More Like this

1. Warming Disrupts Plant–Fungal Endophyte Symbiosis More Severely in Leaves Than Roots

   https://doi.org/10.1111/gcb.70207  

   Edwards, Joseph_D; Kazenel, Melanie_R; Luo, Yiqi; Lynn, Joshua_S; McCulley, Rebecca_L; Souza, Lara; Young, Carolyn; Rudgers, Jennifer_A; Kivlin, Stephanie_N (April 2025, Global Change Biology)

   ABSTRACT Disruptions to functionally important symbionts with global change will negatively impact plant fitness, with broader consequences for species' abundances, distribution, and community composition. Fungal endophytes that live inside plant leaves and roots could potentially mitigate plant heat stress from global warming. Conversely, disruptions of these symbioses could exacerbate the negative impacts of warming. To better understand the consistency and strength of warming‐induced changes to fungal endophytes, we examined fungal leaf and root endophytes in three grassland warming experiments in the US ranging from 2 to 25 years and spanning 2000 km, 12°C of mean annual temperature, and 600 mm of precipitation. We found that experimental warming disrupted symbiosis between plants and fungal endophytes. Colonization of plant tissues by septate fungi decreased in response to warming by 90% in plant leaves and 35% in roots. Warming also reduced fungal diversity and changed community composition in plant leaves, but not roots. The strength, but not direction, of warming effects on fungal endophytes varied by up to 75% among warming experiments. Finally, warming decoupled fungal endophytes from host metabolism by decreasing the correlation between endophyte community and host metabolome dissimilarity. These effects were strongest in the shorter‐term experiment, suggesting endophyte‐host metabolome function may acclimate to warming over decades. Overall, warming‐driven disruption of fungal endophyte community structure and function suggests that this symbiosis may not be a reliable mechanism to promote plant resilience and ameliorate stress responses under global change. 

   more » « less
2. Environmental and host plant effects on taxonomic and phylogenetic diversity of root fungal endophytes

   https://doi.org/10.1093/femsle/fnaf030  

   Farrer, Emily_C; Kulick, Nelle_K; Birnbaum, Christina; Halbrook, Susannah; Bumby, Caitlin_R; Willis, Claire (March 2025, FEMS Microbiology Letters)

   Abstract Nearly all plants are colonized by fungal endophytes, and a growing body of work shows that both environment and host species shape plant-associated fungal communities. However, few studies place their work in a phylogenetic context to understand endophyte community assembly through an evolutionary lens. Here, we investigated environmental and host effects on root endophyte assemblages in coastal Louisiana marshes. We isolated and sequenced culturable fungal endophytes from roots of three to four dominant plant species from each of three sites of varying salinity. We assessed taxonomic diversity and composition as well as phylogenetic diversity (mean phylogenetic distance, MPD) and phylogenetic composition (based on MPD). When we analyzed plant hosts present across the entire gradient, we found that the effect of the environment on phylogenetic diversity (as measured by MPD) was host dependent and suggested phylogenetic clustering in some circumstances. We found that both environment and host plant affected taxonomic composition of fungal endophytes, but only host plant affected phylogenetic composition, suggesting different host plants selected for fungal taxa drawn from distinct phylogenetic clades, whereas environmental assemblages were drawn from similar clades. Our study demonstrates that including phylogenetic, as well as taxonomic, community metrics can provide a deeper understanding of community assembly in endophytes. 

   more » « less
3. Influence of Plant Host and Organ, Management Strategy, and Spore Traits on Microbiome Composition

   https://doi.org/10.1094/PBIOMES-08-19-0045-R  

   Gdanetz, Kristi; Noel, Zachary; Trail, Frances (January 2021, Phytobiomes Journal)

   null (Ed.)

   Microbiomes from maize and soybean were characterized in a long-term three-crop rotation research site, under four different land management strategies, to begin unraveling the effects of common farming practices on microbial communities. The fungal and bacterial communities of leaves, stems, and roots in host species were characterized across the growing season using amplicon sequencing and compared with the results of a similar study on wheat. Communities differed across hosts and among plant growth stages and organs, and these effects were most pronounced in the bacterial communities of the wheat and maize phyllosphere. Roots consistently showed the highest number of bacterial operational taxonomic units compared with aboveground organs, whereas the α-diversity of fungi was similar between above- and belowground organs. Network analyses identified putatively influential members of the microbial communities of the three host plant species. The fungal taxa specific to roots, stems, or leaves were examined to determine whether the specificity reflected their life histories based on previous studies. The analysis suggests that fungal spore traits are drivers of organ specificity in the fungal community. Identification of influential taxa in the microbial community and understanding how community structure of specific crop organs is formed will provide a critical resource for manipulations of microbial communities. The ability to predict how organ-specific communities are influenced by spore traits will enhance our ability to introduce them sustainably. 

   more » « less
4. The Rhizosphere Responds: Rich Fen Peat and Root Microbial Ecology after Long-Term Water Table Manipulation

   https://doi.org/10.1128/AEM.00241-21  

   Rupp, Danielle L.; Lamit, Louis J.; Techtmann, Stephen M.; Kane, Evan S.; Lilleskov, Erik A.; Turetsky, Merritt R. (May 2021, Applied and Environmental Microbiology)

   Stams, Alfons J. (Ed.)

   ABSTRACT Hydrologic shifts due to climate change will affect the cycling of carbon (C) stored in boreal peatlands. Carbon cycling in these systems is carried out by microorganisms and plants in close association. This study investigated the effects of experimentally manipulated water tables (lowered and raised) and plant functional groups on the peat and root microbiomes in a boreal rich fen. All samples were sequenced and processed for bacterial, archaeal (16S DNA genes; V4), and fungal (internal transcribed spacer 2 [ITS2]) DNA. Depth had a strong effect on microbial and fungal communities across all water table treatments. Bacterial and archaeal communities were most sensitive to the water table treatments, particularly at the 10- to 20-cm depth; this area coincides with the rhizosphere or rooting zone. Iron cyclers, particularly members of the family Geobacteraceae , were enriched around the roots of sedges, horsetails, and grasses. The fungal community was affected largely by plant functional group, especially cinquefoils. Fungal endophytes (particularly Acephala spp.) were enriched in sedge and grass roots, which may have underappreciated implications for organic matter breakdown and cycling. Fungal lignocellulose degraders were enriched in the lowered water table treatment. Our results were indicative of two main methanogen communities, a rooting zone community dominated by the archaeal family Methanobacteriaceae and a deep peat community dominated by the family Methanomicrobiaceae . IMPORTANCE This study demonstrated that roots and the rooting zone in boreal fens support organisms likely capable of methanogenesis, iron cycling, and fungal endophytic association and are directly or indirectly affecting carbon cycling in these ecosystems. These taxa, which react to changes in the water table and associate with roots and, particularly, graminoids, may gain greater biogeochemical influence, as projected higher precipitation rates could lead to an increased abundance of sedges and grasses in boreal fens. 

   more » « less
5. Drivers of bacterial and fungal root endophyte communities: understanding the relative influence of host plant, environment, and space

   https://doi.org/10.1093/femsec/fiad034  

   Brigham, Laurel M.; Bueno de Mesquita, Clifton P.; Spasojevic, Marko J.; Farrer, Emily C.; Porazinska, Dorota L.; Smith, Jane G.; Schmidt, Steven K.; Suding, Katharine N. (March 2023, FEMS Microbiology Ecology)

   Abstract Bacterial and fungal root endophytes can impact the fitness of their host plants, but the relative importance of drivers for root endophyte communities is not well known. Host plant species, the composition and density of the surrounding plants, space, and abiotic drivers could significantly affect bacterial and fungal root endophyte communities. We investigated their influence in endophyte communities of alpine plants across a harsh high mountain landscape using high-throughput sequencing. There was less compositional overlap between fungal than bacterial root endophyte communities, with four ‘cosmopolitan’ bacterial OTUs found in every root sampled, but no fungal OTUs found across all samples. We found that host plant species, which included nine species from three families, explained the greatest variation in root endophyte composition for both bacterial and fungal communities. We detected similar levels of variation explained by plant neighborhood, space, and abiotic drivers on both communities, but the plant neighborhood explained less variation in fungal endophytes than expected. Overall, these findings suggest a more cosmopolitan distribution of bacterial OTUs compared to fungal OTUs, a structuring role of the plant host species for both communities, and largely similar effects of the plant neighborhood, abiotic drivers, and space on both communities. 

   more » « less