, indicating spatial heterogeneity in the field. Mycorrhizal fungal communities in maize roots were autocorrelated within approximately 1 m, but at greater distances, AMF community composition of roots differed between plants. Our findings indicate that spatial variation and heterogeneity in the field has a greater effect on the structure of AMF communities than host plant cultivar or modification by Bt toxin genes.

Partner selection in the mycorrhizal mutualism

Partner selection in the mycorrhizal symbiosis is thought to be a key factor stabilising the mutualism. Both plant hosts and mycorrhizal fungi have been shown to preferentially allocate resources to higher quality partners. This can help maintain underground cooperation, although it is likely that different plant species vary in the spatial precision with which they can select partners. Partner selection in the mycorrhizal symbiosis is presumably context-dependent and can be mediated by factors like (relative) resource abundance and resource fluctuations, competition among mycorrhizas, arrival order and cultivation history. Such factors complicate our current understanding of the importance of partner selection and its effectiveness in stimulating mutualistic cooperation.

Decrease in diversity and changes in community composition of arbuscular mycorrhizal fungi in roots of apple trees with increasing orchard management intensity across a regional scale

Understanding which factors drive the diversity and community composition of arbuscular mycorrhizal fungi (AMF) is important due to the role of these soil micro-organisms in ecosystem functioning and current environmental threats to AMF biodiversity. Additionally, in agro-ecosystems, this knowledge may help to evaluate their use in making agriculture more sustainable. Here, we used 454-pyrosequencing of small subunit rRNA gene amplicons to quantify AMF diversity and community composition in the roots of cultivated apple trees across 24 orchards in central Belgium. We aimed at identifying the factors (soil chemical variables, organic vs. conventional farming, and geographical location) that affect AMF diversity and community composition. In total, 110 AMF OTUs were detected, of which the majority belonged to the Glomeraceae (73%) and the Claroideoglomeraceae (19%). We show that soil characteristics and farming system, rather than the geographical location of the orchards, shape AMF communities on apple trees. Particularly, plant-available P content of the soil was associated with lower AMF diversity. In orchards with a lower plant-available P content of the soil (P < 100 mg/kg soil), we also found a significantly higher AMF diversity in organically managed orchards as compared to conventionally managed orchards. Finally, the degree of nestedness of the AMF communities was related to plant-available P and N content of the soil, pointing at a progressive loss of AMF taxa with increasing fertilization. Overall, we conclude that a combination of organic orchard management and moderate fertilization may preserve diverse AMF communities on apple trees and that AMF in the roots of apple trees appear not to be dispersal limited at the scale of central Belgium.

The largest subunit of RNA polymerase II as a new marker gene to study assemblages of arbuscular mycorrhizal fungi in the field

Due to the potential of arbuscular mycorrhizal fungi (AMF, Glomeromycota) to improve plant growth and soil quality, the influence of agricultural practice on their diversity continues to be an important research question. Up to now studies of community diversity in AMF have exclusively been based on nuclear ribosomal gene regions, which in AMF show high intra-organism polymorphism, seriously complicating interpretation of these data. We designed specific PCR primers for 454 sequencing of a region of the largest subunit of RNA polymerase II gene, and established a new reference dataset comprising all major AMF lineages. This gene is known to be monomorphic within fungal isolates but shows an excellent barcode gap between species. We designed a primer set to amplify all known lineages of AMF and demonstrated its applicability in combination with high-throughput sequencing in a long-term tillage experiment. The PCR primers showed a specificity of 99.94% for glomeromycotan sequences. We found evidence of significant shifts of the AMF communities caused by soil management and showed that tillage effects on different AMF taxa are clearly more complex than previously thought. The high resolving power of high-throughput sequencing highlights the need for quantitative measurements to efficiently detect these effects.

Is root DNA a reliable proxy to assess arbuscular mycorrhizal community structure?

Arbuscular mycorrhizal (AM) fungi are widespread plant symbionts that extensively colonize both soil and roots. Given their influence on ecosystem processes, such as plant growth, soil carbon storage, and nutrient cycling, there is great interest in understanding the drivers of their community structure. AM fungal communities are increasingly characterized by selectively amplifying their DNA from plant roots, thus assuming that AM fungal community structure within roots provides a reliable portrait of the total (i.e., soil + roots) community. Through numerical simulations, we test this assumption using published data. We show that community structure and diversity is well preserved when analyzing only a subset of the community biomass (i.e., roots or soil), provided that the community shows a typical skewed abundance distribution, with few very dominant species and a high prevalence of rare species. Given that this community structure has been shown to be common in natural AM fungal communities, the present work would suggest that characterizing AM fungal communities using only roots or soil can provide a reliable portrait of the overall community. However, we show through additional analyses that the proportion of sample biomass used for molecular methods must be over a minimal threshold to properly characterize the community. Using published molecular data sets, we validate those results, which suggest that typical molecular protocols using low amounts of biomass may strongly influence AM fungal community characterization. Finally, we also discuss other assumptions implied by the molecular analysis of AM fungal communities, and point out urgent knowledge gaps.

Inclusive fitness in agriculture

Trade-offs between individual fitness and the collective performance of crop and below-ground symbiont communities are common in agriculture. Plant competitiveness for light and soil resources is key to individual fitness, but higher investments in stems and roots by a plant community to compete for those resources ultimately reduce crop yields. Similarly, rhizobia and mycorrhizal fungi may increase their individual fitness by diverting resources to their own reproduction, even if they could have benefited collectively by providing their shared crop host with more nitrogen and phosphorus, respectively. Past selection for inclusive fitness (benefits to others, weighted by their relatedness) is unlikely to have favoured community performance over individual fitness. The limited evidence for kin recognition in plants and microbes changes this conclusion only slightly. We therefore argue that there is still ample opportunity for human-imposed selection to improve cooperation among crop plants and their symbionts so that they use limited resources more efficiently. This evolutionarily informed approach will require a better understanding of how interactions among crops, and interactions with their symbionts, affected their inclusive fitness in the past and what that implies for current interactions.

Evolution of microbial markets

Biological market theory has been used successfully to explain cooperative behavior in many animal species. Microbes also engage in cooperative behaviors, both with hosts and other microbes, that can be described in economic terms. However, a market approach is not traditionally used to analyze these interactions. Here, we extend the biological market framework to ask whether this theory is of use to evolutionary biologists studying microbes. We consider six economic strategies used by microbes to optimize their success in markets. We argue that an economic market framework is a useful tool to generate specific and interesting predictions about microbial interactions, including the evolution of partner discrimination, hoarding strategies, specialized versus diversified mutualistic services, and the role of spatial structures, such as flocks and consortia. There is untapped potential for studying the evolutionary dynamics of microbial systems. Market theory can help structure this potential by characterizing strategic investment of microbes across a diversity of conditions.

Agricultural practices indirectly influence plant productivity and ecosystem services through effects on soil biota

It is well established that agricultural practices alter the composition and diversity of soil microbial communities. However, the impact of changing soil microbial communities on the functioning of the agroecosystems is still poorly understood. Earlier work showed that soil tillage drastically altered microbial community composition. Here we tested, using an experimental grassland (Lolium, Trifolium, Plantago) as a model system, whether soil microbial communities from conventionally tilled (CT) and non-tilled (NT) soils have different influences on plant productivity and nutrient acquisition. We specifically focus on arbuscular mycorrhizal fungi (AMF), as they are a group of beneficial soil fungi that can promote plant productivity and ecosystem functioning and are also strongly affected by tillage management. Soil microbial communities from CT and NT soils varied greatly in their effects on the grassland communities. Communities from CT soil increased overall biomass production more than soil communities from NT soil. This effect was mainly due to a significant growth promotion of Trifolium by CT microorganisms. In contrast to CT soil inoculum, NT soil inoculum increased plant phosphorus concentration and total plant P content, demonstrating that the soil microbial communities from NT fields enhance P uptake. Differences in AM fungal community composition resulting, for instance, in twofold greater hyphal length in NT soil communities when compared to CT, are the most likely explanation for the different plant responses to CT and NT soil inocula. A range of field studies have shown that plant P uptake increases when farmers change to conservation tillage or direct seeding. Our results indicate that this enhanced P uptake results from enhanced hyphal length and an altered AM fungal community. Our results further demonstrate that agricultural management practices indirectly influence ecosystem services and plant community structure through effects on soil biota.

Sustainable agriculture: possible trajectories from mutualistic symbiosis and plant neodomestication

Food demand will increase concomitantly with human population. Food production therefore needs to be high enough and, at the same time, minimize damage to the environment. This equation cannot be solved with current strategies. Based on recent findings, new trajectories for agriculture and plant breeding which take into account the belowground compartment and evolution of mutualistic strategy, are proposed in this opinion article. In this context, we argue that plant breeders have the opportunity to make use of native arbuscular mycorrhizal (AM) symbiosis in an innovative ecologically intensive agriculture.