Fungal endophytes of invasive Phagramites australis populations vary in species composition and fungicide susceptibility

Fungal and metabolome diversity of the rhizosphere and endosphere of Phragmites australis in an AMD-polluted environment

Symbiotic associations with rhizospheric microbial communities coupled with the production of metabolites are key adaptive mechanisms by metallophytes to overcome metal stress. However, little is known about pseudometallophyte Phragmites australis interactions with fungal community despite commonly being applied in wetland phytoremediation of acid mine drainage (AMD). In this study, fungal community diversity and metabolomes production by rhizosphere and root endosphere of P. australis growing under three different AMD pollution gradient were analyzed. Our results highlight the following: 1) Ascomycota and Basidiomycota were dominant phyla, but the diversity and richness of taxa were lower within AMD sites with Penicillium, Candida, Saccharomycetales, Vishniacozyma, Trichoderma, Didymellaceae, and Cladosporium being enriched in the root endosphere and rhizosphere in AMD sites than non-AMD site; 2) non-metric multidimensional scaling (NMDS) of 73 metabolomes revealed spatially defined metabolite exudation by distinct root parts (rhizosphere vs endosphere) rather than AMD sites, with significant variability occurring within the rhizosphere correlating to pH, TDS, Fe, Cr, Cu and Zn content changes; 3) canonical correspondence analysis (CCA) confirmed specific rhizospheric fungal taxonomic changes are driven by pH, TDS, heavy metals, and stress-related metabolomes produced. This is the first report that gives a snapshot on the complex endophytic and rhizospheric fungal community structure and metabolites perturbations that may be key in the adaptability and metal phytoremediation by P. australis under AMD environment.

Phragmites australis Associates with Belowground Fungal Communities Characterized by High Diversity and Pathogen Abundance

Microbial symbionts are gaining attention as crucial drivers of invasive species spread and dominance. To date, much research has quantified the net effects of plant–microbe interactions on the relative success of native and invasive species. However, little is known about how the structure (composition and diversity) of microbial symbionts can differ among native and invasive species, or vary across the invasive landscape. Here, we explore the structure of endosphere and soil fungal communities associated with a monoculture-forming widespread invader, Phragmites australis, and co-occurring native species. Using field survey data from marshes in coastal Louisiana, we tested three hypotheses: (1) Phragmites australis root and soil fungal communities differ from that of co-occurring natives, (2) Phragmites australis monocultures harbor distinct fungal communities at the expanding edge compared to the monodominant center, and (3) proximity to the P. australis invading front alters native root endosphere and soil fungal community structure. We found that P. australis cultivates root and soil fungal communities with higher richness, diversity, and pathogen abundances compared to native species. While P. australis was found to have higher endosphere pathogen abundances at its expanding edge compared to the monodominant center, we found no evidence of compositional changes or pathogen spillover in native species in close proximity to the invasion front. This work suggests that field measurements of fungal endosphere communities in native and invasive plants are useful to help understand (or rule out) mechanisms of invasion.

Quantifying the sharing of foliar fungal pathogens by the invasive plant Ageratina adenophora and its neighbours

Local pathogens can accumulate as asymptomatic endophytes, making it difficult to detect the impacts of invasive species as propagators of disease in the invaded range. We used the invasive plant Ageratina adenophora to assess such accumulation. We intensively collected foliar fungal endophytes and leaf spot pathogens of A. adenophora and co-occurring neighbours and performed an inoculation experiment to evaluate their pathogenicity and host range. Ageratina adenophora harboured diverse necrotrophic pathogens; its communities of endophytes and leaf spot pathogens were different in composition and shared only a small number of fungal species. In the pathogen communities of local plant hosts, 21% of the operational taxonomic units (OTUs), representing 50% of strains, also occurred as leaf spot pathogens and/or endophytes of A. adenophora. The local pathogen community was more similar to the endophytes than to the pathogens of A. adenophora. The inoculation experiment showed that local pathogens could infect A. adenophora leaves asymptomatically and that local plant hosts were susceptible to both A. adenophora endophytes and pathogens. Ageratina adenophora is a highly competent host for local pathogens, and its asymptomatic latent pathogens are fungi primarily shared with local neighbours. This poses challenges for understanding the long-term ecological consequences of plant invasion.

Does salinity affect lifestyle switching in the plant pathogen Fusarium solani?

Symbiotic microbes that live within plant hosts can exhibit a range in function from mutualistic to pathogenic, but the reason for this lifestyle switching remains largely unknown. Here we tested whether environmental stress, specifically salinity, is a factor that can trigger lifestyle switching in a fungus mainly known as a pathogen, Fusarium solani. F. solani was isolated from roots of Phragmites australis (common reed) in saline coastal marshes of Louisiana, USA, and we used Oryza sativa (rice) as a model organism from wetland environments to test the symbiont lifestyle. We plated rice seeds on control plates or plates with F. solani at three levels of salinity (0, 8 and 16 p.p.t.), then assessed germination and seedling growth after 20 days. Salinity strongly reduced percentage germination, slowed the timing of germination and reduced growth of rice. F. solani slowed germination, and it also caused a minor increase in root growth at medium salinity and a minor decrease in root growth at high salinity. Overall, despite being a common pathogen in other crop species (peas, beans, potatoes and many types of cucurbits), we found little evidence that F. solani has a strong pathogenic lifestyle in rice and we found weak evidence that pathogenicity may increase slightly with elevated salinity. These results have implications for both crops and native plant health in the future as soil salinization increases worldwide.

Tissue-Specific and Geographical Variation in Endophytic Fungi of Ageratina adenophora and Fungal Associations With the Environment

To understand the distribution of the cultivable fungal community in plant tissues and the associations of these fungi with their surrounding environments during the geographical expansion of an invasive plant, Ageratina adenophora, we isolated the cultivable fungi from 72 plant tissues, 12 soils, and 12 air samples collected from six areas in Yunnan Province, China. A total of 4066 isolates were investigated, including 1641 endophytic fungi, 233 withered leaf fungi, 1255 fungi from air, and 937 fungi from soil. These fungi were divided into 458 and 201 operational taxonomic units (OTUs) with unique and 97% ITS gene sequence identity, respectively. Phylogenetic analysis showed that the fungi belonged to four phyla, including Ascomycota (94.20%), Basidiomycota (2.71%), Mortierellomycota (3.03%), and Mucoromycota (0.07%). The dominant genera of cultivable endophytic fungi were Colletotrichum (34.61%), Diaporthe (17.24%), Allophoma (8.03%), and Fusarium (4.44%). Colletotrichum and Diaporthe were primarily isolated from mature leaves, Allophoma from stems, and Fusarium from roots, indicating that the enrichment of endophytic fungi is tissue-specific and fungi rarely grew systemically within A. adenophora. In the surrounding environment, Alternaria (21.46%), Allophoma (19.31%), Xylaria (18.45%), and Didymella (18.03%) were dominant in the withered leaves, Cladosporium (22.86%), Trichoderma (14.27%), and Epicoccum (9.83%) were dominant in the canopy air, and Trichoderma (27.27%) and Mortierella (20.46%) were dominant in the rhizosphere soils. Further analysis revealed that the cultivable endophytic fungi changed across geographic areas and showed a certain degree of variation in different tissues of A. adenophora. The cultivable fungi in mature and withered leaves fluctuated more than those in roots and stems. We also found that some cultivable endophytic fungi might undergo tissue-to-tissue migration and that the stem could be a transport tissue by which airborne fungi infect roots. Finally, we provided evidence that the fungal community within A. adenophora was partially shared with the contiguous environment. The data suggested a frequent interaction between fungi associated with A. adenophora and those in surrounding environments, reflecting a compromise driven by both functional requirements for plant growth and local environmental conditions.

Soil conditioning effects of Phragmites australis on native wetland plant seedling survival

Interactions between introduced plants and soils they colonize are central to invasive species success in many systems. Belowground biotic and abiotic changes can influence the success of introduced species as well as their native competitors. All plants alter soil properties after colonization but, in the case of many invasive plant species, it is unclear whether the strength and direction of these soil conditioning effects are due to plant traits, plant origin, or local population characteristics and site conditions in the invaded range. Phragmites australis in North America exists as a mix of populations of different evolutionary origin. Populations of endemic native Phragmites australis americanus are declining, while introduced European populations are important wetland invaders. We assessed soil conditioning effects of native and non-native P. australis populations on early and late seedling survival of native and introduced wetland plants. We further used a soil biocide treatment to assess the role of soil fungi on seedling survival. Survival of seedlings in soils colonized by P. australis was either unaffected or negatively affected; no species showed improved survival in P. australis-conditioned soils. Population of P. australis was a significant factor explaining the response of seedlings, but origin (native or non-native) was not a significant factor. Synthesis: Our results highlight the importance of phylogenetic control when assessing impacts of invasive species to avoid conflating general plant traits with mechanisms of invasive success. Both native (noninvasive) and non-native (invasive) P. australis populations reduced seedling survival of competing plant species. Because soil legacy effects of native and non-native P. australis are similar, this study suggests that the close phylogenetic relationship between the two populations, and not the invasive status of introduced P. australis, is more relevant to their soil-mediated impact on other plant species.

Plant Host and Geographic Location Drive Endophyte Community Composition in the Face of Perturbation

All plants form symbioses with endophytic fungi, which affect host plant health and function. Most endophytic fungi are horizontally transmitted, and consequently, local environment and geographic location greatly influence endophyte community composition. Growing evidence also suggests that identity of the plant host (e.g., species, genotype) can be important in shaping endophyte communities. However, little is known about how disturbances to plants affect their fungal symbiont communities. The goal of this study was to test if disturbances, from both natural and anthropogenic sources, can alter endophyte communities independent of geographic location or plant host identity. Using the plant species white snakeroot (Ageratina altissima; Asteraceae), we conducted two experiments that tested the effect of perturbation on endophyte communities. First, we examined endophyte response to leaf mining insect activity, a natural perturbation, in three replicate populations. Second, for one population, we applied fungicide to plant leaves to test endophyte community response to an anthropogenic perturbation. Using culture-based methods and Sanger sequencing of fungal isolates, we then examined abundance, diversity, and community structure of endophytic fungi in leaves subjected to perturbations by leaf mining and fungicide application. Our results show that plant host individual and geographic location are the major determinants of endophyte community composition even in the face of perturbations. Unexpectedly, we found that leaf mining did not impact endophyte communities in white snakeroot, but fungicide treatment resulted in small but significant changes in endophyte community structure. Together, our results suggest that endophyte communities are highly resistant to biotic and anthropogenic disturbances.

Functional Role of Bacteria from Invasive Phragmites australis in Promotion of Host Growth

We hypothesize that bacterial endophytes may enhance the competitiveness and invasiveness of Phragmites australis. To evaluate this hypothesis, endophytic bacteria were isolated from P. australis. The majority of the shoot meristem isolates represent species from phyla Firmicutes, Proteobacteria, and Actinobacteria. We chose one species from each phylum to characterize further and to conduct growth promotion experiments in Phragmites. Bacteria tested include Bacillus amyloliquefaciens A9a, Achromobacter spanius B1, and Microbacterium oxydans B2. Isolates were characterized for known growth promotional traits, including indole acetic acid (IAA) production, secretion of hydrolytic enzymes, phosphate solubilization, and antibiosis activity. Potentially defensive antimicrobial lipopeptides were assayed for through application of co-culturing experiments and mass spectrometer analysis. B. amyloliquefaciens A9a and M. oxydans B2 produced IAA. B. amyloliquefaciens A9a secreted antifungal lipopeptides. Capability to promote growth of P. australis under low nitrogen conditions was evaluated in greenhouse experiments. All three isolates were found to increase the growth of P. australis under low soil nitrogen conditions and showed increased absorption of isotopic nitrogen into plants. This suggests that the Phragmites microbes we evaluated most likely promote growth of Phragmites by enhanced scavenging of nitrogenous compounds from the rhizosphere and transfer to host roots. Collectively, our results support the hypothesis that endophytic bacteria play a role in enhancing growth of P. australis in natural populations. Gaining a better understanding of the precise contributions and mechanisms of endophytes in enabling P. australis to develop high densities rapidly could lead to new symbiosis-based strategies for management and control of the host.

The role of plant-microbiome interactions in weed establishment and control

The soil microbiome plays an important role in the establishment of weeds and invasive plants. They associate with microorganisms supporting their growth and health. Weed management strategies, like tillage and herbicide treatments, to control weeds generally alter soil structure going alongside with changes in the microbial community. Once a weed population establishes in the field, the plants build up a close relationship with the available microorganisms. Seeds or vegetative organs overwinter in soil and select early in the season their own microbiome before crop plants start to vegetate. Weed and crop plants compete for light, nutrition and water, but may differently interact with soil microorganisms. The development of new sequencing technologies for analyzing soil microbiomes has opened up the possibility for in depth analysis of the interaction between 'undesired' plants and crop plants under different management systems. These findings will help us to understand the functions of microorganisms involved in crop productivity and plant health, weed establishment and weed prevention. Exploitation of the knowledge offers the possibility to search for new biocontrol methods against weeds based on soil and plant-associated microorganisms. This review discusses the recent advances in understanding the functions of microbial communities for weed/invasive plant establishment and shows new ways to use plant-associated microorganisms to control weeds and invasive plants in different land management systems.

Virulence of oomycete pathogens from Phragmites australis-invaded and noninvaded soils to seedlings of wetland plant species

Soil pathogens affect plant community structure and function through negative plant-soil feedbacks that may contribute to the invasiveness of non-native plant species. Our understanding of these pathogen-induced soil feedbacks has relied largely on observations of the collective impact of the soil biota on plant populations, with few observations of accompanying changes in populations of specific soil pathogens and their impacts on invasive and noninvasive species. As a result, the roles of specific soil pathogens in plant invasions remain unknown. In this study, we examine the diversity and virulence of soil oomycete pathogens in freshwater wetland soils invaded by non-native Phragmites australis (European common reed) to better understand the potential for soil pathogen communities to impact a range of native and non-native species and influence invasiveness. We isolated oomycetes from four sites over a 2-year period, collecting nearly 500 isolates belonging to 36 different species. These sites were dominated by species of Pythium, many of which decreased seedling survival of a range of native and invasive plants. Despite any clear host specialization, many of the Pythium species were differentially virulent to the native and non-native plant species tested. Isolates from invaded and noninvaded soils were equally virulent to given individual plant species, and no apparent differences in susceptibility were observed between the collective groups of native and non-native plant species.

Advancing the science of microbial symbiosis to support invasive species management: a case study on Phragmites in the Great Lakes

A growing body of literature supports microbial symbiosis as a foundational principle for the competitive success of invasive plant species. Further exploration of the relationships between invasive species and their associated microbiomes, as well as the interactions with the microbiomes of native species, can lead to key new insights into invasive success and potentially new and effective control approaches. In this manuscript, we review microbial relationships with plants, outline steps necessary to develop invasive species control strategies that are based on those relationships, and use the invasive plant species Phragmites australis (common reed) as an example of how development of microbial-based control strategies can be enhanced using a collective impact approach. The proposed science agenda, developed by the Collaborative for Microbial Symbiosis and Phragmites Management, contains a foundation of sequential steps and mutually-reinforcing tasks to guide the development of microbial-based control strategies for Phragmites and other invasive species. Just as the science of plant-microbial symbiosis can be transferred for use in other invasive species, so too can the model of collective impact be applied to other avenues of research and management.