Seasonal variation in winter wheat field soil arbuscular mycorrhizal fungus communities after non-mycorrhizal crop cultivation

Advances in microbial based bio-inoculum for amelioration of soil health and sustainable crop production

The adoption of sustainable agricultural practices is increasingly imperative in addressing global food security and environmental concerns, with microbial based bio-inoculums emerging as a promising approach for nurturing soil health and fostering sustainable crop production.This review article explores the potential of microbial based bio-inoculumsor biofertilizers as a transformative approach toenhance plant disease resistance and growth. It explores the commercial prospects of biofertilizers, highlighting their role in addressing environmental concerns associated with conventional fertilizers while meeting the growing demand for eco-friendly agricultural practices. Additionally, this review discusses the future prospects of biofertilizers, emphasizing the ongoing advancements in biotechnology and formulation techniques that are expected to enhance their efficacy and applicability. Furthermore, this article provides insights into strategies for the successful acceptance of biofertilizers among farmers, including the importance of quality control, assurance, and education initiatives to raise awareness about their benefits and overcome barriers to adoption. By synthesizing the current research findings and industrial developments, this review offers valuable guidance for stakeholders seeking to exploit the potential of biofertilizers or beneficial microbes to promote soil health, ensure sustainable crop production, and addressing the challenges of modern agriculture.

Glomerales Dominate Arbuscular Mycorrhizal Fungal Communities Associated with Spontaneous Plants in Phosphate-Rich Soils of Former Rock Phosphate Mining Sites

Arbuscular mycorrhizal fungi (AMF) are key drivers of soil functioning. They interact with multiple soil parameters, notably, phosphorus (P). In this work, AMF communities of native plants grown spontaneously on former mining sites either enriched (P sites) or not enriched with P (nP sites) by mining cuttings of rock phosphate (RP) were studied. No significant differences were observed in the root mycorrhizal rates of the plants when comparing P and nP sites. The assessment of AMF diversity and community structure using Illumina MiSeq metabarcoding and targeting 18S rDNA in roots and rhizospheric soils showed a total of 318 Amplicon Sequence Variants (ASVs) of Glomeromycota phylum. No significant difference in the diversity was found between P and nP sites. Glomeraceae species were largely dominant, formed a fungal core of 26 ASVs, and were persistent and abundant in all sites. In the P soils, eight ASVs were identified by indicator species analysis. A trend towards an increase in Diversisporaceae and Claroideoglomeraceae and a reduction in Paraglomeraceae and Glomeraceae were noticed. These results provide new insights into AMF ecology in former RP mining sites; they document that P concentration is a driver of AMF community structures in soils enriched in RP long term but also suggest an influence of land disturbance, ecosystem self-restoration, and AMF life history strategies as drivers of AMF community profiles.

Legacy effects of pre-crop plant functional group on fungal root symbionts of barley

Arbuscular mycorrhizal (AM) fungi, a group of widespread fungal symbionts of crops, could be important in driving crop yield across crop rotations through plant-soil feedbacks (PSF). However, whether preceding crops have a legacy effect on the AM fungi of the subsequent crop is poorly known. We set up an outdoor mesocosm crop rotation experiment that consisted of a first phase growing either one of four pre-crops establishing AM and/or rhizobial symbiosis or not (spring barley, faba bean, lupine, canola), followed by an AM crop, winter barley. After the pre-crop harvest, carbon-rich organic substrates were applied to test whether it attenuated, accentuated or modified the effect of pre-crops. The pre-crop mycorrhizal status, but not its rhizobial status, affected the richness and composition of AM fungi, and this difference, in particular community composition, persisted and increased in the roots of winter barley. The effect of a pre-crop was driven by its single symbiotic group, not its mixed symbiotic group and/or by a crop-species-specific effect. This demonstrates that the pre-crop symbiotic group has lasting legacy effects on the AM fungal communities and may steer the AM fungal community succession across rotation phases. This effect was accentuated by sawdust amendment, but not wheat straw. Based on the previous observation of decreased crop yield after AM pre-crops, our findings suggest negative PSF at the level of the plant symbiotic group driven by a legacy effect of crop rotation history on AM fungal communities, and that a focus on crop symbiotic group offers additional understanding of PSF.

Traversing arbuscular mycorrhizal fungi and Pseudomonas fluorescens for carrot production under salinity

Carrot is a vital supply of dietary fiber, vitamins, and carotenoids, and it is also rich in antioxidants and minerals. Soil salinity significantly reduces the yield and quality of carrots. Mycorrhiza inoculum (AMF) is known to improve morphological and biochemical traits of vegetables even under saline conditions. But the role of AMF in combating soil salinity effect in carrot is not studied in detail. Therefore here, in the first set, carrot seeds are inoculated with microbes in a pot experiment under polyhouse condition. In total, we applied 7 treatments with different combinations of Mycorrhiza inoculum (Glomus mosseae (Gm) and Gigaspora gigantea (Gg)) and phosphate solubilizing bacteria (Pseudomonas fluroscens (Pf)). In pot experiment study the best two treatments were the combination of Gm + Pf + GG and Pf + GG. Both of these treatments were selected for validation under the open field conditions. Primarily, there seems to be a promising opportunity for AMF application to carrots under pot culture as well as under field trials because of promising effect towards morphological parameters, especially root weight, and disparities in nutrients and metabolites. Overall, our study highlights mycorrhizal fungi and other microbes' efficacy in achieving a successful carrot production under salinity stress.

Water management and phenology influence the root-associated rice field microbiota

Microbial communities associated with plants are greatly influenced by water availability in soil. In flooded crops, such as rice, the impact of water management on microbial dynamics is not fully understood. Here, we present a comprehensive study of the rice microbiota investigated in an experimental field located in one of the most productive areas of northern Italy. The microbiota associated with paddy soil and root was investigated using 454 pyrosequencing of 16S, ITS and 18S rRNA gene amplicons under two different water managements, upland (non-flooded, aerobic) and lowland (traditional flooding, anaerobic), at three plant development stages. Results highlighted a major role of the soil water status in shaping microbial communities, while phenological stage had low impacts. Compositional shifts in prokaryotic and fungal communities upon water management consisted in significant abundance changes of Firmicutes, Methanobacteria, Chloroflexi, Sordariomycetes, Dothideomycetes and Glomeromycotina. A vicariance in plant beneficial microbes and between saprotrophs and pathotrophs was observed between lowland and upland. Moreover, through network analysis, we demonstrated different co-abundance dynamics between lowland and upland conditions with a major impact on microbial hubs (strongly interconnected microbes) that fully shifted to aerobic microbes in the absence of flooding.

High-Throughput DNA Sequence-Based Analysis of AMF Communities

Arbuscular mycorrhizal fungi (AMF) are obligate symbionts of most land plants. They have great ecological and economic impacts as they support plant nutrition and water supply, soil structure, and plant resistance to pathogens. Investigating AMF presence and distribution at small and large scales is critical. Therefore, research requires standard protocols to be easily implemented. In this chapter, we describe a workflow for AMF identification by high-throughput sequencing through Illumina MiSeq platform of two DNA target regions: small subunit (SSU) and internal transcribed spacer (ITS). The protocol can apply to both soil and root AMF communities.

Seasonal shifts of arbuscular mycorrhizal fungi in Cocos nucifera roots in Yucatan, Mexico

The diversity and community structure of arbuscular mycorrhizal fungi (AMF) associated with coconut (Cocos nucifera) roots was evaluated by next generation sequencing (NGS) using partial sequences of the 18S rDNA gene and by spore isolation and morphological identification from rhizosphere soil. Root samples from six different Green Dwarf coconut plantations and from one organic plantation surrounded by tropical dry forest along the coastal sand dunes in Yucatan, Mexico, were collected during the rainy and dry seasons. In total, 14 root samples were sequenced with the Illumina MiSeq platform. Additionally, soil samples from the dry season were collected to identify AMF glomerospores. Based on a 95-97% similarity, a total of 36 virtual taxa (VT) belonging to nine genera were identified including one new genus-like clade. Glomus was the most abundant genus, both in number of VT and sequences. The comparison of dry and rainy season samples revealed differences in the richness and composition of AMF communities colonizing coconut roots. Our study shows that the main AMF genera associated with coconut tree roots in all samples were Glomus, Sclerocystis, Rhizophagus, Redeckera, and Diversispora. Based on glomerospore morphology, 22 morphospecies were recorded among which 14 were identified to species. Sclerocystis sinuosa, Sclerocystis rubiformis, Glomus microaggregatum, and Acaulospora scrobiculata were dominant in field rhizosphere samples. This is the first assessment of the composition of AMF communities colonizing coconut roots in rainy and dry seasons. It is of importance for selection of AMF species to investigate for their potential application in sustainable agriculture of coconut.

Amplicon sequencing analysis of arbuscular mycorrhizal fungal communities colonizing maize roots in different cover cropping and tillage systems

Our understanding regarding the influence of intensive agricultural practices, including cover cropping and tillage, on communities of arbuscular mycorrhizal fungi (AMF) is lacking. This would prove to be an obstacle in the improvement of current maize (Zea mays L.) production. Therefore, using amplicon sequencing, we aimed to clarify how AMF communities and their diversity in maize roots vary under different cover cropping systems and two types of tillage (rotary and no tillage). Two kinds of cover crops (hairy vetch and brown mustard) and fallow treatments were established with rotary or no tillage in rotation with maize crops. Tillage and no tillage yielded a set of relatively common AMF operational taxonomic units (OTUs) in the maize crops, representing 78.3% of the total OTUs. The percentage of maize crop OTUs that were specific to only tillage and no tillage were 9.6% and 12.0%, respectively. We found that tillage system significantly altered the AMF communities in maize roots. However, the AMF communities of maize crops among cover cropping treatments did not vary considerably. Our findings indicate that compared with cover cropping, tillage may shape AMF communities in maize more strongly.

A Review of Studies from the Last Twenty Years on Plant–Arbuscular Mycorrhizal Fungi Associations and Their Uses for Wheat Crops

The aim of this work was to summarize the most recent research focused on the study of plant–arbuscular mycorrhizal fungi (AMF) symbiosis, both in a generic context and in the specific context of wheat cultivation. Taking into account the last 20 years, the most significant studies on the main plant advantages taken from this association are reviewed herein. Positive advances that have been reported stem from the mutualistic relationship between the plant and the mycorrhizal fungus, revealing better performance for the host in terms of nutrient uptake and protection from salinity, lack of water, and excess phytotoxic elements. Mycorrhiza studies and the recent progress in research in this sector have shown a possible solution for environmental sustainability: AMF represent a valid alternative to overcome the loss of biological fertility of soils, reduce chemical inputs, and alleviate the effects of biotic and abiotic stress.

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.