New Species of Didymellaceae within Aquatic Plants from Southwestern China

Members of Didymellaceae have a wide geographical distribution throughout different ecosystems, and most species are associated with fruit, leaf, stem and root diseases of land plants. However, species that occur in aquatic plants are not clearly known. During a survey of the diversity of endophytes in aquatic plants in Yunnan, Sichuan, and Guizhou provinces, we obtained 51 isolates belonging to Didymellaceae based on internal transcribed spacer region (ITS) sequences. Further, the phylogenetic positions of these isolates were determined by combined sequences composed of ITS, partial large subunit nrRNA gene (28S nrDNA; LSU), RNA polymerase II second largest subunit (rpb2) and partial beta-tubulin gene (tub2). Combining morphological characteristics and multi-locus phylogenetic analyses, two new varieties belong to Boeremia and 12 new species distributed into seven genera were recognized from 51 isolates, i.e., Cumuliphoma, Didymella, Dimorphoma, Ectophoma, Leptosphaerulina, Remotididymella, and Stagonosporopsis. Among these species, only one species of Stagonosporopsis and two species of Leptosphaerulina show teleomorphic stages on OA, but have no anamorphic state. Each new species is described in detail, and the differences between new species and their phylogenetically related species are discussed here. The high frequency of new species indicates that aquatic plants may be a special ecological niche which highly promotes species differentiation. At the same time, the frequent occurrence of new species may indicate the need for extensive investigation of fungal resources in those aquatic environments where fungal diversity may be underestimated.

Endophytic Colletotrichum Species from Aquatic Plants in Southwest China

Colletotrichum species are plant pathogens, saprobes, and endophytes in many economically important hosts. Many studies have investigated the diversity and pathogenicity of Colletotrichum species in common ornamentals, fruits, and vegetables. However, Colletotrichum species occurring in aquatic plants are not well known. During the investigation of the diversity of endophytic fungi in aquatic plants in southwest China, 66 Colletotrichum isolates were obtained from aquatic plants there, and 26 of them were selected for sequencing and analyses of actin (ACT), chitin synthase (CHS-1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the internal transcribed spacer (ITS) region, and β-tubulin (TUB2) genomic regions. Based on morphological characterization and multi-locus phylogenetic analyses, 13 Colletotrichum species were recognized, namely, C. baiyuense sp. nov., C. casaense sp. nov., C. demersi sp. nov., C. dianense sp. nov., C. fructicola, C. garzense sp. nov., C. jiangxiense, C. karstii, C. philoxeroidis sp. nov., C. spicati sp. nov., C. tengchongense sp. nov., C. vulgaris sp. nov., C. wuxuhaiense sp. nov. Two species complexes, the C. boninense species complex and C. gloeosporioides species complex, were found to be associated with aquatic plants. Pathogenicity tests revealed a broad diversity in pathogenicity and aggressiveness among the eight new Colletotrichum species.

Culture-Based and Culture-Independent Assessments of Endophytic Fungal Diversity in Aquatic Plants in Southwest China

Aquatic ecosystems contain tremendous plant and microbial diversity. However, little is known about endophyte diversity in aquatic plants. In this study, we investigated the diversity of endophytic fungi in aquatic plants in southwest China using both culture-based and culture-independent high-throughput sequencing methods. A total of 1,689 fungal isolates belonging to three phyla and 154 genera were obtained from 15,373 plant tissue segments of 30 aquatic plant species. The most abundant endophytic fungi were those in ascomycete genera Aspergillus, Ceratophoma, Fusarium, Penicillium, Phoma and Plectosporium. No difference in fungal isolation rates was observed among tissues from roots, stems, and leaves. Twenty tissue samples from three most common plant species were further subjected to culture-independent meta-barcode sequencing. The sequence-based analyses revealed a total of 1,074 OTUs belonging to six fungal phyla and 194 genera. Among the three plants, Batrachium bungei harbored the highest number of OTUs. Besides, a total of 66 genera were detected by two methods. Both the culture-dependent and independent methods revealed that aquatic plants in southwest China have abundant endophytic fungal diversity. This study significantly expands our knowledge of the fungal community of aquatic plants.

Endophytic Fungi: Biological Control and Induced Resistance to Phytopathogens and Abiotic Stresses

Plant diseases cause losses of approximately 16% globally. Thus, management measures must be implemented to mitigate losses and guarantee food production. In addition to traditional management measures, induced resistance and biological control have gained ground in agriculture due to their enormous potential. Endophytic fungi internally colonize plant tissues and have the potential to act as control agents, such as biological agents or elicitors in the process of induced resistance and in attenuating abiotic stresses. In this review, we list the mode of action of this group of microorganisms which can act in controlling plant diseases and describe several examples in which endophytes were able to reduce the damage caused by pathogens and adverse conditions. This is due to their arsenal of molecules generated during the interaction by which they form a kind of biological shield in the plant. Furthermore, considering that endophytic fungi can be an important tool in managing for biotic and abiotic stresses due to the large amount of biologically active substances produced, bioprospecting this class of microorganisms is tending to increase and generate valuable products for agriculture.

Molecular evolution of the internal transcribed spacers in red oaks (Quercus sect. Lobatae)

Previous studies of the Internal Transcribed Spacers of the nuclear ribosomal DNA (ITS) in sections Quercus (white oaks), Protobalanus (intermediate or golden cup oaks), Cerris (Cerris oaks), and Ilex (Ilex oaks) suggest that ITS regions undergo full concerted evolution in oaks; however, ITS evolution patterns in red oaks (section Lobatae) are unknown due to scant representation in published work. To determine whether full concerted evolution occurs in red oaks, the purpose of this study was to examine ITS sequences from 40 red oak species. The results show incomplete concerted evolution and the presence of three ITS ribotypes of lengths 505, 609, 601 bp, hereafter referred to as ITS-S (small), I ITS-M (medium), and ITS-L (large), respectively. Thirty species had only one ribotype (ITS-M), nine species had two ribotypes (different combinations of ITS-L, ITS-M, and ITS-S), and only one species had all three ribotypes. Furthermore, examination of these three ribotypes showed that only ITS-M is putatively functional and ITS-L and ITS-S are pseudogenes. Bayesian analysis strongly supported (100%) two pseudogenes clades but provided weak support for the monophyly of a putative functional clade (ITS-M); moreover, within the "functional" clade, species relationships were uncertain and, in most cases, sequences from the same species failed to group together. The results of the current study suggest that ITS may not be appropriate for phylogeny reconstruction of red oaks due to low levels of interspecific variation and incomplete concerted evolution.

Large scale transcriptome analysis reveals interplay between development of forest trees and a beneficial mycorrhiza helper bacterium

BACKGROUND

Pedunculate oak, Quercus robur is an abundant forest tree species that hosts a large and diverse community of beneficial ectomycorrhizal fungi (EMFs), whereby ectomycorrhiza (EM) formation is stimulated by mycorrhiza helper bacteria such as Streptomyces sp. AcH 505. Oaks typically grow rhythmically, with alternating root flushes (RFs) and shoot flushes (SFs). We explored the poorly understood mechanisms by which oaks integrate signals induced by their beneficial microbes and endogenous rhythmic growth at the level of gene expression. To this end, we compared transcript profiles of oak microcuttings at RF and SF during interactions with AcH 505 alone and in combination with the basidiomycetous EMF Piloderma croceum.

RESULTS

The local root and distal leaf responses to the microorganisms differed substantially. More genes involved in the recognition of bacteria and fungi, defence and cell wall remodelling related transcription factors (TFs) were differentially expressed in the roots than in the leaves of oaks. In addition, interaction with AcH 505 and P. croceum affected the expression of a higher number of genes during SF than during RF, including AcH 505 elicited defence response, which was attenuated by co-inoculation with P. croceum in the roots during SF. Genes encoding leucine-rich receptor-like kinases (LRR-RLKs) and proteins (LRR-RLPs), LRR containing defence response regulators, TFs from bZIP, ERF and WRKY families, xyloglucan cell wall transglycolases/hydrolases and exordium proteins were differentially expressed in both roots and leaves of plants treated with AcH 505. Only few genes, including specific RLKs and TFs, were induced in both AcH 505 and co-inoculation treatments.

CONCLUSION

Treatment with AcH 505 induces and maintains the expression levels of signalling genes encoding candidate receptor protein kinases and TFs and leads to differential expression of cell wall modification related genes in pedunculate oak microcuttings. Local gene expression response to AcH 505 alone and in combination with P. croceum are more pronounced when roots are in resting stages, possibly due to the fact that non growing roots re-direct their activity towards plant defence rather than growth.

Fungal endophytes of aquatic macrophytes: diverse host-generalists characterized by tissue preferences and geographic structure

Most studies of endophytic symbionts have focused on terrestrial plants, neglecting the ecologically and economically important plants present in aquatic ecosystems. We evaluated the diversity, composition, host and tissue affiliations, and geographic structure of fungal endophytes associated with common aquatic plants in lentic waters in northern Arizona, USA. Endophytes were isolated in culture from roots and photosynthetic tissues during two growing seasons. A total of 226 isolates representing 60 putative species was recovered from 9,600 plant tissue segments. Although isolation frequency was low, endophytes were phylogenetically diverse and species-rich. Comparisons among the most thoroughly sampled species and reservoirs revealed that isolation frequency and diversity did not differ significantly between collection periods, among species, among reservoirs, or as a function of depth. However, community structure differed significantly among reservoirs and tissue types. Phylogenetic analyses of a focal genus (Penicillium) corroborated estimates of species boundaries and informed community analyses, highlighting clade- and genotype-level affiliations of aquatic endophytes with both sediment- and waterborne fungi, and endophytes of proximate terrestrial plants. Together these analyses provide a first quantitative examination of endophytic associations in roots and foliage of aquatic plants and can be used to optimize survey strategies for efficiently capturing fungal biodiversity at local and regional scales.

Endophytic fungus-vascular plant-insect interactions

Insect association with fungi has a long history. Theories dealing with the evolution of insect herbivory indicate that insects used microbes including fungi as their principal food materials before flowering plants evolved. Subtlety and the level of intricacy in the interactions between insects and fungi indicate symbiosis as the predominant ecological pattern. The nature of the symbiotic interaction that occurs between two organisms (the insect and the fungus), may be either mutualistic or parasitic, or between these two extremes. However, the triangular relationship involving three organisms, viz., an insect, a fungus, and a vascular plant is a relationship that is more complicated than what can be described as either mutualism or parasitism, and may represent facets of both. Recent research has revealed such a complex relationship in the vertically transmitted type-I endophytes living within agriculturally important grasses and the pestiferous insects that attack them. The intricacy of the association depends on the endophytic fungus-grass association and the insect present. Secondary compounds produced in the endophytic fungus-grass association can provide grasses with resistance to herbivores resulting in mutualistic relationship between the fungus and the plant that has negative consequences for herbivorous insects. The horizontally transmitted nongrass type-II endophytes are far less well studied and as such their ecological roles are not fully understood. This forum article explores the intricacy of dependence in such complex triangular relationships drawing from well-established examples from the fungi that live as endophytes in vascular plants and how they impact on the biology and evolution of free-living as well as concealed (e.g., gall-inducing, gall-inhabiting) insects. Recent developments with the inoculation of strains of type-I fungal endophytes into grasses and their commercialization are discussed, along with the possible roles the endophytic fungi play in the galls induced by the Cecidomyiidae (Diptera).

Endophytic fungal diversity in Theobroma cacao (cacao) and T. grandiflorum (cupuaçu) trees and their potential for growth promotion and biocontrol of black-pod disease

The endophytic niches of plants are a rich source of microbes that can directly and indirectly promote plant protection, growth and development. The diversity of culturable endophytic fungi from stems and branches of Theobroma cacao (cacao) and Theobroma grandiflorum (cupuaçu) trees growing in the Amazon region of Brazil was assessed. The collection of fungal endophytic isolates obtained was applied in field experiments to evaluate their potential as biocontrol agents against Phytophthora palmivora, the causal agent of the black-pod rot disease of cacao, one of the most important pathogens in cocoa-producing regions worldwide. The isolated endophytic fungi from 60 traditional, farmer-planted, healthy cacao and 10 cupuaçu plants were cultured in PDA under conditions inducing sporulation. Isolates were classified based upon the morphological characteristics of their cultures and reproductive structures. Spore suspensions from a total of 103 isolates that could be classified at least up to genus level were tested against P. palmivora in pods attached to cacao trees in the field. Results indicated that ∼70% of isolates showed biocontrol effects to a certain extent, suggesting that culturable endophytic fungal biodiversity in this system is of a mostly mutualistic type of interaction with the host. Eight isolates from genera Trichoderma (reference isolate), Pestalotiopsis, Curvularia, Tolypocladium and Fusarium showed the highest level of activity against the pathogen, and were further characterized. All demonstrated their endophytic nature by colonizing axenic cacao plantlets, and confirmed their biocontrol activity on attached pods trials by showing significant decrease in disease severity in relation to the positive control. None, however, showed detectable growth-promotion effects. Aspects related to endophytic biodiversity and host-pathogen-endophyte interactions in the environment of this study were discussed on the context of developing sustainable strategies for biological control of black-pod rot of cacao.

Impacts of plant symbiotic fungi on insect herbivores: mutualism in a multitrophic context

We consider how fungi that form symbiotic associations with plants interact with insect herbivores attacking the same plants. Both endophytes and mycorrhizae have significant impacts on herbivores with which they are in relatively intimate contact, but weaker effects on those from which they are spatially separated. Generalist insects are usually adversely affected by the presence of endophytes and mycorrhizae, whereas specialist insects may often benefit. Effects on feeding guilds vary according to type of fungi; for example, aphids are often negatively affected by endophytes but respond positively to mycorrhizae, and leaf-chewers are usually negatively affected by both types of fungi. There is a strong taxonomic bias in the literature and many interactions remain little studied; laboratory studies predominate over field studies. Although some patterns emerge, there is a large amount of specificity and context dependency in the outcome of interactions, reflecting the influence of fungal and host genotype, fungal, host, and insect species, and environmental factors. Whereas some of the mechanisms underpinning these interactions are relatively well characterized, others remain unclear and await elucidation by molecular and metabolomic techniques.

Moths that vector a plant pathogen also transport endophytic fungi and mycoparasitic antagonists

Claviceps paspali, a common fungal pathogen of Paspalum grasses, attracts moth vectors by producing sugary exudates in the grass florets it infects. These exudates also support mycoparasitic Fusarium species that may negatively influence C. paspali fitness. We examined the potential for moths on which C. paspali depends to also transmit mycoparasitic Fusarium and fungal endophytes, which inhabit asymptomatic plant tissue and may influence host susceptibility to pathogens. We quantified infections by C. paspali, Fusarium spp., and endophytic fungi associated with Paspalum spp. at focal sites in the southeastern USA and used data from the nuclear internal transcribed spacer (ITS rDNA) to compare communities of plant-associated and moth-borne fungi. ITS sequences of moth-borne fungi were identical to reference sequences of mycoparasitic Fusarium heterosporum and to three distinct endophytic fungi isolated from Paspalum species. Our results demonstrate an unexpected overlap of fungal communities between disparate locations and among plant species and plant tissues, and suggest an unexpected role of moths, which vector a plant pathogen, to transmit other guilds of fungi. In turn, the potential for insects to transmit plant pathogens as well as mycoparasites and endophytic fungi suggests complex interactions underlying a commonly observed grass-pathogen system.

Herbivores cause a rapid increase in hereditary symbiosis and alter plant community composition

Microbial symbioses are ubiquitous in nature. Hereditary symbionts warrant particular attention because of their direct effects on the evolutionary potential of their hosts. In plants, hereditary fungal endophytes can increase the competitive ability, drought tolerance, and herbivore resistance of their host, although it is unclear whether or how these ecological benefits may alter the dynamics of the endophyte symbiosis over time. Here, we demonstrate that herbivores alter the dynamics of a hereditary symbiont under field conditions. Also, we show that changes in symbiont frequency were accompanied by shifts in the overall structure of the plant community. Replicated 25-m2 plots were enriched with seed of the introduced grass, Lolium arundinaceum at an initial frequency of 50% infection by the systemic, seed-transmitted endophyte Neotyphodium coenophialum. Over 54 months, there was a significantly greater increase in endophyte-infection frequency in the presence of herbivores (30% increase) than where mammalian and insect herbivory were experimentally reduced by fencing and insecticide application (12% increase). Under ambient mammalian herbivory, the above-ground biomass of nonhost plant species was reduced compared with the mammal-exclusion treatment, and plant composition shifted toward greater relative biomass of infected, tall fescue grass. These results demonstrate that herbivores can drive plant-microbe dynamics and, in doing so, modify plant community structure directly and indirectly.

Diversity of culturable phyllosphere bacteria on beech and oak: the effects of lepidopterous larvae

The community composition of epiphytic heterotrophic bacteria on leaves of beech and oak, which were either damaged by lepidopterous larvae or remained undamaged, was investigated. In addition, the ability of these bacteria to utilize inorganic nitrogen was studied. The bacteria were isolated on nutrient agar and systematically identified with biochemical and physiological tests. Rarefaction plots and the Shannon-Wiener function revealed that species diversity was significantly higher on leaves of damaged beech compared to undamaged leaves, but no differences were found on leaves of oak. The portion of bacterial isolates showing a strong response to ammonia and nitrate was significantly larger on leaves of oak than on those of beech. Furthermore, significantly more isolates with a high capability to assimilate both nitrogen compounds were found on leaves attacked by the folivorous larvae compared to those not attacked on oak. It is suggested that the changes in the microbial community in response to folivorous insects might affect the extent of nutrient cycling exceeding eventually the scale of a leaf.