Colonization and community structure of arbuscular mycorrhizal fungi in maize roots at different depths in the soil profile respond differently to phosphorus inputs on a long-term experimental site

Oilseed flax cultivation: optimizing phosphorus use for enhanced growth and soil health

Introduction

Oilseed flax (Linum usitatissimum L.) yields are phosphate (P) fertilizer-limited, especially in the temperate semiarid dryland regions of North China. However, there are limited studies on the effects of P-fertilizer inputs on plant growth and soil microorganisms in flax planting systems.

Methods

To address this gap, a field experiment was conducted with four treatments: no P addition and application of 40, 80, and 120 kg P ha-¹, respectively. The aim was to investigate the influence of various P fertilizer inputs on yield, plant dry matter, P use efficiency, as well as the population of soil arbuscular mycorrhizal fungi (AMF) and bacteria in dryland oilseed flax.

Results

Our results show that the P addition increased the dry matter, and the yield of oilseed increased by ~200% at 120 kg P ha-1 addition with inhibition on the growth of AMF hyphae. The moderate P supply (80 kg ha-1) was adequate for promoting P translocation, P use efficiency, and P recovery efficiency. Soil pH, available P, and available K significantly (p< 0.05) promoted the abundance of the dominant taxa (Acidobacteria_GP6, Sphingobacteria and Bacteroidetes). In addition, it is imperative to comprehend the mechanism of interaction between phosphorus-fertilizer inputs and microbiota in oilseed flax soil.

Discussion

This necessitates further research to quantify and optimize the moderate phosphorus supply, regulate soil microbes to ensure high phosphorus utilization, and ultimately establish a sustainable system for oilseed flax cultivation in the local area.

Effect of AMF Inoculation on Reducing Excessive Fertilizer Use

Excessive use of chemical fertilizer is a global concern. Arbuscular mycorrhizal fungi (AMF) are considered a potential solution due to their symbiotic association with crops. This study assessed AMF's effects on maize yield, fertilizer efficiency, plant traits, and soil nutrients under different reduced-fertilizer regimes in medium-low fertility fields. We found that phosphorus supplementation after a 30% fertilizer reduction enhanced AMF's positive impact on grain yield, increasing it by 3.47% with pure chemical fertilizers and 6.65% with mixed fertilizers. The AMF inoculation did not significantly affect the nitrogen and phosphorus fertilizer use efficiency, but significantly increased root colonization and soil mycelium density. Mixed fertilizer treatments with phosphorus supplementation after fertilizer reduction showed greater mycorrhizal effects on plant traits and soil nutrient contents compared to chemical fertilizer treatments. This study highlights that AMF inoculation, closely linked to fertilization regimes, can effectively reduce fertilizer use while sustaining or enhancing maize yields.

Prairie restoration promotes the abundance and diversity of mutualistic arbuscular mycorrhizal fungi

Predicting how biological communities assemble in restored ecosystems can assist in conservation efforts, but most research has focused on plants, with relatively little attention paid to soil microbial organisms that plants interact with. Arbuscular mycorrhizal (AM) fungi are an ecologically significant functional group of soil microbes that form mutualistic symbioses with plants and could therefore respond positively to plant community restoration. To evaluate the effects of plant community restoration on AM fungi, we compared AM fungal abundance, species richness, and community composition of five annually cultivated, conventionally managed agricultural fields with paired adjacent retired agricultural fields that had undergone prairie restoration 5-9 years prior to sampling. We hypothesized that restoration stimulates AM fungal abundance and species richness, particularly for disturbance-sensitive taxa, and that gains of new taxa would not displace AM fungal species present prior to restoration due to legacy effects. AM fungal abundance was quantified by measuring soil spore density and root colonization. AM fungal species richness and community composition were determined in soils and plant roots using DNA high-throughput sequencing. Soil spore density was 2.3 times higher in restored prairies compared to agricultural fields, but AM fungal root colonization did not differ between land use types. AM fungal species richness was 2.7 and 1.4 times higher in restored prairies versus agricultural fields for soil and roots, respectively. The abundance of Glomeraceae, a disturbance-tolerant family, decreased by 25% from agricultural to restored prairie soils but did not differ in plant roots. The abundance of Claroideoglomeraceae and Diversisporaceae, both disturbance-sensitive families, was 4.6 and 3.2 times higher in restored prairie versus agricultural soils, respectively. Species turnover was higher than expected relative to a null model, indicating that AM fungal species were gained by replacement. Our findings demonstrate that restoration can promote a relatively rapid increase in the abundance and diversity of soil microbial communities that had been degraded by decades of intensive land use, and community compositional change can be predicted by the disturbance tolerance of soil microbial taxonomic and functional groups.

Effect of Rootstock Genotype and Arbuscular Mycorrhizal Fungal (AMF) Species on Early Colonization of Apple

The effect of plant cultivar on the degree of mycorrhization and the benefits mediated by arbuscular mycorrhizal fungi (AMF) have been documented in many crops. In apple, a wide variety of rootstocks are commercially available; however, it is not clear whether some rootstock genotypes are more susceptible to mycorrhization than others and/or whether AMF species identity influences rootstock compatibility. This study addresses these questions by directly testing the ability/efficacy of four different AMF species (Rhizophagus irregularis, Septoglomus deserticola, Claroideoglomus claroideum or Claroideoglomus etunicatum) to colonize a variety of commercially available Geneva apple rootstock genotypes (G.11, G.41, G.210, G.969, and G.890). Briefly, micropropagated plantlets were inoculated with individual species of AMF or were not inoculated. The effects of the rootstock genotype/AMF interaction on mycorrhization, plant growth, and/or leaf nutrient concentrations were assessed. We found that both rootstock genotype and the identity of the AMF are significant sources of variation affecting the percentage of colonization. However, these factors largely operate independently in terms of the extent of root colonization. Among the AMF tested, C. etunicatum and R. irregularis represented the most compatible fungal partners, regardless of apple rootstock genotype. Among the rootstocks tested, semi-dwarfing rootstocks appeared to have an advantage over dwarfing rootstocks in regard to establishing and maintaining associations with AMF. Nutrient uptake and plant growth outcomes were also influenced in a rootstock genotype/AMF species-specific manner. Our findings suggest that matching host genetics with compatible AMF species has the potential to enhance agricultural practices in nursery and orchard systems.

Effects of Humic Substances and Mycorrhizal Fungi on Drought-Stressed Cactus: Focus on Growth, Physiology, and Biochemistry

Utilizing water resources rationally has become critical due to the expected increase in water scarcity. Cacti are capable of surviving with minimal water requirements and in poor soils. Despite being highly drought-resistant, cacti still faces limitations in realizing its full potential under drought-stress conditions. To this end, we investigated the interactive effect of humic substances (Hs) and arbuscular mycorrhizal fungi (AMF) on cactus plants under drought stress. In the study, a cactus pot experiment had three irrigation levels (W1: no irrigation, W2: 15% of field capacity, and W3: 30% of field capacity) and two biostimulants (Hs soil amendment and AMF inoculation), applied alone or combined. The findings show that the W1 and W2 regimes affected cactus performance. However, Hs and/or AMF significantly improved growth. Our results revealed that drought increased the generation of reactive oxygen species. However, Hs and/or AMF application improved nutrient uptake and increased anthocyanin content and free amino acids. Furthermore, the soil's organic matter, phosphorus, nitrogen, and potassium contents were improved by the application of these biostimulants. Altogether, using Hs alone or in combination with AMF can be an effective and sustainable approach to enhance the tolerance of cactus plants to drought conditions, while also improving the soil quality.

Niche differentiation of Mucoromycotinian and Glomeromycotinian arbuscular mycorrhizal fungi along a 2-million-year soil chronosequence

Current literature suggests ecological niche differentiation between co-occurring Mucoromycotinian arbuscular mycorrhizal fungi (M-AMF) and Glomeromycotinian AMF (G-AMF), but experimental evidence is limited. We investigated the influence of soil age, water availability (wet and dry), and plant species (native Microlaena stipoides and exotic Trifolium subterraneum) on anatomical root colonisation and DNA profiles of M-AMF and G-AMF under glasshouse conditions. We grew seedlings of each species in soils collected from the four stages of a soil chronosequence, where pH decreases from the youngest to oldest stages, and phosphorus (P) is low in the youngest and oldest, but high in the intermediate stages. We scored the percentage of root length colonised and used DNA metabarcoding to profile fungal richness and community composition associated with treatment combinations. Soil age, water availability, and plant species were important influencers of root colonisation, although no M-AMF were visible following staining of M. stipoides roots. Soil age and host plant influenced fungal richness and community composition. However, response to soil age, potential host species, and water availability differed between M-AMF and G-AMF. Root colonisation of T. subterraneum by M-AMF and G-AMF was inversely correlated with soil P level. Community composition of M-AMF and G-AMF was structured by soil age and, to a lesser extent, plant species. Richness of M-AMF and G-AMF was negatively, and positively, correlated with available P, respectively. These findings are experimental evidence of ecological niche differentiation of M-AMF and G-AMF and invite further exploration into interactive effects of abiotic and biotic factors on their communities along successional trajectories.

A transcriptional activator from Rhizophagus irregularis regulates phosphate uptake and homeostasis in AM symbiosis during phosphorous starvation

Introduction

Phosphorus (P) is one of the most important nutrient elements for plant growth and development. Under P starvation, arbuscular mycorrhizal (AM) fungi can promote phosphate (Pi) uptake and homeostasis within host plants. However, the underlying mechanisms by which AM fungal symbiont regulates the AM symbiotic Pi acquisition from soil under P starvation are largely unknown. Here, we identify a HLH domain containing transcription factor RiPho4 from Rhizophagus irregularis.

Methods

To investigate the biological functions of the RiPho4, we combined the subcellular localization and Yeast One-Hybrid (Y1H) experiments in yeasts with gene expression and virus-induced gene silencing approach during AM symbiosis.

Results

The approach during AM symbiosis. The results indicated that RiPho4 encodes a conserved transcription factor among different fungi and is induced during the in planta phase. The transcription of RiPho4 is significantly up-regulated by P starvation. The subcellular localization analysis revealed that RiPho4 is located in the nuclei of yeast cells during P starvation. Moreover, knock-down of RiPho4 inhibits the arbuscule development and mycorrhizal Pi uptake under low Pi conditions. Importantly, RiPho4 can positively regulate the downstream components of the phosphate (PHO) pathway in R. irregularis.

Discussion

In summary, these new findings reveal that RiPho4 acts as a transcriptional activator in AM fungus to maintain arbuscule development and regulate Pi uptake and homeostasis in the AM symbiosis during Pi starvation.

Response of the wheat mycobiota to flooding revealed substantial shifts towards plant pathogens

Rainfall extremes are intensifying as a result of climate change, leading to increased flood risk. Flooding affects above- and belowground ecosystem processes, representing a substantial threat to crop productivity under climate change. Plant-associated fungi play important roles in plant performance, but their response to abnormal rain events is unresolved. Here, we established a glasshouse experiment to determine the effects of flooding stress on the spring wheat-mycobiota complex. Since plant phenology could be an important factor in the response to hydrological stress, flooding was induced only once and at different plant growth stages, such as tillering, booting and flowering. We assessed the wheat mycobiota response to flooding in three soil-plant compartments (phyllosphere, roots and rhizosphere) using metabarcoding. Key soil and plant traits were measured to correlate physiological plant and edaphic changes with shifts in mycobiota structure and functional guilds. Flooding reduced plant fitness, and caused dramatic shifts in mycobiota assembly across the entire plant. Notably, we observed a functional transition consisting of a decline in mutualist abundance and richness with a concomitant increase in plant pathogens. Indeed, fungal pathogens associated with important cereal diseases, such as Gibberella intricans, Mycosphaerella graminicola, Typhula incarnata and Olpidium brassicae significantly increased their abundance under flooding. Overall, our study demonstrate the detrimental effect of flooding on the wheat mycobiota complex, highlighting the urgent need to understand how climate change-associated abiotic stressors alter plant-microbe interactions in cereal crops.

SlSPX1-SlPHR complexes mediate the suppression of arbuscular mycorrhizal symbiosis by phosphate repletion in tomato

Forming mutualistic symbioses with arbuscular mycorrhizae (AMs) improves the acquisition of mineral nutrients for most terrestrial plants. However, the formation of AM symbiosis usually occurs under phosphate (Pi)-deficient conditions. Here, we identify SlSPX1 (SYG1 (suppressor of yeast GPA1)/Pho81(phosphate 81)/XPR1 (xenotropic and polytropic retrovirus receptor 1) as the major repressor of the AM symbiosis in tomato (Solanum lycopersicum) under phosphate-replete conditions. Loss of SlSPX1 function promotes direct Pi uptake and enhances AM colonization under phosphate-replete conditions. We determine that SlSPX1 integrates Pi signaling and AM symbiosis by directly interacting with a set of arbuscule-induced SlPHR proteins (SlPHR1, SlPHR4, SlPHR10, SlPHR11, and SlPHR12). The association with SlSPX1 represses the ability of SlPHR proteins to activate AM marker genes required for the arbuscular mycorrhizal symbiosis. SlPHR proteins exhibit functional redundancy, and no defective AM symbiosis was detected in the single mutant of SlPHR proteins. However, silencing SlPHR4 in the Slphr1 mutant background led to reduced AM colonization. Therefore, our results support the conclusion that SlSPX1-SlPHRs form a Pi-sensing module to coordinate the AM symbiosis under different Pi-availability conditions.

Zinc nutrition and arbuscular mycorrhizal symbiosis effects on maize (Zea mays L.) growth and productivity

Zinc (Zn) is an essential micronutrient required to enhance crop growth and yield. In the arid – semiarid region, Zn deficiency is expected due to alkaline calcareous soil. Contrarily, Zn toxicity is also becoming an environmental concern due to increasing anthropogenic activities (metal smelting, copper industry, etc.). Therefore, balanced Zn application is necessary to save resources and achieve optimum crop growth and yield. Most scientists suggest biological approaches to overcome the problem of Zn toxicity and deficiency. These biological approaches are mostly environment-friendly and cost-effective. In these biological approaches, the use of arbuscular mycorrhizae fungi (AMF) symbiosis is becoming popular. It can provide tolerance to the host plant against Zn-induced stress. Inoculation of AMF helps in balance uptake of Zn and enhances the growth and yield of crops. On the other hand, maize (Zea mays L.) is an important cereal crop due to its multifarious uses. As maize is an effective host for mycorrhizae symbiosis, that’s why this review was written to elaborate on the beneficial role of arbuscular mycorrhizal fungi (AMF). The review aimed to glance at the recent advances in the use of AMF to enhance nutrient uptake, especially Zn. It was also aimed to discuss the mechanism of AMF to overcome the toxic effect of Zn. We have also discussed the detailed mechanism and physiological improvement in the maize plant. In conclusion, AMF can play an imperative role in improving maize growth, yield, and balance uptake of Zn by alleviating Zn stress and mitigating its toxicity.

Towards sustainable agriculture: rhizosphere microbiome engineering

Soil microbiomes are extremely complex, with dense networks of interconnected microbial species underpinning vital functions for the ecosystem. In advanced agricultural research, rhizosphere microbiome engineering is gaining much attention, as the microbial community has been acknowledged to be a crucial partner of associated plants for their health fitness and yield. However, single or combined effects of a wide range of soil biotic and abiotic factors impact the success of engineered microbiomes, as these microbial communities exhibit uneven structural and functional networks in diverse soil conditions. Therefore, once a deep understanding of major influential factors and corresponding microbial responses is developed, the microbiome can be more effectively manipulated and optimized for cropping benefits. In this mini-review, we propose the concept of a microbiome-mediated smart agriculture system (MiMSAS). We summarize some of the advanced strategies for engineering the rhizosphere microbiome to withstand the stresses imposed by dominant abiotic and biotic factors. This work will help the scientific community gain more clarity about engineered microbiome technologies for increasing crop productivity and environmental sustainability.Key points• Individual or combined effects of soil biotic and abiotic variables hamper the implementation of engineered microbiome technologies in the field.• As a traditional approach, reduced-tillage practices coinciding with biofertilization can promote a relatively stable functional microbiome.• Increasing the complexity and efficiency of the synthetic microbiome is one way to improve its field-application success rate.• Plant genome editing/engineering is a promising approach for recruiting desired microbiomes for agricultural benefit.

It takes three to tango: the importance of microbes, host plant, and soil management to elucidate manipulation strategies for the plant microbiome

The world’s population is expected to grow to almost 10 billion by 2050, placing unprecedented demands on agriculture and natural resources. The risk in food security is also aggravated by climate change and land degradation, which compromise agricultural productivity. In recent years, our understanding of the role of microbial communities on ecosystem functioning, including plant-associated microbes, has advanced considerably. Yet, translating this knowledge into practical agricultural technologies is challenged by the intrinsic complexity of agroecosystems. Here, we review current strategies for plant microbiome manipulation, classifying them into three main pillars: (i) introducing and engineering microbiomes, (ii) breeding and engineering the host plant, and (iii) selecting agricultural practices that enhance resident soil and plant-associated microbial communities. In each of these areas, we analyze current trends in research, as well as research priorities and future perspectives.

Impact of Phosphorus Fertilization on Tomato Growth and Arbuscular Mycorrhizal Fungal Communities

Understanding the impact of phosphorus (P) addition on arbuscular mycorrhizal fungi (AMF) is crucial to understanding tomato (Solanum lycopersicum L.) P nutrition. However, it remains unknown how P fertilization is associated with the structure of AMF communities on tomato plants. Thus, we investigated whether levels of P fertilizer interacted with the colonization and structure of AMF in tomato roots in a field trial. In this study, we established three different amounts of P fertilizer treatments (0 kg ha-1, 50 kg ha-1, and 100 kg ha-1). We investigated AMF root colonization and community structure, as well as plant growth in tomatoes at seven weeks following transplantation. The structure of the AMF communities in the roots of tomato were determined by MiSeq amplicon sequencing. As expected, P fertilizer input enhanced the P uptake and plant biomass. In contrast, the P fertilizer level did not affect the AMF root colonization and diversity or the structure of the AMF communities in the tomato. However, we found a negative correlation between AMF colonization and richness in the roots of the tomato plants. Therefore, we need to investigate whether and how AMF communities and P fertilization develop more effective P management for tomato plants.

Depth structures the community of arbuscular mycorrhizal fungi amplified from grapevine (Vitis vinifera L.) roots

The diversity of arbuscular mycorrhizal fungi (AMF) associating with grapevines has been determined previously, yet little is known of how the community in roots is shaped by depth in the soil or where roots occur in different management zones of the vineyard (vine row versus alley). The influence of depth, management zone, and time of year on the community of AMF in grape roots was examined. I also tested the potential influence of the alley vegetation on AMF in grapevines by comparing the taxa amplified from roots of other plants retrieved from the alley surface soil to those from grapevines growing in the same zone. Depth shaped the AMF community in grapevine roots more than the management zone based on dissimilarity among all grapevine samples. Time of the growing season did not, although AMF taxa richness was greater in grapevine roots collected in late summer (veraison) than it was in late spring (bloom). The number of abundant AMF taxa in grapevine roots from the uppermost soil depth in the vine row was substantially lower in late spring than in late summer, and this was related to high soil nitrate in late spring. The alley vegetation comprised primarily grass, and clover plants harbored a different AMF community in roots than did intermingled grapevine roots. The change in the AMF community in a single perennial host (grape) that occurred with depth in this study resulted from a shift among common taxa as opposed to the appearance of unique taxa in the subsoil.

Subsoil Arbuscular Mycorrhizal Fungi for Sustainability and Climate-Smart Agriculture: A Solution Right Under Our Feet?

With growing populations and climate change, assuring food and nutrition security is an increasingly challenging task. Climate-smart and sustainable agriculture, that is, conceiving agriculture to be resistant and resilient to a changing climate while keeping it viable in the long term, is probably the best solution. The role of soil biota and particularly arbuscular mycorrhizal (AM) fungi in this new agriculture is believed to be of paramount importance. However, the large nutrient pools and the microbiota of subsoils are rarely considered in the equation. Here we explore the potential contributions of subsoil AM fungi to a reduced and more efficient fertilization, carbon sequestration, and reduction of greenhouse gas emissions in agriculture. We discuss the use of crop rotations and cover cropping with deep rooting mycorrhizal plants, and low-disturbance management, as means of fostering subsoil AM communities. Finally, we suggest future research goals that would allow us to maximize these benefits.

Cover cropping can be a stronger determinant than host crop identity for arbuscular mycorrhizal fungal communities colonizing maize and soybean

Background

Understanding the role of communities of arbuscular mycorrhizal fungi (AMF) in agricultural systems is imperative for enhancing crop production. The key variables influencing change in AMF communities are the type of cover crop species or the type of subsequent host crop species. However, how maize and soybean performance is related to the diversity of AMF communities in cover cropping systems remains unclear. We therefore investigated which cover cropping or host identity is the most important factor in shaping AMF community structure in subsequent crop roots using an Illumina Miseq platform amplicon sequencing.

Methods

In this study, we established three cover crop systems (Italian ryegrass, hairy vetch, and brown mustard) or bare fallow prior to planting maize and soybean as cash crops. After cover cropping, we divided the cover crop experimental plots into two subsequent crop plots (maize and soybean) to understand which cover cropping or host crop identity is an important factor for determining the AMF communities and diversity both in maize and soybeans.

Results

We found that most of the operational taxonomic units (OTUs) in root samples were common in both maize and soybean, and the proportion of common generalists in this experiment for maize and soybean roots was 79.5% according to the multinomial species classification method (CLAM test). The proportion of OTUs specifically detected in only maize and soybean was 9.6% and 10.8%, respectively. Additionally, the cover cropping noticeably altered the AMF community structure in the maize and soybean roots. However, the differentiation of AMF communities between maize and soybean was not significantly different.

Discussion

Our results suggest cover cropping prior to planting maize and soybean may be a strong factor for shaping AMF community structure in subsequent maize and soybean roots rather than two host crop identities. Additionally, we could not determine the suitable rotational combination for cover crops and subsequent maize and soybean crops to improve the diversity of the AMF communities in their roots. However, our findings may have implications for understanding suitable rotational combinations between cover crops and subsequent cash crops and further research should investigate in-depth the benefit of AMF on cash crop performances in cover crop rotational systems.

Arbuscular mycorrhizal fungi alleviate the heavy metal toxicity on sunflower (Helianthus annuus L.) plants cultivated on a heavily contaminated field soil at a WEEE-recycling site

An 8-week pot experiment was conducted to investigate the growth and responses of sunflower (Helianthus annuus L.) to arbuscular mycorrhizal (AM) fungal inoculations on a heavily heavy metal (HM)-contaminated (H) soil and a lightly HM-enriched (L) soil, both of which were collected from a waste electrical and electronic equipment (WEEE)-recycling site. Compared with the L soil, the H soil induced significantly larger (P<0.05) concentrations of Cd, Cu, Pb, Cr, Zn and Ni in sunflower (except for root Cr and shoot Ni), which impaired the thylakoid lamellar folds in leaves. The biomasses and P concentrations of shoots and roots, as well as the total P acquisitions per pot were all significantly decreased (P<0.05). Both Funneliformis mosseae (Fm) and F. caledonium (Fc) inoculation significantly increased (P<0.05) root mycorrhizal colonization. For the L soil, AM fungal inoculations had no significant effects on the soil-plant system, except for a decrease of soil pH and increases of soil available P and DTPA-extractable Zn concentrations with the Fm-inoculated treatment. For the H soil, however, AM fungal inoculations significantly increased (P<0.05) the biomasses and P concentrations of shoots and roots, as well as the total P acquisitions per pot, and significantly reduced (P<0.05) the concentrations of HMs in shoots (except for Cu and Pb with Fm- and Fc- inoculated treatments, respectively) and alleviated the toxicity symptoms of HMs in thylakoid structure of leaves. AM fungal inoculations in the H soil also significantly increased (P<0.05) the shoot uptake of HMs (except for Cr), and tended to decrease the total concentrations of HMs in soils. This suggests the potential application of AM fungi for both reducing HM stress and promoting phytoextraction of HM-contaminated soils caused by WEEE recycling.

N-P fertilization did not reduce AMF abundance or diversity but alter AMF composition in an alpine grassland infested by a root hemiparasitic plant

Fertilization has been shown to have suppressive effects on arbuscular mycorrhizal fungi (AMF) and root hemiparasites separately in numerous investigations, but its effects on AMF in the presence of root hemiparasites remain untested. In view of the contrasting nutritional effects of AMF and root hemiparasites on host plants, we tested the hypothesis that fertilization may not show strong suppressive effects on AMF when a plant community was infested by abundant hemiparasitic plants. Plants and soil samples were collected from experimental field plots in Bayanbulak Grassland, where N and P fertilizers had been applied for three continuous years for control against a spreading root hemiparasite, Pedicularis kansuensis. Shoot and root biomass of each plant functional group were determined. Root AMF colonization levels, soil spore abundance, and extraradical hyphae length density were measured for three soil depths (0-10 cm, 10-20 cm, 20-30 cm). Partial 18S rRNA gene sequencing was used to detect AMF diversity and community composition. In addition, we analyzed the relationship between relative abundance of different AMF genera and environmental factors using Spearman's correlation method. In contrast to suppressive effects reported by many previous studies, fertilization showed no significant effects on AMF root colonization or AMF species diversity in the soil. Instead, a marked increase in soil spore abundance and extraradical hyphae length density were observed. However, fertilization altered relative abundance and AMF composition in the soil. Our results support the hypothesis that fertilization does not significantly influence the abundance and diversity of AMF in a plant community infested by P. kansuensis.

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.

Root type and soil phosphate determine the taxonomic landscape of colonizing fungi and the transcriptome of field-grown maize roots

Different root types of plants are colonized by a myriad of soil microorganisms, including fungi, which influence plant health and performance. The distinct functional and metabolic characteristics of these root types may influence root type-inhabiting fungal communities. We performed internal transcribed spacer (ITS) DNA profiling to determine the composition of fungal communities in field-grown axial and lateral roots of maize (Zea mays) and in response to two different soil phosphate (P) regimes. In parallel, these root types were subjected to transcriptome profiling by RNA sequencing (RNA-Seq). We demonstrated that fungal communities were influenced by soil P levels in a manner specific to root types. Moreover, maize transcriptome sequencing revealed root type-specific shifts in cell wall metabolism and defense gene expression in response to high P. Furthermore, lateral roots specifically accumulated defense-related transcripts at high P levels. This observation was correlated with a shift in fungal community composition, including a reduction in colonization by arbuscular mycorrhizal fungi, as observed in ITS sequence data and microscopic evaluation of root colonization. Our findings suggest soil nutrient-dependent changes in functional niches within root systems and provide new insights into the interaction of individual root types with soil microbiota.

Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi

The arrival of 454 sequencing represented a major breakthrough by allowing deeper sequencing of environmental samples than was possible with existing Sanger approaches. Illumina MiSeq provides a further increase in sequencing depth but shorter read length compared with 454 sequencing. We explored whether Illumina sequencing improves estimates of arbuscular mycorrhizal (AM) fungal richness in plant root samples, compared with 454 sequencing. We identified AM fungi in root samples by sequencing amplicons of the SSU rRNA gene with 454 and Illumina MiSeq paired-end sequencing. In addition, we sequenced metagenomic DNA without prior PCR amplification. Amplicon-based Illumina sequencing yielded two orders of magnitude higher sequencing depth per sample than 454 sequencing. Initial analysis with minimal quality control recorded five times higher AM fungal richness per sample with Illumina sequencing. Additional quality control of Illumina samples, including restriction of the marker region to the most variable amplicon fragment, revealed AM fungal richness values close to those produced by 454 sequencing. Furthermore, AM fungal richness estimates were not correlated with sequencing depth between 300 and 30,000 reads per sample, suggesting that the lower end of this range is sufficient for adequate description of AM fungal communities. By contrast, metagenomic Illumina sequencing yielded very few AM fungal reads and taxa and was dominated by plant DNA, suggesting that AM fungal DNA is present at prohibitively low abundance in colonised root samples. In conclusion, Illumina MiSeq sequencing yielded higher sequencing depth, but similar richness of AM fungi in root samples, compared with 454 sequencing.

Barcoded NS31/AML2 primers for sequencing of arbuscular mycorrhizal communities in environmental samples

PREMISE OF THE STUDY

Arbuscular mycorrhizal fungi (AMF) are globally important root symbioses that enhance plant growth and nutrition and influence ecosystem structure and function. To better characterize levels of AMF diversity relevant to ecosystem function, deeper sequencing depth in environmental samples is needed. In this study, Illumina barcoded primers and a bioinformatics pipeline were developed and applied to study AMF diversity and community structure in environmental samples.

METHODS

Libraries of small subunit ribosomal RNA fragment amplicons were amplified from environmental DNA using a single-step PCR reaction with barcoded NS31/AML2 primers. Amplicons were sequenced on an Illumina MiSeq sequencer using version 2, 2 × 250-bp paired-end chemistry, and analyzed using QIIME and RDP Classifier.

RESULTS

Sequencing captured 196 to 6416 operational taxonomic units (OTUs; depending on clustering parameters) representing nine AMF genera. Regardless of clustering parameters, ∼20 OTUs dominated AMF communities (78-87% reads) with the remaining reads distributed among other OTUs. Analyses also showed significant biogeographic differences in AMF communities and that community composition could be linked to specific edaphic factors.

DISCUSSION

Barcoded NS31/AML2 primers and Illumina MiSeq sequencing provide a powerful approach to address AMF diversity and variations in fungal assemblages across host plants, ecosystems, and responses to environmental drivers including global change.