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1. Seasonal Dynamics of Core Fungi in the Switchgrass Phyllosphere, and Co-Occurrence with Leaf Bacteria

   https://doi.org/10.1094/PBIOMES-07-20-0051-R  

   Bowsher, Alan W.; Benucci, Gian Maria; Bonito, Gregory; Shade, Ashley (January 2021, Phytobiomes Journal)

   null (Ed.)

   Plant leaves harbor complex microbial communities that influence plant health and productivity. Nevertheless, a detailed understanding of phyllosphere community assembly and drivers is needed, particularly for phyllosphere fungi. Here, we investigated seasonal dynamics of epiphytic phyllosphere fungal communities in switchgrass (Panicum virgatum L.), a focal bioenergy crop. We also leverage previously published data on switchgrass phyllosphere bacterial communities from the same experimental plants, allowing us to compare fungal and bacterial dynamics and explore interdomain network associations in the switchgrass phyllosphere. Overall, we found a strong impact of sampling date on fungal community composition, with multiple taxonomic levels exhibiting clear temporal patterns in relative abundance. In addition, leaf nitrogen concentration, leaf dry matter content, plant height, and minimum daily air temperature explained significant variation in phyllosphere fungal communities, likely due to their correlation with sampling date. Finally, among the core taxa, fungi–bacteria network associations were much more common than bacteria–bacteria associations, suggesting the importance of interdomain phylogenetic diversity in microbiome assembly. Although our findings highlight the complexity of phyllosphere microbiome assembly, the clear temporal patterns in lineage-specific fungal abundances give promise to the potential for accurately predicting shifts in fungal phyllosphere communities throughout the growing season, a key research priority for sustainable agriculture. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license . 

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2. Ectomycorrhizal fungi alter soil food webs and the functional potential of bacterial communities

   https://doi.org/10.1128/msystems.00369-24  

   Berrios, Louis; Bogar, Glade D; Bogar, Laura M; Venturini, Andressa M; Willing, Claire E; Del_Rio, Anastacia; Ansell, T Bertie; Zemaitis, Kevin; Velickovic, Marija; Velickovic, Dusan; et al (May 2024, mSystems)

   Gao, Cheng (Ed.)

   ABSTRACT Most of Earth’s trees rely on critical soil nutrients that ectomycorrhizal fungi (EcMF) liberate and provide, and all of Earth’s land plants associate with bacteria that help them survive in nature. Yet, our understanding of how the presence of EcMF modifies soil bacterial communities, soil food webs, and root chemistry requires direct experimental evidence to comprehend the effects that EcMF may generate in the belowground plant microbiome. To this end, we grewPinus muricataplants in soils that were either inoculated with EcMF and native forest bacterial communities or only native bacterial communities. We then profiled the soil bacterial communities, applied metabolomics and lipidomics, and linked omics data sets to understand how the presence of EcMF modifies belowground biogeochemistry, bacterial community structure, and their functional potential. We found that the presence of EcMF (i) enriches soil bacteria linked to enhanced plant growth in nature, (ii) alters the quantity and composition of lipid and non-lipid soil metabolites, and (iii) modifies plant root chemistry toward pathogen suppression, enzymatic conservation, and reactive oxygen species scavenging. Using this multi-omic approach, we therefore show that this widespread fungal symbiosis may be a common factor for structuring soil food webs.IMPORTANCEUnderstanding how soil microbes interact with one another and their host plant will help us combat the negative effects that climate change has on terrestrial ecosystems. Unfortunately, we lack a clear understanding of how the presence of ectomycorrhizal fungi (EcMF)—one of the most dominant soil microbial groups on Earth—shapes belowground organic resources and the composition of bacterial communities. To address this knowledge gap, we profiled lipid and non-lipid metabolites in soils and plant roots, characterized soil bacterial communities, and compared soils amended either with or without EcMF. Our results show that the presence of EcMF changes soil organic resource availability, impacts the proliferation of different bacterial communities (in terms of both type and potential function), and primes plant root chemistry for pathogen suppression and energy conservation. Our findings therefore provide much-needed insight into how two of the most dominant soil microbial groups interact with one another and with their host plant. 

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3. Comparing Sediment Microbial Communities of Arctic Beaver Ponds to Tundra Lakes and Streams

   https://doi.org/10.1029/2023JG007408  

   Shannon, Kelly C.; Christman, Natasha R.; Crump, Byron C.; Carey, Michael P.; Koch, Joshua; Lapham, Laura L.; O’Donnell, Jonathan; Poulin, Brett A.; Tape, Ken D.; Clark, Jason A.; et al (August 2023, Journal of Geophysical Research: Biogeosciences)

   Abstract In recent decades the habitat of North American beaver (Castor canadensis) has expanded from boreal forests into Arctic tundra ecosystems. Beaver ponds in Arctic watersheds are known to alter stream biogeochemistry, which is likely coupled with changes in the activity and composition of microbial communities inhabiting beaver pond sediments. We investigated bacterial, archaeal, and fungal communities in beaver pond sediments along tundra streams in northwestern Alaska (AK), USA and compared them to those of tundra lakes and streams in north‐central Alaska that are unimpacted by beavers.β‐glucosidase activity assays indicated higher cellulose degradation potential in beaver ponds than in unimpacted streams and lakes within a watershed absent of beavers. Beta diversity analyses showed that dominant lineages of bacteria and archaea in beaver ponds differed from those in tundra lakes and streams, but dominant fungal lineages did not differ between these sample types. Beaver pond sediments displayed lower relative abundances of Crenarchaeota and Euryarchaeota archaea and of bacteria from typically anaerobic taxonomic groups, suggesting differences in rates of fermentative organic matter (OM) breakdown, syntrophy, and methane generation. Beaver ponds also displayed low relative abundances of Chytridiomycota (putative non‐symbiotic) fungi and high relative abundances of ectomycorrhizal (plant symbionts) Basidiomycota fungi, suggesting differences in the occurrence of plant and fungi mutualistic interactions. Beaver ponds also featured microbes with taxonomic identities typically associated with the cycling of nitrogen and sulfur compounds in higher relative abundances than tundra lakes and streams. These findings help clarify the microbiological implications of beavers expanding into high latitude regions. 

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4. Co-inoculations of bacteria and mycorrhizal fungi often drive additive plant growth responses

   https://doi.org/10.1093/ismeco/ycae104  

   Berrios, Louis; Venturini, Andressa_M; Ansell, Tillson_Bertie; Tok, Esther; Johnson, William; Willing, Claire_E; Peay, Kabir_G (August 2024, ISME Communications)

   Abstract Controlled greenhouse studies have shown the numerous ways that soil microbes can impact plant growth and development. However, natural soil communities are highly complex, and plants interact with many bacterial and fungal taxa simultaneously. Due to logistical challenges associated with manipulating more complex microbiome communities, how microbial communities impact emergent patterns of plant growth therefore remains poorly understood. For instance, do the interactions between bacteria and fungi generally yield additive (i.e. sum of their parts) or nonadditive, higher order plant growth responses? Without this information, our ability to accurately predict plant responses to microbial inoculants is weakened. To address these issues, we conducted a meta-analysis to determine the type (additive or higher-order, nonadditive interactions), frequency, direction (positive or negative), and strength that bacteria and mycorrhizal fungi (arbuscular and ectomycorrhizal) have on six phenotypic plant growth responses. Our results demonstrate that co-inoculations of bacteria and mycorrhizal fungi tend to have positive additive effects on many commonly reported plant responses. However, ectomycorrhizal plant shoot height responds positively and nonadditively to co-inoculations of bacteria and ectomycorrhizal fungi, and the strength of additive effects also differs between mycorrhizae type. These findings suggest that inferences from greenhouse studies likely scale to more complex field settings and that inoculating plants with diverse, beneficial microbes is a sound strategy to support plant growth. 

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5. Forest structural diversity is linked to soil microbial diversity

   https://doi.org/10.1002/ecs2.4702  

   Lang, Ashley_K; LaRue, Elizabeth_A; Kivlin, Stephanie_N; Edwards, Joseph_D; Phillips, Richard_P; Gallion, Joey; Kong, Nicole; Parker, John_D; McCormick, Melissa_K; Domke, Grant; et al (November 2023, Ecosphere)

   Abstract Efforts to catalog global biodiversity have often focused on aboveground taxonomic diversity, with limited consideration of belowground communities. However, diversity aboveground may influence the diversity of belowground communities and vice versa. In addition to taxonomic diversity, the structural diversity of plant communities may be related to the diversity of soil bacterial and fungal communities, which drive important ecosystem processes but are difficult to characterize across broad spatial scales. In forests, canopy structural diversity may influence soil microorganisms through its effects on ecosystem productivity and root architecture, and via associations between canopy structure, stand age, and species richness. Given that structural diversity is one of the few types of diversity that can be readily measured remotely (e.g., using light detection and ranging—LiDAR), establishing links between structural and microbial diversity could facilitate the detection of belowground biodiversity hotspots. We investigated the potential for using remotely sensed information about forest structural diversity as a predictor of soil microbial community richness and composition. We calculated LiDAR‐derived metrics of structural diversity as well as a suite of stand and soil properties from 38 forested plots across the central hardwoods region of Indiana, USA, to test whether forest canopy structure is linked with the community richness and diversity of four key soil microbial groups: bacteria, fungi, arbuscular mycorrhizal (AM) fungi, and ectomycorrhizal (EM) fungi. We found that the density of canopy vegetation is positively associated with the taxonomic richness (alpha diversity) of EM fungi, independent of changes in plant taxonomic richness. Further, structural diversity metrics were significantly correlated with the overall community composition of bacteria, EM, and total fungal communities. However, soil properties were the strongest predictors of variation in the taxonomic richness and community composition of microbial communities in comparison with structural diversity and tree species diversity. As remote sensing tools and algorithms are rapidly advancing, these results may have important implications for the use of remote sensing of vegetation structural diversity for management and restoration practices aimed at preserving belowground biodiversity. 

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