Effect of Organic Carbon and Nitrogen on the Interactions of Morchella spp. and Bacteria Dispersing on Their Mycelium

Genome assembly of M. spongiola and comparative genomics of the genus Morchella provide initial insights into taxonomy and adaptive evolution

Morchella spongiola is a highly prized mushroom for its delicious flavor and medical value and is one of the most flourishing, representative, and dominant macrofungi in the Qilian Mountains of the Qinghai-Tibet Plateau subkingdoms (QTPs). However, the understanding of M. spongiola remains largely unknown, and its taxonomy is ambiguous. In this study, we redescribed a unique species of M. spongiola, i.e., micromorphology, molecular data, genomics, and comparative genomics, and the historical biogeography of M. spongiola were estimated for 182 single-copy homologous genes. A high-quality chromosome-level reference genome of M. spongiola M12-10 was obtained by combining PacBio HiFi data and Illumina sequencing technologies; it was approximately 57.1 Mb (contig N50 of 18.14 Mb) and contained 9775 protein-coding genes. Comparative genome analysis revealed considerable conservation and unique characteristics between M. spongiola M12-10 and 32 other Morchella species. Molecular phylogenetic analysis indicated that M. spongiola M12-10 is similar to the M. prava/Mes-7 present in sandy soil near rivers, differentiating from black morels ~ 43.06 Mya (million years ago), and diverged from M. parva/Mes-7 at approximately 12.85 Mya (in the Miocene epoch), which is closely related to the geological activities in the QTPs (in the Neogene). Therefore, M. spongiola is a unique species rather than a synonym of M. vulgaris/Mes-5, which has a distinctive grey-brown sponge-like ascomata. This genome of M. spongiola M12-10 is the first published genome sequence of the species in the genus Morchella from the QTPs, which could aid future studies on functional gene identification, germplasm resource management, and molecular breeding efforts, as well as evolutionary studies on the Morchella taxon in the QTPs.

Associated bacterial communities, confrontation studies, and comparative genomics reveal important interactions between Morchella with Pseudomonas spp

Members of the fungal genus Morchella are widely known for their important ecological roles and significant economic value. In this study, we used amplicon and genome sequencing to characterize bacterial communities associated with sexual fruiting bodies from wild specimens, as well as vegetative mycelium and sclerotia obtained from Morchella isolates grown in vitro. These investigations included diverse representatives from both Elata and Esculenta Morchella clades. Unique bacterial community compositions were observed across the various structures examined, both within and across individual Morchella isolates or specimens. However, specific bacterial taxa were frequently detected in association with certain structures, providing support for an associated core bacterial community. Bacteria from the genus Pseudomonas and Ralstonia constituted the core bacterial associates of Morchella mycelia and sclerotia, while other genera (e.g., Pedobacter spp., Deviosa spp., and Bradyrhizobium spp.) constituted the core bacterial community of fruiting bodies. Furthermore, the importance of Pseudomonas as a key member of the bacteriome was supported by the isolation of several Pseudomonas strains from mycelia during in vitro cultivation. Four of the six mycelial-derived Pseudomonas isolates shared 16S rDNA sequence identity with amplicon sequences recovered directly from the examined fungal structures. Distinct interaction phenotypes (antagonistic or neutral) were observed in confrontation assays between these bacteria and various Morchella isolates. Genome sequences obtained from these Pseudomonas isolates revealed intriguing differences in gene content and annotated functions, specifically with respect to toxin-antitoxin systems, cell adhesion, chitinases, and insecticidal toxins. These genetic differences correlated with the interaction phenotypes. This study provides evidence that Pseudomonas spp. are frequently associated with Morchella and these associations may greatly impact fungal physiology.

The cultivation regimes of Morchella sextelata trigger shifts in the community assemblage and ecological traits of soil bacteria

The successful large-scale cultivation of morel mushrooms (Morchella sextelata) requires a comprehensive understanding of the soil bacterial communities associated with morel-farming beds, as the interactions between fungi and bacteria play a crucial role in shaping the soil microbiome. In this study, we investigated the temporal distribution and ecological characteristics of soil bacteria associated with morel fruiting bodies at different stages, specifically the conidial and primordial stages, under two cropping regimes, non-continuous cropping (NCC) and continuous cropping (CC). Our findings revealed a significant reduction in the yield of morel primordia during the third year following 2 years of CC (0.29 ± 0.25 primordia/grid), in comparison to the NCC regime (12.39 ± 6.09 primordia/grid). Furthermore, inoculation with morel mycelia had a notable impact on soil bacterial diversity, decreasing it in the NCC regime and increasing the number of generalist bacterial members in the CC regime. The latter regime also led to the accumulation of nutrients in the soil beds, resulting in a shift from a stochastic to a deterministic process in the composition of the bacterial community, which differed from the NCC regime. Additionally, mycelial inoculation had a positive effect on the abundance of potential copiotrophic/denitrifying and N-fixing bacteria while decreasing the abundance of oligotrophic/nitrifying bacteria. Interestingly, this effect was more pronounced in the NCC regime than in the CC regime. These results suggest that the increase in potential copiotrophic/denitrifying and N-fixing bacteria facilitated the decomposition of nutrients in exogenous nutrient bags by morel mushrooms, thereby maintaining nitrogen balance in the soil. Overall, our study provides valuable insights into the interactions between morel mycelia and the associated soil bacteriome as well as the influence of different cultivation regimes on these interactions. These findings contribute to our understanding of the complex dynamics of the soil microbiome and can inform strategies for optimizing morel mushroom cultivation.

Dazomet changes microbial communities and improves morel mushroom yield under continuous cropping

Morels (Morchella spp.) are highly prized and popular edible mushrooms. The outdoor cultivation of morels in China first developed at the beginning of the 21st century. Several species, such as Morchella sextelata, M. eximia, and M. importuna, have been commercially cultivated in greenhouses. However, the detriments and obstacles associated with continuous cropping have become increasingly serious, reducing yields and even leading to a complete lack of fructification. It has been reported that the obstacles encountered with continuous morel cropping may be related to changes in the soil microbial community. To study the effect of dazomet treatment on the cultivation of morel under continuous cropping, soil was fumigated with dazomet before morel sowing. Alpha diversity and beta diversity analysis results showed that dazomet treatment altered the microbial communities in continuous cropping soil, which decreased the relative abundance of soil-borne fungal pathogens, including Paecilomyces, Trichoderma, Fusarium, Penicillium, and Acremonium, increased the relative abundance of beneficial soil bacteria, including Bacillius and Pseudomonas. In addition, the dazomet treatment significantly increased the relative abundance of morel mycelia in the soil and significantly improved morel yield under continuous cropping. These results verified the relationship between the obstacles associated with continuous cropping in morels and the soil microbial community and elucidated the mechanism by which the obstacle is alleviated when using dazomet treatment.

Decline in Morel Production upon Continuous Cropping Is Related to Changes in Soil Mycobiome

The black morel Morchella sextelata (Morchellaceae, Pezizales) is a valuable edible mushroom that can be cultivated on a large scale, but a severe yield decline is observed during continuous cropping. The effect of long-term cropping on soil-borne diseases and the dysbiosis of the microbiome and how these biotic factors affect the morel yield are not well understood. To help fill this knowledge gap, we designed an indoor experiment to investigate the influence of black morel cropping regimes on soil physicochemical properties, richness and distribution of fungal community, and morel primordial production. In this study, we employed rDNA metabarcoding and microbial network analysis to evaluate the effect of non-continuous and continuous cropping regimes on the fungal community during three developmental stages of black morel production, namely, the bare soil mycelium, mushroom conidial, and primordial stages. The results showed that during the first year, M. sextelata mycelium overwhelmed the resident soil fungal community by reducing the alpha diversity and niche breadth of soil fungal patterns by a greater amount compared to the continuous cropping regime, leading to high crop yield of 12.39 ± 6.09/quadrat but less complex soil mycobiome. To sustain continuous cropping, exogenous nutrition bags and morel mycelial spawn were consecutively added to the soil. The additional nutrient input stimulated the growth of fungal saprotrophic decomposers. The degrading activity of soil saprotrophs, including M.sextelata, caused a significant increase in soil nutrient content. This led to an inhibitory effect on the formation of morel primordia, resulting in a sharp decline to 0.29 ± 0.25/quadrat and 0.17 ± 0.24/quadrat, respectively, in the final morel cropping. Our findings provided a dynamic overview of the soil fungal community during morel mushroom production, allowing us to identify beneficial and detrimental fungal taxa in the soil mycobiome involved in morel cultivation. The information acquired from this study can be applied to mitigate the adverse impact of continuous cropping on the yield of black morel.

Mycelial Growth-promoting Potential of Extracellular Metabolites of Paraburkholderia spp. Isolated from Rhizopogon roseolus Sporocarp

This study aimed to investigate the effect of potential metabolite(s) produced by Paraburkholderia spp. isolated from the Rhizopogon roseolus (shouro mushroom) sporocarp on the mycelial growth of R. roseolus. For this purpose, we selected two molecularly identified bacteria: P. fungorum GIB024 and P. caledonica KN1. Direct confrontation assay at three different distances, a pour plate method that sampled bacterial spent broth either with and without agitation at 25 °C, and an indirect confrontation assay was carried out in order to assess the R. roseolus growth-promoting ability of Paraburkholderia spp. These assessments were carried out in a 1:5 diluted Melin-Norkran-modified medium with glucose (hs-dMMN) and without glucose (ls-dMMN). GIB024 promoted the growth of R. roseolus in ls-dMMN in short distance, whereas KN1 inhibited the growth of the fungus in that condition. In hs-dMMN, both bacteria have neutral or slightly promotion effect toward R. roseolus. We determined from the spent broth analysis that Paraburkholderia spp. that grew axenically under static conditions had a more pronounced mycelial growth-promoting effect on R. roseolus than under agitation conditions. We also found that high concentration of spent broth resulted in a decrease in mycelial growth-promoting ability. Volatile metabolite(s) produced by both bacteria did not promote the mycelial growth of R. roseolus. In conclusion, Paraburkholderia spp. exhibited a species- and nutrient (sugar)-dependent ability to promote the mycelial growth of R. roseolus, and the bacterial soluble metabolite(s) play a crucial role in their growth-promoting ability.

Morel Production Associated with Soil Nitrogen-Fixing and Nitrifying Microorganisms

True morels (Morchella, Pezizales) cultivated in soil are subject to complex influences from soil microbial communities. To explore the characteristics of soil microbial communities on morel cultivation, and evaluate whether these microbes are related to morel production, we collected 23 soil samples from four counties in Sichuan and Yunnan Provinces, China. Based on ITS and 16S rDNA amplicon sequencing, the alpha diversity analysis indicated that the biodiversity of morel cultivation soil showed a downward trend compared with the bare soil. The results also showed that there were no significant differences in soil microbial communities between OC (bare soil) and OO (after one-year suspension of sowing). This means that, after about one year of stopping sowing, the component and structure of soil that once cultivated morel would be restored. In co-occurrence networks, some noteworthy bacterial microbes involved in nitrogen fixation and nitrification have been identified in soils with high morel yields, such as Arthrobacter, Bradyhizobium, Devosia, Pseudarthrobacter, Pseudolabrys, and Nitrospira. In contrast, in soils with low or no morel yield, some pathogenic fungi accounted for a high proportion, including Gibberella, Microidium, Penicillium, Sarocladium, Streptomyces, and Trichoderma. This study provided valuable information for the isolation and culturing of some beneficial microbes for morel cultivation in further study and, potentially, to harness the power of the microbiome to improve morel production and health.

Cooperative herbivory between two important pests of rice

Normally, when different species of herbivorous arthropods feed on the same plant this leads to fitness-reducing competition. We found this to be different for two of Asia's most destructive rice pests, the brown planthopper and the rice striped stem borer. Both insects directly and indirectly benefit from jointly attacking the same host plant. Double infestation improved host plant quality, particularly for the stemborer because the planthopper fully suppresses caterpillar-induced production of proteinase inhibitors. It also reduced the risk of egg parasitism, due to diminished parasitoid attraction. Females of both pests have adapted their oviposition behaviour accordingly. Their strong preference for plants infested by the other species even overrides their avoidance of plants already attacked by conspecifics. This cooperation between herbivores is telling of adaptations resulting from the evolution of plant-insect interactions, and points out mechanistic vulnerabilities that can be targeted to control these major pests.

Changes in soil bacteria functional ecology associated with Morchella rufobrunnea fruiting in a natural habitat

Morchella rufobrunnea is a saprobic edible mushroom, found in a range of ecological niches, indicating nutritional adjustment to different habitats and possible interaction with soil prokaryotic microbiome (SPM). Using the 16S rRNA gene, we examined the SPM of M. rufobrunnea that appeared in a natural habitat in Northern Israel. Three sample types were included: bare soil without mushroom, soil beneath young mushroom initials and soil beneath the mature fruiting body. Morchella rufobrunnea developmental stage was significantly associated with changes in bacterial populations (PERMANOVA, p < 0.0005). Indicator analysis with point-biserial correlation coefficient found 180 operational taxonomic units (OTU) uniquely associated with distinct stages of development. The Functional Annotation of Prokaryotic Taxonomy (FAPROTAX) database helped to infer ecological roles for indicator OTU. The functional ecological progression begins with establishment of a photoautotrophic N-fixing bacterial mat on bare soil. Pioneer heterotrophs including oligotrophs, acidifying nutrient mobilizers and nitrifiers are congruent with appearance of young M. rufobrunnea initials. Under the mature fruiting body, the population changed to saprobes, organic-N degraders, denitrifiers, insect endosymbionts and fungal antagonists. Based on this work, M. rufobrunnea may be able to influence SPM and change the soil nutritional profile.

Functional Diversity of the Litter-Associated Fungi from an Oxalate-Carbonate Pathway Ecosystem in Madagascar

The oxalate-carbonate pathway (OCP) is a biogeochemical process linking oxalate oxidation and carbonate precipitation. Currently, this pathway is described as a tripartite association involving oxalogenic plants, oxalogenic fungi, and oxalotrophic bacteria. While the OCP has recently received increasing interest given its potential for capturing carbon in soils, there are still many unknowns, especially regarding the taxonomic and functional diversity of the fungi involved in this pathway. To fill this gap, we described an active OCP site in Madagascar, under the influence of the oxalogenic tree Tamarindus indica, and isolated, identified, and characterized 50 fungal strains from the leaf litter. The fungal diversity encompassed three phyla, namely Mucoromycota, Ascomycota, and Basidiomycota, and 23 genera. Using various media, we further investigated their functional potential. Most of the fungal strains produced siderophores and presented proteolytic activities. The majority were also able to decompose cellulose and xylan, but only a few were able to solubilize inorganic phosphate. Regarding oxalate metabolism, several strains were able to produce calcium oxalate crystals while others decomposed calcium oxalate. These results challenge the current view of the OCP by indicating that fungi are both oxalate producers and degraders. Moreover, they strengthen the importance of the role of fungi in C, N, Ca, and Fe cycles.

Experimental Analysis of Interactions Among Saprotrophic Fungi from A Phosphorous-Poor Desert Oasis in the Chihuahuan Desert

Fungal ecological interactions play a key role in structuring community assemblages. These associations may involve both antagonistic and synergistic relationships, which are commonly influenced by abiotic factors such as nutrient conditions. However, information for extreme, oligotrophic systems remain poor. Herein, interactions among key members of the aquatic transient fungal community (Aspergillus niger, Cladosporium sp., and Coprinellus micaceus) of a low-nutrient freshwater system in the Cuatro Ciénegas Basin, Mexico were studied. Pairwise interaction bioassays were explored in vitro under different nutrient conditions, including carbohydrates-rich, carbohydrates and amino peptides-rich, and low nutrients. Our results indicated that antagonistic patterns prevail among the studied taxa. However, nutrient-dependent changes were observed in Cladosporium sp. shifting to synergy under carbohydrates-rich conditions, suggesting changes in the fungal community composition as a result of nutrient enrichment. Remarkably, our findings contrast with previous work demonstrating mainly synergistic interactions between our tested fungal isolates and co-occurring autochthonous bacteria (Aeromonas spp. and Vibrio sp.) under low-nutrient conditions. This observation may indicate that bacteria and fungi exhibit distinct community-level responses, driven by nutrient conditions. This contributes to the knowledge of fungal community dynamics and interspecific interactions in an oligotrophic ecosystem, highlighting the relevance of nutrient-based shifts and antagonistic interactions in ecosystem dynamics.

Self-immobilized biomixture with pellets of Aspergillus niger Y3 and Arthrobacter. sp ZXY-2 to remove atrazine in water: A bio-functions integration system

The microorganism Arthrobacter. ZXY-2 exhibits excellent degradation efficiency for atrazine in free cells. However, its poor fixability makes it hard to be kept and recycled in water. To conquer the problem, this work employed mycelial pellets of Aspergillus niger Y3 to immobilize ZXY-2, which formed a self-immobilized biomixture (SIB) to remove atrazine. SIB could completely degrade 57.3 mg/L atrazine within 10 h. The SIB exhibited the highest degradation efficiency at pH = 7 and 40 °C. Degradation of atrazine with initial concentrations of 57.3 mg/L and 17.5 mg/L was described well by zero and first-order reaction kinetics, respectively. The recycling experiments demonstrated that SIB could be recycled for 5 batches. The results of SEM, FT-IR, and zeta potential analysis showed that porous structure, functional groups, and electronegativity of SIB all contributed to its stable formation. Therefore, this study demonstrates that SIB could be formed stably and could remove atrazine efficiently.