PacBio sequencing of Glomeromycota rDNA: a novel amplicon covering all widely used ribosomal barcoding regions and its applicability in taxonomy and ecology of arbuscular mycorrhizal fungi

Diversity of Arbuscular Mycorrhizal Fungi of the Rhizosphere of Lycium barbarum L. from Four Main Producing Areas in Northwest China and Their Effect on Plant Growth

Arbuscular mycorrhizal fungi (AMF) can help plants absorb more mineral nutrients after they colonize plant roots, and the mycelia harmonize the soil structure and physical and chemical properties by secreting compounds. AMF species co-evolve with their habitat's geographic conditions and hosts; this gradually causes differences in the AMF species. By using Melzer's reagent to analyze the morphology and using Illumina Miseq sequencing technology to perform the molecular identification of AMF communities among the four typical L. barbarum planting areas (Zhongning, Guyuan, Jinghe, and Dulan) investigated, the variety of L. barbarum roots and rhizosphere AMF communities was greater in the Zhongning area, and every region additionally had endemic species. The successfully amplified AMF was re-applied to the L. barbarum seedlings. We found that the total dry weight and accumulation of potassium increased significantly (p < 0.05), and the root volume and number of root branches were significantly higher in the plants that were inoculated with Paraglomus VTX00375 in the pot experiment, indicating that AMF improves root development and promotes plant growth. We have investigated AMF germplasm species in four regions, and we are committed to the development of native AMF resources. The multiplication and application of AMF will be conducive to realizing the potential role of biology in the maintenance of agroecology.

Diversity of Arbuscular Mycorrhizal Fungi in Distinct Ecosystems of the North Caucasus, a Temperate Biodiversity Hotspot

BACKGROUND

Investigations that are focused on arbuscular mycorrhizal fungus (AMF) biodiversity is still limited. The analysis of the AMF taxa in the North Caucasus, a temperate biodiversity hotspot, used to be limited to the genus level. This study aimed to define the AMF biodiversity at the species level in the North Caucasus biotopes.

METHODS

The molecular genetic identification of fungi was carried out with ITS1 and ITS2 regions as barcodes via sequencing using Illumina MiSeq, the analysis of phylogenetic trees for individual genera, and searches for operational taxonomic units (OTUs) with identification at the species level. Sequences from MaarjAM and NCBI GenBank were used as references.

RESULTS

We analyzed >10 million reads in soil samples for three biotopes to estimate fungal biodiversity. Briefly, 50 AMF species belonging to 20 genera were registered. The total number of the AM fungus OTUs for the "Subalpine Meadow" biotope was 171/131, that for "Forest" was 117/60, and that for "River Valley" was 296/221 based on ITS1/ITS2 data. The total number of the AM fungus species (except for virtual taxa) for the "Subalpine Meadow" biotope was 24/19, that for "Forest" was 22/13, and that for "River Valley" was 28/24 based on ITS1/ITS2 data. Greater AMF diversity, as well as number of OTUs and species, in comparison with that of forest biotopes, characterized valley biotopes (disturbed ecosystems; grasslands). The correlation coefficient between "Percentage of annual plants" and "Glomeromycota total reads" r = 0.76 and 0.81 for ITS1 and ITS2, respectively, and the correlation coefficient between "Percentage of annual plants" and "OTUs number (for total species)" was r = 0.67 and 0.77 for ITS1 and ITS2, respectively.

CONCLUSION

High AMF biodiversity for the river valley can be associated with a higher percentage of annual plants in these biotopes and the active development of restorative successional processes.

GlobalAMFungi: a global database of arbuscular mycorrhizal fungal occurrences from high-throughput sequencing metabarcoding studies

Arbuscular mycorrhizal (AM) fungi are crucial mutualistic symbionts of the majority of plant species, with essential roles in plant nutrient uptake and stress mitigation. The importance of AM fungi in ecosystems contrasts with our limited understanding of the patterns of AM fungal biogeography and the environmental factors that drive those patterns. This article presents a release of a newly developed global AM fungal dataset (GlobalAMFungi database, https://globalamfungi.com) that aims to reduce this knowledge gap. It contains almost 50 million observations of Glomeromycotinian AM fungal amplicon DNA sequences across almost 8500 samples with geographical locations and additional metadata obtained from 100 original studies. The GlobalAMFungi database is built on sequencing data originating from AM fungal taxon barcoding regions in: i) the small subunit rRNA (SSU) gene; ii) the internal transcribed spacer 2 (ITS2) region; and iii) the large subunit rRNA (LSU) gene. The GlobalAMFungi database is an open source and open access initiative that compiles the most comprehensive atlas of AM fungal distribution. It is designed as a permanent effort that will be continuously updated by its creators and through the collaboration of the scientific community. This study also documented applicability of the dataset to better understand ecology of AM fungal taxa.

Glomeromycota associations with bamboos (Bambusoideae) worldwide, a qualitative systematic review of a promising symbiosis

Background

Around the world, bamboos are ecologically, economically, and culturally important plants, particularly in tropical regions of Asia, America, and Africa. The association of this plant group with arbuscular mycorrhizal fungi belonging to the phylum Glomeromycota is still a poorly studied field, which limits understanding of the reported ecological and physiological benefits for the plant, fungus, soil, and ecosystems under this symbiosis relationship.

Methods

Through a qualitative systematic review following the PRISMA framework for the collection, synthesis, and reporting of evidence, this paper presents a compilation of the research conducted on the biology and ecology of the symbiotic relationship between Glomeromycota and Bambusoideae from around the world. This review is based on academic databases enriched with documents retrieved using different online databases and the Google Scholar search engine.

Results

The literature search yielded over 6,000 publications, from which 18 studies were included in the present review after a process of selection and validation. The information gathered from the publications included over 25 bamboo species and nine Glomeromycota genera from eight families, distributed across five countries on two continents.

Conclusion

This review presents the current state of knowledge regarding the symbiosis between Glomeromycota and Bambusoideae, while reflecting on the challenges and scarcity of research on this promising association found across the world.

Morphological and Molecular Characterizations of Arbuscular Mycorrhizal Fungi and Their Influence on Soil Physicochemical Properties and Plant Nutrition

Pulses are considered a remarkable and stable source of nutrients, which are being presently extensively cultivated and consumed in different parts of the world. Pulses belong to the family Leguminosae and are a rich source of nutrients such as phosphorus (P) and nitrogen (N) for best growth via symbiotic relationship with bacteria and AMF (arbuscular mycorrhizal fungi). The aim of the current study was evaluating the influence of AMF diversity associated with various pulses (French bean, mung bean, kidney bean, peas, soybean, peanuts, and grams). Furthermore, AMF characterization was done using morphological features of spores and sequencing of the rDNA gene, which confirmed the existence of 10 different AMF taxa. Among the different genera, the genus Glomus was observed to be the most dominant with 30% species followed by Gigaspora (22%), Sclerocystis (12%), Acaulospora (8%), Rhizophagus and Septoglomus (7%), Diversispora (5%), and Claroideoglomus, Archaeospora, and Ambispora (3%). Furthermore, soil physicochemical analysis and percentage of AMF colonization results revealed the fact that the phosphorus content (inversely proportional to the AMF diversity) was a determining factor of AMF diversity. The highest amount of available phosphorus (62.825 mg kg-1) in the district Swabi resulted in a low rate of AMF colonization (6.66 ± 11.54%) with a comparatively higher rate of AMF colonization (50.66 ± 1.15%) found in the soil of the district Chitral having a low phosphorus content (17.3 ± 7.6 mg kg-1). Nutrient uptake by pulses including nitrogen (2.4 ± 1.3%), phosphorus (13.5 ± 7.6 mg kg -1), potassium (99.5 ± 25.8 mg kg -1), zinc (1.4 ± 0.5 mg kg -1), moisture (2.3 ± 1.3%), crude fats (5.6 ± 2.8%), ash (4 ± 1.2%), and proteins (13.6 ± 9.01%) determined the fact that AMF species diversity is positively correlated to the plant mineral nutrition. From the current study, it is concluded that AMF inoculation to the soil fields is beneficial to ensure the sustainability and productivity of pulse crops in diverse environmental conditions without polluting the soil.

Influence of scat ageing on the gut microbiome: how old is too old?

BACKGROUND

The study of the host-microbiome by the collection of non-invasive samples has the potential to become a powerful tool for conservation monitoring and surveillance of wildlife. However, multiple factors can bias the quality of data recovered from scats, particularly when field-collected samples are used given that the time of defecation is unknown. Previous studies using scats have shown that the impact of aerobic exposure on the microbial composition is species-specific, leading to different rates of change in microbial communities. However, the impact that this aging process has on the relationship between the bacterial and fungal composition has yet to be explored. In this study, we measured the effects of time post-defecation on bacterial and fungal compositions in a controlled experiment using scat samples from the endangered koala (Phascolarctos cinereus).

RESULTS

We found that the bacterial composition remained stable through the scat aging process, while the fungal composition did not. The absence of an increase in facultative anaerobes and the stable population of obligate anaerobic bacteria were likely due to our sampling from the inner portion of the scat. We report a cluster of fungal taxa that colonises scats after defecation which can dilute the genetic material from the autochthonous mycoflora and inhibit recovery.

CONCLUSION

We emphasize the need to preserve the integrity of scat samples collected in the wild and combat the effects of time and provide strategies for doing so.

Metabarcoding Reveals Impact of Different Land Uses on Fungal Diversity in the South-Eastern Region of Antioquia, Colombia

Changes in soil fungal communities caused by land use have not been sufficiently studied in South American Andosols, which are considered key food production areas. Since fungal communities play an important role in soil functionality, this study analysed 26 soil samples of Andosols collected from locations devoted to conservation, agriculture and mining activities in Antioquia, Colombia, to establish differences between fungal communities as indicators of soil biodiversity loss using Illumina MiSeq metabarcoding on nuclear ribosomal ITS2 region. A non-metric multidimensional scaling allowed to explore driver factors of changes in fungal communities, while the significance of these variations was assessed by PERMANOVA. Furthermore, the effect size of land use over relevant taxa was quantified. Our results suggest a good coverage of fungal diversity with a detection of 353,312 high-quality ITS2 sequences. We found strong correlations of Shannon and Fisher indexes with dissimilarities on fungal communities (r = 0.94). These correlations allow grouping soil samples according to land use. Variations in temperature, air humidity and organic matter content lead to changes in abundances of relevant orders (Wallemiales and Trichosporonales). The study highlights specific sensitivities of fungal biodiversity features in tropical Andosols, which may serve as a basis for robust assessments of soil quality in the region.

Pesticide soil microbial toxicity: setting the scene for a new pesticide risk assessment for soil microorganisms (IUPAC Technical Report)

Pesticides constitute an integral part of modern agriculture. However, there are still concerns about their effects on non-target organisms. To address this the European Commission has imposed a stringent regulatory scheme for new pesticide compounds. Assessment of the aquatic toxicity of pesticides is based on a range of advanced tests. This does not apply to terrestrial ecosystems, where the toxicity of pesticides on soil microorganisms, is based on an outdated and crude test (N mineralization). This regulatory gap is reinforced by the recent methodological and standardization advances in soil microbial ecology. The inclusion of such standardized tools in a revised risk assessment scheme will enable the accurate estimation of the toxicity of pesticides on soil microorganisms and on associated ecosystem services. In this review we (i) summarize recent work in the assessment of the soil microbial toxicity of pesticides and point to ammonia-oxidizing microorganisms (AOM) and arbuscular mycorrhizal fungi (AMF) as most relevant bioindicator groups (ii) identify limitations in the experimental approaches used and propose mitigation solutions, (iii) identify scientific gaps and (iv) propose a new risk assessment procedure to assess the effects of pesticides on soil microorganisms.

Phenol and Polyaromatic Hydrocarbons Are Stronger Drivers Than Host Plant Species in Shaping the Arbuscular Mycorrhizal Fungal Component of the Mycorrhizosphere

Changes in soil microbial communities in response to hydrocarbon pollution are critical indicators of disturbed ecosystem conditions. A core component of these communities that is functionally adjusted to the life-history traits of the host and environmental factors consists of arbuscular mycorrhizal fungi (AMF). AMF communities associated with Poa trivialis and Phragmites australis growing at a phenol and polynuclear aromatic hydrocarbon (PAH)-contaminated site and at an uncontaminated site were compared based on LSU rDNA sequencing. Dissimilarities in species composition and community structures indicated soil pollution as the main factor negatively affecting the AMF diversity. The AMF communities at the contaminated site were dominated by fungal generalists (Rhizophagus, Funneliformis, Claroideoglomus, Paraglomus) with wide ecological tolerance. At the control site, the AMF communities were characterized by higher taxonomic and functional diversity than those exposed to the contamination. The host plant identity was the main driver distinguishing the two AMF metacommunities. The AMF communities at the uncontaminated site were represented by Polonospora, Paraglomus, Oehlia, Nanoglomus, Rhizoglomus, Dominikia, and Microdominikia. Polonosporaceae and Paraglomeraceae were particularly dominant in the Ph. australis mycorrhizosphere. The high abundance of early diverging AMF could be due to the use of primers able to detect lineages such as Paraglomeracae that have not been recognized by previously used 18S rDNA primers.

The Potential Applications of Commercial Arbuscular Mycorrhizal Fungal Inoculants and Their Ecological Consequences

Arbuscular mycorrhizal fungal (AMF) inoculants are sustainable biological materials that can provide several benefits to plants, especially in disturbed agroecosystems and in the context of phytomanagement interventions. However, it is difficult to predict the effectiveness of AMF inoculants and their impacts on indigenous AMF communities under field conditions. In this review, we examined the literature on the possible outcomes following the introduction of AMF-based inoculants in the field, including their establishment in soil and plant roots, persistence, and effects on the indigenous AMF community. Most studies indicate that introduced AMF can persist in the target field from a few months to several years but with declining abundance (60%) or complete exclusion (30%). Further analysis shows that AMF inoculation exerts both positive and negative impacts on native AMF species, including suppression (33%), stimulation (38%), exclusion (19%), and neutral impacts (10% of examined cases). The factors influencing the ecological fates of AMF inoculants, such as the inherent properties of the inoculum, dosage and frequency of inoculation, and soil physical and biological factors, are further discussed. While it is important to monitor the success and downstream impacts of commercial inoculants in the field, the sampling method and the molecular tools employed to resolve and quantify AMF taxa need to be improved and standardized to eliminate bias towards certain AMF strains and reduce discrepancies among studies. Lastly, inoculant producers must focus on selecting strains with a higher chance of success in the field, and having little or negligible downstream impacts.

DNA barcoding of fungal specimens using PacBio long-read high-throughput sequencing

Molecular methods are increasingly used to identify species that lack conspicuous macro- or micromorphological characters. Taxonomic and ecological research teams barcode large numbers of collected voucher specimens annually. In this study we assessed the efficiency of long-read high throughput sequencing (HTS) as opposed to the traditionally used Sanger method for taxonomic identification of multiple vouchered fungal specimens. We also evaluated whether this method can provide reference information about intra-individual gene polymorphism. We developed a workflow based on a test set of 423 basidiomycete specimens (representing 195 species), the PacBio HTS method, and ribosomal rRNA operon internal transcribed spacer (ITS) and 28S rRNA gene (LSU) markers. The PacBio HTS had a higher success rate than Sanger sequencing at a comparable cost. Species identification based on PacBio reads was usually straightforward, because the dominant operational taxonomic unit (OTU) typically represented the targeted organism. The PacBio HTS also enabled us to detect widespread polymorphism within the ITS marker. We conclude that multiplex DNA barcoding of the fungal ITS and LSU markers using PacBio HTS is a useful tool for taxonomic identification of large amounts of collected voucher specimens at a competitive price. Furthermore, PacBio HTS accurately recovers various alleles and paralogs, which can provide crucial information for species delimitation and population-level studies.

Illumina MiSeq Sequencing Reveals Correlations among Fruit Ingredients, Environmental Factors, and AMF Communities in Three Lycium Barbarum Producing Regions of China

The symbiotic relationship of arbuscular mycorrhizal fungi (AMF) is important for Lycium barbarum, a highly nutritious and medicinal crop. However, the influence of environmental factors on AMF communities remains largely elusive. Based on MiSeq sequencing, we analyzed AMF communities in rhizosphere soils of L. barbarum with growth synchronization in three typical L. barbarum cultivation sites in China. The Zhongning region has poor soils with a high richness of AMF communities. Geographical environmental variances lead to differences in AMF communities which in turn affects the active ingredients of L. barbarum fruit. Furthermore, different genera of AMF showed significant correlations with environmental factors and fruit ingredients. The three genera, Claroideoglomus, Dominikia, and Funneliformis correlated to environmental factors and fruits ingredients in a similar manner affecting the whole sugar (TS) and flavonoids (FLA) contents in the fruits of L. barbarum. Also, these showed a significantly positive correlation with soil pH. This fact was unknown so far due to different soil acidity/alkalinity in different studies. IMPORTANCE The climatic and ecological environment is a complex phenomenon, involving various environmental factors that regulate the diversity and population distribution structure of AMF communities affecting plant growth, crop composition, and yield. Current studies on the effects of environmental factors on AMF communities have mainly focused on soil conditions and host plants. Fewer studies have been conducted on the correlation between temperature, enzyme activity, plant fruiting, and AMF communities. The present study investigated the diversity of AMF communities and the influence of environmental factors on their distribution patterns, which showed similar effects on some AMF species. The results suggest that screening AMF fungicides that meet the target may significantly help soil restoration reducing the use of chemical fertilizers and a large amount of human and material resources.

Best practices in metabarcoding of fungi: From experimental design to results

The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview of current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By reanalysing published data sets, we demonstrate that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, a finding that is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared to the ITS2 subregion. Finally, we show that specific methods for compositional data analyses provide more reliable estimates of shifts in community structure. We conclude that metabarcoding analyses of fungi are especially promising for integrating fungi into the full microbiome and broader ecosystem functioning context, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.

Environmental identification of arbuscular mycorrhizal fungi using the LSU rDNA gene region: an expanded database and improved pipeline

Arbuscular mycorrhizal fungi (AMF; Glomeromycota) are difficult to culture; therefore, establishing a robust amplicon-based approach to taxa identification is imperative to describe AMF diversity. Further, due to low and biased sampling of AMF taxa, molecular databases do not represent the breadth of AMF diversity, making database matching approaches suboptimal. Therefore, a full description of AMF diversity requires a tool to determine sequence-based placement in the Glomeromycota clade. Nonetheless, commonly used gene regions, including the SSU and ITS, do not enable reliable phylogenetic placement. Here, we present an improved database and pipeline for the phylogenetic determination of AMF using amplicons from the large subunit (LSU) rRNA gene. We improve our database and backbone tree by including additional outgroup sequences. We also improve an existing bioinformatics pipeline by aligning forward and reverse reads separately, using a universal alignment for all tree building, and implementing a BLAST screening prior to tree building to remove non-homologous sequences. Finally, we present a script to extract AMF belonging to 11 major families as well as an amplicon sequencing variant (ASV) version of our pipeline. We test the utility of the pipeline by testing the placement of known AMF, known non-AMF, and Acaulospora sp. spore sequences. This work represents the most comprehensive database and pipeline for phylogenetic placement of AMF LSU amplicon sequences within the Glomeromycota clade.

Multiple Arbuscular Mycorrhizal Fungal Consortia Enhance Yield and Fatty Acids of Medicago sativa: A Two-Year Field Study on Agronomic Traits and Tracing of Fungal Persistence

Arbuscular mycorrhizal fungi are promoted as biofertilizers due to potential benefits in crop productivity, and macro- and microelement uptake. However, crop response to arbuscular mycorrhizal fungi (AMF) inoculation is context-dependent, and AMF diversity and field establishment and persistence of inoculants can greatly contribute to variation in outcomes. This study was designed to test the hypotheses that multiple and local AMF inoculants could enhance alfalfa yield and fatty acids (FA) compared to exotic isolates either single or in the mixture. We aimed also to verify the persistence of inoculated AMF, and which component of the AMF communities was the major driver of plant traits. Therefore, a field experiment of AMF inoculation of alfalfa (Medicago sativa L.) with three single foreign isolates, a mixture of the foreign isolates (FMix), and a highly diverse mixture of local AMF (LMix) was set up. We showed that AMF improved alfalfa yield (+ 68%), nutrient (+ 147% N content and + 182% P content in forage), and FA content (+ 105%). These positive effects persisted for at least 2 years post-inoculation and were associated with enhanced AMF abundance in roots. Consortia of AMF strains acted in synergy, and the mixture of foreign AMF isolates provided greater benefits compared to local consortia (+ 20% forage yield, + 36% forage N content, + 18% forage P content, + 20% total FA in forage). Foreign strains of Funneliformis mosseae and Rhizophagus irregularis persisted in the roots of alfalfa 2 years following inoculation, either as single inoculum or as a component of the mixture. Among inoculants, F. mosseae BEG12 and AZ225C and the FMix exerted a higher impact on the local AMF community compared with LMix and R. irregularis BEG141. Finally, the stimulation of the proliferation of a single-taxa (R. irregularis cluster1) induced by all inoculants was the main determinant of the host benefits. Crop productivity and quality as well as field persistence of inoculated AMF support the use of mixtures of foreign AMF. On the other hand, local mixtures showed a lower impact on native AMF. These results pave the way for extending the study on the effect of AMF mixtures for the production of high-quality forage for the animal diet.

New taxa in Glomeromycota: Polonosporaceae fam. nov., Polonospora gen. nov., and P. polonica comb. nov

Phylogenetic analyses of sequences of the nuc rDNA small subunit (18S), internal transcribed spacer (ITS1-5.8S-ITS2 = ITS), and large subunit (28S) region (= 18S-ITS-28S), as well as sequences of this region concatenated with sequences of the largest subunit of RNA polymerase II (RPB1) gene, proved that the species originally described as Acaulospora polonica (phylum Glomeromycota) represents a new genus and a new family of the ancient order Archaeosporales, here introduced into the Glomeromycota under the names Polonospora and Polonosporaceae, respectively. The phylogenetic analyses and BLASTn queries also indicated that the Polonosporaceae with P. polonica comb. nov. still contains several morphologically undescribed taxa at the ranks of genus and species, which have a worldwide distribution.