Community composition of arctic root-associated fungi mirrors host plant phylogeny

Primer pairs, PCR conditions, and peptide nucleic acid clamps affect fungal diversity assessment from plant root tissues

High-throughput sequencing has become a prominent tool to assess plant-associated microbial diversity. Still, some technical challenges remain in characterising these communities, notably due to plant and fungal DNA co-amplification. Fungal-specific primers, Peptide Nucleic Acid (PNA) clamps, or adjusting PCR conditions are approaches to limit plant DNA contamination. However, a systematic comparison of these factors and their interactions, which could limit plant DNA contamination in the study of plant mycobiota, is still lacking. Here, three primers targeting the ITS2 region were evaluated alone or in combination with PNA clamps both on nettle (Urtica dioica) root DNA and a mock community. PNA clamps did not improve the richness or diversity of the fungal communities but increased the number of fungal reads. Among the tested factors, the most significant was the primer pair. Specifically, the 5.8S-Fun/ITS4-Fun pair exhibited a higher OTU richness but fewer fungal reads. Our study demonstrates that the choice of primers is critical for limiting plant and fungal DNA co-amplification. PNA clamps increase the number of fungal reads when ITS2 is targeted but do not result in higher fungal diversity recovery at high sequencing depth. At lower read depths, PNA clamps might enhance microbial diversity quantification for primer pairs lacking fungal specificity.

Plant species identity and mycorrhizal type explain the root-associated fungal pathogen community assembly of seedlings based on functional traits in a subtropical forest

Introduction

As a crucial factor in determining ecosystem functioning, interaction between plants and soil-borne fungal pathogens deserves considerable attention. However, little attention has been paid into the determinants of root-associated fungal pathogens in subtropical seedlings, especially the influence of different mycorrhizal plants.

Methods

Using high-throughput sequencing techniques, we analyzed the root-associated fungal pathogen community for 19 subtropical forest species, including 10 ectomycorrhizal plants and 9 arbuscular mycorrhizal plants. We identified the roles of different factors in determining the root-associated fungal pathogen community. Further, we identified the community assembly process at species and mycorrhizal level and managed to reveal the drivers underlying the community assembly.

Results

We found that plant species identity, plant habitat, and plant mycorrhizal type accounted for the variations in fungal pathogen community composition, with species identity and mycorrhizal type showing dominant effects. The relative importance of different community assembly processes, mainly, homogeneous selection and drift, varied with plant species identity. Interestingly, functional traits associated with acquisitive resource-use strategy tended to promote the relative importance of homogeneous selection, while traits associated with conservative resource-use strategy showed converse effect. Drift showed the opposite relationships with functional traits compared with homogeneous selection. Notably, the relative importance of different community assembly processes was not structured by plant phylogeny. Drift was stronger in the pathogen community for ectomycorrhizal plants with more conservative traits, suggesting the predominant role of stochastic gain and loss in the community assembly.

Discussion

Our work demonstrates the determinants of root-associated fungal pathogens, addressing the important roles of plant species identity and plant mycorrhizal type. Furthermore, we explored the community assembly mechanisms of root-associated pathogens and stressed the determinant roles of functional traits, especially leaf phosphorus content (LP), root nitrogen content (RN) and root tissue density (RTD), at species and mycorrhizal type levels, offering new perspectives on the microbial dynamics underlying ecosystem functioning.

An Integrative Study of Mycobiome in Different Habitats from a High Arctic Region: Diversity, Distribution, and Functional Role

In the Arctic ecosystems, fungi are crucial for interactions between soil and plants, the cycling of nutrients, and the transport of carbon. To date, no studies have been conducted to thoroughly examine the mycobiome and its functional role in various habitats of the High Arctic region. The aim was to unravel the mycobiome in the nine habitats (i.e., soil, lichen, vascular plant, moss, freshwater, seawater, marine sediment, dung, and marine alga) in the Ny-Ålesund Region (Svalbard, High Arctic) using a high-throughput sequencing approach. A total of 10,419 ASVs were detected. Among them, 7535 ASVs were assigned to unidentified phyla, while the remaining 2884 ASVs were assigned to 11 phyla, 33 classes, 81 orders, 151 families, 278 genera, and 261 species that were known. The distribution of the mycobiome was driven by habitat specificity, indicating that habitat filtering is a crucial factor influencing the fungal assemblages at a local scale in this High Arctic region. Six growth forms and 19 fungal guilds were found. The ecological guild (e.g., lichenized, ectomycorrhizal) and growth form (e.g., yeast, thallus photosynthetic) varied significantly among various habitats. In addition, the occurrence of 31 fungal species that are considered to be potential pathogens was determined. These results will increase our understanding of fungal diversity and its functional significance in this distinctive High Arctic area and thereby establish the groundwork for prediction about how the mycobiome will alter in various environments as a result of anticipated climate change.

Source and acquisition of rhizosphere microbes in Antarctic vascular plants

Rhizosphere microbial communities exert critical roles in plant health, nutrient cycling, and soil fertility. Despite the essential functions conferred by microbes, the source and acquisition of the rhizosphere are not entirely clear. Therefore, we investigated microbial community diversity and potential source using the only two native Antarctic plants, Deschampsia antarctica (Da) and Colobanthus quitensis (Cq), as models. We interrogated rhizosphere and bulk soil microbiomes at six locations in the Byers Peninsula, Livingston Island, Antarctica, both individual plant species and their association (Da.Cq). Our results show that host plant species influenced the richness and diversity of bacterial communities in the rhizosphere. Here, the Da rhizosphere showed the lowest richness and diversity of bacteria compared to Cq and Da.Cq rhizospheres. In contrast, for rhizosphere fungal communities, plant species only influenced diversity, whereas the rhizosphere of Da exhibited higher fungal diversity than the Cq rhizosphere. Also, we found that environmental geographic pressures (i.e., sampling site, latitude, and altitude) and, to a lesser extent, biotic factors (i.e., plant species) determined the species turnover between microbial communities. Moreover, our analysis shows that the sources of the bacterial communities in the rhizosphere were local soils that contributed to homogenizing the community composition of the different plant species growing in the same sampling site. In contrast, the sources of rhizosphere fungi were local (for Da and Da.Cq) and distant soils (for Cq). Here, the host plant species have a specific effect in acquiring fungal communities to the rhizosphere. However, the contribution of unknown sources to the fungal rhizosphere (especially in Da and Da.Cq) indicates the existence of relevant stochastic processes in acquiring these microbes. Our study shows that rhizosphere microbial communities differ in their composition and diversity. These differences are explained mainly by the microbial composition of the soils that harbor them, acting together with plant species-specific effects. Both plant species acquire bacteria from local soils to form part of their rhizosphere. Seemingly, the acquisition process is more complex for fungi. We identified a significant contribution from unknown fungal sources due to stochastic processes and known sources from soils across the Byers Peninsula.

Effects of continuous and rotational cropping practices on soil fungal communities in pineapple cultivation

Background

Rotational cropping practices can change the fungal structure and diversity of cropping soil, and these changes can promote crop development. However, only a few studies have explored the effects of rotational cropping of pineapple on soil fungal diversity.

Methods

In this study, we investigated fungal diversity in continuous and rotational cropping soil of pineapple in Xuwen and Leizhou of China in summer and winter through high throughput sequencing of the fungal internal transcribed spacer region.

Results

The diversity and richness of the fungal community were observed to be significantly increased after rotational cropping in Xuwen and Leizhou in summer, whereas no changes were observed in winter. Furthermore, Ascomycota, Basidiomycota, Zygomcota, and Chytridiomycota were the dominant phyla, and Chaetomium, Penicillium, Fusarium, Trichoderma, and Cryptococcus were the dominant genera in the continuous and rotational cropping soil of pineapple, respectively, in both summer and winter. Chytridiomycota at phylum level and Gibberella at genus level were observed in rotational cropping soil; however, Ascomycota at the phylum level and Chaetomium at the genus level were the most abundant fungi, and their abundance dramatically decreased in continuous cropping soil. Redundancy analysis revealed that rotational cropping reduced the correlation between environmental parameters and the fungal community in winter. In addition, several fungal biomarkers were found in Xuwen in both continuous and rotational cropping soil samples, including Sporobolomyces, Aspergillus, Corynascus sp JHG 2007, and Corynascus at the genus level, Penicillium and fungal sp p1s11 at the species level in rotational cropping soil, and ales family Incertae sedis and Sordariomycetes at the class level in continuous cropping soil. These results revealed the changes in the structure and diversity of fungal community in continuous and rotational cropping practices for pineapple cultivation, which may be associated with crop yield and quality.

Unearthing the plant-microbe quid pro quo in root associations with beneficial fungi

Mutualistic symbiotic associations between multicellular eukaryotes and their microbiota are driven by the exchange of nutrients in a quid pro quo manner. In the widespread arbuscular mycorrhizal (AM) symbiosis involving plant roots and Glomeromycotina fungi, the mycobiont is supplied with carbon through photosynthesis, which in return supplies the host plant with essential minerals such as phosphorus (P). Most terrestrial plants are largely dependent on AM fungi for nutrients, which raises the question of how plants that are unable to form a functional AM sustain their P nutrition. AM nonhost plants can form alternative, evolutionarily younger, mycorrhizal associations such as the ectomycorrhiza, ericoid and orchid mycorrhiza. However, it is unclear how plants such as the Brassicaceae species Arabidopsis thaliana, which do not form known mycorrhizal symbioses, have adapted to the loss of these essential mycorrhizal traits. Isotope tracing experiments with root-colonizing fungi have revealed the existence of new 'mycorrhizal-like' fungi capable of transferring nutrients such as nitrogen (N) and P to plants, including Brassicaceae. Here, we provide an overview of the biology of trophic relationships between roots and fungi and how these associations might support plant adaptation to climate change.

Ecology and potential functions of plant-associated microbial communities in cold environments

Complex microbial communities are associated with plants and can improve their resilience under harsh environmental conditions. In particular, plants and their associated communities have developed complex adaptation strategies against cold stress. Although changes in plant-associated microbial community structure have been analysed in different cold regions, scarce information is available on possible common taxonomic and functional features of microbial communities across cold environments. In this review, we discuss recent advances in taxonomic and functional characterization of plant-associated microbial communities in three main cold regions, such as alpine, Arctic and Antarctica environments. Culture-independent and culture-dependent approaches are analysed, in order to highlight the main factors affecting the taxonomic structure of plant-associated communities in cold environments. Moreover, biotechnological applications of plant-associated microorganisms from cold environments are proposed for agriculture, industry and medicine, according to biological functions and cold adaptation strategies of bacteria and fungi. Although further functional studies may improve our knowledge, the existing literature suggest that plants growing in cold environments harbor complex, host-specific and cold-adapted microbial communities, which may play key functional roles in plant growth and survival under cold conditions.

Host-Environment Interplay Shapes Fungal Diversity in Mosquitoes

Mosquito larvae encounter diverse assemblages of bacteria (i.e., "microbiota") and fungi in the aquatic environments that they develop in. However, while a number of studies have addressed the diversity and function of microbiota in mosquito life history, relatively little is known about mosquito-fungus interactions outside several key fungal entomopathogens. In this study, we used high-throughput sequencing of internal transcribed spacer 2 (ITS2) metabarcode markers to provide the first simultaneous characterization of the fungal communities in field-collected Aedes albopictus larvae and their associated aquatic environments. Our results reveal unprecedented variation in fungal communities among adjacent but discrete larval breeding habitats. Our results also reveal a distinct fungal community assembly in the mosquito gut versus other tissues, with gut-associated fungal communities being most similar to those present in the environment where larvae feed. Altogether, our results identify the environment as the dominant factor shaping the fungal community associated with mosquito larvae, with no evidence of environmental filtering by the gut. These results also identify mosquito feeding behavior and fungal mode of nutrition as potential drivers of tissue-specific fungal community assembly after environmental acquisition. IMPORTANCE The Asian tiger mosquito, Aedes albopictus, is the dominant mosquito species in the United States and an important vector of arboviruses of major public health concern. One aspect of mosquito control to curb mosquito-borne diseases has been the use of biological control agents such as fungal entomopathogens. Recent studies also demonstrate the impact of mosquito-associated microbial communities on various mosquito traits, including vector competence. However, while much research attention has been dedicated to understanding the diversity and function of mosquito-associated bacterial communities, relatively little is known about mosquito-associated fungal communities. A better understanding of the factors that drive fungal community diversity and assembly in mosquitoes will be essential for future efforts to target mosquito-associated bacteria and fungi for mosquito and mosquito-borne disease control.