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1. Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses

   https://doi.org/10.7717/peerj.7744  

   Benucci, Gian Maria; Longley, Reid; Zhang, Peng; Zhao, Qi; Bonito, Gregory; Yu, Fuqiang (January 2019, PeerJ)

   Morels ( Morchella spp.) are iconic edible mushrooms with a long history of human consumption. Some microbial taxa are hypothesized to be important in triggering the formation of morel primordia and development of fruiting bodies, thus, there is interest in the microbial ecology of these fungi. To identify and compare fungal and prokaryotic communities in soils where Morchella sextelata is cultivated in outdoor greenhouses, ITS and 16S rDNA high throughput amplicon sequencing and microbiome analyses were performed. Pedobacter , Pseudomonas , Stenotrophomonas , and Flavobacterium were found to comprise the core microbiome of M. sextelata ascocarps. These bacterial taxa were also abundant in the soil beneath growing fruiting bodies. A total of 29 bacterial taxa were found to be statistically associated to Morchella fruiting bodies. Bacterial community network analysis revealed high modularity with some 16S rDNA operational taxonomic unit clusters living in specialized fungal niches (e.g., pileus, stipe). Other fungi dominating the soil mycobiome beneath morels included Morchella , Phialophora , and Mortierella . This research informs understanding of microbial indicators and potential facilitators of Morchella ecology and fruiting body production. 

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

   https://doi.org/10.3389/ffunb.2023.1285531  

   Cailleau, Guillaume; Hanson, Buck T.; Cravero, Melissa; Zhioua, Sami; Hilpish, Patrick; Ruiz, Celia; Robinson, Aaron J.; Kelliher, Julia M.; Morales, Demosthenes; Gallegos-Graves, La Verne; et al (December 2023, Frontiers in Fungal Biology)

   Members of the fungal genusMorchellaare 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 fromMorchellaisolates grownin vitro. These investigations included diverse representatives from both Elata and EsculentaMorchellaclades. Unique bacterial community compositions were observed across the various structures examined, both within and across individualMorchellaisolates 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 genusPseudomonasandRalstoniaconstituted the core bacterial associates ofMorchellamycelia and sclerotia, while other genera (e.g.,Pedobacterspp.,Deviosaspp., andBradyrhizobiumspp.) constituted the core bacterial community of fruiting bodies. Furthermore, the importance ofPseudomonasas a key member of the bacteriome was supported by the isolation of severalPseudomonasstrains from mycelia duringin vitrocultivation. Four of the six mycelial-derivedPseudomonasisolates 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 variousMorchellaisolates. Genome sequences obtained from thesePseudomonasisolates 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 thatPseudomonasspp. are frequently associated withMorchellaand these associations may greatly impact fungal physiology. 

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3. Soil microbial community response to ectomycorrhizal dominance in diverse neotropical montane forests

   https://doi.org/10.1007/s00572-023-01134-4  

   Edwards, Joseph D.; Krichels, Alexander H.; Seyfried, Georgia S.; Dalling, James; Kent, Angela D.; Yang, Wendy H. (January 2024, Mycorrhiza)

   Abstract Ectomycorrhizal (EM) associations can promote the dominance of tree species in otherwise diverse tropical forests. These EM associations between trees and their fungal mutualists have important consequences for soil organic matter cycling, yet the influence of these EM-associated effects on surrounding microbial communities is not well known, particularly in neotropical forests. We examined fungal and prokaryotic community composition in surface soil samples from mixed arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) stands as well as stands dominated by EM-associatedOreomunnea mexicana(Juglandaceae) in four watersheds differing in soil fertility in the Fortuna Forest Reserve, Panama. We hypothesized that EM-dominated stands would support distinct microbial community assemblages relative to the mixed AM-EM stands due to differences in carbon and nitrogen cycling associated with the dominance of EM trees. We expected that this microbiome selection in EM-dominated stands would lead to lower overall microbial community diversity and turnover, with tighter correspondence between general fungal and prokaryotic communities. We measured fungal and prokaryotic community composition via high-throughput Illumina sequencing of theITS2(fungi) and16SrRNA (prokaryotic) gene regions. We analyzed differences in alpha and beta diversity between forest stands associated with different mycorrhizal types, as well as the relative abundance of fungal functional groups and various microbial taxa. We found that fungal and prokaryotic community composition differed based on stand mycorrhizal type. There was lower prokaryotic diversity and lower relative abundance of fungal saprotrophs and pathogens in EM-dominated than AM-EM mixed stands. However, contrary to our prediction, there was lower homogeneity for fungal communities in EM-dominated stands compared to mixed AM-EM stands. Overall, we demonstrate that EM-dominated tropical forest stands have distinct soil microbiomes relative to surrounding diverse forests, suggesting that EM fungi may filter microbial functional groups in ways that could potentially influence plant performance or ecosystem function. 

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4. Stochastic and deterministic processes shape bioenergy crop microbiomes along a vertical soil niche

   https://doi.org/10.1111/1462-2920.16269  

   Benucci, Gian Maria; Beschoren da Costa, Pedro; Wang, Xinxin; Bonito, Gregory (February 2023, Environmental Microbiology)

   Abstract Sustainable biofuel cropping systems aim to address climate change while meeting energy needs. Understanding how soil and plant‐associated microbes respond to these different cropping systems is key to promoting agriculture sustainability and evaluating changes in ecosystem functions. Here, we leverage a long‐term biofuel cropping system field experiment to dissect soil and root microbiome changes across a soil‐depth gradient in poplar, restored prairie and switchgrass to understand their effects on the microbial communities. High throughput amplicon sequencing of the fungal internal transcribed spacer (ITS) and prokaryotic 16S DNA regions showed a common trend of root and soil microbial community richness decreasing and evenness increasing with depth. Ecological niche (root vs. soil) had the strongest effect on community structure, followed by depth, then crop. Stochastic processes dominated the structuring of fungal communities in deeper soil layers while operational taxonomic units (OTUs) in surface soil layers were more likely to co‐occur and to be enriched by plant hosts. Prokaryotic communities were dispersal limited at deeper depths. Microbial networks showed a higher density, connectedness, average degree and module size in deeper soils. We observed a decrease in fungal‐fungal links and an increase of bacteria–bacteria links with increasing depth in all crops, particularly in the root microbiome. 

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5. Microbial Communities in the Changing Vegetation of the Chihuahuan Desert

   Embury, Emily L (February 2024, ProQuest)

   The encroachment of woody shrubs into grasslands is a phenomenon that has been occurring in the Chihuahuan Desert since the 1800s. Research shows that extensive livestock grazing and increased drought levels have acted as the main drivers of the grassland-to-shrubland transition. Very few studies have considered the impacts of such vegetation changes on microbial communities. Microbes play important ecosystem roles in nutrient cycling and carbon sequestration but also have the potential to act as pathogens. As the role of microbes in ecosystems is so important, it is crucial to understand the potential impacts of shrub encroachment on microbes and vice versa. Additionally, dryland microbes in general are understudied and as drylands cover over 40% of Earth’s land, understanding these microbes is of great ecological importance. The goal of this study was to assess microbial communities in shrub encroached systems in the Chihuahuan Desert to improve understanding of the ecological impacts of encroachment and increase general knowledge of dryland microbes. To conduct this study, soil samples were collected from sites dominated by black grama grass (Bouteloua eriopoda), sites dominated by honey mesquite shrubs (Prosopis glandulosa), and transition sites with both black grama and mesquite. DNA from soil samples was sequenced for bacteria (16S) and fungi (ITS2). Soil sampling was conducted through five sampling periods across a 10-month range to assess any potential seasonal variation in the microbial communities. In addition to DNA sequencing, microbial biomass and other environmental variables were collected. Statistical analyses were conducted to assess potential differences in microbial communities between vegetation types and seasons. Analyses included assessments of alpha and beta diversity, co-occurrence networks, and differential abundance analyses. Results show that there are significant changes in the microbial communities across vegetation types and seasons. Unique fungal and bacterial communities were identified in association with the different vegetation types, demonstrating that differences in vegetation influence microbial communities. Additionally, findings show that microbial communities are strongly impacted by seasons, showing decreases in biomass and changes to community composition in warm summer months compared to cooler months. Additionally, results show higher proportions of fungal pathogens in grass sites compared to other sites. Overall, this study demonstrates that microbial communities are influenced by shrub encroachment. As dryland microbial communities are often understudied, these findings can provide valuable insight into the ecology of dryland microbes and shrub-encroached systems. 

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