Ectomycorrhizosphere Soils Research Articles

Metagenomics offers insights into the rhizospheric bacterial diversity of mushrooms from a tropical forest and temperate forest of India

Bacteria promote mushroom growth by providing growth factors and vitamins, preventing pathogen growth, and enhancing spore distribution. Soil bacteria involved in the nitrogen cycle showed association with the abundance of ectomycorrhizal fungi. Uncultured microorganisms comprise a significant proportion of complex soil ecosystem. Nanopore sequencing Technologies used a genome-resolved metagenomics approach to evaluate the rhizospheric bacterial diversity of these mushrooms from the tropical forests of West Bengal (India) and the temperate forests of West Kameng districts in Arunachal Pradesh, India. The ectomycorrhizosphere soil of tropical forest has higher abundance of nitrogen fixing bacteria such as Bradyrhizobium diazoefficiens, B. erythrophlei, and B. elkanii whereas the ectomycorrhizosphere soil of temperate forest has higher abundance of Candidatus Solibacter usitatus, Rhodoplanes sp. Z2-YC6860, Candidatus Koribacter versatilis, Bacillus cereus, Granulicella tundricola, G. mallensis, Bradyrhizobium icense, Bradyrhizobium sp. SK17, Acidobacterium capsulatum, Bacillus weihaiensis, Terriglobus saanensis, Planococcus sp. MB-3u-03, Bradyrhizobium sp. CCGE-LA001, and Bradyrhizobium japonicum These microorganisms have deep impact in the growth and development of ectomycorrhizal partners (trees and mushrooms) and be called as mycorrhiza helper bacteria (MHB).

Black Truffles Affect Quercus aliena Physiology and Root-Associated nirK- and nirS-Type Denitrifying Bacterial Communities in the Initial Stage of Inoculation.

Truffles (Tuber spp.) are edible ectomycorrhizal fungi with high economic value. Bacteria in ectomycorrhizosphere soils are considered to be associated with the nutrient uptake of truffles and hosts. Whether Tuber spp. inoculation can affect the growth of Quercus aliena, the ectomycorrhizosphere soil, and the rhizosphere nirK and nirS-denitrifier communities at the ectomycorrhizae formation stage is still unclear. Therefore, we inoculated Q. aliena with the black truffles Tuber melanosporum and Tuber indicum, determined the physiological activity and morphological indices of Q. aliena seedlings, analyzed the physicochemical properties of ectomycorrhizosphere soils, and applied DNA sequencing to assess the nirK and nirS- denitrifier community structure in ectomycorrhizosphere soils. Peroxidase activity was higher in the seedlings inoculated with T. melanosporum than in the T. indicum inoculation and uninoculated control treatments. The available phosphorus contents were lower and nitrate contents were higher in those with truffle inoculation, and T. melanosporum treatment differed more from the control than the T. indicum treatment. The richness of the nirK-community was highest in the T. indicum treatment and lowest in the uninoculated treatment. The differences in nirK-community composition across treatments were not statistically significant, but the nirS communities were different. The nirS-type bacteria correlated with three environmental factors (pH, available phosphorus, and nitrate contents), whereas the nirK-type bacteria were only associated with the nitrate contents. Generally, this work revealed that inoculation with Tuber spp. would change a few nutrient contents and richness of nirK-type bacteria and had little effects on growth of Q. aliena seedlings in the initial stage of inoculation. The results of this study may provide in-depth insights into the relationships between Tuber spp. and hosts, which should be taken into account when developing truffle production methods.

Cataloguing the bacterial diversity in the active ectomycorrhizal zone of Astraeus from a dry deciduous forest of Shorea.

The plant microbiome has been considered one of the most researched areas of microbial biodiversity, yet very little information is available on the microbial communities prevailing in the mushroom's ectomycorrhizosphere. Ectomycorrhizal symbioses often result in the formation of a favourable niche which enables the thriving of various microbial symbionts where these symbionts endorse functions, such as quorum sensing, biofilm formation, volatile microbial compound (VOC) production, regulation of microbial gene expression, symbiosis and virulence. The identification of hidden uncultured microbial communities around the active ectomycorrhizal zone of Astraeus from dry deciduous sal forest of Jharkhand, India was carried out using MinION Oxford Nanopore sequencing of 16S rRNA amplicons genes. High richness of Operational Taxonomic Units (1,905 OTUs) was observed. We recorded 25 distinct phyla. Proteobacteria (36%) was the most abundant phylum, followed by Firmicutes (28%), Actinobacteria (10%) and Bacteroidetes (6%), whereas Gammaproteobacteria was the most abundant class of bacterial communities in the active ectomycorrhizal zone. The ectomycorrhizosphere soil has abundant phosphate-solubilising bacteria (PSB). This is the first report of the ectomycorrhizosphere microbiome associated with Astraeus.

Tuber melanosporum shapes nirS-type denitrifying and ammonia-oxidizing bacterial communities in Carya illinoinensis ectomycorrhizosphere soils.

BackgroundNirS-type denitrifying bacteria and ammonia-oxidizing bacteria (AOB) play a key role in the soil nitrogen cycle, which may affect the growth and development of underground truffles. We aimed to investigate nirS-type denitrifying bacterial and AOB community structures in the rhizosphere soils of Carya illinoinensis seedlings inoculated with the black truffle (Tuber melanosporum) during the early symbiotic stage.MethodsThe C. illinoinensis seedlings inoculated with or without T. melanosporum were cultivated in a greenhouse for six months. Next-generation sequencing (NGS) technology was used to analyze nirS-type denitrifying bacterial and AOB community structures in the rhizosphere soils of these seedlings. Additionally, the soil properties were determined.ResultsThe results indicated that the abundance and diversity of AOB were significantly reduced due to the inoculation of T. melanosporum, while these of nirS-type denitrifying bacteria increased significantly. Proteobacteria were the dominant bacterial groups, and Rhodanobacter, Pseudomonas, Nitrosospira and Nitrosomonas were the dominant classified bacterial genera in all the soil samples. Pseudomonas was the most abundant classified nirS-type denitrifying bacterial genus in ectomycorrhizosphere soils whose relative abundance could significantly increase after T. melanosporum inoculation. A large number of unclassified nirS-type denitrifying bacteria and AOB were observed. Moreover, T. melanosporum inoculation had little effect on the pH, total nitrogen (TN), nitrate-nitrogen (NOn}{}{}_{3}^{-}-N) and ammonium-nitrogen (NHn}{}{}_{4}^{+}-N) contents in ectomycorrhizosphere soils. Overall, our results showed that nirS-type denitrifying bacterial and AOB communities in C. illinoinensis rhizosphere soils were significantly affected by T. melanosporum on the initial stage of ectomycorrhizal symbiosis, without obvious variation of soil N contents.

Mycorrhization of Quercus acutissima with Chinese black truffle significantly altered the host physiology and root-associated microbiomes.

BackgroundOur aim was to explore how the ectomycorrhizae of an indigenous tree,Quercus acutissima, with a commercial truffle, Chinese black truffle (Tuber indicum), affects the host plant physiology and shapes the associated microbial communities in the surrounding environment during the early stage of symbiosis.MethodsTo achieve this, changes in root morphology and microscopic characteristics, plant physiology indices, and the rhizosphere soil properties were investigated when six-month-old ectomycorrhizae were synthesized. Meanwhile, next-generation sequencing technology was used to analyze the bacterial and fungal communities in the root endosphere and rhizosphere soil inoculated with T. indicum or not.ResultsThe results showed that colonization by T. indicum significantly improved the activity of superoxide dismutase in roots but significantly decreased the root activity. The biomass, leaf chlorophyll content and root peroxidase activity did not obviously differ. Ectomycorrhization of Q. acutissima with T. indicum affected the characteristics of the rhizosphere soil, improving the content of organic matter, total nitrogen, total phosphorus and available nitrogen. The bacterial and fungal community composition in the root endosphere and rhizosphere soil was altered by T. indicum colonization, as was the community richness and diversity. The dominant bacteria in all the samples were Proteobacteria and Actinobacteria, and the dominant fungi were Eukaryota_norank, Ascomycota, and Mucoromycota. Some bacterial communities, such as Streptomyces, SM1A02, and Rhizomicrobium were more abundant in the ectomycorrhizae or ectomycorrhizosphere soil. Tuber was the second-most abundant fungal genus, and Fusarium was present at lower amounts in the inoculated samples.DiscussionOverall, the symbiotic relationship between Q. acutissima and T. indicum had an obvious effect on host plant physiology, soil properties, and microbial community composition in the root endosphere and rhizosphere soil, which could improve our understanding of the symbiotic relationship between Q. acutissima and T. indicum, and may contribute to the cultivation of truffle.

Chinese Black Truffle (Tuber indicum) Alters the Ectomycorrhizosphere and Endoectomycosphere Microbiome and Metabolic Profiles of the Host Tree Quercus aliena.

Truffles are one group of the most famous ectomycorrhizal fungi in the world. There is little information on the ecological mechanisms of truffle ectomycorrhizal synthesis in vitro. In this study, we investigated the ecological effects of Tuber indicum – Quercus aliena ectomycorrhizal synthesis on microbial communities in the host plant roots and the surrounding soil using high-throughput sequencing and on the metabolic profiles of host plant roots using metabolomics approaches. We observed an increase in the diversity and richness of prokaryotic communities and a decrease in richness of fungal communities in the presence of T. indicum. The microbial community structures in the host roots and the surrounding soil were altered by ectomycorrhizal synthesis in the greenhouse. Bacterial genera Pedomicrobium, Variibacter, and Woodsholea and fungal genera Aspergillus, Phaeoacremonium, and Pochonia were significantly more abundant in ectomycorhizae and the ectomycorrhizosphere soil compared with the corresponding T. indicum-free controls (P < 0.05). Truffle-colonization reduced the abundance of some fungal genera surrounding the host tree, such as Acremonium, Aspergillus, and Penicillium. Putative prokaryotic metabolic functions and fungal functional groups (guilds) were also differentiated by ectomycorrhizal synthesis. The ectomycorrhizal synthesis had great impact on the measured soil physicochemical properties. Metabolic profiling analysis uncovered 55 named differentially abundant metabolites between the ectomycorhizae and the control roots, including 44 upregulated and 11 downregulated metabolites. Organic acids and carbohydrates were two major upregulated metabolites in ectomycorhizae, which were found formed dense interactions with other metabolites, suggesting their crucial roles in sustaining the metabolic functions in the truffle ectomycorrhization system. This study revealed the effects of truffle-colonization on the metabolites of ectomycorrhiza and illustrates an interactive network between truffles, the host plant, soil and associated microbial communities, shedding light on understanding the ecological effects of truffles.

Tuber indicum shapes the microbial communities of ectomycorhizosphere soil and ectomycorrhizae of an indigenous tree (Pinus armandii).

The aim of this study was to investigate the effect of an ectomycorrhizal fungus (Tuber indicum) on the diversity of microbial communities associated with an indigenous tree, Pinus armandii, and the microbial communities in the surrounding ectomycorhizosphere soil. High-throughput sequencing was used to analyze the richness of microbial communities in the roots or rhizosphere of treatments with or without ectomycorrhizae. The results indicated that the bacterial diversity of ectomycorhizosphere soil was significantly lower compared with the control soil. Presumably, the dominance of truffle mycelia in ectomycorhizosphere soil (80.91%) and ectomycorrhizae (97.64%) was the main factor that resulted in lower diversity and abundance of endophytic pathogenic fungi, including Fusarium, Monographella, Ustilago and Rhizopus and other competitive mycorrhizal fungi, such as Amanita, Lactarius and Boletus. Bacterial genera Reyranena, Rhizomicrobium, Nordella, Pseudomonas and fungal genera, Cuphophyllus, Leucangium, Histoplasma were significantly more abundant in ectomycorrhizosphere soil and ectomycorrhizae. Hierarchical cluster analysis of the similarities between rhizosphere and ectomycorrhizosphere soil based on the soil properties differed significantly, indicating the mycorrhizal synthesis may have a feedback effect on soil properties. Meanwhile, some soil properties were significantly correlated with bacterial and fungal diversity in the rhizosphere or root tips. Overall, this work illustrates the interactive network that exists among ectomycorrhizal fungi, soil properties and microbial communities associated with the host plant and furthers our understanding of the ecology and cultivation of T. indicum.

Degradation of the polycyclic aromatic hydrocarbon (PAH) fluorene is retarded in a Scots pine ectomycorrhizosphere.

• Polycyclic aromatic hydrocarbons (PAHs) are an important class of persistent organic pollutants (POPs) in the environment and accumulate in forest soils. These soils are often dominated by ectomycorrhizal (EcM) roots, but little is known about how EcM fungi degrade PAHs, or the overall effect of field colonized EcM roots on the fate of PAHs. • The ability of eight EcM fungi to degrade PAHs in liquid culture spiked with 14 C labelled PAHs was investigated. Microcosms were used to determine the impact of naturally colonized mycorrhizal pine seedlings on PAH mineralization and volatilization. • Only two EcM fungi (Thelephora terrestris and Laccaria laccata) degraded at least one PAH and none were able to mineralize the PAHs in pure culture. Where degradation occurred, the compounds were only mono-oxygenated. EcM pine seedlings did not alter naphthalene mineralization or volatilization but retarded fluorene mineralization by 35% compared with unplanted, ectomycorrhizosphere soil inoculated, microcosms. • The EcM fungi possessed limited PAH degrading abilities, which may explain why EcM dominated microcosms retarded fluorene mineralization. This observation is considered in relation to the 'Gadgil-effect', where retarded litter decomposition has been observed in the presence of EcM roots.

Properties of soils influenced by ectomycorrhizal fungi in hybrid spruce [Picea glauca × engelmannii (Moench.) Voss

Soil properties of rhizosphere zones in coniferous forests are influenced by the presence of ectomycorrhizae. To elucidate the role of ectomycorrhizae (ECM) on the alteration of chemical and mineralogical properties of soils, soil pH, total C and N, cation exchange capacity, and the contents of mica, chlorite, and kaolinite, 2:1 type expandable clays, and amorphous minerals were compared in two soils, soils influenced by ectomycorrhizal fungi (ECS) and non-ectomycorrhizosphere soils (N-ECM) of Picea glauca x engelmannii (Moench.) Voss. Specifically, the two ECS soils were dominated by (1) Piloderma spp. (ECS-A) and (2) Inocybe lacera-like and Hebeloma-like morphotypes or where Piloderma spp. colonization was &lt;1% (ECS-B). Our results showed that pH was lower in ECS compared to N-ECM samples. Total C and N were significantly higher in ECS soils than N-ECM samples. Cation exchange capacity as well as exchangeable K+, and Na+ were higher in ECS compared to N-ECM soils. X-ray diffraction analysis showed that the amount of 2:1 expanding clays (vermiculite and smectite) was higher in ECS than N-ECM samples and results suggest that there is an enhanced transformation of mica and chlorite to 2:1 type expandable clays in ECS samples when compared to N-ECM samples. The differences in chemical and mineralogical properties between ECS and N-ECM soils, in our study, support earlier studies that show ectomycorrhizal fungi can alter the properties of soils in the rhizosphere zone. Key words: ectomycorrhizosphere soils, soil properties, Piloderma spp.

Mineral weathering in ectomycorrhizosphere of subalpine fir ( Abies lasiocarpa (Hook.) Nutt.) as revealed by soil solution composition

The soil solution is considered an important index of nutrient availability, because it mimics the field conditions when plant roots obtained their nutrition, and reflects the weatherability of a particular soil mineral. The composition of soil solution is sensitive to physical, biological and chemical changes to soil systems, including the presence of fungal hyphae and rhizomorphs from ectomycorrhizal colonization. The objective of this paper is to compare the soil solution composition extracted from two ectomycorrhizosphere soils (or soil environment in the vicinity of ectomycorrhizae) to non-ectomycorrhizosphere soil of subalpine fir ( Abies lasiocarpa (Hook.) Nutt.) in the Ae horizon of Gray Luvisol in northern British Columbia. We extracted the soil solution from ectomycorrhizosphere of Piloderma spp. (ECS-A), Mycelium radicis atrovirens-cottony yellow-brown types (or where Piloderma spp. colonization was <2%) (ECS-B), and from non-ectomycorrhizosphere soils (N-ECM). These soils had been equilibrated anaerobically at field capacity for three weeks at room temperature. The content of major cations in solution, regardless of soil sample, followed the order Ca 2+ > K + > Mg 2+. We found that the concentrations as well as the activities of these cations followed the order ECS-A > ECS-B > N-ECM. A similar trend is true for K″, a parameter for the availability of soil K +. These trends are consistent to the results of geochemical models of more negative saturation index (or enhanced weathering) for muscovite, chlorite, anorthite and K-feldspars in ECS-A and ECS-B compared to N-ECM soils. Low pH in the ectomycorrhizosphere sample is believed to be responsible for the differential breakdown of soil minerals and the increased availability of K +, Ca 2+ and Mg 2+ in soil solution. The results from this study could have practical application in forestry, such as in use of fungal inoculation for improved survival of seedlings, especially in areas that shows deficiency of potassium and calcium.

Chemical and mineral composition of ectomycorrhizosphere soils of subalpine fir (Abieslasiocarpa (Hook.) Nutt.) in the Ae horizon of a Luvisol

Differences in the properties of bulk forest and rhizosphere soils are often attributed to ectomycorrhizal association, or the symbiosis characterized by a fungal sheath surrounding the root (mantle) and intercellular root colonization (Hartig net). We compared the soil pH, total C, N, cation exchange capacity, and the contents of mica, chlorite, kaolinite, 2:1 expandable clays, feldspars and amorphous materials between two ectomycorrhizosphere soils (or soil environment in the vicinity of ectomycorrhizae (ECM)) and non-ectomycorrhizosphere soils to study the influence of ectomycorrhizae on chemical and mineralogical properties of soils. The two ectomycorrhizosphere soils were characterized by ectomycorrhizal colonization dominated by (1) Piloderma spp., and (2) Mycelium radicis atrovirensand cottony yellow-brown (MRA-CYB) types or where Piloderma spp. colonization was &lt;2%. Our results showed that total C and N were higher in ectomycorrhizosphere than non-ectomycorrhizosphere soils, and the ectomycorrhizosphere soils dominated by Piloderma spp. had almost twice the total C and N as ectomycorrhizosphere soils with MRA-CYB. Soil pH was lower by half a pH unit in ectomycorrhizosphere soils compared to non-ectomycorrhizosphere soils. Cation exchange capacity as well as exchangeable Ca2+, Mg2+ and K+ were lower in non-ectomycorrhizosphere soil compared to ectomycorrhizosphere soils. We also found that cation exchange capacity, exchangeable Ca2+, Mg2+ and K+ values in soils dominated by Piloderma spp. were higher compared to ectomycorrhizosphere soils with insignificant Piloderma spp. Our results suggest that transformation rate of mica and chlorite to 2:1 expandable clays was predominant in ectomycorrhizosphere compared to non-ectomycorrhizosphere soils, likely as a result of high production of organic acids and direct extraction of K+ and Mg2+ by fungal hyphae. In ectomycorrhizoplane samples, it is suggested that K+ and possibly amorphous Al2O3 and Fe2O3 could reconstitute the degraded mica and chlorite through the formation of hydroxy-interlayered 2:1 clays. Key words: Ectomycorrhizosphere soils, subalpine fir, Piloderma spp.