Site‐specific responses of foliar fungal microbiomes to nutrient addition and herbivory at different spatial scales

The plant microbiome can affect host function in many ways and characterizing the ecological factors that shape endophytic (microbes living inside host plant tissues) community diversity is a key step in understanding the impacts of environmental change on these communities. Phylogenetic relatedness among members of a community offers a way of quantifying phylogenetic diversity of a community and can provide insight into the ecological factors that shape endophyte microbiomes. We examined the effects of experimental nutrient addition and herbivory exclusion on the phylogenetic diversity of foliar fungal endophyte communities of the grass species Andropogon gerardii at four sites in the Great Plains of the central USA. Using amplicon sequencing, we characterized the effects of fertilization and herbivory on fungal community phylogenetic diversity at spatial scales that spanned within‐host to between sites across the Great Plains. Despite increasing fungal diversity and richness, at larger spatial scales, fungal microbiomes were composed of taxa showing random phylogenetic associations. Phylogenetic diversity did not differ systematically when summed across increasing spatial scales from a few meters within plots to hundreds of kilometers among sites. We observed substantial shifts in composition across sites, demonstrating distinct but similarly diverse fungal communities were maintained within sites across the region. In contrast, at the scale of within leaves, fungal communities tended to be comprised of closely related taxa regardless of the environment, but there were no shifts in phylogenetic composition among communities. We also found that nutrient addition (fertilization) and herbivory have varying effects at different sites. These results suggest that the direction and magnitude of the outcomes of environmental modifications likely depend on the spatial scale considered, and can also be constrained by regional site differences in microbial diversity and composition.     

Disturbance to desert soil ecosystems contributes to dust-mediated impacts at regional scales

This review considers the regional scale of impacts arising from disturbance to desert soil ecosystems. Deserts occupy over one-third of the Earth’s terrestrial surface, and biological soil covers are critical to stabilization of desert soils. Disturbance to these can contribute to massive destabilization and mobilization of dust. This results in dust storms that are transported across inter-continental distances where they have profound negative impacts. Dust deposition at high altitudes causes radiative forcing of snowpack that leads directly to altered hydrological regimes and changes to freshwater biogeochemistry. In marine environments dust deposition impacts phytoplankton diazotrophy, and causes coral reef senescence. Increasingly dust is also recognized as a threat to human health.     

Endophytic Fungal Communities Associated with Vascular Plants in the High Arctic Zone Are Highly Diverse and Host-Plant Specific

This study assessed the diversity and distribution of endophytic fungal communities associated with the leaves and stems of four vascular plant species in the High Arctic using 454 pyrosequencing with fungal-specific primers targeting the ITS region. Endophytic fungal communities showed high diversity. The 76,691 sequences obtained belonged to 250 operational taxonomic units (OTUs). Of these OTUs, 190 belonged to Ascomycota, 50 to Basidiomycota, 1 to Chytridiomycota, and 9 to unknown fungi. The dominant orders were Helotiales, Pleosporales, Capnodiales, and Tremellales, whereas the common known fungal genera were Cryptococcus, Rhizosphaera, Mycopappus, Melampsora, Tetracladium, Phaeosphaeria, Mrakia, Venturia, and Leptosphaeria. Both the climate and host-related factors might shape the fungal communities associated with the four Arctic plant species in this region. These results suggested the presence of an interesting endophytic fungal community and could improve our understanding of fungal evolution and ecology in the Arctic terrestrial ecosystems.     

Diversity and dynamics of fungal endophytes in leaves, stems and roots of Stellera chamaejasme L. in northwestern China

This study was conducted to explore fungal endophyte communities inhabiting a toxic weed (Stellera chamaejasme L.) from meadows of northwestern China. The effects of plant tissue and growth stage on endophyte assemblages were characterized. Endophytes were recovered from 50 % of the samples, with a total of 714 isolates. 41 operational taxonomical units (OTUs) were identified, consisting of 40 OTUs belonging primarily to Ascomycota and 1 OTU belonging to Basidiomycota. Pleosporales and Hypocreales were the orders contributing the most species to the endophytic assemblages. The total colonization frequency and species richness of endophytic fungi were higher in roots than in leaves and stems. In addition, for the plant tissues, the structure of fungal communities differed significantly by growth stages of leaf emergence and dormancy; for the plant growth stages, the structure of fungal communities differed significantly by plant tissues. This study demonstrates that S. chamaejasme serves as a reservoir for a wide variety of fungal endophytes that can be isolated from various plant tissues.     

Fungal endophyte communities in two tropical forests of southern India: diversity and host affiliation

Fifteen tree species from a tropical dry thorn forest and fifteen tree species from a tropical dry deciduous forest in the Mudumalai Wildlife Sanctuary, Nilgiri Biosphere Reserve, southern India, were surveyed for their foliar endophyte communities during the dry and wet seasons. Surface sterilized leaf segments of uniform dimension were plated on nutrient agar and culturable endophytes growing from the segments were identified. Endophyte diversity was greater in the dry thorn forest than in the dry deciduous forest in the dry season. Although the isolation frequency of culturable endophytes increased for both forests during the wet season, the assemblages were represented not by any unique fungal species but by the commonly occurring ones. Furthermore, although individual leaves were densely colonized by endophytes, only a few species of endophytes colonized the whole leaves; and, only a few fungal species dominated the foliar endophytic communities and were common for both forests during both dry and wet seasons. Thus, even under wet conditions that favour dispersal and infection by fungi, the endophyte diversity increased only marginally, an indication that certain tropical forests are not hyperdiverse with reference to fungal endophytes. This should be considered when using culturable endophyte diversity as a surrogate for estimating global fungal diversity.     

High diversity and low specificity of fungi associated with seedless epiphytic plants

Epiphytes, which grow on other plants for support, make up a large portion of Earth's plant diversity. Like other plants, their surfaces and interiors are colonized by diverse assemblages of fungi that can benefit their hosts by increasing tolerance for abiotic stressors and resistance to disease or harm them as pathogens. Fungal communities associated with epiphytic plants and the processes that structure these communities are poorly known. To address this, we sampled seven epiphytic seedless plant taxa in a Costa Rican rainforest and examined the effects of host identity and microhabitat on external and endophytic fungal communities. We found low host specificity for both external and endophytic fungi and weak differentiation between epiphytic and neighboring epilithic plant hosts. High turnover in fungi within and between hosts and habitats reveals that epiphytic plant-associated fungal communities are highly diverse and suggests that they are structured by stochastic processes.     

黑老虎内生真菌及根际土壤真菌的群落结构与生态功能分析

为探讨黑老虎(Kadsura coccinea)根际土壤和组织内生真菌菌群的组成及其生态功能，该研究采用ITS高通量测序技术对成熟黑老虎(根、茎、叶)内生真菌及根际土壤真菌群落结构、多样性和生态功能进行了分析。结果表明：(1)从12个样品中共获得2 241个可操作分类单元(OTU),涉及10门、41纲、95目、212科、367属，内生真菌(根、茎、叶)和根际土壤真菌OTU数分别为386、536、258、1 435个，其中共有的OTU为18个。在门水平上，黑老虎内生真菌及根际土壤真菌优势群落均为子囊菌门和担子菌门，其中子囊菌门在叶和茎中占比分别高达96.99%和95.37%;在属水平上，黑老虎根际土壤真菌中腐生真菌被孢霉属占比较高(为13.5%),叶和茎等生长旺盛的组织中子囊菌门未分类属和痂囊腔菌属占比较高。(2)α多样性分析结果显示，黑老虎根际土壤真菌群落的丰度和多样性明显高于内生真菌，茎中内生真菌丰度显著高于根和叶，而根、茎和叶组织间内生真菌多样性差异不显著；PCoA分析结果显示，叶和茎的真菌群落结构相似性更高。(3)利用FUNGuild数据库进行的功能预测分析结果显示，黑老虎根际土...     

Diversity,community composition,and bioactivity of cultivable fungal endophytes in saline and dry soils in deserts

Fungal endophyte communities are poorly investigated in extreme habitats such as deserts. We used cultivation and Sanger sequencing to investigate the effects of environmental variables on the endophytic fungal communities of eight Iranian desert plants. Host species was the main factor shaping the endophyte composition, while soil type additionally affected endophytes of above- and below-ground organs. Redundancy analysis showed that soil pH and electric conductivity determine fungal endophyte communities in plants in dry and saline soils. In a follow-up experiment, we showed that these endophytes could be used in crop production under salinity/drought stress and as biocontrol agents. Although compared to other ecosystems, the endophytic fungi associated with the studied Iranian desert plants are of low diversity, our results suggest that they probably play an essential role in the survival of their hosts. Further investigation is necessary to evaluate the potential benefits and applicability of such endophytes in agricultural practices in drylands.     

A comparison of fungal endophytic community diversity in tree leaves of rural and urban temperate forests of Kanto district,eastern Japan

To clarify the effects of forest fragmentation and a change in tree species composition following urbanization on endophytic fungal communities, we isolated fungal endophytes from the foliage of nine tree species in suburban (Kashiwa City, Chiba) and rural (Mt. Wagakuni, Ibaraki; Mt. Takao, Tokyo) forests and compared the fungal communities between sites and host tree species. Host specificity was evaluated using the index of host specificity (Si), and the number of isolated species, total isolation frequency, and the diversity index were calculated. From just one to several host-specific species were recognized in all host tree species at all sites. The total isolation frequency of all fungal species on Quercus myrsinaefolia, Quercus serrata, and Chamaecyparis obtusa and the total isolation frequency of host-specific species on Q. myrsinaefolia, Q. serrata, and Eurya japonica were significantly lower in Kashiwa than in the rural forests. The similarity indices (nonmetric multidimensional scaling (NMS) and C_MH) of endophytic communities among different tree species were higher in Kashiwa, as many tree species shared the same fungal species in the suburban forest. Endophytic fungi with a broad host range were grouped into four clusters suggesting their preference for conifer/broadleaves and evergreen/deciduous trees. Forest fragmentation and isolation by urbanization have been shown to cause the decline of host-specific fungal species and a decrease in β diversity of endophytic communities, i.e., endophytic communities associated with tree leaves in suburban forests were found to be depauperate.     

Fungal Assemblages Associated with Roots of Halophytic and Non-halophytic Plant Species Vary Differentially Along a Salinity Gradient

Structure of fungal communities is known to be influenced by host plants and environmental conditions. However, in most cases, the dynamics of these variation patterns are poorly understood. In this work, we compared richness, diversity, and composition between assemblages of endophytic and rhizospheric fungi associated to roots of two plants with different lifestyles: the halophyte Inula crithmoides and the non-halophyte I. viscosa (syn. Dittrichia viscosa L.), along a spatially short salinity gradient. Roots and rhizospheric soil from these plants were collected at three points between a salt marsh and a sand dune, and fungi were isolated and characterized by ITS rDNA sequencing. Isolates were classified in a total of 90 operational taxonomic units (OTUs), belonging to 17 fungal orders within Ascomycota and Basidiomycota. Species composition of endophytic and soil communities significantly differed across samples. Endophyte communities of I. crithmoides and I. viscosa were only similar in the intermediate zone between the salt marsh and the dune, and while the latter displayed a single, generalist association of endophytes, I. crithmoides harbored different assemblages along the gradient, adapted to the specific soil conditions. In the lower salt marsh, root assemblages were strongly dominated by a single dark septate sterile fungus, also prevalent in other neighboring salt marshes. Interestingly, although its occurrence was positively correlated to soil salinity, in vitro assays revealed a strong inhibition of its growth by salts. Our results suggest that host lifestyle and soil characteristics have a strong effect on endophytic fungi and that environmental stress may entail tight plant-fungus relationships for adaptation to unfavorable conditions.     

Fungal community composition shifts along a leaf degradation gradient in a European beech forest

Aims

The fungal communities in living and decomposed leaves of European Beech (Fagus sylvatica) were compared to identify the phyllosphere fungi involved in litter decomposition at a site in Bavaria, Germany.

Methods

New primers were designed to cover a broad range of fungal ribosomal DNA sequence diversity. Following ‘environmental PCR’, clone libraries from each of five samples of living leaves (surface-sterilized and untreated), freshly fallen, initially and highly decomposed leaves, were screened using RFLP fingerprinting.

Results

Statistical analysis (ANOSIM) revealed that the fungal communities colonizing living (a) and initially decomposed leaves (c) significantly differed between each other and from freshly fallen (b) and highly decomposed leaves (d). Fungal assemblages of a and d were statistically indistinguishable from each other and from the endophyllous fungal community in living leaves.

Conclusions

The results showed that endophyllous fungi play a role throughout the whole decomposition process of beech leaf litter. Therefore, clarification of the life cycle of certain endophytic and/or soil fungi may only be achieved by considering both phyllosphere and soil habitats.     

紫花针茅根际和体内真菌群落结构及与土壤环境因子的相关性研究

[目的] 探究青藏高原不同地区高寒草原紫花针茅根际和体内真菌群落的组成、多样性等特征,及与土壤环境因子（理化性质和酶活性）间的相互关系。[方法] 从青藏高原不同地区采集紫花针茅样品,应用土壤化学方法分析根际土壤理化性质和酶活性,并采用Illumina Miseq高通量测序技术,解析根际土壤和体内真菌群落组成和丰度、Alpha多样性和菌群结构,同时分析了紫花针茅根际真菌种群多样性与土壤环境因子的相关性,厘清了影响紫花针茅根际真菌区系的土壤环境因素。[结果] 三个采样地的根际土壤呈中性偏碱,土壤理化性质和酶活性变化各异。高通量测序共得到314801条有效序列和4491个OTUs;XZ样地的紫花针茅真菌多样性和丰富度相对偏低,GS样地最高。在门分类水平上,子囊菌门Ascomycota和担子菌门Basidiomycota是主要内生真菌类群,占总菌群的88.28%。不同采样地区紫花针茅体内真菌群落结构存在明显差异,而根际土壤真菌群落结构差异不大。相关性分析表明,紫花针茅真菌多样性与土壤pH、有效钾、铁、钙、镁、多酚氧化酶、过氧化物酶和脱氢酶呈显著（P<0.05）或极显著（P<0.01）正相关,而与海拔、土壤酸性磷酸酶呈极显著负相关。RDA分析发现,紫花针茅根际土壤真菌不同,影响的土壤环境因子也不同。[结论] 青藏高原高寒草地紫花针茅根际和体内栖息着丰富的真菌群落,其组成和多样性受多种土壤环境因子影响,且影响不同真菌群落的主要土壤环境因子也不同。本研究对于有益微生物资源的开发、利用及保护具有重要意义,并为紫花针茅草原保育和合理开发利用提供科学依据。     

Endophytic fungi from Peruvian highland and lowland habitats form distinctive and host plant-specific assemblages

Biodiversity and biogeography of leaf-inhabiting endophytic fungi have not been resolved yet. This is because host specificity, life cycles and species concepts, in this heterogeneous ecological guild of plant-associated microfungi, are far from being understood. Even though it is known that culture-based collection techniques are often biased, this has been the method of choice for studying fungal endophytes. Isolation of fungal endophytes only through culture-based methods could potentially mask slow growing species as well as species with low prevalence, preventing the capture of the communities’ real diversity and composition. This bias can be partially resolved by the use of cultivation-independent approaches such as direct sequencing of plant tissue by next generation techniques. Irrespective of the chosen sampling method, an efficient analysis of community ecology is urgently needed in order to evaluate the driving forces acting on fungal endophytic communities. In the present study, endophytic ascomyceteous fungi from three different plant genera (Vasconcellea microcarpa, Tillandsia spp., and Hevea brasiliensis) distributed in Peru, were isolated through culture-based sampling techniques and sequenced for their ITS rDNA region. These data sets were used to assess host preferences and biogeographic patterns of endophytic assemblages. This study showed that the effect of the host’s genetic background (identity) has a significant effect on the composition of the fungal endophytic community. In other words, the composition of the fungal endophytic community was significantly related to their host’s taxonomic identity. However, this was not true for all endophytic groups, since we found some endophytic groups (e.g. Xylariales and Pleosporales) occurring in more than one host genus. Findings from this study promote the formulation of hypotheses related to the effect of altitudinal changes on the endophytic communities along the Eastern Andean slopes. These hypotheses and perspectives for fungal biodiversity research and conservation in Peru are addressed and discussed.     

Widespread dust deposition on North American peatlands coincident with European land-clearance

Ecosystems around the world are being subjected to numerous human disturbances. Climate change and land degradation are the most obvious of these disturbances and have received much attention. However, easily overlooked, indirect disturbances can also alter ecosystem structure and function. Dust deposition is a prime example of an easily overlooked disturbance process. We hypothesized that historic European settlement and land-clearance in eastern North America led to widespread wind erosion of upland soils and subsequent dust deposition onto otherwise undisturbed peatlands, potentially fertilizing these naturally nutrient-poor ecosystems and causing shifts in plant communities. We tested these hypotheses by analyzing 11 peat profiles collected across a broad region of eastern North America. We documented a strong correlation between the concentrations of Ambrosia pollen grains and microscopic mineral particles, interpreting this as a signal of dust deposition coincident with European settlement and land-clearance. Analysis of Sphagnum macrofossils revealed substantial site-to-site variability in both the degree and the direction of ecological response to dust deposition, but suggested that increasing magnitude of dust deposition increased the likelihood of a decline in the relative abundance of Sphagnum. Results also suggested that raised bogs were more sensitive to dust deposition than kettle peatlands. We conclude that European settlement and land-clearance resulted in widespread dust deposition on peatlands, leading to ecological changes in some of these ecosystems, and leaving behind a coherent dust horizon in the late-Holocene peatland stratigraphy of eastern North America. This easily overlooked indirect disturbance process could be ongoing today in areas of widespread soil disturbance and could potentially further alter dust-receiving ecosystems.     

Relocation,high‐latitude warming and host genetic identity shape the foliar fungal microbiome of poplars

Micro‐organisms associated with plants and animals affect host fitness, shape community structure and influence ecosystem properties. Climate change is expected to influence microbial communities, but their reactions are not well understood. Host‐associated micro‐organisms are influenced by the climate reactions of their hosts, which may undergo range shifts due to climatic niche tracking, or may be actively relocated to mitigate the effects of climate change. We used a common‐garden experiment and rDNA metabarcoding to examine the effect of host relocation and high‐latitude warming on the complex fungal endophytic microbiome associated with leaves of an ecologically dominant boreal forest tree (Populus balsamifera L.). We also considered the potential effects of poplar genetic identity in defining the reactions of the microbiome to the treatments. The relocation of hosts to the north increased the diversity of the microbiome and influenced its structure, with results indicating enemy release from plausible pathogens. High‐latitude warming decreased microbiome diversity in comparison with natural northern conditions. The warming also caused structural changes, which made the fungal communities distinct in comparison with both low‐latitude and high‐latitude natural communities, and increased the abundance of plausible pathogens. The reactions of the microbiome to relocation and warming were strongly dependent on host genetic identity. This suggests that climate change effects on host–microbiome systems may be mediated by the interaction of environmental factors and the population genetic processes of the hosts.     

Microbial Mechanisms Mediating Increased Soil C Storage under Elevated Atmospheric N Deposition

Future rates of anthropogenic N deposition can slow the cycling and enhance the storage of C in forest ecosystems. In a northern hardwood forest ecosystem, experimental N deposition has decreased the extent of forest floor decay, leading to increased soil C storage. To better understand the microbial mechanisms mediating this response, we examined the functional genes derived from communities of actinobacteria and fungi present in the forest floor using GeoChip 4.0, a high-throughput functional-gene microarray. The compositions of functional genes derived from actinobacterial and fungal communities was significantly altered by experimental nitrogen deposition, with more heterogeneity detected in both groups. Experimental N deposition significantly decreased the richness and diversity of genes involved in the depolymerization of starch (∼12%), hemicellulose (∼16%), cellulose (∼16%), chitin (∼15%), and lignin (∼16%). The decrease in richness occurred across all taxonomic groupings detected by the microarray. The compositions of genes encoding oxidoreductases, which plausibly mediate lignin decay, were responsible for much of the observed dissimilarity between actinobacterial communities under ambient and experimental N deposition. This shift in composition and decrease in richness and diversity of genes encoding enzymes that mediate the decay process has occurred in parallel with a reduction in the extent of decay and accumulation of soil organic matter. Our observations indicate that compositional changes in actinobacterial and fungal communities elicited by experimental N deposition have functional implications for the cycling and storage of carbon in forest ecosystems.     

Rainfall homogenizes while fruiting increases diversity of spore deposition in Mediterranean conditions

There is a lack of knowledge regarding the main factors modulating fungal spore deposition in forest ecosystems. We have described the local spatio-temporal dynamics of fungal spore deposition along a single fruiting season and its relation with fruit body emergence and rainfall events. Passive spore traps were weekly sampled during autumn and analysed by metabarcoding of the ITS2 region in combination with qPCR. There were larger compositional changes of deposited spores across sampling weeks than amongst sampling plots. Spore diversity and abundance correlated with mushroom emergence and weekly rainfall. Spore compositional changes were related to rainfall, with lower spatial compositional heterogeneity across plots during weeks with higher rainfall. Soil saprotrophs, and amongst them, puffball species, showed the strongest positive correlation with rainfall across fungal guilds. We saw high fine-scale temporal changes of deposited spores, and both mushroom emergence and rainfall may be important factors driving airborne spore deposition.     

Geographical and seasonal influences on the distribution of fungal endophytes in Quercus ilex

A systematic survey of the endophytic assemblages of Quercus ilex in central Spain has been performed, with the goal of evaluating the importance of geographical and seasonal factors on these fungal communities. Four sampling sites were selected; one of them was sampled twice, in the spring and the autumn. The collected plant material consisted of bark, twigs and leaves from eight trees per site. Fungal strains were isolated with the use of a surface-sterilization method with sodium hypochlorite. A total of 2921 fungal strains grouped into 149 'species' or morphological types were recovered. The 10 dominant species, with isolation frequencies >1.5%, were Pyrenochaeta sp., Periconiella anamorph of Biscogniauxia mediterranea (De Not.) Kuntze, Pseudonectria sp., Cryptosporiopsis quercina Petrak, Alternaria alternata (Fr:) Keissl., two undetermined coelomycetes, Penicillium funiculosum Thom, Diplodia mutila Fr. apud Mont. and Ascochyta sp. Medians of fungal species per tree were significantly different among the sampled sites. The isolation frequencies of the dominant species, as well as other less frequent species, were significantly dependent on the sampling site. The degree of endophytic infection and the diversity of fungal species were significantly higher in the spring. The frequencies of all dominant species at one of the sites depended significantly on the season, except for C. quercina , Acremonium sclerotigenum (F & V Moreau ex Valenta) Gams. and D. mutila . Cluster analysis of the whole endophytic mycoflora of the sampled trees suggested that the geographical factor affects the endophytic distribution patterns more significantly than the seasonal factor.     

Endophytic fungi associated with leaves of Betulaceae in Japan

Diversity and species composition of endophytic fungi on leaves of 11 tree species in Betulaceae were studied, with reference to climatic, tree species, and seasonal variations. A total of 186 fungal isolates were obtained from 190 leaves collected in a subalpine forest, a cool temperate forest, and a subtropical forest in Japan, and were divided into 46 operational taxonomic units (OTUs) according to the base sequences of D1-D2 region of large subunit rDNA. The 2 most frequent OTUs were Muscodor sp. and Nemania sp. in Xylariaceae, followed by Gnomonia sp., Glomerella acutata , Apiosporopsis sp., Asteroma sp., and Cladosporium cladosporioides . The similarities of OTU composition in endophytic fungal assemblages on leaves of Betulaceae were generally low among the forests of different climatic regions. Fungal OTU compositions were relatively similar between 2 Betula species in the subalpine forest, whereas 7 tree species in the cool temperate forest were divided into 3 groups according to the similarity of endophytic fungal assemblages on the leaves, with 4 Carpinus species assigned into 2 of the 3 groups. The similarity of endophytic fungal assemblages between August and October was relatively high in the subalpine forest, whereas the seasonal changes were generally greater (i.e., the similarities among sampling dates were lower) in the cool temperate forest.     

银杏叶部内生真菌多样性的研究

为了解我国特有植物银杏的叶部组织中内生真菌菌群的多样性和演替变化,分别于春、夏、秋季从江苏和山东两省的五个主要银杏栽培地采集健康叶片进行了内生真菌的研究。结果表明:所分离出的1971株内生真菌可归于32属,以交链孢属Alternaria(18.01%)、叶点霉属Phyllosticta(14.66%)和丝核菌属Rhizoctonia(14.56%)为优势菌群。在内生真菌的类群及组成上存在着部位、地区以及季节的差异性,也呈现一定的规律性。多样性指数的计算反映出所获得的银杏叶部内生真菌菌群具有不同的丰富度及均匀度,同时有一定的相似性。