Abstract Arbuscular Mycorrhizal Research Articles

Fungal symbiont diversity drives growth of Holcus lanatus depending on soil nutrient availability

Abstract Arbuscular mycorrhizal (AM) fungi frequently colonise plant roots and can affect plant morphology and physiology through their contribution to plant nutrition. However, the functional role of AM fungi in the presence of other microbial symbionts, including widespread Mucoromycotina ‘fine root endophytes’ (MFRE) fungi, remains largely unknown. While both AM fungi and MFRE transfer nutrients, including nitrogen, from inorganic and organic sources to host plants, their combined effects on co‐colonised plants have only been investigated in liverworts. Here, we compare the morphology and physiology of the grass Holcus lanatus grown with an AM fungal community versus a more diverse symbiotic fungal community containing both AM fungi and MFRE. Holcus lanatus plants were grown in the presence of either a diverse MFRE+AM fungi soil inoculum or a multi‐species AM fungal inoculum. Plant traits associated with growth were quantified, along with fungal transfer of 15N tracer to plants from a variety of sources (ammonium chloride, alanine, glycine and algal necromass). Holcus lanatus grown with the AM fungal community had greater root and shoot growth during early development and prior to the addition of 15N‐labelled sources, compared with plants grown with the more diverse symbiotic fungal community. When nitrogen sources were made available to the fungal symbionts in the pot microcosms, plants growing with the MFRE+AM fungi soil inoculum had a faster growth rate than plants growing with the AM fungal community. At harvest, H. lanatus grown with the AM fungal community had a larger biomass, and there were no differences in 15N tracer assimilation in plants across the two fungal community treatments. Our results demonstrate that the diversity of fungal inocula in conjunction with soil nutrient availability determine the benefits derived by plants from diverse fungal symbionts. Our research contributes to understanding host plant outcomes in diverse multi‐symbiont scenarios. Read the free Plain Language Summary for this article on the Journal blog.

ARBUSCULAR MYCORRHIZA-INDUCED KINASES AMK8 and AMK24 associate with the receptor-like kinase KINASE3 to regulate arbuscular mycorrhizal symbiosis in Lotus japonicus.

Arbuscular mycorrhizal (AM) symbiosis is a widespread, ancient mutualistic association between plants and fungi, and facilitates nutrient uptake into plants. Cell surface receptor-like kinases (RLKs) and receptor-like cytoplasmic kinases (RLCKs) play pivotal roles in transmembrane signaling, while few RLCKs are known to function in AM symbiosis. Here, we show that 27 out of 40 AM-induced kinases (AMKs) are transcriptionally upregulated by key AM transcription factors in Lotus japonicus. Nine AMKs are only conserved in AM-host lineages, among which the SPARK-RLK-encoding gene KINASE3 (KIN3) and the RLCK paralogues AMK8 and AMK24 are required for AM symbiosis. KIN3 expression is directly regulated by the AP2 transcription factor CTTC MOTIF-BINDING TRANSCRIPTION FACTOR1 (CBX1), which regulates the reciprocal exchange of nutrients in AM symbiosis, via the AW-box motif in the KIN3 promoter. Loss of function mutations in KIN3, AMK8, or AMK24 result in reduced mycorrhizal colonization in L. japonicus. AMK8 and AMK24 physically interact with KIN3. KIN3 and AMK24 are active kinases and AMK24 directly phosphorylates KIN3 in vitro. Moreover, CRISPR-Cas9-mediated mutagenesis of OsRLCK171, the sole homolog of AMK8 and AMK24 in rice (Oryza sativa), leads to diminished mycorrhization with stunted arbuscules. Overall, our results reveal a crucial role of the CBX1-driven RLK/RLCK complex in the evolutionarily conserved signaling pathway enabling arbuscule formation.

OsSYMRK Plays an Essential Role in AM Symbiosis in Rice (Oryza sativa).

Arbuscular mycorrhizal (AM) fungi establish mutualistic symbiosis with a wide range of terrestrial plants, including rice. However, the mechanisms underlying the initiation of AM symbiosis are yet to be elucidated, particularly in nonleguminous plants. We previously demonstrated that chitin elicitor receptor kinase 1 (OsCERK1), a lysin motif receptor-like kinase essential for chitin-triggered immunity, also plays a key role in AM symbiosis in rice. However, the mechanisms underlying the regulation of switching between immunity and symbiosis by OsCERK1 are yet to be fully elucidated. SYMBIOSIS RECEPTOR-LIKE KINASE (SYMRK)/DOES NOT MAKE INFECTIONS 2 (DMI2) is a leucine-rich repeat receptor-like kinase associated with both root nodule symbiosis and AM symbiosis in legumes. The homolog of SYMRK in rice, OsSYMRK, has a shorter form than that in legumes because OsSYMRK lacks a malectin-like domain (MLD). The MLD reportedly contributes to symbiosis in Lotus japonicus; however, the contribution of OsSYMRK to AM symbiosis in rice remains unclear. Phylogenetic analyses indicated that the MLD of SYMRK/DMI2 is widely conserved even in mosses and ferns but absent in commelinids, including rice. To understand the function of OsSYMRK, we produced an Ossymrk knockout mutant using genome editing technology. AM colonization was mostly abolished in Ossymrk with a more severe phenotype than Oscerk1. Ca2+ spiking against chitin tetramer was also diminished in Ossymrk. In contrast, comparable defense responses against chitin heptamer to the wild type were observed in Ossymrk. Bimolecular fluorescence complementation studies demonstrating an interaction between OsSYMRK and OsCERK1 indicate that OsSYMRK may play an important role in switching from immunity to symbiosis through the interaction with OsCERK1 in rice.

Mycorrhizal fungi alter root exudation to cultivate a beneficial microbiome for plant growth

Abstract Arbuscular mycorrhizal (AM) fungi traditionally form symbioses with most plant species. Although AM fungi have critical effects on microbial communities, the pathways showing how AM fungi shape rhizosphere bacterial communities and their functions are rarely explored. Here, through three systematic experiments, AM fungi–bacteria interactions were first investigated in the rhizosphere of Lotus japonicus, then the interactions were confirmed by a second experiment with wild‐type and a mycorrhiza‐defective mutant ljcbx of L. japonicus. The mechanisms were presented by adding core bacteria and AM fungi to the plant rhizosphere in the third experiment. We found that AM fungi–bacteria interactions enhanced host plant growth and identified a core bacterial group that uniquely enhanced host plant growth. Adding core bacteria and AM fungi promoted host growth and nutrient acquisition compared to adding AM fungi or core bacteria independently. Allelopathic substances secreted by AM fungal colonizing host roots to recruit the rhizosphere bacteria were detected by the multi‐omics joint analysis, showing that arachidonic acid was the main allelopathic substance that affected AM fungi–bacteria interactions. Our findings provide direct evidence that mycorrhizal infection simulated root exudation, such as arachidonic acid, recruited a beneficial microbiome to the host rhizosphere, increasing plant growth and soil nutrient turnover. Read the free Plain Language Summary for this article on the Journal blog.

Defense responses of arbuscular mycorrhizal fungus-colonized poplar seedlings against gypsy moth larvae: a multiomics study

Arbuscular mycorrhizal (AM) fungi may help protect plants against herbivores; however, their use for the pest control of woody plants requires further study. Here, we investigated the effect of Glomus mosseae colonization on the interactions between gypsy moth larvae and Populus alba × P. berolinensis seedlings and deciphered the regulatory mechanisms underlying the mycorrhizal-induced resistance in the leaves of mycorrhizal poplar using RNA-seq and nontargeted metabolomics. The resistance assay showed that AM fungus inoculation protected poplar seedlings against gypsy moth larvae, as evidenced by the decreased larval growth and reduced larval survival. A transcriptome analysis revealed that differentially expressed genes (DEGs) were involved in jasmonic acid biosynthesis (lipoxygenase, hydroperoxide dehydratase, and allene oxide cyclase) and signal transduction (jasmonate-ZIM domain and transcription factor MYC2) and identified the genes that were upregulated in mycorrhizal seedlings. Except for chalcone synthase and anthocyanidin synthase, which were downregulated in mycorrhizal seedlings, all DEGs related to flavonoid biosynthesis were upregulated, including 4-coumarate-CoA ligase, chalcone isomerase, flavanone 3-hydroxylase, flavonol synthase, and leucoanthocyanidin reductase. The metabolome analysis showed that several metabolites with insecticidal properties, including coumarin, stachydrine, artocarpin, norizalpinin, abietic acid, 6-formylumbelliferone, and vanillic acid, were significantly accumulated in the mycorrhizal seedlings. These findings suggest the potential of mycorrhiza-induced resistance for use in pest management of woody plants and demonstrate that the priming of JA-dependent responses in poplar seedlings contributes to mycorrhiza-induced resistance to insect pests.

The mycorrhizal-induced growth promotion and insect resistance reduction in Populus alba × P. berolinensis seedlings: a multi-omics study.

Arbuscular mycorrhizal (AM) fungi are an alternative to chemical insecticides or fertilizers, and there is an urgent need to extend the application of AM fungi to woody plants. This study aims to investigate the growth and resistance against the gypsy moth larvae (Lymantria dispar) in Glomus intraradices-colonized Populus alba × P. berolinensis seedlings, and to unravel the transcriptome and metabolome phenotypes recruited by AM fungus colonization that affect plant growth and insect resistance. Our results showed a positive mycorrhizal growth response, i.e., growth and biomass of mycorrhizal seedlings were enhanced. However, AM fungus inoculation reduced the resistance of poplar to gypsy moth larvae, as evidenced by the decreased carbon/nitrogen ratio in leaves, as well as the increased larval growth and shortened larval developmental duration. Transcriptome analysis revealed that in both auxin and gibberellin signaling transductions, all nodes were responsive to AM symbiosis and most differentially expressed genes belonging to effectors were up-regulated in mycorrhizal seedlings. Furthermore, the two key enzymes (4-coumarate-CoA ligase and trans-cinnamate 4-monooxygenase) involved in the synthesis of p-Coumaroyl-CoA, an initial metabolite in flavonoid biosynthesis and the first rate-limiting enzyme (chalcone synthase) in flavonoid biosynthesis, were down-regulated at the transcriptional level. Consistent with the transcriptome results, metabolome analysis found that the amounts of all differentially accumulated flavonoid compounds (e.g., catechin and quercetin) identified in mycorrhizal seedlings were decreased. Taken together, these findings highlight the diverse outcomes of AM fungi-host plant-insect interaction and reveal the regulatory network of the positive mycorrhizal growth response and mycorrhizal-induced reduction of insect resistance in poplar.

Arbuscular Mycorrhizal Colonization in Five Tropical Forest Tree Legumes of Chittagong University Campus in Bangladesh

Arbuscular mycorrhizal (AM) colonization in five tropical forest tree legumes (Gliricidia sepium, Dalbergia sissoo, Indigofera tysmanii, Delonix regia and Samanea saman) was investigated in Chittagong University (CU) campus. The results of the present study clearly suggests that, Vesicular AM fungi (VAM) are common in all the studied forest tree species, and that the studied forest tree species differ in their rates of AM formation. The intensity of colonization is maximum (98%) in I. tysmonii followed by D. sissoo (95%), D. regia (63%), S. saman (59%) and G. sepium (52%). Coiled structures of hyphae were recorded in D. regia. Arbuscule formation was recorded in D. sissooand in I. tysmonii. Mycorrhizal spores were found in rhizosphere soils of all the sites. Glomus, Acaulospora, Entrophospora and Gigaspora spores were identified in all the hosts. Forest plants differ in their rates of AM formation. Edhapic conditions like moisture content, soil pH also influence the extent of root colonization.Keyword: Mycorrhizae, Legume, Colonization, Edhapic condition, Rhizosphere, Underground networking.

Low indigenous AM fungal activity would be a necessary but not sufficient condition for effective utilization of exogenous AM fungal inoculum to forage corn

ABSTRACT Arbuscular mycorrhizal (AM) fungi is expected to be utilized in low input agriculture for their function to supply nutrients and water to host plants. AM fungal inoculum has been provided, but it has been known that their effect is context dependent. To clarify the factors that determine the effect of AM fungal inoculation to forage corn, a pot experiment was conducted using different indigenous AM fungal infection potential that evaluated with a modified infection unit method. Because we hypothesized that low indigenous AM fungal infection potential would be required to obtain significant inoculation effect, we prepared soils with different indigenous AM fungal infection potential by mixing sterile and non-sterile soils with different ratio. AM fungal colonization of non-inoculated series were increased with increase of indigenous AM fungal infection potential. Inoculation effect to increase of AM fungal colonization to corn root was generally larger in soils with low indigenous AM fungal infection potential and with low phosphorus (P) level, however, the effect was not very prominent in the soil with moderate P levels. Plant growth and plant P uptake showed similar trend with AM fungal colonization, i.e., enhanced P uptake and increase in plant dry matter were obtained when change in AM fungal colonization was larger. Therefore, low indigenous AM fungal infection potential would be required but not a sufficient condition to obtain AM fungal inoculation effect to forage corn.

Conservation of Picrorrhiza kurroa with arbuscular mycorrhizal fungi: An endangered and highly economic medicinal herb of Himalaya

Arbuscular mycorrhizal (AM) fungi are prevalent from arctic to tropics in most agricultural and natural ecosystems, play an important role in the conservation of some valuable medicinal plants. Picrorrhiza kurroa Royle ex Benth is distinguished endangered medicinal herb, naturally distributed in alpine and sub-alpine region of Himalayas. In present investigation, spores density of AM fungi along root colonization were studied from the rhizospheric soils of P. kurroa collected from different locations of Himachal Pradesh. Highest spore number (60) was found in the soil samples collected from forest nursery Rajkunda while AM root space colonization was highest in the samples of forest nursery Devidhar. The biodiversity of AM fungi was studied; the number of AM species was also highest in these two forest nursery samples. Funneliformis mosseae and Acaulospora laevis were dominant species associated with P. kurroa. After mass multiplication of F. mosseae and A. laevis, bioinoculation experiment was performed on Picrorrhiza kurroa seedlings for the biomass production and nutrient uptake analysis. Seedlings were inoculated with single and in combined mycorrhizal treatments with different combinations of farmyard manure and vermicompost. All inoculated seedlings showed significant biomass production than control seedlings. Root length (8.7cm), fresh and dry biomass was observed to be maximum in the plants inoculated with F. mosseae and vermicompost @ 10t ha−1 while percent AM root colonization was highest (60.33) in the roots of plants inoculated with F. mosseae plus A. laevis with vermicompost @10t ha−1. The phosphorus content was more in seedlings inoculated with consortium of two native AM fungi followed by F. mosseae and A. laevis, separately. In overall, consortium of native AM fungi i.e. F. mosseae and A. laevis was found to be best for the conservation of the P. kurroa in the presence of vermicompost and FYM, respectively.

Benefits of arbuscular mycorrhizal fungi in reducing organic contaminant residues in crops: Implications for cleaner agricultural production

Arbuscular mycorrhizal (AM) fungi (AMF) can not only improve soil and plant health, but also alter the accumulation of contaminants in plants. Here, the effects of AMF on the contents of organic contaminants and the underlying mechanisms are summarized. Data show that AMF widely occur in sites contaminated with organic chemicals. In most cases, AMF improve plant tolerance to organic contaminants and enhance crop growth, leading to increased biomass of the crops. Overall, AMF decrease organic contaminant residues in crop shoots, but often cause increased accumulation of contaminants, especially persistent organic pollutants (POPs), in crop roots. The benefits and mechanisms behind AMF’s role in ameliorating organic contaminant residues in crops can be summarized as follows: (1) increased biomass via improved mineral nutrition and water availability; (2) alleviation of oxidative stress induced by contaminants; (3) enhanced activities of contaminant degradation-related enzymes; (4) accumulation and sequestration of contaminants by AMF structures; (5) glomalin-related soil protein (GRSP)-triggered changes in bioavailability of contaminants; (6) stimulation of contaminant-degrading microorganisms in soil; (7) improved soil structure; and (8) reduced pesticide application via enhanced crop resistance to pathogens and improved competition with weeds. Finally, future challenges and perspectives regarding AMF’s contribution to crop safety are proposed.

Nitrogen fertilization altered arbuscular mycorrhizal fungi abundance and soil erosion of paddy fields in the Taihu Lake region of China.

Arbuscular mycorrhizal (AM) fungi were of importance in mitigating soil erosion, which was highly influenced by biotic and abiotic factors, such as host plant growth and soil nutrient. To investigate the impact of nitrogen (N) fertilization on seasonal variance in AM colonization and soil erosion, we conducted a field experiment with rice cultivation under four N fertilizer levels (0kgNha-1, 270kgNha-1, 300kgNha-1, and 375kgNha-1 plus organic fertilizers) in the Taihu Lake region, China. We investigated AM colonization before rice transplantation, during rice growth, and after rice harvest. We also assessed soil splash erosion of intact soil cores sampled at tillering and after rice harvest. We found that AM colonization (indicated by percentage of root length colonization) varied from 15 to 73%, which was attributed to rice growth, N fertilization, and their interaction. Soil loss due to splash erosion was cut down by organic N fertilizer at tillering, while higher inorganic N fertilization significantly increased soil loss after rice harvest. Additionally, we found significantly negative relationships of AM colonization to soil loss but positive relationships to soil aggregate stability. We highlighted the potential role of AM fungi in decreasing soil erosion and suggested that high N fertilization should be considered carefully when seeking after high yields.

Changes of mycorrhizal fungal community occurring during the natural restoration after the chi-chi earthquake in Taiwan

Arbuscular mycorrhizal (AM) fungi influence the plant establishment after disturbances, however, there were no reports on the succession of soil AM fungal communities after earthquakes. This study was carried out to monitor the changes of AM fungal species composition during plant succession after earthquakes. After a major earthquake, the ‘Chi-Chi’ event of 1999, a total of 4238 AM fungal spores belonging to 13 species were recorded. Higher AM fungal spore density was found in the crest area of the affected mountainside and the AM fungal community was significantly different between the crest and valley area. Scutellospora nigra, Acaulospora scrobiculata and Acaulospora tuberculata were dominant in the early succession stage. Glomus ambisporum, Glomus deserticola and Acaulospora mellea were more abundant in the late successional stage. These results demonstrated the dynamics of AM fungal community during succession and vegetation recovery.

Arbuscular mycorrhizal fungi with reference to different cultivars of Sesamum indicum L.

Arbuscular mycorrhizal (AM) fungi are the symbiotic association with plant roots and support plant growth through increased nutrient transport besides offering many other benefits. In the present investigation the role of AM fungi has been worked out in relation to six cultivars of Sesamum indicum L. The data reports the association of six AM fungi, root colonization plant height and yield. Gowri cultivar has exhibited more colonization, plant height, yield, oil content and other factors. Quantitative data of AM fungi has also been presented along with soil-physico-chemical factors.

MAXIMIZING THE SHELF LIFE OF MONOXENICALLY PRODUCED CARRIER-BASED AM FUNGAL BIO-INOCULA FOR MAINTAINING ITS LONG-TERM VIABILITY

Arbuscular mycorrhizal (AM) fungi are often applied as bio-inoculants due to their plant growth promoting benefits. The objectives of the present work were to maximize the shelf life of monoxenically produced carrier-based AM fungal bio-inocula of Rhizoglomus intraradices and Funneliformis mosseae. Shelf life of in vitro produced inoculum was studied by assessing the infectivity potential of in vitro produced inocula in an optimum carrier formulation (vermiculite: cow dung powder: wood powder: wood ash in the ratio of 20:8:2:1) during storage at three different temperatures viz., 4 °C, 25 °C and room temperature (RT). The re-germination potential of in vitro produced spores from carrier-based inocula to in vitro conditions was also examined. The in vitro produced inocula stored at 25 °C remained viable up to 6 mo in the organic carrier formulation. 100 % germination was recorded when the spores of both AM species were cultured back to in vitro conditions indicating high viability, and efficiency of the carrier formulation in maintaining vigour of in vitro produced propagules.

Arbuscular mycorrhizal fungal communities associated with two dominant species differ in their responses to long‐term nitrogen addition in temperate grasslands

Abstract Arbuscular mycorrhizal (AM) fungi are important components of grassland ecosystems and are sensitive to enhanced atmospheric nitrogen (N) deposition. Enhanced N deposition has been widely reported to reduce species richness and alter species composition across different types of grasslands world‐wide. Despite extensive studies on effects of N deposition on AM fungal communities of grasslands, few studies have specifically focused on effects of N deposition on AM fungi associated with dominant species in grasslands. We investigated long‐term (12‐year) effects of N addition (80 kg ha−1 year−1) on AM fungal community richness in roots and rhizosphere biomass of two dominant plant species (forb Artemisia frigida and grass Stipa krylovii) in temperate steppes of northern China. We found that AM fungi associated with the two dominant plant species differed in their responses to N addition. Nitrogen addition led to a significant reduction in AM fungal richness colonized in roots, and biomass in the rhizosphere of A. frigida, while N addition had little impacts on AM fungi colonized in roots and rhizosphere of S. krylovii. Nitrogen addition significantly reduced AM fungal colonization in roots and AM fungal spore density in the rhizosphere soils of A. frigida. In contrast, N addition had no effect on AM fungal colonization in roots and spore density in the rhizosphere of S. krylovii. Nitrogen addition markedly suppressed photosynthetic rates in A. frigida due to excessive foliar accumulation of manganese. The N‐induced reduction in photosynthetic rates reduced allocation of C into roots in A. frigida, leading to a lower root/shoot ratio, and suppression of AM fungal community associated with A. frigida. The inhibition of AM fungi would render A. frigida less competitive in terms of acquisition of mineral nutrients in soils, thus contributing to its loss in the steppe community under conditions of elevated N deposition. These findings provide a mechanistic explanation for N‐evoked differential responses of AM fungal communities associated with A. frigida and S. krylovii by linking soil properties and host plants to AM fungal communities. A plain language summary is available for this article.

Growth and Photosynthetic Responses of Litchi Seedlings to Arbuscular Mycorrhizal Fungal Inoculation: Differences between Two Genotypes

Arbuscular mycorrhizal (AM) fungi are beneficial symbiotic soil microorganisms and AM technology can find its potential application in the nursery of horticultural industry. When AM fungi have been successfully applied to many wood fruit tree species, little information is available in litchi (Litchi chinensis Sonn.). In this study, the seedlings of two litchi genotypes (‘Baila’ and ‘Heiye’) were inoculated with two AM fungal species (Rhizophagus irregularis and Gigaspora margarita) in the nursery conditions, and the growth and photosynthetic responses of seedlings to AM fungal inoculation were investigated. Results indicated that AM fungi significantly promoted the plant growth of ‘Heiye’ seedlings in terms of biomass, plant height, stem diameter and leaf number, while they slightly decreased these parameters of ‘Baila’. The inoculation effect can be explained by the changes in photosynthetic characteristics induced by AM fungi, because AM fungi increased Amax, Aqe, LSP and decreased LCP of ‘Heiye’ but did not affected those of ‘Baila’. Pn was not affected by AM fungi, however, regression analysis indicated a weaker relationship between biomass and Pn than those between biomass and Amax, LSP or LCP. Our results strongly suggest that AM fungi can differentially affect the seedling growth of litchi genotypes mainly via their effects on photosynthetic characteristics, and that precautions should be taken to select appropriate genotypes as rootstock if AM technology is applied in litchi nursery.

Can Cd translocation in Oryza sativa L. be attenuated by arbuscular mycorrhizal fungi in the presence of EDTA?

Arbuscular mycorrhizal (AM) fungi play an important role in plant tolerance of heavy metal contamination. In this study, a pot experiment was conducted to illustrate the effects of the two AM fungi species Funneliformis mosseae (Fm) and Rhizophagus irregularis (Ri) on plant growth of Oryza sativa L. either with or without ethylenediamine tetraacetate (EDTA) addition and during exposure to five Cd concentrations (in the range of 0-5mgkg-1). The results showed that Fm inoculation achieved greater mycorrhizal colonization and mycorrhizal dependency indexes than Ri inoculation. In addition, the effects of AM fungi on Cd biosorption and translocation in rice were also investigated in the presence of EDTA. Despite cooperative adsorption, the Freundlich isotherm could describe the biosorption effects of Cd on rice roots regardless of AM fungi inoculation or EDTA addition. Cd concentrations in mycorrhizal roots increased but decreased in mycorrhizal shoots in contrast to the control treatment. Although EDTA addition negatively inhibited the uptake of Cd to mycorrhizal shoots, lower translocation factor (TF) and bioconcentration factor (BCF) were still observed in treatments with EDTA compared to control treatment. Our findings suggest that Ri and Fm inoculation enhanced Cd immobilization in the roots, thus preventing Cd entry into the food chain during exposure to low and high Cd stress, respectively.

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering.

Arbuscular mycorrhizal (AM) fungi form mutualisms with plant roots that increase plant growth and shape plant communities. Each AM fungal cell contains a large amount of genetic diversity, but it is unclear if this diversity varies across evolutionary lineages. We found that sequence variation in the nuclear large-subunit (LSU) rRNA gene from 29 isolates representing 21 AM fungal species generally assorted into genus- and species-level clades, with the exception of species of the genera Claroideoglomus and Entrophospora However, there were significant differences in the levels of sequence variation across the phylogeny and between genera, indicating that it is an evolutionarily constrained trait in AM fungi. These consistent patterns of sequence variation across both phylogenetic and taxonomic groups pose challenges to interpreting operational taxonomic units (OTUs) as approximations of species-level groups of AM fungi. We demonstrate that the OTUs produced by five sequence clustering methods using 97% or equivalent sequence similarity thresholds failed to match the expected species of AM fungi, although OTUs from AbundantOTU, CD-HIT-OTU, and CROP corresponded better to species than did OTUs from mothur or UPARSE. This lack of OTU-to-species correspondence resulted both from sequences of one species being split into multiple OTUs and from sequences of multiple species being lumped into the same OTU. The OTU richness therefore will not reliably correspond to the AM fungal species richness in environmental samples. Conservatively, this error can overestimate species richness by 4-fold or underestimate richness by one-half, and the direction of this error will depend on the genera represented in the sample. Arbuscular mycorrhizal (AM) fungi form important mutualisms with the roots of most plant species. Individual AM fungi are genetically diverse, but it is unclear whether the level of this diversity differs among evolutionary lineages. We found that the amount of sequence variation in an rRNA gene that is commonly used to identify AM fungal species varied significantly between evolutionary groups that correspond to different genera, with the exception of two genera that are genetically indistinguishable from each other. When we clustered groups of similar sequences into operational taxonomic units (OTUs) using five different clustering methods, these patterns of sequence variation caused the number of OTUs to either over- or underestimate the actual number of AM fungal species, depending on the genus. Our results indicate that OTU-based inferences about AM fungal species composition from environmental sequences can be improved if they take these taxonomically structured patterns of sequence variation into account.

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.

Parameters for Selecting Efficient Arbuscular Mycorrhizal Fungi for Plants Under Microcosm Conditions

Arbuscular mycorrhizal (AM) fungi are mutualistic symbionts imparting a number of benefits to plants and are being advocated for being potential biofertilizer in the agriculture and forestry sectors. Superior AM fungi for forestry tree species (Acacia nilotica var. cupressiformis, Albizzia lebbeck and Eucalyptus tereticornis) and horticultural plant species (Capsicum annum, Allium cepa and Fragaria ananassa) were evaluated in a completely randomized design microcosm trial involving AM species of native and exotic origin. Out of ten AM fungal species used with forest species, G. intraradices (AM-1004) and mixed indigenous AM fungi (AM-1209) were found to give the highest P uptake in shoots, whereas in horticultural plants AM-1004 and AM-1207 (commercial inoculum, Mycorise) followed by mixed indigenous AM fungi (AM-1209) gave the highest P uptake in shoots. The shoot dry weight in these superior AM-mediated plants also indicated greater response and were highly correlated with P uptake (r = 0.53–0.88) and to a lesser extent with root colonization (r = 0.41–0.81). P uptake in the early growth stage (6–8 weeks) of AM-inoculated plants can be used as an indicator to evaluate superior AM fungi for growth promotion of forestry and horticultural plant species.