Contrasting common measures of arbuscular mycorrhizal fungal root colonization

The influence of a soil amendment on the abundance and interaction of arbuscular mycorrhizal fungi with arable soils and host winter wheat

Arbuscular mycorrhizal (AM) fungi have been shown to be associated with an estimated 70 % of vascular terrestrial plants. Such relationships have been shown to be sensitive to soil disturbance, for example, tillage in the preparation of a seed bed. From the application of arable soil management, AM fungal populations have been shown to be negatively impacted in abundance and diversity, reducing plant growth and development. The present study aims to utilise two sources (multipurpose compost and a commercial inocula) of mycorrhizal fungi for the amendment of arable soils supporting Zulu winter wheat under controlled conditions and quantify plant growth responses. A total of nine fields across three participating farms were sampled, each farm practicing either conventional, reduced, or zero tillage soil management exclusively. Soil textures were assessed for each sampled soil. Via the employment of AM fungal symbiosis quantification methods, AM fungi were compared between soil amendments and their effects on crop growth and development. The present study was able to quantify a mean 6 cm increase to crop height (P<0.001), 10 cm reduction to root length corresponding with a 2.45-fold increase in AM fungal arbuscular structures (P<0.001), a 1.15-fold increase in soil glomalin concentration corresponding to a 1.26-fold increase in soil carbon, and a 1.32-fold increase in the relative abundance of molecular identified AM fungal sequences for compost amended soils compared to control samples. Mycorrhizal inocula, however, saw no change to crop height or root length, AM fungal arbuscules were reduced by 1.43-fold, soil glomalin was additionally reduced by 1.55-fold corresponding to a reduction in soil carbon by 1.31-fold, and a reduction to relative AM fungal species abundance by 1.26-fold. The present study can conclude the addition of compost as an arable soil amendment is more beneficial for the restoration of AM fungi beneficial to wheat production and soil carbon compared to the addition of a commercial mycorrhizal inocula.

Mycorrhizal response of Solanum tuberosum to homokaryotic versus dikaryotic arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi (AMF) are obligate plant symbionts of most land plants. In these organisms, thousands of nuclei that are either genetically similar (homokaryotic) or derived from two distinct parents (dikaryotic) co-exist in a large syncytium. Here, we investigated the impact of these two nuclear organizations on the mycorrhizal response of potatoes (Solanum tuberosum) by inoculating four potato cultivars with eight Rhizophagus irregularis strains individually (four homokaryotic and four dikaryotic). By evaluating plant and fungal fitness-related traits four months post inoculation, we found that AMF genetic organization significantly affects the mycorrhizal response of host plants. Specifically, homokaryotic strains lead to higher total, shoot, and tuber biomass and a higher number of tubers, compared to dikaryotic strains. However, fungal fitness-related traits showed no clear differences between homokaryotic and dikaryotic strains. Nucleotype content analysis of single spores confirmed that the nucleotype ratio of AMF heterokaryon spores can shift depending on host identity. Together, these findings continue to highlight significant ecological differences derived from the two distinct genetic organizations in AMF.

Quantification of arbuscular mycorrhizal fungi root colonization in wheat, tomato, and leek using absolute qPCR

Arbuscular mycorrhizal fungi (AMF) form symbioses with most terrestrial plants and are known to have a positive effect on plant growth and health. Different methodologies have been developed to assess the AMF-plant symbiosis. The most applied method, which involves staining of roots and microscopic observation of the AMF structures, is tedious and time-consuming and the results are highly dependent on the observer. Using quantitative polymerase chain reaction (qPCR) to quantify AMF root colonization represents a reliable, high-throughput technique that allows the assessment of numerous samples. Quantification with qPCR can be performed through two methods: relative quantification and absolute quantification. In relative quantification, the target gene is normalized with a reference gene. On the other hand, absolute quantification involves the use of a standard curve, for which template DNA is serially diluted. In a previous paper, we validated the primer pair AMG1F and AM1 for a relative quantification approach to assess AMF root colonization in Petunia. Here, we tested the same primers with an absolute quantification approach and compared the results with the traditional microscopy method. We evaluated the qPCR method with three different crops, namely, wheat (cv. Colmetta and Wiwa), tomato, and leek. We observed a strong correlation between microscopy and qPCR for Colmetta (r = 0.90, p < 0.001), Wiwa (r = 0.94, p < 0.001), and tomato (r = 0.93, p < 0.001), but no correlation for leek (r = 0.27, p = 0.268). This highlights the importance of testing the primer pair for each specific crop.

Changes of root AMF community structure and colonization levels under distribution pattern of geographical substitute for four Stipa species in arid steppe

The establishment of symbiotic relationship between arbuscular mycorrhizal fungi (AMF) and roots is a mutually beneficial process and plays an important role in plant succession in ecosystems. However, there is less understanding of information about the AMF community in roots under vegetation succession on a large regional scale, especially the spatial variation in the AMF community and its potential ecological functions. Here, we elucidated the spatial variations in root AMF community structure and root colonization along a distribution pattern of four zonal Stipa species in arid and semiarid grassland systems and explored key factors regulating AMF structure and mycorrhizal symbiotic interactions. Four Stipa species established a symbiosis with AMF, and annual mean temperature (MAT) and soil fertility were the main positive and negative driving factors of AM colonization, respectively. The Chao richness and Shannon diversity of AMF community in the root system of Stipa species tended to increase firstly from S. baicalensis to S. grandis and then decreased from S. grandis to S. breviflora. While evenness of root AMF and root colonization showed a trend of increasing from S. baicalensis to S. breviflora, and biodiversity was principally affected by soil total phosphorus (TP), organic phosphorus (Po) and MAT. It is emphasized that Stipa species have certain dependence on AMF, especially in a warming environment, and the root AMF community structure among the four Stipa taxa was different. Additionally, the composition and spatial distribution of root AMF in host plants varied with MAT, annual mean precipitation (MAP), TP and host plant species. These results will broaden our understanding of the relationship between plant and AMF communities and their ecological role, and provide basic information for the application of AMF in the conservation and rehabilitation of forage plants in degraded semiarid grasslands.

Characterization of Arbuscular Mycorrhizal Effector Proteins

Plants are colonized by various fungi with both pathogenic and beneficial lifestyles. One type of colonization strategy is through the secretion of effector proteins that alter the plant's physiology to accommodate the fungus. The oldest plant symbionts, the arbuscular mycorrhizal fungi (AMF), may exploit effectors to their benefit. Genome analysis coupled with transcriptomic studies in different AMFs has intensified research on the effector function, evolution, and diversification of AMF. However, of the current 338 predicted effector proteins from the AM fungus Rhizophagus irregularis, only five have been characterized, of which merely two have been studied in detail to understand which plant proteins they associate with to affect the host physiology. Here, we review the most recent findings in AMF effector research and discuss the techniques used for the functional characterization of effector proteins, from their in silico prediction to their mode of action, with an emphasis on high-throughput approaches for the identification of plant targets of the effectors through which they manipulate their hosts.

Deep learning-based quantification of arbuscular mycorrhizal fungi in plant roots

Soil fungi establish mutualistic interactions with the roots of most vascular land plants. Arbuscular mycorrhizal (AM) fungi are among the most extensively characterised mycobionts to date. Current approaches to quantifying the extent of root colonisation and the abundance of hyphal structures in mutant roots rely on staining and human scoring involving simple yet repetitive tasks which are prone to variation between experimenters. We developed Automatic Mycorrhiza Finder (AMFinder) which allows for automatic computer vision-based identification and quantification of AM fungal colonisation and intraradical hyphal structures on ink-stained root images using convolutional neural networks. AMFinder delivered high-confidence predictions on image datasets of roots of multiple plant hosts (Nicotiana benthamiana, Medicago truncatula, Lotus japonicus, Oryza sativa) and captured the altered colonisation in ram1-1, str, and smax1 mutants. A streamlined protocol for sample preparation and imaging allowed us to quantify mycobionts from the genera Rhizophagus, Claroideoglomus, Rhizoglomus and Funneliformis via flatbed scanning or digital microscopy, including dynamic increases in colonisation in whole root systems over time. AMFinder adapts to a wide array of experimental conditions. It enables accurate, reproducible analyses of plant root systems and will support better documentation of AM fungal colonisation analyses. AMFinder can be accessed at https://github.com/SchornacklabSLCU/amfinder.

Sustainable improvement of soil health utilizing biochar and arbuscular mycorrhizal fungi: A review

Conservation of soil health and crop productivity is the central theme for sustainable agriculture practices. It is unrealistic to expect that the burgeoning crop production demands will be met by a soil ecosystem that is increasingly unhealthy and constrained. Therefore, the present review is focused on soil amendment techniques, using biochar in combination with arbuscular mycorrhizal fungi (AMF), which is an indispensable biotic component that maintains plant-soil continuum. Globally significant progress has been made in elucidating the physical and chemical properties of biochar; along with its role in carbon sequestration. Similarly, research advances on AMF include its evolutionary background, functions, and vital roles in the soil ecosystem. The present review deliberates on the premise that biochar and AMF have the potential to become cardinal to management of agro-ecosystems. The wider perspectives of various agronomical and environmental backgrounds are discussed. The present state of knowledge, different aspects and limitations of combined biochar and AMF applications (BC + AMF), mechanisms of interaction between biochar and AMF, effects on plant growth, challenges and future opportunities of BC + AMF applications are critically reviewed. Given the severely constrained nature of soil health, the roles of BC + AMF in agriculture, bioremediation and ecology have also been examined. In spite of the potential benefits, the functionality and dynamics of BC + AMF in soil are far from being fully elucidated.

VBA-AMF: A VBA Program Based on the Magnified Intersections Method for Quantitative Recording of Root Colonization by Arbuscular Mycorrhizal Fungi

The extent of mycorrhizal fungi colonization is an important factor for determining the function of mycorrhizal fungi in fungi-host interaction, and quantifying the extent of mycorrhizal fungi colonization is a fundamental and essential task for researchers engaged in mycorrhizal studies. Intersect methods, such as the gridline intersect and magnified intersections methods, are accurate and objective, and are widely used to assess the colonization status of arbuscular mycorrhizal (AM) fungus. However, no convenient procedures or add-ins for Excel spreadsheets have been developed to simplify these methods. Here, we propose a procedure using the Visual Basic for Application (VBA) program in Excel that is based on the magnified intersections method, which we refer to as VBA-AMF (arbuscular mycorrhizal fungi). Time-saving and convenience are the two most prominent advantages of the VBA-AMF procedure, as it enables researchers to compute the colonization rate of AM fungi in roots, and consequently the extent of root colonization by AM fungi. VBA-AMF can also be modified to measure the status of other fungal colonizations in plant roots following the same strategy.