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1. Host genotype controls ecological change in the leaf fungal microbiome

   https://doi.org/10.1371/journal.pbio.3001681  

   VanWallendael, Acer; Benucci, Gian Maria; da Costa, Pedro Beschoren; Fraser, Linnea; Sreedasyam, Avinash; Fritschi, Felix; Juenger, Thomas E.; Lovell, John T.; Bonito, Gregory; Lowry, David B. (August 2022, PLOS Biology)

   Dong, Xinnian (Ed.)

   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. 

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2. Fungal Communities and Functional Guilds Shift Along an Elevational Gradient in the Southern Appalachian Mountains

   https://doi.org/10.1007/s00248-017-1116-6  

   Veach, Allison M.; Stokes, C. Elizabeth; Knoepp, Jennifer; Jumpponen, Ari; Baird, Richard (December 2017, Microbial Ecology)

   Nitrogen deposition alters forest ecosystems particularly in high elevation, montane habitats where nitrogen deposition is greatest and continues to increase. We collected soils across an elevational (788–1940 m) gradient, encompassing both abiotic (soil chemistry) and biotic (vegetation community) gradients, at eight locations in the southern Appalachian Mountains of southwestern North Carolina and eastern Tennessee. We measured soil chemistry (total N, C, extractable PO4, soil pH, cation exchange capacity [ECEC], percent base saturation [% BS]) and dissected soil fungal communities using ITS2 metabarcode Illumina MiSeq sequencing. Total soil N, C, PO4, % BS, and pH increased with elevation and plateaued at approximately 1400 m, whereas ECEC linearly increased and C/N decreased with elevation. Fungal communities differed among locations and were correlated with all chemical variables, except PO4, whereas OTU richness increased with total N. Several ecological guilds (i.e., ectomycorrhizae, saprotrophs, plant pathogens) differed in abundance among locations; specifically, saprotroph abundance, primarily attributable to genus Mortierella, was positively correlated with elevation. Ectomycorrhizae declined with total N and soil pH and increased with total C and PO4 where plant pathogens increased with total N and decreased with total C. Our results demonstrate significant turnover in taxonomic and functional fungal groups across elevational gradients which facilitate future predictions on forest ecosystem change in the southern Appalachians as nitrogen deposition rates increase and regional temperature and precipitation regimes shift. 

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3. Altered precipitation has asymmetric impacts on annual plant communities in warm and cool growing seasons

   https://doi.org/10.1525/elementa.2021.00014  

   Spasojevic, Marko J.; Homyak, Peter M.; Jenerette, G. Darrel; Goulden, Mike L.; McFaul, Shane; Madsen-McQueen, Tesa; Schauer, Lisa; Solis, Miguel (January 2022, Elementa: Science of the Anthropocene)

   While altered precipitation regimes can greatly impact biodiversity and ecosystem functioning, we lack a comprehensive view of how these impacts are mediated by changes to the seasonality of precipitation (i.e., whether it rains more/less in one season relative to another). Over 2 years, we examined how altered seasonal precipitation influenced annual plant biomass and species richness, Simpson’s diversity, and community composition of annual plant communities in a dryland ecosystem that receives both winter and summer rainfall and has distinct annual plant communities in each season. Using a rainfall exclusion, collection, and distribution system, we excluded precipitation and added water during each season individually and compared responses to control plots which received ambient summer and winter precipitation. In control plots, we found five times greater annual plant biomass, twice as many species, and higher diversity in winter relative to summer. Adding water increased annual plant biomass in summer only, did not change richness or diversity in either summer or winter, and modestly shifted community composition. Excluding precipitation in either season reduced annual plant biomass, richness, and Simpson’s diversity. However, in the second winter season, biomass was higher in the plots where precipitation was excluded in the previous summer seasons suggesting that reduced productivity in the summer may facilitate biomass in the winter. Our results suggest that increased precipitation in summer may have stronger short-term impacts on annual plant biodiversity and ecosystem function relative to increased winter precipitation. In contrast, decreasing precipitation may have ubiquitous negative effects on annual plants across both summer and winter but may lead to increased biomass in the following off-seasons. These patterns suggest that annual plant communities exhibit asymmetries in their community and ecosystem responses to altered seasonal precipitation and that considering the seasonality of precipitation is important for predicting the effects of altered precipitation regimes. 

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4. 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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5. Fragmentation disrupts microbial effects on native plant community productivity

   https://doi.org/10.1111/1365-2745.14097  

   Kiesewetter, Kasey N.; Otano, Leydiana; Afkhami, Michelle E. (April 2023, Journal of Ecology)

   Abstract Anthropogenic habitat fragmentation—the breaking up of natural landscapes—is a pervasive threat to biodiversity and ecosystem function world‐wide. Fragmentation results in a mosaic of remnant native habitat patches embedded in human‐modified habitat known as the ‘matrix’. By introducing novel environmental conditions in matrix habitats and reducing connectivity of native habitats, fragmentation can dramatically change how organisms experience their environment. The effects of fragmentation can be especially important in urban landscapes, which are expanding across the globe. Despite this surging threat and the importance of microbiomes for ecosystem services, we know very little about how fragmentation affects microbiomes and even less about their consequences for plant–microbe interactions in urban landscapes.By combining field surveys, microbiome sequencing and experimental mesocosms, we (1) investigated how microbial community diversity, composition and functional profiles differed between 15 native pine rockland fragments and the adjacent urban matrix habitat, (2) identified habitat attributes that explained significant variation in microbial diversity of native core habitat compared to urban matrix and (3) tested how changes in urbanized and low connectivity microbiomes affected plant community productivity.We found urban and native microbiomes differed substantively in diversity, composition and functional profiles, including symbiotic fungi decreasing 81% and pathogens increasing 327% in the urban matrix compared to native habitat. Furthermore, fungal diversity rapidly declined as native habitats became increasingly isolated, with ~50% of variation across the landscape explained by habitat connectivity alone. Interestingly, microbiomes from native habitats increased plant productivity by ~300% while urban matrix microbiomes had no effect, suggesting that urbanization may decouple beneficial plant–microbe interactions. In addition, microbial diversity within native habitats explained significant variation in plant community productivity, with higher productivity linked to more diverse microbiomes from more connected, larger fragments.Synthesis. Taken together, our study not only documents significant changes in microbial diversity, composition and functions in the urban matrix, but also supports that two aspects of habitat fragmentation—the introduction of a novel urban matrix and reduced habitat connectivity—disrupt microbial effects on plant community productivity, highlighting preservation of native microbiomes as critical for productivity in remnant fragments. 

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