Above- and belowground fungal biodiversity of Populus trees on a continental scale

Understanding drivers of terrestrial fungal communities over large scales is an important challenge for predicting the fate of ecosystems under climate change and providing critical ecological context for bioengineering plant-microbe interactions in model systems. We conducted an extensive molecular and microscopy field study across the contiguous United States measuring natural variation in the Populus fungal microbiome among tree species, plant niche compartments and key symbionts. Our results show clear biodiversity hotspots and regional endemism of Populus-associated fungal communities explained by a combination of climate, soil and geographic factors. Modelling climate change impacts showed a deterioration of Populus mycorrhizal associations and an increase in potentially pathogenic foliar endophyte diversity and prevalence. Geographic differences among these symbiont groups in their sensitivity to environmental change are likely to influence broader forest health and ecosystem function. This dataset provides an above- and belowground atlas of Populus fungal biodiversity at a continental scale.

Plant Seeds Commonly Host Bacillus spp., Potential Antagonists of Phytopathogens

In agriculture, horticulture and plantation forestry, Bacillus species are the most commonly applied antagonists and biopesticides, targeting plant pathogens and insect pests, respectively. Bacillus isolates are also used as bacterial plant biostimulants, or BPBs. Such useful isolates of Bacillus are typically sourced from soil. Here, we show that Bacillus - and other antagonistic microbes - can be sourced from a broad range of plant seeds. We found that culturable Bacillus isolates are common in the seeds of 98 plant species representing 39 families (i.e., 87% of the commonly cultured bacteria belonged to Bacillales). We also found that 83% of the commonly cultured fungi from the seeds of the 98 plant species belonged to just three orders of fungi-Pleosporales, Hypocreales and Eurotiales-that are also associated with antagonism. Furthermore, we confirmed antagonism potential in agaro with seed isolates of Bacillus from Pinus monticola as a representative case. Eight isolates each of seed Bacillus, seed fungi, and foliar fungi, all from P. monticola, were paired in a total of 384 possible pair-wise interactions (with seed and foliar fungi as the targets). Seed Bacillus spp. were the strongest antagonists of the seed and foliar fungi, with a mean interaction strength 2.8 times greater than seed fungi (all either Eurotiales or Hypocreales) and 3.2 times greater than needle fungi. Overall, our study demonstrates that seeds host a taxonomically narrow group of culturable, antagonistic bacteria and fungi.

Facilitating Reforestation Through the Plant Microbiome: Perspectives from the Phyllosphere

Tree planting and natural regeneration contribute to the ongoing effort to restore Earth's forests. Our review addresses how the plant microbiome can enhance the survival of planted and naturally regenerating seedlings and serve in long-term forest carbon capture and the conservation of biodiversity. We focus on fungal leaf endophytes, ubiquitous defensive symbionts that protect against pathogens. We first show that fungal and oomycetous pathogen richness varies greatly for tree species native to the United States (n = 0-876 known pathogens per US tree species), with nearly half of tree species either without pathogens in these major groups or with unknown pathogens. Endophytes are insurance against the poorly known and changing threat of tree pathogens. Next, we review studies of plant phyllosphere feedback, but knowledge gaps prevent us from evaluating whether adding conspecific leaf litter to planted seedlings promotes defensive symbiosis, analogous to adding soil to promote positive feedback. Finally, we discuss research priorities for integrating the plant microbiome into efforts to expand Earth's forests.

The core seed mycobiome of Pseudotsuga menziesii var. menziesii across provenances of the Pacific Northwest, USA

Fungal symbionts occur in all plant tissues, and many aid their host plants with critical functions, including nutrient acquisition, defense against pathogens, and tolerance of abiotic stress. "Core" taxa in the plant mycobiome, defined as fungi present across individuals, populations, or time, may be particularly crucial to plant survival during the challenging seedling stage. However, studies on core seed fungi are limited to individual sampling sites, raising the question of whether core taxa exist across large geographic scales. We addressed this question using both culture-based and culture-free techniques to identify the fungi found in individual seeds collected from nine provenances across the range of coastal Douglas-fir (Pseudotsuga menziesii var. menziesii), a foundation tree species in the Pacific Northwest and a globally important timber crop that is propagated commercially by seed. Two key findings emerged: (i) Seed mycobiome composition differed among seed provenances. (ii) Despite variation in the seed mycobiome, we detected four core members, none of which is a known pathogen of Douglas-fir: Trichoderma spp., Hormonema macrosporum, Mucor plumbeus, and Talaromyces rugulosus. Our results support the concept of a core seed microbiome, yet additional work is needed to determine the functional consequences of core taxa for seedling germination, growth, survival, and competition.

Elevated carbon dioxide reduces a common soybean leaf endophyte

Free-air CO2 enrichment (FACE) experiments have elucidated how climate change affects plant physiology and production. However, we lack a predictive understanding of how climate change alters interactions between plants and endophytes, critical microbial mediators of plant physiology and ecology. We leveraged the SoyFACE facility to examine how elevated [CO2 ] affected soybean (Glycine max) leaf endophyte communities in the field. Endophyte community composition changed under elevated [CO2 ], including a decrease in the abundance of a common endophyte, Methylobacterium sp. Moreover, Methylobacterium abundance was negatively correlated with co-occurring fungal endophytes. We then assessed how Methylobacterium affected the growth of co-occurring endophytic fungi in vitro. Methylobacterium antagonized most co-occurring fungal endophytes in vitro, particularly when it was more established in culture before fungal introduction. Variation in fungal response to Methylobacterium within a single fungal operational taxonomic unit (OTU) was comparable to inter-OTU variation. Finally, fungi isolated from elevated vs. ambient [CO2 ] plots differed in colony growth and response to Methylobacterium, suggesting that increasing [CO2 ] may affect fungal traits and interactions within the microbiome. By combining in situ and in vitro studies, we show that elevated [CO2 ] decreases the abundance of a common bacterial endophyte that interacts strongly with co-occurring fungal endophytes. We suggest that endophyte responses to global climate change will have important but largely unexplored implications for both agricultural and natural systems.

Leaf Endophytes of Populus trichocarpa Act as Pathogens of Neighboring Plant Species

The conventional definition of endophytes is that they do not cause disease, whereas pathogens do. Complicating this convention, however, is the poorly explored phenomenon that some microbes are endophytes in some plants but pathogens in others. Black cottonwood or poplar (Populus trichocarpa) and wheat (Triticum aestivum) are common wild and crop plants, respectively, in the Pacific Northwest USA. The former anchors wild, riparian communities, whereas the latter is an introduced domesticate of commercial importance in the region. We isolated Fusarium culmorum – a well-known pathogen of wheat causing both blight and rot – from the leaf of a black cottonwood tree in western Washington. The pathogenicity of this cottonwood isolate and of a wheat isolate of F. culmorum were compared by inoculating both cottonwood and wheat in a greenhouse experiment. We found that both the cottonwood and wheat isolates of F. culmorum significantly reduced the growth of wheat, whereas they had no impact on cottonwood growth. Our results demonstrate that the cottonwood isolate of F. culmorum is endophytic in one plant species but pathogenic in another. Using sequence-based methods, we found an additional 56 taxa in the foliar microbiome of cottonwood that matched the sequences of pathogens of other plants of the region. These sequence-based findings suggest, though they do not prove, that P. trichocarpa may host many additional pathogens of other plants.

Analysis of leaf microbiome composition of near-isogenic maize lines differing in broad-spectrum disease resistance

Plant genotype strongly affects disease resistance, and also influences the composition of the leaf microbiome. However, these processes have not been studied and linked in the microevolutionary context of breeding for improved disease resistance. We hypothesised that broad-spectrum disease resistance alleles also affect colonisation by nonpathogenic symbionts. Quantitative trait loci (QTL) conferring resistance to multiple fungal pathogens were introgressed into a disease-susceptible maize inbred line. Bacterial and fungal leaf microbiomes of the resulting near-isogenic lines were compared with the microbiome of the disease-susceptible parent line at two time points in multiple fields. Introgression of QTL from disease-resistant lines strongly shifted the relative abundance of diverse fungal and bacterial taxa in both 3-wk-old and 7-wk-old plants. Nevertheless, the effects on overall community structure and diversity were minor and varied among fields and years. Contrary to our expectations, host genotype effects were not any stronger in fields with high disease pressure than in uninfected fields, and microbiome succession over time was similar in heavily infected and uninfected plants. These results show that introgressed QTL can greatly improve broad-spectrum disease resistance while having only limited and inconsistent pleiotropic effects on the leaf microbiome in maize.

Fungal functional ecology: bringing a trait-based approach to plant-associated fungi

Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (Fun^Fun ). Fun^Fun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.

Contingency rules for pathogen competition and antagonism in a genetically based, plant defense hierarchy

Plant defense against pathogens includes a range of mechanisms, including, but not limited to, genetic resistance, pathogen-antagonizing endophytes, and pathogen competitors. The relative importance of each mechanism can be expressed in a hierarchical view of defense. Several recent studies have shown that pathogen antagonism is inconsistently expressed within the plant defense hierarchy. Our hypothesis is that the hierarchy is governed by contingency rules that determine when and where antagonists reduce plant disease severity.Here, we investigated whether pathogen competition influences pathogen antagonism using Populus as a model system. In three independent field experiments, we asked whether competition for leaf mesophyll cells between a Melampsora rust pathogen and a microscopic, eriophyid mite affects rust pathogen antagonism by fungal leaf endophytes. The rust pathogen has an annual, phenological disadvantage in competition with the mite because the rust pathogen must infect its secondary host in spring before infecting Populus. We varied mite-rust competition by utilizing Populus genotypes characterized by differential genetic resistance to the two organisms. We inoculated plants with endophytes and allowed mites and rust to infect plants naturally.Two contingency rules emerged from the three field experiments: (a) Pathogen antagonism by endophytes can be preempted by host genes for resistance that suppress pathogen development, and (b) pathogen antagonism by endophytes can secondarily be preempted by competitive exclusion of the rust by the mite. Synthesis: Our results point to a Populus defense hierarchy with resistance genes on top, followed by pathogen competition, and finally pathogen antagonism by endophytes. We expect these rules will help to explain the variation in pathogen antagonism that is currently attributed to context dependency.

Resistance to an eriophyid mite in an interspecific hybrid pedigree of Populus

Schizoempodium mesophyllincola is an eriophyid mite that feeds in leaves of Populus trichocarpa in the central part of this cottonwood tree’s range (i.e., coastal British Columbia, Washington and Oregon) in the Pacific Northwest (PNW) of North America, and on some interspecific hybrids planted in short-rotation, intensive forestry in the region. The mite, a leaf vagrant, sucks the contents of spongy mesophyll cells, causing leaf discoloration, or “bronzing.” Here, we investigate the inheritance pattern of resistance to leaf bronzing using a three-generation Populus trichocarpa x P. deltoides hybrid pedigree. We found that resistance to the mite is an exaptation in that its source in two related F₂ families of the TxD hybrid pedigree was the non-native host, P. deltoides. Two grandparental genotypes of the latter, ‘ILL-5’ and ‘ILL-129’, were completely free of the bronzing symptom and that phenotype was inherited in a Mendelian manner in the F₁ and F₂. Resistance to S. mesophyllincola is similar to resistance to many other regional pathogens of P. trichocarpa (e.g., Melampsora occidentalis, Venturia inopina, Sphaerulina populicola, and Taphrina sp.) in that it is inherited from the non-native grandparent (e.g., P. deltoides, P. nigra, or P. maximowiczii) in three-generation, hybrid pedigrees. In addition to finding evidence for Mendelian inheritance, we found two QTLs with LOD scores 5.03 and 3.12 mapped on linkage groups (LG) III and I, and they explained 6.7 and 4.2% of the phenotypic variance, respectively. The LG I QTL is close to, or synonymous with, one for resistance to sap-feeding arthropods and leaf developmental traits as expressed in a British study utilizing the same pedigree.

A Hypothetical Bottleneck in the Plant Microbiome

The plant microbiome may be bottlenecked at the level of endophytes of individual seeds. Strong defense of developing seeds is predicted by optimal defense theory, and we have experimentally demonstrated exclusionary interactions among endophytic microbes infecting individual seeds of Centaurea stoebe. Having found a single, PDA-culturable microbe per seed or none in an exploratory study with Centaurea stoebe, we completed a more extensive survey of an additional 98 plant species representing 39 families. We again found that individual, surface-sterilized seeds of all species hosted only one PDA-culturable bacterial or fungal endophyte per seed, or none. PDA-unculturables were not determined but we expect them to also be bottlenecked in individual seeds, as they too should be governed by exclusionary interactions. If the bottleneck were confirmed with high-throughput sequencing of individual seeds then it would make sense to further investigate the Primary Symbiont Hypothesis (PSH). This includes the prediction that primary symbionts (i.e., the winners of the exclusionary battles among seed endophytes) have strong effects on seedlings depending on symbiont identity.

Protocols for Investigating the Leaf Mycobiome Using High-Throughput DNA Sequencing

High-throughput sequencing of taxon-specific loci, or DNA metabarcoding, has become an invaluable tool for investigating the composition of plant-associated fungal communities and for elucidating plant-fungal interactions. While sequencing fungal communities has become routine, there remain numerous potential sources of systematic error that can introduce biases and compromise metabarcoding data. This chapter presents a protocol for DNA metabarcoding of the leaf mycobiome based on current best practices to minimize errors through careful laboratory practices and validation.

Research priorities for harnessing plant microbiomes in sustainable agriculture

Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is to integrate beneficial plant microbiomes-i.e., those enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance-into agricultural production. This integration will require a large-scale effort among academic researchers, industry researchers, and farmers to understand and manage plant-microbiome interactions in the context of modern agricultural systems. Here, we identify priorities for research in this area: (1) develop model host-microbiome systems for crop plants and non-crop plants with associated microbial culture collections and reference genomes, (2) define core microbiomes and metagenomes in these model systems, (3) elucidate the rules of synthetic, functionally programmable microbiome assembly, (4) determine functional mechanisms of plant-microbiome interactions, and (5) characterize and refine plant genotype-by-environment-by-microbiome-by-management interactions. Meeting these goals should accelerate our ability to design and implement effective agricultural microbiome manipulations and management strategies, which, in turn, will pay dividends for both the consumers and producers of the world food supply.

Fungal endophytes: modifiers of plant disease

Many recent studies have demonstrated that non-pathogenic fungi within plant microbiomes, i.e., endophytes ("endo" = within, "phyte" = plant), can significantly modify the expression of host plant disease. The rapid pace of advancement in endophyte ecology warrants a pause to synthesize our understanding of endophyte disease modification and to discuss future research directions. We reviewed recent literature on fungal endophyte disease modification, and here report on several emergent themes: (1) Fungal endophyte effects on plant disease span the full spectrum from pathogen antagonism to pathogen facilitation, with pathogen antagonism most commonly reported. (2) Agricultural plant pathosystems are the focus of research on endophyte disease modification. (3) A taxonomically diverse group of fungal endophytes can influence plant disease severity. And (4) Fungal endophyte effects on plant disease severity are context-dependent. Our review highlights the importance of fungal endophytes for plant disease across a broad range of plant pathosystems, yet simultaneously reveals that complexity within plant microbiomes presents a significant challenge to disentangling the biotic environmental factors affecting plant disease severity. Manipulative studies integrating eco-evolutionary approaches with emerging molecular tools will be poised to elucidate the functional importance of endophytes in natural plant pathosystems that are fundamental to biodiversity and conservation.

Common foliar fungi of Populus trichocarpa modify Melampsora rust disease severity

Nonpathogenic foliar fungi (i.e. endophytes and epiphytes) can modify plant disease severity in controlled experiments. However, experiments have not been combined with ecological studies in wild plant pathosystems to determine whether disease-modifying fungi are common enough to be ecologically important. We used culture-based methods and DNA sequencing to characterize the abundance and distribution of foliar fungi of Populus trichocarpa in wild populations across its native range (Pacific Northwest, USA). We conducted complementary, manipulative experiments to test how foliar fungi commonly isolated from those populations influence the severity of Melampsora leaf rust disease. Finally, we examined correlative relationships between the abundance of disease-modifying foliar fungi and disease severity in wild trees. A taxonomically and geographically diverse group of common foliar fungi significantly modified disease severity in experiments, either increasing or decreasing disease severity. Spatial patterns in the abundance of some of these foliar fungi were significantly correlated (in predicted directions) with disease severity in wild trees. Our study reveals that disease modification is an ecological function shared by common foliar fungal symbionts of P. trichocarpa. This finding raises new questions about plant disease ecology and plant biodiversity, and has applied potential for disease management.

Genetics-based interactions among plants, pathogens, and herbivores define arthropod community structure

Plant resistance to pathogens or insect herbivores is common, but its potential for indirectly influencing plant-associated communities is poorly known. Here, we test whether pathogens' indirect effects on arthropod communities and herbivory depend on plant resistance to pathogens and/or herbivores, and address the overarching interacting foundation species hypothesis that genetics-based interactions among a few highly interactive species can structure a much larger community. In a manipulative field experiment using replicated genotypes of two Populus species and their interspecific hybrids, we found that genetic variation in plant resistance to both pathogens and insect herbivores modulated the strength of pathogens' indirect effects on arthropod communities and insect herbivory. First, due in part to the pathogens' differential impacts on leaf biomass among the two Populus species and the hybrids, the pathogen most strongly impacted arthropod community composition, richness, and abundance on the pathogen-susceptible tree species. Second, we found similar patterns comparing pathogen-susceptible and pathogen-resistant genotypes within species. Third, within a plant species, pathogens caused a fivefold greater reduction in herbivory on insect-herbivore-susceptible plant genotypes than on herbivore-resistant genotypes, demonstrating that the pathogen-herbivore interaction is genotype dependent. We conclude that interactions among plants, pathogens, and herbivores can structure multitrophic communities, supporting the interacting foundation species hypothesis. Because these interactions are genetically based, evolutionary changes in genetic resistance could result in ecological changes in associated communities, which may in turn feed back to affect plant fitness.

A taxonomic and phylogenetic revision of Penicillium section Aspergilloides

Species belonging to Penicillium section Aspergilloides have a world-wide distribution with P. glabrum, P. spinulosum and P. thomii the most well-known species of this section. These species occur commonly and can be isolated from many substrates including soil, food, bark and indoor environments. The taxonomy of these species has been investigated several times using various techniques, but species delimitation remains difficult. In the present study, 349 strains belonging to section Aspergilloides were subjected to multilocus molecular phylogenetic analyses using partial β-tubulin (BenA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) sequences. Section Aspergilloides is subdivided into 12 clades and 51 species. Twenty-five species are described here as new and P. yezoense, a species originally described without a Latin diagnosis, is validated. Species belonging to section Aspergilloides are phenotypically similar and most have monoverticillate conidiophores and grow moderately or quickly on agar media. The most important characters to distinguish these species were colony sizes on agar media, growth at 30 °C, ornamentation and shape of conidia, sclerotium production and stipe roughness.