Desert plants, arbuscular mycorrhizal fungi and associated bacteria: Exploring the diversity and role of symbiosis under drought.

Desert plants, such as Agave tequilana, A. salmiana and Myrtillocactus geometrizans, can survive harsh environmental conditions partly due to their symbiotic relationships with microorganisms, including arbuscular mycorrhizal fungi (AMF). Interestingly, some of these fungi also harbour endosymbiotic bacteria. Our research focused on investigating the diversity of these AMFs and their associated bacteria in these plants growing in arid soil. We found that agaves have a threefold higher AMF colonization than M. geometrizans. Metabarcoding techniques revealed that the composition of AMF communities was primarily influenced by the plant host, while the bacterial communities were more affected by the specific plant compartment or niche they inhabited. We identified both known and novel endofungal bacterial taxa, including Burkholderiales, and confirmed their presence within AMF spores using multiphoton microscopy. Our study also explored the effects of drought on the symbiosis between A. tequilana and AMF. We discovered that the severity of drought conditions could modulate the strength of this symbiosis and its outcomes for the plant holobiont. Severe drought conditions prevented the formation of this symbiosis, while moderate drought conditions promoted it, thereby conferring drought tolerance in A. tequilana. This research sheds light on the diversity of AMF and associated bacteria in Crassulacean Acid Metabolism (CAM) plants and underscores the crucial role of drought as a factor modulating the symbiosis between A. tequilana and AMF. Further research is needed to understand the role of endofungal bacteria in this response.

New Cortinariaceae species associated with Dicymbe, Aldina, and Pakaraimaea in Guyana.

Species of the ectomycorrhizal (ECM) family Cortinariaceae (Agaricales, Agaricomycetes, Basidiomycota) have long been considered impoverished or absent from lowland tropical rainforests. Several decades of collecting in forests dominated by ECM trees in South America's Guiana Shield is countering this view, with discovery of numerous Cortinariaceae species. To date, ~12 morphospecies of this family have been found in the central Pakaraima Mountains of Guyana. Here, we describe three of these as new species of Cortinarius and two as new species of Phlegmacium from forests dominated by the ECM tree genera Dicymbe (Fabaceae subfam. Detarioideae), Aldina (Fabaceae subfam. Papilionoideae), and Pakaraimaea (Cistaceae). Macromorphological, micromorphological, habitat, and DNA sequence data are provided for each new species.

Grazing exclusion-induced changes in soil fungal communities in a highly desertified Brazilian dryland.

Soil desertification poses a critical ecological challenge in arid and semiarid climates worldwide, leading to decreased soil productivity due to the disruption of essential microbial community processes. Fungi, as one of the most important soil microbial communities, play a crucial role in enhancing nutrient and water uptake by plants through mycorrhizal associations. However, the impact of overgrazing-induced desertification on fungal community structure, particularly in the Caatinga biome of semiarid regions, remains unclear. In this study, we assessed the changes in both the total fungal community and the arbuscular mycorrhizal fungal community (AMF) across 1. Natural vegetation (native), 2. Grazing exclusion (20 years) (restored), and 3. affected by overgrazing-induced degradation (degraded) scenarios. Our assessment, conducted during both the dry and rainy seasons in Irauçuba, Ceará, utilized Internal Transcribed Spacer (ITS) gene sequencing via Illumina® platform. Our findings highlighted the significant roles of the AMF families Glomeraceae (∼71% of the total sequences) and Acaulosporaceae (∼14% of the total sequences) as potential key taxa in mitigating climate change within dryland areas. Moreover, we identified the orders Pleosporales (∼35% of the total sequences) and Capnodiales (∼21% of the total sequences) as the most abundant soil fungal communities in the Caatinga biome. The structure of the total fungal community differed when comparing native and restored areas to degraded areas. Total fungal communities from native and restored areas clustered together, suggesting that grazing exclusion has the potential to improve soil properties and recover fungal community structure amid global climate change challenges.

Distinct orchid mycorrhizal fungal communities among co-occurring Vanilla species in Costa Rica: root substrate and population-based segregation.

Despite being the second largest family of flowering plants, orchids represent community structure variation in plant-microbial associations, contributes to niche partitioning in metacommunity assemblages. Yet, mycorrhizal communities and interactions remain unknown for orchids that are highly specialized or even obligated in their associations with their mycorrhizal partners. In this study, we sought to compare orchid mycorrhizal fungal (OMF) communities of three co-occurring hemiepiphytic Vanilla species (V. hartii, V. pompona, and V. trigonocarpa) in tropical forests of Costa Rica by addressing the identity of their OMF communities across species, root types, and populations, using high-throughput sequencing. Sequencing the nuclear ribosomal internal transcribed spacer (nrITS) yielded 299 fungal Operational Taxonomic Units (OTUs) from 193 root samples. We showed distinct segregation in the putative OMF (pOMF) communities of the three coexisting Vanilla hosts. We also found that mycorrhizal communities associated with the rare V. hartii varied among populations. Furthermore, we identified Tulasnellaceae and Ceratobasidiaceae as dominant pOMF families in terrestrial roots of the three Vanilla species. In contrast, the epiphytic roots were mainly dominated by OTUs belonging to the Atractiellales and Serendipitaceae. Furthermore, the pOMF communities differed significantly across populations of the widespread V. trigonocarpa and showed patterns of distance decay in similarity. This is the first report of different pOMF communities detected in roots of wild co-occurring Vanilla species using high-throughput sequencing, which provides evidence that three coexisting Vanilla species and their root types exhibited pOMF niche partitioning, and that the rare and widespread Vanilla hosts displayed diverse mycorrhizal preferences.

Four new species of Russula subsection Roseinae from tropical montane forests in western Panama.

Species of the genus Russula are key components of ectomycorrhizal ecosystems worldwide. Nevertheless, their diversity in the tropics is still poorly known. This study aims to contribute to the knowledge of the diversity of Russula species classified in subsection Roseinae based on specimens recently collected in tropical montane rainforests in western Panama. A five gene multilocus phylogeny based on the nuclear markers ITS nrDNA, MCM7, RPB1, RPB2 and TEF-1α was constructed to identify the systematic position of 22 collections from Panama. Four new species, Russula cornicolor, Russula cynorhodon, Russula oreomunneae and Russula zephyrovelutipes are formally described and illustrated. None of the four species are sister species and they are more closely related to North American or Asian species. Two of the newly described species were associated with the ectomycorrhizal tree species Oreomunnea mexicana, while the other two species were associated with Quercus species. All four species are so far only known from mountains in western Panama.

Diversity and community structure of ectomycorrhizal fungi in Pinus thunbergii coastal forests bordering the Yellow Sea of China.

Ectomycorrhizas play a fundamental role in the function of forest ecosystems, being essential for plant nutrition absorption and soil quality. Many afforestation and reforestation programmes have begun to recover and maintain coastal forests in China, using pine species including Pinus thunbergii. We investigated the ectomycorrhizal colonization status of P. thunbergii in coastal pine forests of the Yellow Sea of China. We identified a total of 53 ectomycorrhizal fungal species in 74 soil samples collected from three sites and found that Thelephoraceae (10 spp.) and Russulaceae (8 spp.) were the most species-rich ectomycorrhizal fungal lineages. Russula sp. 1 was the most abundant species, accounting for 15.3% of the total ectomycorrhizal tips identified. Most of the remaining species were rare. At this small scale, host identity had no significant effect on the ectomycorrhizal fungal community composition (A = 0.036, P = 0.258), but sampling sites did (A = 0.135, P = 0.041). In addition, Na+ and K+ content and soil pH had significant effects on the ectomycorrhizal fungal community. The ectomycorrhizal fungal community associated with different host plants will become an important new direction for research, as ectomycorrhiza may have the potential to improve host capacity to establish in salt-stressed environments. This will provide a theoretical basis and technical support for saline soil reforestation and rehabilitation using pine species with compatible, native ectomycorrhizal fungi in Yellow Sea coastal areas.

Impact of land use history on the arbuscular mycorrhizal fungal diversity in arid soils of Argentinean farming fields.

Arbuscular mycorrhizal fungi (AMF) are a key soil functional group, with an important potential to increase crop productivity and sustainable agriculture including food security. However, there is clear evidence that land uses, crop rotations and soil features affect the AMF diversity and their community functioning in many agroecosystems. So far, the information related to AMF biodiversity in ecosystems like the Argentinean Puna, an arid high plateau where plants experience high abiotic stresses, is still scarce. In this work, we investigated morphological and molecular AMF diversity in soils of native corn, bean and native potato Andean crops, under a familiar land use, in Chaupi Rodeo (Jujuy, Argentina), without agrochemical supplements but with different histories of crop rotation. Our results showed that AMF morphological diversity was not only high and variable among the three different crop soils but also complemented by Illumina MiSeq data. The multivariate analyses highlighted that total fungal diversity is significantly affected by the preceding crop plants and the rotation histories, more than from the present crop species, while AMF communities are significantly affected by preceding crop only in combination with the effect of nitrogen and calcium soil concentration. This knowledge will give useful information on appropriate familiar farming.

Mutualist and pathogen traits interact to affect plant community structure in a spatially explicit model.

Empirical studies show that plant-soil feedbacks (PSF) can generate negative density dependent (NDD) recruitment capable of maintaining plant community diversity at landscape scales. However, the observation that common plants often exhibit relatively weaker NDD than rare plants at local scales is difficult to reconcile with the maintenance of overall plant diversity. We develop a spatially explicit simulation model that tracks the community dynamics of microbial mutualists, pathogens, and their plant hosts. We find that net PSF effects vary as a function of both host abundance and key microbial traits (e.g., host affinity) in ways that are compatible with both common plants exhibiting relatively weaker local NDD, while promoting overall species diversity. The model generates a series of testable predictions linking key microbial traits and the relative abundance of host species, to the strength and scale of PSF and overall plant community diversity.

Septoglomus mexicanum, a new species of arbuscular mycorrhizal fungi from semiarid regions in Mexico.

Septoglomus mexicanum is here described as a new species of arbuscular mycorrhizal fungi (AMF; Glomeromycota) based on morphological and phylogenetic analyses. It was isolated from rhizospheric soil of two endemic Mexican legumes: Prosopis laevigata and Mimosa luisana, which grow in semiarid regions of central Mexico. Septoglomus mexicanum is characterized by forming globose spores of (154.5-)202.8(-228.9) µm diam and a spore wall consisting of four layers (SWL1-SWL4): outer wall layer (SWL1) hyaline, evanescent, (1.7-)3.2(-4.3) µm thick; SWL2 laminate and smooth, orange to reddish orange, (3.1-)4.5(-6.1) µm thick; SWL3 laminate, smooth, reddish orange to reddish brown, (4.1-)5.1(-5.7) µm thick; and SWL4 hyaline, semiflexible, (0.93-)1.2(-1.4) µm thick. None of the spore wall layers stain with Melzer's reagent. The subtending hypha has a color from yellowish to golden and presents a septum on spore base. Septoglomus mexicanum can be distinguished from all other Septoglomus species by spore size and color, by spore wall structure (four layers), and by color change of the subtending hypha. Phylogenetic analysis based on the AMF extended DNA barcode covering a 1.5-kb fragment of the small subunit (SSU), internal transcribed spacer region (ITS1-5.8S-ITS2), and the large subunit (LSU) of rRNA genes places S. mexicanum in the genus Septoglomus, separated from other described Septoglomus species, especially S. turnauae, with whom it could be confused morphologically. All available sequences in public databases suggest that this new fungal species has not yet been previously detected. Thus, there are currently 149 Glomeromycota species registered in Mexico, representing 47.4% of the known species worldwide.

Is arbuscular mycorrhizal fungal species community affected by cotton growth management systems in the Brazilian Cerrado?

Conventional cotton production in western Bahia, Brazil, involves intensive use of agricultural inputs and mechanization, which may affect arbuscular mycorrhizal fungi (AMF). This work aimed at studying the impact of conventional and organic cotton production in the AMF of western Bahia. Soil samples were obtained from conventional white cotton and colored cotton organic production systems as well as from native Cerrado areas, close to the white cotton fields, and from the subcaducifolia vegetation, close to the organic colored cotton farms. The most frequent species in the conventional farming areas belonged to the genera Acaulospora (10 spp.); Glomus (8 spp.); Dentiscutata (3 spp.); Ambispora, Pacispora and Scutellospora (2 spp. each), as well as Claroideoglomus etunicatum, Diversispora sp., Entrophospora infrequens, Gigaspora sp., Orbispora pernambucana, Paradentiscutata maritima, and Paraglomus occultum. Eighteen species were found in the organic farming areas, with the predominance of Glomus (5 spp.) and Acaulospora (5 spp.), and with Claroideoglomus, Dentiscutata, Gigaspora, Corymbiglomus, Orbispora, Paraglomus, Scutellospora, and Simiglomus (1 spp. each). Paraglomus bolivianum was first reported in Cerrado. In the native vegetation, nine species were found, with the predominance of Glomus and Acaulospora. The highest number of AMF species was found in the organic farming areas, which deserves further investigation.

Plant-soil feedback of two legume species in semi-arid Brazil.

Positive feedback between arbuscular mycorrhizal fungal (AMF) and vascular plants can contribute to plant species establishment, but how this feedback affects plant invasion by Prosopis juliflora SW. (DC.), or resistance to invasion by Mimosa tenuiflora (Willd.) Poir in Brazilian semi-arid region is not well known. In this work, we tested how modified and native AMF communities affect the establishment of P. juliflora and M. tenuiflora plants. We examined the effects of inoculation with modified and native AMF communities on number of AMF spores, root colonization, number of N-fixing nodules, plant dry biomass, plant phosphorous concentration, and plant responsiveness to mycorrhizas of P. juliflora and M. tenuiflora. We found that the modified AMF community enhanced the root colonization, plant dry biomass, and plant phosphorous concentration of invasive P. juliflora, whereas native AMF enhanced M. tenuiflora. Our results demonstrate that the invasive P. juliflora alters soil AMF community composition, and this change generates positive feedback to the invasive P. juliflora itself and decreases AMF associations with native M. tenuiflora.

Edaphic Factors Influence the Distribution of Arbuscular Mycorrhizal Fungi Along an Altitudinal Gradient of a Tropical Mountain.

Changes in relief in montane areas, with increasing altitude, provide different biotic and abiotic conditions, acting on the species of arbuscular mycorrhizal fungi (AMF). The objective of this work was to determine the influence of altitude, edaphic factors, and vegetation on the AMF species in a mountainous area. The list of AMF species was obtained from morphological identification of the spores, with 72 species recovered from field samples and trap cultures. Lower levels of Shannon's diversity occurred only at lower altitude; however, there was no difference in AMF richness. The structure of the AMF assembly between the two highest altitudes was similar and differed in relation to the lower altitude. There was variation in the distribution of AMF species, which was related to soil texture and chemical factors along the altitude gradient. Some species, genera, and families were indicative of a certain altitude, showing the preference of fungi for certain environmental conditions, which may aid in decisions to conserve montane ecosystems.

Systematic study of truffles in the genus Ruhlandiella, with the description of two new species from Patagonia.

Ruhlandiella is a genus of exothecial, ectomycorrhizal fungi in the order Pezizales. Ascomata of exothecial fungi typically lack a peridium and are covered with a hymenial layer instead. Ruhlandiella species have nonoperculate asci and highly ornamented ascospores. The genus was first described by Hennings in 1903 to include the single species, R. berolinensis. Since then, mycologists have uncovered Ruhlandiella species in many locations around the globe, including Australia, Spain, Italy, and the USA. Currently, there are four recognized species: R. berolinensis, R. peregrina, R. reticulata, and R. truncata. All were found near Eucalyptus or Melaleuca trees of Australasian origin. Recently, we discovered two new species of Ruhlandiella in Nothofagaceae forests in South America. They regularly form mitotic spore mats directly on soil in the forests of Patagonia. Here, we formally describe these new species and construct the phylogeny of Ruhlandiella and related genera using a multilocus phylogenetic analysis. We also revise the taxonomy of Ruhlandiella and provide an identification key to accepted species of Ruhlandiella.

Distinct arbuscular mycorrhizal fungal communities associate with different manioc landraces and Amazonian soils.

Manioc (Manihot esculenta Crantz) is an important tropical crop that depends on arbuscular mycorrhizal (AM) association for its nutrition. However, little is known about the richness and species composition of AM fungal communities associating with manioc and possible differences across soils and manioc landraces. We studied the diversity and composition of AM fungal communities present in the roots of different manioc landraces and surrounding soils in indigenous shifting cultivation fields on different Amazonian soil types. A total of 126 AM fungal virtual taxa (VT; phylogenetically defined taxonomic units) were recovered from soil and root samples using 454 sequencing of AM fungal SSU rRNA gene amplicons. Different AM fungal communities occurred in different soil types. Minor differences occurred in the composition of AM fungal community associating with different manioc landraces, but AM fungal richness was not different among them. There was a low similarity between the AM fungal communities colonizing manioc roots and those recorded in the soil, independently of differences in soil properties or the manioc landrace evaluated. Rhizophagus manihotis and Glomus VT126 were the most abundant AM fungal species colonizing manioc roots. Contrasting with the results of earlier spore-based investigations, all the AM fungi identified as indicator species of particular manioc landraces were morphologically unknown Glomus species. In conclusion, different manioc landraces growing in common conditions associated with distinct AM fungal communities, whereby AM fungal communities in soils did not necessarily reflect the AM fungal communities colonizing manioc roots.

Soil lead pollution modifies the structure of arbuscular mycorrhizal fungal communities.

The impact of lead (Pb) pollution on native communities of arbuscular mycorrhizal fungi (AMF) was assessed in soil samples from the surroundings of an abandoned Pb smelting factory. To consider the influence of host identity, bulk soil surrounding plant roots soil samples of predominant plant species (Sorghum halepense, Bidens pilosa, and Tagetes minuta) growing in Pb-polluted soils and in an uncontaminated site were selected. Molecular diversity was assessed by sequencing the 18S rDNA region with primers specific to AMF (AMV4.5NF/AMDGR) using Illumina MiSeq. A total of 115 virtual taxa (VT) of AMF were identified in this survey. Plant species did not affect AMF diversity patterns. However, soil Pb content was negatively correlated with VT richness per sample. Paraglomeraceae and Glomeraceae were the predominant families while Acaulosporaceae, Ambisporaceae, Archaeosporaceae, Claroideoglomeraceae, Diversisporaceae, and Gigasporaceae were less abundant. Acaulosporaceae and Glomeraceae were negatively affected by soil Pb, but Paraglomeraceae relative abundance increased under increasing soil Pb content. Overall, 26 indicator taxa were identified; four of them were previously reported in Pb-polluted soils (VT060; VT222; VT004; VT380); and five corresponded to cultured spores of Scutellospora castaneae (VT041), Diversispora spp. and Tricispora nevadensis (VT060), Diversispora epigaea (VT061), Glomus proliferum (VT099), and Gl. indicum (VT222). Even though AMF were present in Pb-polluted soils, community structure was strongly altered via the differential responses of taxonomic groups of AMF to Pb pollution. These taxon-specific differences in tolerance to soil Pb content should be considered for future phytoremediation strategies based on the selection and utilization of native Glomeromycota.

Agroecological coffee management increases arbuscular mycorrhizal fungi diversity.

Agroecology aims to maintain ecosystem services by minimizing the impact of agriculture and promoting the use of biological potential. Arbuscular mycorrhizal fungi (AMF) are elements which are key to improving crop productivity and soil quality. It is pertinent to understand how agricultural management in the tropics affects the AMF spatio-temporal community composition, especially in crops of global importance, such as coffee (Coffea arabica L.). Soil and root samples were collected from three localities under three management systems (agroecological, conventional and forest fragment), during the phenological stages of coffee (flowering, grain filling, harvesting). Spores were extracted for morphological identification and molecular community analysis by PCR-DGGE. Dendrograms were prepared and the bands were sequenced and analyzed by bioinformatics. No differences were observed in the richness of morphospecies between management systems, localities and period, but little is known about tropical species. Molecular analysis showed that the agroecological management system was similar to natural forest and with a higher diversity indices than conventional management. Locality and period of sample affect AMF community composition. It is necessary to associate classical taxonomic evaluations with molecular biological techniques because different approaches can lead to different outcomes. This study contributes to the understanding of the impact of agriculture management systems on AMF and provides evidence that agroecology is a management system applicable to sustainable coffee production.

Characteristics of root-cultivable endophytic fungi from Rhododendron ovatum Planch.

Ericoid mycorrhiza can improve the competitiveness of their host plants at the ecosystem level. The ability of ericoid mycorrhizal fungi to thrive under harsh environmental conditions suggests that they are capable of decomposing plant organic matter. This study aims to characterize 2 strains of root-cultivable endophytic fungi, RooDK1 and RooDK6, from Rhododendron ovatum Planch using colony and hyphal morphology, molecular analysis, observations of mycorrhiza, and investigations of adaptation to different sources of organic matter. Nitrogen utilization was also investigated by assessing protease production and growth on different nitrogen sources. Morphological studies indicated that both species are ericoid mycorrhizal fungi; our molecular studies confirmed RooDK1 as Oidiodendron maius and classified RooDK6 as Pezicula ericae. We observed that only RooDK1 can assist in host plant survival by degrading organic matter. This species also secretes protease and has the highest nitrate reductase activity of these 2 endophytes. Thus, RooDK1 has a greater ability to help the host plants thrive in a harsh habitat.

Community composition of arbuscular mycorrhizal fungi associated with native plants growing in a petroleum-polluted soil of the Amazon region of Ecuador.

Arbuscular mycorrhizal fungi (AMF) are worldwide distributed plant symbionts. However, their occurrence in hydrocarbon-polluted environments is less investigated, although specific communities may be present with possible interest for remediation strategies. Here, we investigated the AMF community composition associated with the roots of diverse plant species naturally recolonizing a weathered crude oil pond in the Amazon region of Ecuador. Next generation 454 GS-Junior sequencing of an 800 bp LSU rRNA gene PCR amplicon was used. PCR amplicons were affiliated to a maximum-likelihood phylogenetic tree computed from 1.5 kb AMF reference sequences. A high throughput phylogenetic annotation approach, using an evolutionary placement algorithm (EPA) allowed the characterization of sequences to the species level. Fifteen species were detected. Acaulospora species were identified as dominant colonizers, with 73% of relative read abundance, Archaeospora (19.6%) and several genera from the Glomeraceae (Rhizophagus, Glomus macrocarpum-like, Sclerocystis, Dominikia and Kamienskia) were also detected. Although, a diverse community belonging to Glomeraceae was revealed, they represented <10% of the relative abundance in the Pond. Seventy five % of the species could not be identified, suggesting possible new species associated with roots of plants under highly hydrocarbon-polluted conditions.

Two Lactarius species (subgenus Plinthogalus) in ectomycorrhizal association with tropical Quercus trees in eastern Mexico.

Two species of Lactarius are documented from fragments of tropical lowland oak forest in central Veracruz. Lactarius trichodermoides, described here as new, was found in association with Quercus sapotifolia and Lactarius subplinthogalus with Quercus glaucescens. Both Lactarius species were identified morphologically and supported by phylogenetic analyses of nuc rDNA internal transcribed spacers (ITS1-5.8S-ITS2) and D1-D2 domains of nuc 28S rDNA sequences. Confirmation of mycobionts in ectomycorrhizal (ECM) associations was verified by molecular identification of ECM root tips. Detailed macroscopic and microscopic descriptions and photographs and illustrations of basidiomes and ectomycorrhizas are presented. The new binomial Lactarius chiangmaiensis is proposed for L. subplinthogalus var. chiangmaiensis.

The enigmatic Cortinarius magellanicus complex occurring in Nothofagaceae forests of the Southern Hemisphere.

Cortinarius magellanicus Speg. is an edible, ectomycorrhizal fungus, widely distributed in Argentina, Chile and New Zealand. However, earlier studies already indicated that the epithet 'magellanicus' might have been applied in a wide sense, thus circumscribing several species. A neotype was designated by Moser and Horak (1975) due Spegazzini's type was lost. Argentinian Nothofagaceae forests' samples, from autumn of 2017, morphologically recognized as C. magellanicus were used for a phylogenetic analysis, including sequences from type material and closely related species. Our results showed that C. magellanicus represents a complex of species, with at least three phylogenetic lineages, each with strong regionalism and distinct host associations. Cortinarius magellanicus s. str. is restricted to Patagonia of Argentina and Chile. The misidentified reports from New Zealand and Australia represent distinct and different lineages. In the present contribution, the re-description of C. magellanicus is based on neotype material and two new species are proposed. Cortinarius vitreopileatus var. similissimus is described as variety from New Zealand resembling C. magellanicus, however without close phylogenetic relationship to it. The taxonomic delimitation for C. magellanicus species complex is of high relevance due to the abundance of these fungi and their ectomycorrhizal role in Nothofagaceae forests in Gondwanian region.