Pine species determine fungal microbiome composition in a common garden experiment

Spatiotemporal dynamics reveal high turnover and contrasting assembly processes in fungal communities across contiguous habitats of tropical forests

BACKGROUND

The variation in fungal community composition within a single habitat space has been extensively studied in forest ecosystems. However, the spatial and temporal distribution of fungi across contiguous habitats, particularly at a local scale and in tropical regions, remains underexplored. In this study, we examined the fungal community composition across multiple habitats proximal to each other over two seasons in seven Fagaceae species in Taiwanese broadleaf forests. We tested how local spatial scale and habitat influence community assembly.

RESULTS

Using a metabarcoding approach, we sequenced ITS2 regions from 864 samples collected from four distinct habitats-leaves, twigs, litter, and soil. We identified 11,600 fungal amplicon sequence variants (ASVs), with community composition differing significantly between habitats proximal to each other. Generalized dissimilarity modeling (GDM) revealed that spatial distance, interacting with precipitation, was the strongest predictor of fungal turnover, particularly in the phyllosphere. Normalized Stochasticity Ratio (NST) analyses further highlighted contrasting assembly processes, with deterministic influences dominating in the phyllosphere habitat, while stochasticity prevailed in soil and litter. Random forest analysis accurately classified habitats based on ASVs' relative abundances, with strong predictors were mostly habitat-specific ASVs prevalent in soil. Misclassified samples were due to secondary contact of fungi between adjacent habitats. Co-occurrence network analysis revealed more complex and deterministic networks in leaf and twig habitats, while soil was driven by stochastic processes and contained most habitat-specific ASVs. A Cladosporium sp. emerged as a keystone species, maintaining network stability across forests.

CONCLUSION

This study reveals how local spatial variation and habitat shape distinct fungal communities in tropical forests, with deterministic processes dominating in some habitats and stochasticity playing a key role in others. We show extremely high turnover in fungal community are present over very short distances and that local fungal taxa are strong habitat predictors. These findings highlight the importance of studying coexisting habitats to gain a deeper understanding of fungal biogeography and ecosystem function.

Foliar Fungal Endophyte Communities of Scottish Plantation Pines

The diversity of foliar fungal endophyte communities was examined in three economically and ecologically important pine species in Scotland: Scots pine, Corsican pine and lodgepole pine. Two plantation sites comprising all three species were selected in climatically contrasting parts of Scotland and were sampled in late spring by collecting healthy needles from two age classes. Surface sterilisation was carried out before obtaining cultures of fungal isolates, and representatives of common sterile morphotypes were sequenced to determine taxonomic placement. Overall relative proportions of the dominant taxa across sites, tree species and needle age classes were as follows: Anthostomella spp. (52%), Lophodermium seditiosum (17%) and Desmazierella acicola (7%). Many other less frequent taxa were recovered. The results agreed with previous endophyte studies in that the combined effects of site and tree species produced unique endophytic fungal assemblages. Phylogenetic analyses revealed potential sub-species variation associated with site in Anthostomella pinea. Our findings point to the potential naturalisation of European fungal endophytic species (e.g., Anthostomella spp.) in Scottish pine plantations, particularly in association with Corsican pine.

The strong seasonality of soil microbial community structure in declining Mediterranean pine forests depends more on soil conditions than on tree vitality

The soil microbiome plays an important role in forest functioning. However, the impact of drought-induced dieback and tree death on soil microbial biomass, community structure, and functional composition is unknown. We also lack understanding on how soil microbiota varies seasonally in such declining stands. We used Phospholipid Fatty Acids (PLFA) analysis to quantify soil microbial biomass and study its seasonal changes in three Mediterranean forests showing dieback and dominated by three pine species (Pinus halepensis Mill, Pinus pinaster Ait. and Pinus sylvestris L.). We also measured microclimatic parameters and soil physical and chemical parameters under trees with different vigor, assessed as canopy defoliation degree, and related them to seasonal changes in the soil microbial community. We found marked differences in soil microbial community structure, total biomass, and the relative abundance of major functional groups among forests. First, soil microbial biomass peaked either in the dry summer (P. halepensis) or in autumn (P. pinaster and P. sylvestris). Accordingly, the relative abundance of most functional groups, excluding Arbuscular mycorrhizal fungi, displayed substantial variation between seasons. In addition, the relative abundance of fungi and Gram-positive bacteria exhibited an opposite pattern compared to actinomycetes and Gram-negative bacteria. Second, soil physical and chemical parameters had a significant impact on within-site PLFA variation, although their influence was less important than that of seasonal variation. Third, differences between defoliated and healthy trees were minor and restricted to averaged ratios between different PLFA markers. Overall, the structure, biomass and relative abundance of major functional groups of the soil microbiome vary considerably among stand types and seasons in forests showing ongoing dieback and high mortality. However, while the seasonal dynamics show predictable patterns, which should be accounted for in future studies, the within-site variation is highly variable and mainly depends on soil physical and chemical parameters.

Evaluating the Biocontrol Efficacy and Antioxidant Potential of Phellinus caribaeo-quercicola-A First Report Dual-Action Endophyte From Inula racemosa Hook. F

Phellinus caribaeo-quercicola is a basidiomycetous fungus, isolated as an endophyte in this study from the healthy and symptomless leaves of Inula racemosa Hook. f., an important medicinal herb growing in Kashmir Himalaya. This study combines morphological, molecular and phylogenetic techniques to identify the fungal endophyte, using the ITS sequence of nrDNA. A detached leaf assay was conducted to assess the pathogenicity of the fungal endophyte suggesting its mutually symbiotic relationship with the host. The authors also investigated the antifungal potential of the isolated endophytic strain to ascertain its use as a biocontrol agent. The study shows that P. caribaeo-quercicola INL3-2 strain exhibits biocontrol activity against four key fungal phytopathogens that cause significant agronomic and economic losses: Aspergillus flavus, Aspergillus niger, Fusarium solani, and Fusarium oxysporum. Notably, P. caribaeo-quercicola INL3-2 strain is highly effective against A. flavus, with an inhibition percentage of 57.63%. In addition, this study investigates the antioxidant activity of P. caribaeo-quercicola INL3-2 strain crude extracts using ethyl acetate and methanol as solvents. The results showed that the methanolic fraction of P. caribaeo-quercicola exhibits potential as an antioxidant agent, with an IC50 value of 171.90 ± 1.15 µg/mL. This investigation is first of its kind and marks the initial report of this fungal basidiomycete, P. caribaeo-quercicola, as an endophyte associated with a medicinal plant. The findings of this study highlight the potential of P. caribaeo-quercicola INL3-2 strain as a dual-action agent with both biocontrol and antioxidant properties consistent with the medicinal properties of Inula racemosa. This endophytic fungus could be a promising source of natural compounds for use in agriculture, medicine, and beyond.

Comparative metabarcoding and biodiversity of gut-associated fungal assemblages of Dendroctonus species (Curculionidae: Scolytinae)

The genus Dendroctonus is a Holarctic taxon composed of 21 nominal species; some of these species are well known in the world as disturbance agents of forest ecosystems. Under the bark of the host tree, these insects are involved in complex and dynamic associations with phoretic ectosymbiotic and endosymbiotic communities. Unlike filamentous fungi and bacteria, the ecological role of yeasts in the bark beetle holobiont is poorly understood, though yeasts were the first group to be recorded as microbial symbionts of these beetles. Our aim was characterize and compare the gut fungal assemblages associated to 14 species of Dendroctonus using the internal transcribed spacer 2 (ITS2) region. A total of 615,542 sequences were recovered yielding 248 fungal amplicon sequence variants (ASVs). The fungal diversity was represented by 4 phyla, 16 classes, 34 orders, 54 families, and 71 genera with different relative abundances among Dendroctonus species. The α-diversity consisted of 32 genera of yeasts and 39 genera of filamentous fungi. An analysis of β-diversity indicated differences in the composition of the gut fungal assemblages among bark beetle species, with differences in species and phylogenetic diversity. A common core mycobiome was recognized at the genus level, integrated mainly by Candida present in all bark beetles, Nakazawaea, Cladosporium, Ogataea, and Yamadazyma. The bipartite networks confirmed that these fungal genera showed a strong association between beetle species and dominant fungi, which are key to maintaining the structure and stability of the fungal community. The functional variation in the trophic structure was identified among libraries and species, with pathotroph-saprotroph-symbiotroph represented at the highest frequency, followed by saprotroph-symbiotroph, and saprotroph only. The overall network suggested that yeast and fungal ASVs in the gut of these beetles showed positive and negative associations among them. This study outlines a mycobiome associated with Dendroctonus nutrition and provides a starting point for future in vitro and omics approaches addressing potential ecological functions and interactions among fungal assemblages and beetle hosts.

Beyond the surface: exploring the mycobiome of Norway spruce under drought stress and with Heterobasidion parviporum

The mycobiome, comprising fungi inhabiting plants, potentially plays a crucial role in tree health and survival amidst environmental stressors like climate change and pathogenic fungi. Understanding the intricate relationships between trees and their microbial communities is essential for developing effective strategies to bolster the resilience and well-being of forest ecosystems as we adopt more sustainable forest management practices. The mycobiome can be considered an integral aspect of a tree's biology, closely linked to its genotype. To explore the influence of host genetics and environmental factors on fungal composition, we examined the mycobiome associated with phloem and roots of Norway spruce (Picea abies (L.) Karst.) cuttings under varying watering conditions. To test the "mycobiome-associated-fitness" hypothesis, we compared seedlings artificially inoculated with Heterobasidion parviporum and control plants to evaluate mycobiome interaction on necrosis development. We aimed to 1) identify specific mycobiome species for the Norway spruce genotypes/families within the phloem and root tissues and their interactions with H. parviporum and 2) assess stability in the mycobiome species composition under abiotic disturbances (reduced water availability). The mycobiome was analyzed by sequencing the ribosomal ITS2 region. Our results revealed significant variations in the diversity and prevalence of the phloem mycobiome among different Norway spruce genotypes, highlighting the considerable impact of genetic variation on the composition and diversity of the phloem mycobiome. Additionally, specific mycobiome genera in the phloem showed variations in response to water availability, indicating the influence of environmental conditions on the relative proportion of certain fungal genera in Norway spruce trees. In the root mycobiome, key fungi such as Phialocephala fortinii and Paraphaeosphaeria neglecta were identified as conferring inhibitory effects against H. parviporum growth in Norway spruce genotypes. Furthermore, certain endophytes demonstrated greater stability in root ecosystems under low water conditions than ectomycorrhizal fungi. This knowledge can contribute to developing sustainable forest management practices that enhance the well-being of trees and their ecosystems, ultimately bolstering forest resilience.

Larger presence of ectomycorrhizae detected from pygmy pine ecotype in the fire-frequent pine barrens ecosystem

Pine barrens ecosystem has acidic, sandy, and nutrient-poor soil and is prone to drought and fire. In the New Jersey Pine Barrens, the predominant pitch pine (Pinus rigida) consists of two ecotypes: the regular pitch pines with heights of 4.6-12 m, and the pygmy pines of low stature (1.2-1.8 m) in the New Jersey Pine Plains. Previous ecological studies suggested that the dwarf pines in the Pine Plains that are embedded within the Pine Barrens were an evolutionary adaptation to frequent fire. Pines are obligate ectomycorrhizal (EcM) mutualists, and their root mycobiota may contribute to stress protection and plant health. However, information on the mycobiota associated with plants in the pine barrens ecosystem is lacking. To have a holistic understanding of the evolution and adaptation in this stressed environment, we used both culture-independent metabarcoding and culture-based method to characterize the mycobiota from soil and root of the two ecotypes and to identify core mycobiota. We found that Agaricomycetes, Leotiomycetes, and Mucoromycotina are predominant fungi in the New Jersey Pine Barrens ecosystem, which is rich in root mutualistic fungi. We observed that the pygmy pine roots had significantly higher density of EcM tips than the regular pine roots. This was corroborated by our metabarcoding analysis, which showed that the pygmy pine trees had higher ratio of ectomycorrhiza-forming fungi than the regular-statured pines. We hypothesize that symbiotrophic EcM fungi associated with pygmy pines are capable of mitigating high fire stress in the Pine Plains.

Vaccination of Elms against Dutch Elm Disease—Are the Associated Epiphytes and Endophytes Affected?

Dutch elm disease (DED) is causing extensive mortality of ecologically and culturally valuable elm trees (Ulmus spp.). Treatment of elms with the biological vaccine Dutch Trig® has been found to provide effective protection against DED by stimulating the defensive mechanisms of the trees. We hypothesized that the same mechanisms could also affect non-target organisms associated with elms. We explored the possible effects of vaccination on epiphytes (mainly lichens) and fungal endophytes living in the bark and young xylem of treated elms. Epiphyte cover percentage was assessed visually using a grid placed on the trunks, and a culture-based approach was used to study endophytes. Epiphyte cover was lower on the trunks of vaccinated trees as compared with unvaccinated trees, but the difference was not statistically significant. The presence of slow-growing and uncommon endophytes seemed to be reduced in continuously vaccinated elms; however, the highest endophyte diversity was found in elms four years after cessation of the vaccination treatments. Our findings suggest that although vaccination may shape epiphyte and endophyte communities in elms, its impacts are not straightforward. More detailed studies are, therefore, needed to inform the sustainable application of the vaccine as a part of the integrated management of DED.

Principal Drivers of Fungal Communities Associated with Needles, Shoots, Roots and Adjacent Soil of Pinus sylvestris

The plant- and soil-associated microbial communities are critical to plant health and their resilience to stressors, such as drought, pathogens, and pest outbreaks. A better understanding of the structure of microbial communities and how they are affected by different environmental factors is needed to predict and manage ecosystem responses to climate change. In this study, we carried out a country-wide analysis of fungal communities associated with Pinus sylvestris growing under different environmental conditions. Needle, shoot, root, mineral, and organic soil samples were collected at 30 sites. By interconnecting the high-throughput sequencing data, environmental variables, and soil chemical properties, we were able to identify key factors that drive the diversity and composition of fungal communities associated with P. sylvestris. The fungal species richness and community composition were also found to be highly dependent on the site and the substrate they colonize. The results demonstrated that different functional tissues and the rhizosphere soil of P. sylvestris are associated with diverse fungal communities, which are driven by a combination of climatic (temperature and precipitation) and edaphic factors (soil pH), and stand characteristics.

Beneficial and pathogenic plant-microbe interactions during flooding stress

The number and intensity of flood events will likely increase in the future, raising the risk of flooding stress in terrestrial plants. Understanding flood effects on plant physiology and plant-associated microbes is key to alleviate flooding stress in sensitive species and ecosystems. Reduced oxygen supply is the main constrain to the plant and its associated microbiome. Hypoxic conditions hamper root aerobic respiration and, consequently, hydraulic conductance, nutrient uptake, and plant growth and development. Hypoxia favours the presence of anaerobic microbes in the rhizosphere and roots with potential negative effects to the plant due to their pathogenic behaviour or their soil denitrification ability. Moreover, plant physiological and metabolic changes induced by flooding stress may also cause dysbiotic changes in endosphere and rhizosphere microbial composition. The negative effects of flooding stress on the holobiont (i.e., the host plant and its associated microbiome) can be mitigated once the plant displays adaptive responses to increase oxygen uptake. Stress relief could also arise from the positive effect of certain beneficial microbes, such as mycorrhiza or dark septate endophytes. More research is needed to explore the spiralling, feedback flood responses of plant and microbes if we want to promote plant flood tolerance from a holobiont perspective.

Studying tree response to biotic stress using a multi-disciplinary approach: The pine pitch canker case study

In an era of climate change and global trade, forests sustainability is endangered by several biotic threats. Pine pitch canker (PPC), caused by Fusarium circinatum, is one of the most important disease affecting conifers worldwide. To date, no effective control measures have been found for this disease. Earlier studies on PPC were mainly focused on the pathogen itself or on determining the levels of susceptibility of different hosts to F. circinatum infection. However, over the last years, plenty of information on the mechanisms that may explain the susceptibility or resistance to PPC has been published. This data are useful to better understand tree response to biotic stress and, most importantly, to aid the development of innovative and scientific-based disease control measures. This review gathers and discusses the main advances on PPC knowledge, especially focusing on multi-disciplinary studies investigating the response of pines with different levels of susceptibility to PPC upon infection. After an overview of the general knowledge of the disease, the importance of integrating information from physiological and Omics studies to unveil the mechanisms behind PPC susceptibility/resistance and to develop control strategies is explored. An extensive review of the main host responses to PPC was performed, including changes in water relations, signalling (ROS and hormones), primary metabolism, and defence (resin, phenolics, and PR proteins). A general picture of pine response to PPC is suggested according to the host susceptibility level and the next steps and gaps on PPC research are pointed out.