We constructed nine sets of oligonucleotide primers on the basis of the results of DNA hybridization of cloned genes from Neurospora crassa and Aspergillus nidulans to the genomes of select filamentous ascomycetes and deuteromycetes (with filamentous ascomycete affiliations). Nine sets of primers were designed to amplify segments of DNA that span one or more introns in conserved genes. PCR DNA amplification with the nine primer sets with genomic DNA from ascomycetes, deuteromycetes, basidiomycetes, and plants revealed that five of the primer sets amplified a product only from DNA of the filamentous ascomycetes and deuteromycetes. The five primer sets were constructed from the N. crassa genes for histone 3, histone 4, beta-tubulin, and the plasma membrane ATPase. With these five primer sets, polymorphisms were observed in both the size of and restriction enzyme sites in the amplified products from the filamentous ascomycetes. The primer sets described here may provide useful tools for phylogenetic studies and genome analyses in filamentous ascomycetes and deuteromycetes (with ascomycete affiliations), as well as for the rapid differentiation of fungal species by PCR.

Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes.

Summary 1 Summary All plants in natural ecosystems appear to be symbiotic with fungal endophytes. This highly diverse group of fungi can have profound impacts on plant communities through increasing fitness by conferring abiotic and biotic stress tolerance, increasing biomass and decreasing water consumption, or decreasing fitness by altering resource allocation. Despite more than 100 yr of research resulting in thousands of journal articles, the ecological significance of these fungi remains poorly characterized. Historically, two endophytic groups (clavicipitaceous (C) and nonclavicipitaceous (NC)) have been discriminated based on phylogeny and life history traits. Here, we show that NC-endophytes represent three distinct functional groups based on host colonization and transmission, in planta biodiversity and fitness benefits conferred to hosts. Using this framework, we contrast the life histories, interactions with hosts and potential roles in plant ecophysiology of C- and NC-endophytes, and highlight several key questions for future work in endophyte biology.

https://courses.washington.edu/cfr523/documents/2009TansleyReview.pdf

Fungal endophytes: diversity and functional roles.

Sequencing of the Arabidopsis thaliana root microbiome shows that its composition is strongly influenced by location, inside or outside the root, and by soil type. The association between a land plant and the soil microbes of the root microbiome is important for the plant's well-being. A deeper understanding of these microbial communities will offer opportunities to control plant growth and susceptibility to pathogens, particularly in sustainable agricultural regimes. Two groups, working separately but developing best-practice protocols in parallel, have characterized the root microbiota of the model plant Arabidopis thaliana. Working on two continents and with five different soil types, they reach similar general conclusions. The bacterial communities in each root compartment — the rhizosphere immediately surrounding the root and the endophytic compartment within the root — are most strongly influenced by soil type, and to a lesser degree by host genotype. In natural soils, Arabidopsis plants are preferentially colonized by Actinobacteria, Proteobacteria, Bacteroidetes and Chloroflexi species. And — an important point for future work — Arabidopsis root selectivity for soil bacteria under controlled environmental conditions mimics that of plants grown in a natural environment. Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation1,2,3. Colonization of the root occurs despite a sophisticated plant immune system4,5, suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments from both soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plant–microbe interactions derived from complex soil communities.

/pdf/defining-the-core-arabidopsis-thaliana-root-microbiome-4w59sb3pp3.pdf

Defining the core Arabidopsis thaliana root microbiome

Laccases of fungi attract considerable attention due to their possible involvement in the transformation of a wide variety of phenolic compounds including the polymeric lignin and humic substances. So far, more than a 100 enzymes have been purified from fungal cultures and characterized in terms of their biochemical and catalytic properties. Most ligninolytic fungal species produce constitutively at least one laccase isoenzyme and laccases are also dominant among ligninolytic enzymes in the soil environment. The fact that they only require molecular oxygen for catalysis makes them suitable for biotechnological applications for the transformation or immobilization of xenobiotic compounds.

Fungal laccases - occurrence and properties.

All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.

The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes

We demonstrate that native grass species from coastal and geothermal habitats require symbiotic fungal endophytes for salt and heat tolerance, respectively. Symbiotically conferred stress tolerance is a habitat-specific phenomenon with geothermal endophytes conferring heat but not salt tolerance, and coastal endophytes conferring salt but not heat tolerance. The same fungal species isolated from plants in habitats devoid of salt or heat stress did not confer these stress tolerances. Moreover, fungal endophytes from agricultural crops conferred disease resistance and not salt or heat tolerance. We define habitat-specific, symbiotically-conferred stress tolerance as habitat-adapted symbiosis and hypothesize that it is responsible for the establishment of plants in high-stress habitats. The agricultural, coastal and geothermal plant endophytes also colonized tomato (a model eudicot) and conferred disease, salt and heat tolerance, respectively. In addition, the coastal plant endophyte colonized rice (a model monocot) and conferred salt tolerance. These endophytes have a broad host range encompassing both monocots and eudicots. Interestingly, the endophytes also conferred drought tolerance to plants regardless of the habitat of origin. Abiotic stress tolerance correlated either with a decrease in water consumption or reactive oxygen sensitivity/generation but not to increased osmolyte production. The ability of fungal endophytes to confer stress tolerance to plants may provide a novel strategy for mitigating the impacts of global climate change on agricultural and native plant communities.

/pdf/stress-tolerance-in-plants-via-habitat-adapted-symbiosis-1m46ol6vjj.pdf

Stress tolerance in plants via habitat-adapted symbiosis

All plants studied in natural ecosystems are symbiotic with fungi ([1][1]), which obtain nutrients while either positively, negatively, or neutrally affecting host fitness ([2][2]). Plant adaptation to selective pressures is considered to be regulated by the plant genome ([3][3]). To test whether

http://www.rcn.montana.edu/Publications/Pdf/2002/thermotolerance%20generated%20by%20plant-fungal%20symbiosis.pdf

Thermotolerance Generated by Plant/Fungal Symbiosis

/pdf/the-polymerase-chain-reaction-and-plant-disease-diagnosis-3089hn3bk6.pdf

The polymerase chain reaction and plant disease diagnosis

Melanins are darkly pigmented polymers that protect organisms against environmental stress. Even when not directly involved in pathogenesis, fungal melanin is likely required by melanizing phytopathogens for survival in the environment. However, some phytopathogenic fungi that produce melanized appressoria for host invasion require appressorial melanogenesis for pathogenicity. Much less is known about the role melanins play in pathogenesis during infection by other phytopathogens that do not rely on appressoria for host penetration. Here we focus on one such phytopathogenic fungus, Gaeumannomyces graminis var. tritici, the etiologic agent of the devastating root disease of cereals, take-all. This fungus is lightly pigmented in culture, but requires melanin biosynthesis for pathogenesis, perhaps to produce melanized, ectotrophic macrohyphae on roots. However, the constitutively melanized, asexual Phialophora anamorph of G. graminis var. tritici is nonpathogenic. In addition, melanization of G. graminis var. graminis is not required to produce root disease on its rice host. Explanations for these apparent contradictions are suggested, as are other functions for the melanins of phytopathogenic fungi.

The dark side of the mycelium : Melanins of phytopathogenic fungi

All plants studied in natural ecosystemsare symbiotic with fungi that either resideentirely (endophytes) or partially(mycorrhizae) within plants. Thesesymbioses appear to adapt to biotic andabiotic stresses and may be responsible forthe survival of both plant hosts and fungalsymbionts in high stress habitats. Here wedescribe the role of symbiotic fungi inplant stress tolerance and present astrategy based on adaptive symbiosis topotentially mitigate the impacts of globalchange on plant communities.

http://www.rcn.montana.edu/Publications/Pdf/2004/The%20role%20of%20fungal%20symbioses%20in%20the%20adaptation%20of%20.pdf

Joan M. Henson

Papers

Stress tolerance in plants via habitat-adapted symbiosis

Thermotolerance Generated by Plant/Fungal Symbiosis

The polymerase chain reaction and plant disease diagnosis

The dark side of the mycelium : Melanins of phytopathogenic fungi

The role of fungal symbioses in the adaptation of plants to high stress environments