Dynamics of soil microbiome throughout the cultivation life cycle of morel (Morchella sextelata)

Abstract

Although Morchella sextelata (morel) is a well-known, edible, and medicinal fungus widely cultivated in China, the dynamics and roles of its soil microbiome during cultivation are unclear. Using rhizosphere soil samples collected throughout the M. sextelata cultivation life cycle, we conducted a high-throughput metagenomic sequencing analysis, with an emphasis on variations in soil microbial composition, characteristic biomarkers, and ecological functions. We found that microbial relative abundance, alpha diversity, and structure varied significantly among fungal growth stages. A total of 47 stage-associated biomarkers were identified through a linear discriminant analysis of effect size. In addition, horizontal comparison of soil microbiomes exhibiting successful and failed primordium formation further confirmed primordium-associated microbes with possible key roles in primordium formation. A microbial function analysis revealed that nutrient metabolism-related pathways were enriched during mycelium and fruiting body stages, whereas the signal transduction pathway was enriched during the primordium stage. This result indicates that diverse microbes are required at different growth stages of M. sextelata. Our research has revealed the dynamic scenario of the soil microbiome throughout the cultivation life cycle of M. sextelata. The high-resolution microbial profiles uncovered in the present study provide novel insights that should contribute to the improvement of morel cultivation using microbial inoculants.

Dynamics of the soil microbial community associated with Morchella cultivation: diversity, assembly mechanism and yield prediction

“…Pseudomonas promotes mycelial growth, primordia formation, and high yield (Cho et al, 2003 ; Kim et al, 2008 ; Zarenejad et al, 2012 ). Previous studies have confirmed that Pseudomonas are considered the most common bacteria in soil for cultivating Morchella and the main biomarker at the primordium stage (Zhang C. et al, 2023 ). Pseudomonas can stimulate sclerotium formation (Hayes et al, 2010 ), further promote the growth and fruiting of Morchella (Pion et al, 2013 ; Liu Q. et al, 2017 ; Benucci et al, 2019 ).…”

“…Fire events produce large amounts of wood ash after fires in spring and summer, and this ash contains a high content of water-soluble potassium and can be used as a fertilizer, further making it possible to grow more Morchella in the soil after fires than under conventional cultivation (Li et al, 2017 ). Several researchers have also simulated the environment after a fire or directly added wood ash when cultivating Morchella and found that the growth and development of Morchella require a large amount of potassium fertilizer (Zhang C. et al, 2023 ). Moreover, the soil fungal community was influenced mainly by deterministic processes, and the habitat niche breadth was significantly narrower than that of the bacterial community ( Figure 6A ), indicating that the fungal community in the cultivated soil of Morchella was more sensitive to the bacterial community.…”

“…Potassium fertilizer changed the ecological niche of the soil fungi, leading to imbalanced competition between the major fungal groups and resulting in changes in Morchella yield. The niche width of soil fungi is related to taxonomic richness (Levins, 2020 ; Zhang C. et al, 2023 ). Specifically, under suitable cultivation conditions, especially in environments with high potassium fertilizer content, Morchella mycelia invade the soil and occupy the soil ecological niche, further becoming the dominant species of the soil microbial community.…”

“…However, the cultivation process of morel is unstable, and its planting fields have suffered serious losses in fruiting body yield, even with no harvest, resulting in catastrophic economic losses and seriously hindering the development of the morel agroindustry. Previous studies have shown that the variability in Morchella yield is due to the vitality of cultivated strains, field management models (Zhang C. et al, 2023 ), soil-borne pathogens (Guo et al, 2016 ; He et al, 2017 ; Lan et al, 2020 ), soil physicochemical characteristics (Zhang et al, 2019 ), volatile organic compounds (VOCs) (Yu F. et al, 2022 ), genetic instability (Chai et al, 2017 ), and microbial community evenness (Tan et al, 2021a , b ). Differences in Morchella growth were observed between the different habitats.…”

“…The main reason for the decline in the yield of Morchella under continuous cropping cultivation is also related to the proliferation of pathogenic fungi, which leads to a decrease in soil fungal diversity and ecological niches (Liu et al, 2022 ). Importantly, the pathogen load may increase from the primordium stage to the fruiting body production stage in Morchella (Zhang C. et al, 2023 ). Therefore, exploring the potential relationship between microbial ecology and Morchella yield in soil agroecosystems is essential for the development of the Morchella agroindustry.…”