Impacts of invasive plants on soil fungi and on above- and belowground plant diversity in temperate forests

To investigate the response mechanisms of soil bacterial and fungal communities to the changes of preci-pitation in a desert steppe of Ningxia, we conducted a three-year precipitation control experiment following completely randomized design. There were five treatments, natural precipitation (T0), 50% less in precipitation (T1), 25% less in precipitation (T2), 25% more in precipitation (T3) and 50% more in precipitation (T4). By using Illumina high-throughput sequencing and bioinformatics analysis, we investigated the effects of increased and decreased precipitation on soil bacterial and fungal communities, and examined the correlations between soil physicochemical properties, plant communities and soil bacterial and fungal communities. The result showed that the richness of soil bacteria and fungi was highest in the T4 treatment. In addition, the relative abundance of Chloroflexi, the predominant phyla of soil bacteria was more sensitive to precipitation change. However, the relative abundance of only Ascomycota, a rare fungal taxon, responded to precipitation changes. Results of redundancy analysis showed that the first two axes accounted for 92.8% and 87.4% of the total variance for soil bacterial and fungal community composition, respectively. Precipitation and soil pH were the most important environmental factors driving changes in soil bacterial diversity and community composition. On the one hand, precipitation had a direct positive effect on bacterial diversity and community composition. On the other hand, precipitation changed pH by affecting soil moisture, which in turn had a significant indirect effect on bacterial diversity and community composition. Plant community biomass, plant species richness, and soil pH were the most influential environmental factors affecting fungal diversity and community composition. Precipitation had no direct effect on soil fungal community, but had a significant indirect effect by changing plant community richness and soil pH. The response mechanisms of bacterial and fungal communities in soil differed significantly under different precipitation regimes in the desert grasslands of Ningxia.

Plant diversity and soil properties regulate the microbial community of monsoon evergreen broad-leaved forest under different intensities of woodland use

The responses of soil microbes to climatic and anthropological factors in the Tibetan grasslands

Effects of grassland afforestation on structure and function of soil bacterial and fungal communities

Tropical low-land rainforests are one of the most diverse ecosystems in the world and provide valuable ecosystem services such as climate change mitigation. They are immensely threatened by expanding human land-use. Especially in South-East Asia, deforestation and replacement with cash crop monoculture plantations such as rubber (Hevea brasiliensis) and oil palm (Elaeis guineensis) have led to drastic losses in biodiversity and to ecosystem degradation. Recently, the research focus has increasingly extended to belowground demonstrating strong structuring effects of human land-use on soil microbial communities. Fungi fulfill various ecological functions and their interaction with plants include efficient degradation of dead plant material (saprotrophs), mutualistic mycorrhizal interactions with roots, essential for the nutrient uptake in a majority of land plants, and structuring effects on plant communities (pathogens). Thereby, fungi are often tightly associated with the plant community as a key group of organisms facilitating the flow of nutrients between the below- and aboveground biome. Conversion of tropical lowland rainforests plantations leads to drastic changes in fungal community structures. The magnitude of structuring effects by changes in root or soil properties on the composition of trophic groups (mycorrhiza, saprotrophs and pathogens) remains unknown. The present thesis, conducted on Sumatra (Indonesia), analyses the structuring effects of human land-use in tropical ecosystems on this important group of microorganisms using next generation sequencing methods and root and soil properties. The work is structured into three major research chapters. 
\nIn the first research chapter, I analyzed the effect of land-use intensity on root associated arbuscular mycorrhizal fungi (AM). Anthropogenic land-use severely affects the AM communities in grasslands but tropical forest transformation systems have rarely been studied. I hypothesized that increased land-use intensities negatively affect AM abundance and diversity because of impaired plant fungus interactions at the roots. I further hypothesized that increases in land-use intensity drive the composition of the AM community, causing decline in naturally occurring AM fungi. A land-use intensity index (LUI) based on yield, chemical input and plant richness across four major land-use systems (forest, jungle rubber, rubber and oil palm plantations) was developed and the effect of LUI on AM molecular richness and abundance as well as AM spore abundance and root colonization was tested. Indicator species analysis was used to investigate significant associations between AM species and land-use types. LUI structured the root associated AM community and negatively affected AM diversity and abundance but positively affected AM spore abundance in soil. Distinct land-use types harbored distinct AM communities; however, forest harbored a higher number of indicator species. In conclusion, land-use intensity strongly altered AM communities across land-use systems reducing specialized OTUs. Extensive management practices may help sustain a diverse and abundant AM community.
\nLocal soil and root associated fungal communities often differ considerably. Likely, this is caused by varying magnitude of structuring effects by the plant root community (biotic environmental filter) and edaphic conditions (abiotic environmental filter). However, few studies analyzed the effects of those environmental drivers on root versus soil associated fungal communities across different land-use types. In chapter 2, I tested the hypothesis that root associated fungi respond to changes in root properties more strongly than to changes in soil properties, due to their strong dependence on the root community. In turn, the soil fungal community provides a species pool from which the root community is recruited and this pool is structured mainly by changes in soil properties and stochastic fluctuations. Shifts of different ecological groups of soil and root inhabiting fungi in response to spatial distance as well as changes in soil and root chemistry across different land-use systems (as above, including riparian sites) were investigated. Overall, environmental filters had a stronger effect on the fungal community composition than geographic distance. Unexpectedly, high turnover and low nestedness between local root and soil communities was found. Additionally to a strong structuring effect of soil pH, root chemistry, especially root C/N strongly affected the composition of the root-associated fungal assemblages, while root vitality also affected shifts in soil-residing fungal communities. Root and soil chemistry changes drove divergent turnover of different functional groups (saprotroph, mycorrhiza and plant pathoges) in soil and roots. An important novel result was that assemblages root associated fungal communities were promoted by changes of root chemistry largely independent of the surrounding soil community. Therefore, recovering chemical root traits in intensively managed systems may stabilize the fungal communities against human land-use.
\nThe results of the previous chapters raised the question, whether enrichment of oil palm plantations with other tree species can help to reverse the strong structuring effects of human land-use and partly recover the mycorrhizal community. To address this question, I analyzed the effect of tree species enrichment islands in an intensively managed oil palm plantation on the soil fungal community composition. Islands of native tree species (Parkia speciosa, Archidendron pauciflorum, Durio zibethinus, Peronema canescens, Shorea leprosula, Dyera polyphylla) were planted in an oil palm monoculture and further management was stopped within the islands to allow for natural undergrowth succession. After three years of enrichment cultivation, I tested the hypothesis that tree enrichment alters the taxonomic and functional soil fungal community composition in comparison with that in the soil of intensely managed oil palm plantations. However, no significant effects of tree species richness, or presence of individual tree species on the fungal community composition were found. A small proportion of community variation (< 10 %) was explained by soil abiotic conditions (N, C/N and P) and the majority of variation remained unexplained. These results suggest that abiotic filters as the result of intensively managed land-use constitute a legacy to fungal communities, overruling structuring effects of the vegetation on soil fungal communities within the first years after stopping management.
\nThis thesis demonstrated a severe structuring impact of anthropogenic land-use on the fungal community structures. Soil abiotic properties were a main driver of fungal community composition in roots and soil. For the first time, changes in root chemical traits were linked to changes in the root and soil fungal communities. The results of this thesis underpin that the observed community shifts may result in loss of ecosystem services such as tree nutrient provision and tree health because of impaired AM root colonization. Links between shifts in the fungal community and plant root vitality suggest negative plant soil feedbacks driven by fungal community shifts. Strong bottom-up regulatory effects by root chemical traits especially on the root associated fungal community was demonstrated. However, no structuring effects of three years of plant succession on soil fungal communities in a biodiversity enriched oil palm plantations was found. Time series are required to investigate long term structuring effects of plant top-down regulation of soil fungal communities and the spatial scale at which root traits can affect local soil fungal communities. In summary, this thesis provides valuable new insights in the fungal community assembly processes under human land-use and highlights important areas of future research.

Soil fungal communities play a critical role in ecosystem carbon (C) and nitrogen (N) cycling. Although the effect of plant invasions on ecosystem C and N cycling is well established, its impact on soil fungal communities is not fully understood. The objective of this study was therefore to understand the variations in soil fungal communities as affected by plant invasion, and the mechanisms that drive these changes. We examined the impacts of invasive Spartina alternifolia Loisel. (SA) on soil fungal abundance, diversity, community composition, trophic modes and functional groups in comparison with bare flat (BF) and native Suaeda salsa (Linn.) Pall. (SS), Scirpus mariqueter Tang et Wang (SM), and Phragmites australis (Cav.) Trin. ex Steud. (PA) communities in coastal salt marshes of eastern China, based on analyses of the quantitative polymerase chain reaction (qPCR) and Illumina MiSeq DNA sequences of fungal internal transcribed spacer (ITS) region. SA invasion increased the soil fungal abundance and diversity compared to BF, SS, SM, and PA soils. The increased soil fungal abundance and diversity were highly related to soil organic carbon (C) and nitrogen (N), water-soluble organic carbon (WSOC), litter C:N ratio, and root C:N ratio. Soil fungal community composition was shifted following SA invasion. Specifically, SA invasion significantly enhanced the relative abundance of Basidiomycota, and reduced the relative abundance of Ascomycota compared with BF, SS, SM, and PA soils. Additionally, SA invasion changed soil fungal trophic modes and functional groups. The relative abundance of saprotrophic fungi significantly increased, while the relative abundances of symbiotic and pathotrophic fungi decreased following SA invasion. Our data revealed that SA invasion altered soil fungal abundance, diversity, community composition, trophic modes and functional groups, which were primarily driven by the quality and quantity of plant residues, soil nutrition substrates, as well as soil physicochemical properties. The changes in soil fungal communities, especially their trophic modes and functional groups following SA invasion would greatly affect soil C and N decomposition and accumulation with potential feedback on climate change.

Soil microorganisms play a crucial role in the plant invasion process, acting as both drivers of and responders to plant invasion. However, the effects of plant invasion on the complexity and stability of co-occurrence networks of soil microbial communities remain unclear. Here, we investigated how the invasion of Spartina alterniflora affected the diversity, composition, and co-occurrence networks of soil bacterial and fungal communities in the Yellow River Delta, China. Compared to the native plant (Suaeda salsa), S. alterniflora invasion decreased the α-diversity of soil bacterial communities but did not affect that of fungal communities. The β-diversity of soil bacterial and fungal communities under S. salsa and S. alterniflora habitats also differed dramatically. S. alterniflora invasion increased the relative abundance of the copiotrophic phylum Bacteroidota, whereas decreased the relative abundances of the oligotrophic phyla Acidobacteriota and Gemmatimonadota. Additionally, the relative abundance of Chytridiomycota, known for its role in degrading recalcitrant organic matter, increased substantially within the soil fungal community. Functional predictions revealed that S. alterniflora invasion increased the relative abundance of certain soil bacteria involved in carbon and nitrogen cycling, including aerobic chemoheterotrophy, nitrate reduction, and nitrate respiration. More importantly, S. alterniflora invasion reduced the complexity and stability of both soil bacterial and fungal community networks. The shifts in soil microbial community structure and diversity were mainly induced by soil available nutrients and soil salinity. Overall, our study highlights the profound impacts of S. alterniflora invasion on soil microbial communities, which could further indicate the modification of ecosystem functioning by invasive species.

Summary Soil aggregate stability is an important ecosystem property which deteriorates overtime due to agricultural practices. The cessation of cultivation allows the potential recovery of soil aggregate binding agents such as soil micro‐organisms and biochemical properties. Consequently, an increase in soil aggregate stability is expected. However, this outcome is difficult to predict because the response of each individual soil component and its contribution to soil stability varies. This study utilized a chronosequence of 12 ex‐arable fields in the Bolivian Altiplano, representing six soil ages of abandonment after cessation of potato cultivation, to examine whether soil aggregate stability increases after abandonment and the extent to which changes in soil bacterial and fungal community composition and soil chemical properties are involved in stability recovery. Fields with the longest time since disturbance (15 and 20 years) have a greater proportion of water‐stable aggregates than more recently abandoned fields (1 and 3 years) and exhibit larger differences in bacterial and fungal composition. Total N, , C and organic matter also increased with time since the last intensive agricultural practice. Water‐stable aggregates were strongly correlated with soil fungal community composition. Analysis of covariance is also consistent with the soil fungal community being an important mediator of the recovery of aggregate stability. Synthesis and applications. Soil aggregate stability increased by 50% over the 20 years following disturbance. This recovery was associated with shifts in soil fungal community composition, as is consistent with fungal mediation of this recovery. Land management strategies focusing on restoration of the soil fungal community may enhance soil aggregate stability, a key aspect for soil conservation, restoration, sustainability of agroecosystems and erosion prevention.

Variation and drivers of soil fungal and functional groups among different forest types in warm temperate secondary forests

The annual invasive plant Impatiens glandulifera reduces hyphal biomass of soil fungi in deciduous forests

Fungi have a huge biodiversity and play important roles in soil biogeochemical cycling in island ecosystems. Although island biogeography has been widely studied for macroorganisms, fungal community assembly in true islands and its relationship with island area are less documented. We examined soil fungal communities in 18 oceanic islands of two types (eight non-coral islands and 10 coral islands) using the Illumina MiSeq sequencing technique. Our results showed that fungal α-diversity (species richness) was substantially different among the oceanic islands, with a higher value in non-coral islands than in coral islands. Fungal α-diversity was significantly affected by soil potassium and magnesium (Mg) and plant communities in non-coral islands, whereas only soil Mg significantly affected it in coral islands. Soil fungal community composition was significantly different in the non-coral and coral islands and was influenced by soil property, plant community and spatial distance. The ecological stochasticity model showed that the fungal community assembly was mainly governed by deterministic processes regardless of island type. Fungal β-diversity, but not α-diversity, increased significantly with increasing island area. These findings have implications for the better prediction of soil fungal community dynamics in island systems and biodiversity conservation in fragmented habitats.

How does tree mortality caused by bark beetle (Trypophloeus klimeschi) outbreaks affect changes in soil fungal communities?

Fungal diversity and community composition are mainly related to soil and vegetation factors. However, the relative contribution of the different drivers remains largely unexplored, especially in subtropical forest ecosystems. We studied the fungal diversity and community composition of soils sampled from 12 comparative study plots representing three forest age classes (Young: 10–40 yrs; Medium: 40–80 yrs; Old: ≥80 yrs) in Gutianshan National Nature Reserve in South-eastern China. Soil fungal communities were assessed employing ITS rDNA pyrotag sequencing. Members of Basidiomycota and Ascomycota dominated the fungal community, with 22 putative ectomycorrhizal fungal families, where Russulaceae and Thelephoraceae were the most abundant taxa. Analysis of similarity showed that the fungal community composition significantly differed among the three forest age classes. Forest age class, elevation of the study plots, and soil organic carbon (SOC) were the most important factors shaping the fungal community composition. We found a significant correlation between plant and fungal communities at different taxonomic and functional group levels, including a strong relationship between ectomycorrhizal fungal and non-ectomycorrhizal plant communities. Our results suggest that in subtropical forests, plant species community composition is the main driver of the soil fungal diversity and community composition.

Atmospheric nitrogen (N) deposition is known to alter soil microbial communities, but how canopy and understory N addition affects soil bacterial and fungal communities in different soil layers remains poorly understood. Conducting a 6-year canopy and understory N addition experiment in a temperate forest, we showed that soil bacterial and fungal communities in the organic layer exhibited different responses to N addition. The main effect of N addition decreased soil bacterial diversity and altered bacterial community composition in the organic layer, but not changed fungal diversity and community composition in all layers. Soil pH was the main factor that regulated the responses of soil bacterial diversity and community composition to N addition, whereas soil fungal diversity and community composition were mainly controlled by soil moisture and nutrient availability. In addition, compared with canopy N addition, the understory N addition had stronger effects on soil bacterial Shannon diversity and community composition but had a weaker effect on soil bacteria richness in the organic soil layer. Our study demonstrates that the bacterial communities in the organic soil layer were more sensitive than the fungal communities to canopy and understory N addition, and the conventional method of understory N addition might have skewed the effects of natural atmospheric N deposition on soil bacterial communities. This further emphasizes the importance of considering canopy processes in future N addition studies and simultaneously evaluating soil bacterial and fungal communities in response to global environmental changes.

Microbial communities are closely related to the overall health and quality of soil, but studies on microbial ecology in apple pear orchard soils are limited. In the current study, 28 soil samples were collected from three apple pear orchards, and the composition and structure of fungal and bacterial communities were investigated by high-throughput sequencing. The molecular ecological network showed that the keystone taxa of bacterial communities were Actinobacteria, Proteobacteria, Gemmatimonadetes, Acidobacteria, Nitrospirae, and Chloroflexi, and the keystone taxon of fungal communities was Ascomycota. Mantel tests showed that soil texture and pH were important factors shaping soil bacterial and fungal communities, and soil water soluble organic carbon (WSOC) and nitrate nitrogen (NO3−-N) were also closely related to soil bacterial communities. Canonical correspondence analysis (CCA) and variation partition analysis (VPA) revealed that geographic distance, soil texture, pH, and other soil properties could explain 10.55%, 13.5%, and 19.03% of the overall variation in bacterial communities, and 11.61%, 13.03%, and 20.26% of the overall variation in fungal communities, respectively. The keystone taxa of bacterial and fungal communities in apple pear orchard soils and their strong correlation with soil properties could provide useful clues toward sustainable management of orchards.