Pecan (Carya illinoinensis) is an economically important nut tree native to the Mississippi basin and cultivated worldwide. In North America, species of truffles are regularly found fruiting in ...productive pecan orchards and the truffle genus Tuber appears to be abundant in pecan ectomycorrhizal (EM) communities. As an initial step to determine the feasibility of co-cropping European truffle species with pecan, we evaluated whether mycorrhizae of highly esteemed European truffle species (Tuber aestivum Vittad. T. borchii and T. macrosporum) could be formed on pecan seedlings. Seedlings were inoculated with truffle spores and were grown in a greenhouse for 10 months. Levels of EM colonization were estimated visually and quantified by counting EM tips. Ectomycorrhizae were identified both morphologically and molecularly with species-specific amplification and by sequencing of the ITS region of the nuclear ribosomal DNA (nrDNA). Both T. borchii and T. aestivum spores produced well-formed ectomycorrhizae on pecan seedlings with average root colonization levels of about 62% and 42%, respectively, whereas no ectomycorrhizae of T. macrosporum were formed. The anatomy and morphology of these truffle ectomycorrhizae on pecan was characterized. The co-cropping of T. aestivum and T. borchii may hold promise as an additional stream of revenue to pecan growers, although, further studies are needed to assess whether this symbiosis is maintained after planting in the field and whether truffle production can be supported by this host species.
•Small mammals facilitate mutualisms between truffle-forming fungi and trees.•Using a molecular method we identified 81 species of truffles in chipmunk diet.•Truffle species richness in chipmunk scat ...did not increase with unlogged patch size.•Truffle species richness in chipmunk scat decreased across the summer months.•Chipmunks provide an important ecosystem service in wood producing forests.
Intensive management of forests for wood modifies forest biodiversity, affecting the composition of plant and animal communities as well as microorganisms such as bacteria and fungi. Ectomycorrhizal fungi (EMF) form mutualistic relationships with trees, but there is evidence that the abundance and diversity of EMF declines under intensive forest management. The dispersal of some EMF, including that of truffles, depends on small mammals consuming their fruiting bodies and dispersing spores through feces. To better understand provisioning of this ecosystem service within intensively managed forests, we applied high-throughput, DNA amplicon sequencing to scat collected from Townsend’s chipmunks (Neotamias townsendii) inhabiting retention patches in recently clearcut-conifer stands. Across two summers, we collected 165 chipmunk scat samples from 43 clearcut-conifer stands in the Pacific Northwest (USA). We identified 81 truffle species representing 16 families, which included many rare and uncommon taxa. Retention patch sizes varied from 9 to 222 trees (0.002–0.83 ha) but we did not detect an effect of retention patch size on the richness of truffles in chipmunk scat samples. However, truffle richness was slightly higher in scat samples collected from chipmunks in retention patches compared to individuals sampled in adjacent clearcuts. Furthermore, the abundance of certain truffle species in chipmunk scat varied in relation to retention patch size and location (riparian or upland), suggesting retention forestry practices may influence truffle community composition. Throughout the sampling season, we detected a 44% decline in truffle species richness and a significant reduction in abundance (i.e., sequence reads) for > 50% of common truffle taxa. Our application of high-throughput sequencing of scat effectively captured variation in truffle species consumption by chipmunks. Our results confirm that common small mammals play an important role in the dispersal of EMF across recently logged forests (<8 years since harvest) and indicate that retaining relatively small (∼10 tree) green-tree patches may promote truffle dispersal by providing small mammal habitat.
The process of fermenting tofu extends back thousands of years and is an indispensable part of Chinese culture. Despite a cultural resurgence in fermented foods and interest in microbiomes, there is ...little knowledge on the microbial diversity represented in fermented ‘hairy’ tofu, known locally in China as Mao tofu. High-throughput metagenomic sequencing of the ITS, LSU and 16S rDNA was used to determine Mao tofu’s fungal and bacterial community diversity across four wet markets in Yunnan, China. The results show that hairy tofu in this region consists of around 170 fungal and 365 bacterial taxa, and that microbial taxa differ between markets. Diversity also differed based on the specific niche of the tofu block, comparing the outside rind-like niche to that of the inside of the tofu block. Machine learning random forest models were able to accurately classify both the market and niche of sample origin. An over-abundance of yeast and Geotrichum was found, and Mucor (Mucoromycota) was abundant in the outside rind-like niche, which consists of the visible ‘hairy’ mycelium. The majority of the bacterial OTUs belonged to Proteobacteria, Firmicutes, and Bacteroidetes, with Acinetobacter, Lactobacillus, Sphingobacterium and Flavobacterium the most abundant genera. Putative fungal pathogens of plants (Cercospora, Diaporthe, Fusarium) and animals (Metarhizium, Entomomortierella, Pyxidiophora, Candida, Clavispora) were also detected, as were putative bacterial pathogens identified as Legionella. Non-fungal eukaryotic taxa detected by LSU amplicon sequencing included soybean (Glycine max), Protozoa, Metazoa (e.g., Nematoda and Platyhelminthes), Rhizaria and Chromista, indicating that additional biodiversity exists in the hairy tofu microbiome.
Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and ...antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass (
Panicum virgatum
). We also sampled a replicated subset of genotypes across 3 additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association (GWA) mapping and RNA sequencing to show that 3 cysteine-rich receptor-like kinases (crRLKs) were linked to a genetic locus associated with microbiome structure. We confirmed GWAS results in an independent set of genotypes for both the internal transcribed spacer (ITS) and large subunit (LSU) ribosomal DNA markers. Fungal pathogens were central to microbial covariance networks, and genotypes susceptible to pathogens differed in their expression of the 3 crRLKs, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome.
Many truffle species in the genus Tuber are endemic to North America. Some of these have commercial value such as Tuber oregonense and Tuber gibbosum, commonly known as Oregon white truffles. Most of ...what is known about the ecology of these truffles comes from observational data. These truffle species form ectomycorrhizas with Douglas-fir (Pseudotsuga menziesii) and sometimes fruit abundantly in early successional forest regrowth. The goal of this study was to characterize fungal communities and soils associated with truffle-producing Douglas-fir sites. We extracted DNA from roots of five trees at four different truffle-producing Douglas-fir sites (nâ=â20). We amplified the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA (nrDNA) and sequenced amplicons with 454 pyrosequencing. After quality filtering, we assembled 15,713 sequences into 150 fungal operational taxonomic units (OTUs). Pezizomycetes (Tuber and Pyronemataceae) were the most abundant taxa detected followed by Helotiales. Agaricomycetes represented most by Thelephoraceae, Russulaceae, and Inocybaceae were also abundant. A total of five Tuber species were detected. T. oregonense was the most abundant OTU, followed by T. gibbosum and Wilcoxina mikolae. Fungal root endophytes were also detected and well represented by Chalara and Phialocephala spp. Fungal community structure and soil chemistry differed between sites. This study represents the first characterization of the fungal communities in Douglas-fir stands producing Oregon white truffles. We found that Tuber species can be dominant ectomycorrhizal symbionts of Douglas-fir. Truffle fungi are also important in forest health, food webs, and as a non-timber forest resource that can contribute to rural economies.
The effects on bacterial, yeast and fungal communities present within an agricultural soil treated with a pig slurry-derived digestate were studied using a multidisciplinary (biochemical and 454 ...pyrosequencing platform) approach.
Biochemical analyses showed a significant increase of CO2 emissions from soil 5 days after the amendment with digestate, whereas soil microbial biomass (C-biomass) increased significantly only after 12 and 30 days. PLFAs analysis revealed a significant increase in Gram-negative bacteria 90 days after the amendment.
Results from 454 pyrosequencing revealed the presence of OTUs attributed to bacteria, yeasts and filamentous fungi. Proteobacteria, Bacteroidetes and Firmicutes exhibited a significant predominance in the first 5 days, whereas Ascomycota became predominant 90 days after the amendment.
Overall, both bacterial and yeast + fungal richness exhibited a decreasing trend from 0 to 90 days after the amendment. Canonical analysis of principal coordinates showed that the cumulative effect of amendment and incubation time explained approximately 45% and 36% of the total variance observed in the bacterial and yeast + fungal communities, respectively. The correlation among some bacterial and fungal OTUs suggested the probable existence of specific biological interactions among different phyla.
The results reported represent a picture of the changes of soil microbial diversity in relation with some agronomic practices, such as organic amendments.
•An early increase of CO2 emissions were observed after soil amendment.•Gram-negative bacteria exhibited a long-term increase after soil amendment.•Proteobacteria, Bacteroidetes and Firmicutes predominated in the early stages.•Ascomycota became predominant 90 days after amendment.•A few relationships between bacterial and fungal OTUs were found.
Abstract Fungicides reduce fungal pathogen populations and are essential to food security. Understanding the impacts of fungicides on crop microbiomes is vital to minimizing unintended consequences ...while maintaining their use for plant protection. However, fungicide disturbance of plant microbiomes has received limited attention, and has not been examined in different agricultural management systems. We used amplicon sequencing of fungi and prokaryotes in maize and soybean microbiomes before and after foliar fungicide application in leaves and roots from plots under long-term no-till and conventional tillage management. We examined fungicide disturbance and resilience, which revealed consistent non-target effects and greater resiliency under no-till management. Fungicides lowered pathogen abundance in maize and soybean and decreased the abundance of Tremellomycetes yeasts, especially Bulleribasidiaceae, including core microbiome members. Fungicide application reduced network complexity in the soybean phyllosphere, which revealed altered co-occurrence patterns between yeast species of Bulleribasidiaceae, and Sphingomonas and Hymenobacter in fungicide treated plots. Results indicate that foliar fungicides lower pathogen and non-target fungal abundance and may impact prokaryotes indirectly. Treatment effects were confined to the phyllosphere and did not impact belowground microbial communities. Overall, these results demonstrate the resilience of no-till management to fungicide disturbance, a potential novel ecosystem service provided by no-till agriculture.
Abstract
Truffle growers devote great efforts to improve black truffle productivity, developing agronomic practices such as ‘truffle nests’ (peat amendments that are supplemented with truffle spore ...inoculum). It has been hypothesized that improved fruiting associated with nests is linked to stimulation of truffle mycelia previously established in soil or to changes generated in soil fungal community. To assess this, we used real-time PCR to quantify black truffle extraradical mycelium during 2 years after nests installation. We also characterized the fungal community via high-throughput amplicon sequencing of the ITS region of rRNA genes. We found that neither the abundance of truffle mycelium in nests nor in the soil—nest interphase was higher than in the bulk soil, which indicates that nests do not improve mycelial growth. The fungal community in nests showed lower richness and Shannon index and was compositionally different from that of soil, which suggests that nests may act as an open niche for fungal colonization that facilitates truffle fruiting. The ectomycorrhizal fungal community showed lower richness in nests. However, no negative relationships between amount of truffle mycelium and reads of other ectomycorrhizal fungi were found, thus countering the hypothesis that ectomycorrhizal competition plays a role in the nest effect.
Truffle nests did not increase black truffle mycelial growth, but generated a less diverse fungal community, acting as an open niche for fungal colonization and seemingly alleviating ectomycorrhizal competition.
Tuber macrosporum Vittad. is not a common truffle species, but with remarkable organoleptic qualities and much economic interest. After the addition of truffle spore slurry, 30 seedlings of Quercus ...robur L., Quercus cerris L. and Corylus avellana L. were grown inside a greenhouse for 11 months before evaluation of the mycorrhizal level. Two different potting mixes were used: a natural soil-based potting mix for Q. robur, Q. cerris and C. avellana and a peat-based potting mix for Q. robur. Quercus robur planted in soil potting mix was the most receptive towards the truffle spore inoculum, with a level of formation of T. macrosporum ectomycorrhizas (ECMs) of approximately 14 %, ranging from a minimum of ∼4 % to a maximum of ∼44 % in different seedlings. No T. macrosporum ECMs developed on Q. cerris (soil potting mix) or on Q. robur (peat potting mix), whereas a low percentage of ECMs was detected on only three C. avellana (soil potting mix) seedlings. The fungus Sphaerosporella brunnea (Alb. & Schwein.) Svrček & Kubička was also detected as a contaminant on almost half the truffle-inoculated seedlings. A new detailed description of the morphological and anatomical characteristics of T. macrosporum ECMs and their DNA-based verification with species-specific markers were also reported.
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