Scale-Dependent Influences of Distance and Vegetation on the Composition of Aboveground and Belowground Tropical Fungal Communities

Shifts of understory vegetation induced by thinning drive the expansion of soil rare fungi

The gap formation due to forest thinning regulates the understorey microclimate, ground vegetation, and soil biodiversity. However, little is known about abundant and rare taxa's various patterns and assemblage mechanisms under thinning gaps. Thinning gaps with increasing sizes (0, 74, 109, and 196 m2) were established 12 years ago in a 36-year-old spruce plantation in a temperate mountain climate. Soil fungal and bacterial communities were analyzed by MiSeq sequencing and related to soil physicochemical properties and aboveground vegetation. The functional microbial taxa were sorted by FAPROTAX and Fungi Functional Guild database. The bacterial community stabilized under varied thinning intensities and was not different from the control plots, whereas the richness of the rare fungal taxa was at least 1.5-fold higher in the large gaps than in the small ones. Total phosphorus and dissolved organic carbon were the main factors influencing microbial communities in soil under various thinning gaps. The diversity and richness of the entire fungal community and rare fungal taxa increased with the understorey vegetation coverage and shrub biomass after thinning. Gap formation by thinning stimulated the understorey vegetation, the rare saprotroph (Undefined Saprotroph), and mycorrhizal fungi (Ectomycorrhizal-Endophyte-Ericoid Mycorrhizal-Litter Saprotroph-Orchid Mycorrhizal and Bryophyte Parasite-Lichen Parasite-Ectomycorrhizal-Ericoid Mycorrhizal-Undefined Saprotroph), which may accelerate nutrient cycling in forest ecosystems. However, the abundance of Endophyte-Plant Pathogens increased by eight times, which showed the potential risk for the artificial spruce forests. Thus, fungi may be the driving force of forest restoration and nutrient cycling under the increasing intensity of thinning and may induce plant diseases. Therefore, vegetation coverage and microbial functional diversity should be considered to evaluate the sustainability of the artificial forest ecosystem and forest restoration.

Habitat and tree species identity shape aboveground and belowground fungal communities in central European forests

Introduction

Trees interact with fungi in mutualistic, saprotrophic, and pathogenic relationships. With their extensive aboveground and belowground structures, trees provide diverse habitats for fungi. Thus, tree species identity is an important driver of fungal community composition in forests.

Methods

Here we investigate how forest habitat (bark surface vs. soil) and tree species identity (deciduous vs. coniferous) affect fungal communities in two Central European forests. We assess differences and interactions between fungal communities associated with bark surfaces and soil, in forest plots dominated either by Fagus sylvatica, Picea abies, or Pinus sylvestris in two study regions in southwestern and northeastern Germany.

Results

ITS metabarcoding yielded 3,357 fungal amplicon sequence variants (ASVs) in the northern and 6,088 in the southern region. Overall, soil communities were 4.7 times more diverse than bark communities. Habitat type explained 48-69% of the variation in alpha diversity, while tree species identity explained >1-3%. NMDS ordinations showed that habitat type and host tree species structured the fungal communities. Overall, few fungal taxa were shared between habitats, or between tree species, but the shared taxa were highly abundant. Network analyses, based on co-occurrence patterns, indicate that aboveground and belowground communities form distinct subnetworks.

Discussion

Our study suggests that habitat (bark versus soil) and tree species identity are important factors structuring fungal communities in temperate European forests. The aboveground (bark-associated) fungal community is currently poorly known, including a high proportion of reads assigned to "unknown Ascomycota" or "unknown Dothideomycetes." The role of bark as a habitat and reservoir of unique fungal diversity in forests has been underestimated.

Rare Taxa Drive the Response of Soil Fungal Guilds to Soil Salinization in the Taklamakan Desert

Salinization poses great threats to soil fungal communities that would cause the losses of ecosystems services. Soil fungal communities are composed of different functional guilds such as saprotrophic, symbiotrophic, and pathotrophic fungi, and each guild includes many rare taxa and a few abundant taxa. Despite of low abundance, rare taxa may be crucial in determining the responses of entire soil fungal communities to salinization. However, it remains poorly understood how rare taxa mediate the impacts of soil salinization on soil fungal community structure. Here, we took advantage of a salinity gradient in a desert ecosystem ranging from 0.60 to 31.09 g kg^-1 that was created by a 12-year saline-water irrigation and assessed how the rare vs. abundant taxa of soil saprotrophic, symbiotrophic, and pathotrophic fungi respond to soil salinization through changes in the community biodiversity and composition. We found that the rare taxa of soil saprotrophic, symbiotrophic, and pathographic fungi were more sensitive to changes in soil salinity compared to the abundant taxa. In addition, the community composition of rare taxa of the saprotrophic and pathotrophic fungi not the symbiotrophic fungi was positively associated with soil salinity change. However, the symbiotrophic fungi showed greater variations in the species richness along the salinity gradient. These findings highlight the importance to differentiate rare taxa in predicting how the biodiversity and functional groups of soil fungal communities respond to soil salinization.

Contrasting Patterns and Drivers of Soil Fungal Communities between Two Ecosystems Divided by the Treeline

The treeline is a sensitive region of the terrestrial ecosystem responding to climate change. However, studies on the composition and formation mechanisms of soil fungal communities across the treeline are still lacking. In this study, we investigated the patterns of soil fungal community composition and interactions among functional guilds above and below the treeline using Illumina high-throughput sequencing and ecological network analysis. The results showed that there were significant differences in the soil environment and soil fungal community composition between the two ecosystems above and below the treeline. At the local scale of this study, geographic distance and environmental factors affected the composition of the soil fungal community. Soil temperature was an important environmental predictor of soil fungal community composition. Species in soil fungal communities in the subalpine meadow were more closely related to each other compared to those in the montane forest. Furthermore, the soil fungal community in montane forest was more stable. Our findings contribute to a better understanding of how mountain ecological functions respond to global climate change.

Fungi in soil and understory have coupled distribution patterns

Ecological processes that control fungal distribution are not well understood because many fungi can persist in a wide variety of dissimilar habitats which are seldom sampled simultaneously. Geographic range size is reflective of species’ resource usage, and for plants and animals, there is a robust positive correlation between niche-breadth and range-size. It remains unknown whether this pattern is true for fungi. To investigate the fungal niche breadth–range size relationship we identified habitat specialists and generalists from two habitats (plant leaves and soil) and asked whether habitat specialization influenced fungal biogeography. We sampled fungi from the soil and phylloplane of tropical forests in Vanuatu and used DNA metabarcoding of the fungal ITS1 region to examine rarity, range size, and habitat connectivity. Fungal communities from the soil and phylloplane are spatially autocorrelated and the spatial distribution of individual fungal OTU are coupled between habitats. Habitat breadth (generalist fungi) did not result in larger range sizes but did correlate positively with occurrence frequency. Fungi that were frequently found were also found in high abundance, a common observation in similar studies of plants and animals. Fungal abundance-occupancy relationships differed by habitat and habitat-specificity. Soil specialists were found to be locally abundant but restricted geographically. In contrast, phylloplane generalists were found to be abundant over a large range in multiple habitats. These results are discussed in the context of differences between habitat characteristics, stability and spatial distribution. Identifying factors that drive spatial variation is key to understanding the mechanisms that maintain biodiversity in forests.

Spatial factors and plant attributes influence soil fungal community distribution patterns in the lower reaches of the Heihe River Basin, Northwest China

Inland river basins include critical habitats and provide various ecosystem services in extremely arid lands. However, we know little about the distribution patterns of soil fungal communities in these river basins. We investigated the distribution patterns of soil fungal communities from the riparian oasis zone (ROZ) to the circumjacent desert zone (CDZ) at the lower reaches of the Heihe River. The results indicated that soil fungal communities were mainly dominated by the phyla Ascomycota and Basidiomycota across all samples. The dominant soil fungi taxa were significantly different between ROZ and CDZ habitats at both the phylum and genus levels. Fungal alpha diversity was mainly affected by spatial factors and plant functional traits, and Pearson correlation analysis revealed that fungal alpha diversity was more closely related to plant functional traits than soil properties. Furthermore, fungal community structure was best explained by spatial factors and plant attributes (including plant diversity and plant functional traits). Together, our findings provide new insights into the significance of spatial factors and plant attributes for predicting distributions of fungal communities in arid inland river basins, which will help us better understand the functions and services of these ecosystems.