喀斯特森林常见树种倒木分解对土壤真菌群落组成及分布规律的影响

BackgroundLong-term cultivation of ginseng can cause severe crop disorders and soil sickness. Crop rotation is an effective agricultural management measure to improve soil sustainability and decrease pathogens. However, the suitable ginseng rotation system and the changes in soil microbial community and soil characteristics under the rotation system need to be further explored.MethodsTo explore suitable ginseng crop rotation systems and improve soil utilization, Allium fistulosum and Brassica napus were planted on ginseng cultivation soil for one year. The effects of the two crops on the chemical properties and enzyme activities of the ginseng cultivation soil were evaluated by chemical analysis. In addition, amplicon sequencing targeting 16 s rDNA genes of bacteria and ITS of fungi has been used to characterize the functional and compositional diversity of microbial communities.ResultsThe results elucidated that the levels of available phosphorus (AP) and available potassium (AK) in the soil increased significantly after one year of cultivation for both crops and Allium fistulosum cultivation may also have reduced soil salinity. In addition, the effects of the two crops on the activities of key soil enzymes were different. Catalase (CAT), urease (URE), and acid phosphatase (A-PHO) activities were significantly reduced and sucrase (SUC), and laccase (LAC) activities were significantly increased after Allium fistulosum planting. While A-PHO activity was significantly increased and LAC activity was significantly decreased after Brassica napus planting. Allium fistulosum significantly reduced the abundance of soil fungal communities. The cultivation of Allium fistulosum and Brassica napus significantly altered the composition of soil bacterial and fungal communities, where changes in the abundance of dominant microorganisms, such as Ascomycota, and Mortierellomycota, etc., were closely related to soil chemistry and enzyme activity. Moreover, both significantly reduced the abundance of the pathogenic fungus Ilyonectria.ConclusionsOur study clarified the effects of Allium fistulosum and Brassica napus on the microbial community and physicochemical properties of ginseng cultivated soil and provides a basis for the sustainable application of ginseng cultivation soil and the development of ginseng crop rotation systems.

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 fungi are a diverse group of organisms extremely crucial to forest nutrient cycling and carbon (C) storage. The elevational pattern of soil microbial diversity has been widely studied, but how soil properties, elevation, and their association affect fungal community in subalpine forests remain to be explored. Here, soil fungal community diversity was investigated using high-throughput sequencing along an elevation gradient (3500–4300 m a.s.l.) in the Abies georgei var. smithii forests, a typical subalpine forest type in the Segila Mountains of Southeast Tibet. Elevation significantly affected the soil properties. Available phosphorus (P), total nitrogen (N), and soil organic C (SOC) increased whereas pH decreased with elevation. A U-shaped pattern for fungal diversity was found in topsoil while a slight monotonically decreasing pattern in subsoil layer across the elevation gradient. Basidiomycota, Ascomycota, and Mortierellomycota were the top three dominant phyla, and ectomycorrhizal fungi were the dominant functional fungi group in the A. georgei forest soils. Significant negative correlations were observed between fungal OTUs richness and NO 3 - ( r = −0.431, p < 0.01), indicating that soil N availability is an important factor for fungal diversity. Based on redundancy analysis, soil factors explained 32.1% of the total variations in composition structure of fungal community. Soil pH, moisture, and fertilities (i.e., SOC, TN, TP, NO 3 - ) were independent factors affecting the fungal community composition. Collectively, the alterations in soil environmental factor across elevations are essential in shaping the soil fungal diversity and community composition in the A. georgei forests in Segila Mountains, Southeast Tibet. • Elevation significantly increased soil organic C and nutrients while decreased pH. • Topsoil fungal richness showed a U-shaped pattern with increasing elevation. • Ectomycorrhizal fungi (EcM) were the dominant functional group across elevation. • NO 3 - was the prominent driving factor on fungal diversity in the A. georgei forests.

Soil microbes are the primary drivers of the material cycling of the forest ecosystem, and understanding how microbial structure and composition change across succession assists in clarifying the mechanisms behind succession dynamics. However, the response of soil microbial communities and assembly processes to succession is poorly understood in subtropical forests. Thus, through the “space instead of time” and high throughput sequencing method, the dynamics of the soil bacterial and fungal communities and assembly process along the succession were studied, where five succession stages, including Abandoned lands (AL), Deciduous broad-leaved forests (DB), Coniferous forests (CF), Coniferous broad-leaved mixed forests (CB), and Evergreen broad-leaved forests (EB), were selected in a subtropical forest on the western slope of Wuyi Mountain, southern China. The results demonstrated that succession significantly decreased soil bacterial α-diversity but had little effect on fungal α-diversity. The composition of soil bacterial and fungal communities shifted along with the succession stages. LEfSe analysis showed the transition from initial succession microbial communities dominated by Firmicutes, Bacteroidota, Ascomycota, and Chytridiomycota to terminal succession communities dominated by Actinobacteriota and Basidiomycota. Distance-based redundancy analysis (db-RDA) revealed that soil total organic carbon (TOC) was the main factor explaining variability in the structure of soil bacterial communities, and multiple soil environmental factors such as the TOC, soil total nitrogen (TN), C:N ratio, and pH co-regulated the structure of fungi. The null models illustrated that deterministic processes were dominant in the soil bacterial communities, while the stochastic processes contributed significantly to the soil fungal communities during succession. Collectively, our results suggest that different patterns are displayed by the soil bacterial and fungal communities during the succession. These findings enhance our comprehension of the processes that drive the formation and maintenance of soil microbial diversity throughout forest succession.

Different fertilization regimes can substantially influence soil fungal community composition, yet fewer studies try to control for the effects of nitrogen input. Here, we investigated the impact of fertilization with equal nitrogen upon soil properties and soil fungal diversity and community composition in the North China Plain in a long-term field experiment. Long-term (32 years) fertilization regimes were applied with equal amounts of nitrogen: no chemical fertilizer or organic manure; chemical fertilization only; organic manure fertilization only, and; combination of 1/2 chemical fertilizer and 1/2 organic manure. Then we investigated the influence of these four fertilization regimes to soil properties, fungal diversity and community composition. The results showed that applying organic manure significantly influenced soil properties. Illumina MiSeq sequencing and its analysis revealed that organic manure fertilization significantly changed soil fungal alpha diversity, but chemical fertilization did not. Although soil fungal community composition did not differ significantly among all the fertilization regimes at the phylum and class levels, they did show differences in the abundance of dominant fungi. Yet at the genus level, soil fungal community composition, abundance, and beta diversity was affected by all fertilization regimes. Application of organic manure also reduced the abundance of soil-born fungal pathogens such as Fusarium. Our results suggest that long-term application of organic manure could markedly improve soil properties, altering soil fungal community composition and its diversity. Moreover, organic manure fertilization could limit soil-born fungal diseases, to further contribute to soil ecosystem sustainability.

Wildfires are unpredictable disturbances with profound effects on soil properties and microbial communities within forest ecosystems. However, knowledge of post-fire microbial communities in karst forests remains limited. In this study, microbial amplicon sequencing techniques were employed to investigate the impact of wildfires on the composition, diversity, function, and co-occurrence network of soil microbial communities in karst forest landscapes and to identify the key soil physicochemical factors affecting the post-fire microbial communities. The wildfire affected the fungal community to a greater extent than the bacterial community, with the former shifting from a dominance of Basidiomycota to Ascomycota at the phylum level, while the relative abundance of Actinobacteria increased significantly in the bacterial community. Moreover, the wildfire increased the α-diversity of the microbial community and changed the β-diversity. Network analysis indicated significant reductions in the complexity of microbial community networks and the hub microbiome in burned soils compared to those of unburned soils. Functional predictions indicated an increase in the highly abundant functional taxa of chemoheterotrophic and aerobic chemoheterotrophic bacteria, along with a significant rise in saprotrophic functional fungal taxa following the fire. In addition, soil organic matter, total nitrogen, total phosphorus, and soil water content emerged as key soil physicochemical factors affecting post-fire soil microbial communities in the karst forest. Overall, this study revealed the structural and functional characteristics of soil microbial communities and their key influencing factors after a fire in a karst forest, which will provide a valuable theoretical basis for ecosystem restoration after a wildfire.IMPORTANCEDespite the significant impacts of wildfires on forest ecosystems, most existing studies have largely focused on boreal and Mediterranean coniferous forest types, with limited research on the impacts of coniferous and broadleaf forest types in subtropical karst regions. This study reveals the effects of wildfires on soil microbial communities of coniferous and broadleaf forest types in a karst forest. The results of this study not only improve the understanding of the effects of wildfires on the composition, diversity, function, and network of soil microbial communities but also provide a meaningful theoretical basis for post-fire ecosystem restoration in the karst forest.

Understanding responses of soil fungal community characteristics to vegetation restoration is essential for optimizing artificial restoration strategies in alpine mining ecosystems. Despite its ecological significance, current comprehension regarding the structure composition and assembly mechanisms of soil fungal communities following vegetation restoration in these fragile ecosystems remains insufficient. We used the high-throughput sequencing and null model analysis to determine the variations and environmental drivers of soil fungal community structures and assembly processes across different restoration chronosequences (natural plant sites, unrestored sites, 2-year restoration sites, and 6-year restoration sites) in a semiarid alpine coal mining region. Artificial vegetation restoration significantly enhanced the α diversity of soil fungal communities while reducing β diversity. However, with prolonged restoration duration, we observed a significant decrease in α diversity accompanied by a corresponding increase in β diversity. Moreover, artificial restoration induced substantial modifications in soil fungal community composition. Taxonomic analysis demonstrated a distinct shift in dominant specialist species from Ascomycota in unrestored, natural plant, and 2-year restoration sites to Glomeromycota in 6-year restoration sites. Dispersal limitation and homogeneity selection were the predominant mechanism governing soil fungal community assembly, with its relative contributions varying significantly across restoration stages. In natural plant communities and unrestored sites, the structure of soil fungal community was primarily governed by dispersal limitation. The 2-year restoration sites exhibited a marked transition, with homogeneous selection emerging as the dominant assembly process, primarily influenced by soil sand content, total phosphorus (TP), total potassium (TK), and belowground biomass (BGB). This transition was accompanied by a significant reduction in the contribution of dispersal limitation. As restoration progressed, the importance of homogeneous selection gradually decreased, while dispersal limitation regained prominence, with community structure being predominantly regulated by soil clay content, soil moisture content (SMC), and TP. Our results underscore the critical role of soil texture and phosphorus availability in shaping soil fungal community dynamics throughout the revegetation process.

Phosphorus (P) in soil is important in the process by which soil microbial communities regulate soil enzyme activity. We aim to explore how short-term P fertilization affects the composition and functionality of the soil fungal community, offering insights into the complex responses of soil fungi to fertilization. Soil samples from a long-term experiment with no P fertilization were collected for pot experiments. The pot experiment included four treatments: non-P fertilizer (NK), chemical P fertilizer (NPK), 1/2 organic fertilizer + 1/2 chemical fertilizer (MNP), and organic fertilizer (M). High-throughput sequencing was employed to analyze the composition, diversity, and functionality of soil fungal communities. Results showed that short-term P addition significantly increased the soil fungal Shannon and Pielou e indices, with increases of 34.48%~59.00% and 29.79%~53.19%, respectively. Ascomycota and Basidiomycota were the most abundant fungal phyla, whereas Cladosporium and Emericellopsis were the most abundant genera. The main factors affecting soil fungal community composition were total nitrogen (TN) and organic matter (OM). A linear discriminant analysis effect size (LEfSe) analysis indicated that Mortierellomycota were significantly enriched under the NPK treatment. A FUNGuild analysis revealed that, compared to the NK treatment, the relative abundance of Animal Pathogen–Endophyte–Lichen Parasite–Plant Pathogen–Wood Saprotroph was reduced by 67.54%, 46.93%, and 44.10% under NPK, MNP, and M treatments, respectively. The relative abundance of Plant Pathogen was less than 1% in the NPK and the MNP treatments. These results indicate that short-term P addition increased soil nutrient levels and soil fungal community diversity. Chemical P fertilizer significantly improved the fungal community structure in yellow paddy soils, enhancing beneficial fungi and suppressing pathogens.

Tropical secondary forests currently represent over half of the world's remaining tropical forests and are critical candidates for maintaining global biodiversity and enhancing potential carbon-use efficiency (CUE) and, thus, carbon sequestration. However, these ecosystems can exhibit multiple successional pathways, which have hindered our understanding of the soil microbial drivers that facilitate improved CUE. To begin to address this, we examined soil % C; % N; C:N ratio; soil microbial biomass C (Cmic); NO3-; NH4+; pH; % moisture; % sand, silt, and clay; and elevation, along with soil bacterial and fungal community composition, and determined which soil abiotic properties structure the soil Cmic and the soil bacterial and fungal communities across a primary forest, 33-year-old secondary forest, and 22-year-old young secondary in the Northern Zone of Costa Rica. We provide evidence that soil microbial communities were mostly distinct across the habitat types and that these habitats appear to have affected the soil ectomycorrhizal fungi and the soil microbial groups associated with the degradation of complex carbon compounds. We found that soil Cmic levels increased along the management gradient from young, to old secondary, to primary forest. In addition, the changes in soil Cmic and soil fungal community structure were significantly related to levels of soil NO3-. Our analyses showed that even after 33years of natural forest regrowth, the clearing of tropical forests can have persistent effects on soil microbial communities and that it may take a longer time than we realized for secondary forests to develop carbon-utilization efficiencies similar to that of a primary forest. Our results also indicated that forms of inorganic N may be an important factor in structuring soil Cmic and the soil microbial communities, leading to improved CUE in regenerating secondary forests. This study is the first in the region to highlight some of the factors which appear to be structuring the soil Cmic and soil microbial communities such that they are more conducive for enhanced CUE in secondary forests.

The soil food web is essential for the functioning of terrestrial ecosystems. The application of naphthalene is a commonly employed experimental treatment for expelling soil fauna to examine faunal effects on litter decomposition processes, for which is it assumed that naphthalene has negligible effects on soil microbial communities. An experiment was conducted to examine the potential soil-fauna-repellent effect of naphthalene application (100 g/m2/month, TR) on a soil fungal community during litter decomposition. The results showed that TR greatly suppressed the abundance and taxonomic richness of soil fauna by 83.7 ± 14.2% and 48.1 ± 17.2%, respectively, and reduced the rates of poplar leaf litter decomposition compared to the control (CK, without naphthalene treatment). Among the fungal communities, the abundance of Thelephorales in the TR soil was suppressed, while the abundance of Capnodiales was stimulated, although TR did not significantly alter the carbon and nitrogen content in the soil microbial biomass nor the diversity of soil fungal communities and the most abundant fungal phylum. Thus, both the suppressed soil arthropod abundance and altered soil fungal community might contribute to the observed slowdown in litter decomposition. These results suggest that naphthalene, as a soil fauna repellent, can alter the abundance of specific taxa in a soil fungal community, thereby impeding the effort to elucidate the contribution of soil fauna to ecosystem functioning (e.g., with respect to litter decomposition).

To understand how the soil microbial community structure responds to vegetation restoration in alpine mining areas, this study specifically examines the grassland ecosystem in the Qianmalong mining area of the Qilian Mountains after five years of artificial restoration. High-throughput sequencing methods were employed to analyze soil bacteria and fungi microbial characteristics in diverse grassland communities. Combined with modifications in vegetation diversity as well as soil physicochemical properties, the impact of vegetation restoration on soil microbiome diversity in this alpine mining area was investigated. The findings indicated that the dominant plants were Cyperus rotundus, Carex spp., and Elymus nutans. As the extent of the grassland's restoration increased, the number of plant species, importance values, and plant community diversity showed an increasing trend. The plant functional groups were mainly dominated by Cyperaceae, followed by Poaceae. Plant height, density, plant cover, frequency, and aboveground biomass showed an increasing trend, and soil water content (SWC) increased. While soil pH and soil electrical conductivity (EC) exhibited a declining trend, available phosphorus (AP), total phosphorus (TP), total nitrogen (TN), nitrate nitrogen (NO3-N), soil organic carbon (SOC), and soil water content (SWC) showed an increasing trend. The dominant bacterial communities were Actinobacteriota, Proteobacteria, Acidobacteriota, Chloroflexi, Firmicutes, and Gemmatimonadota, while the dominant fungal communities were Ascomycota, Mortierellomycota, Basidiomycota, unclassified_k_Fungi, and Glomeromycota. Significant differences were detected within soil microbial community composition among different degrees of restoration grasslands, with bacteria generally dominating over fungi. SWC, TP, and TN were found to be the main soil physicochemical factors affecting the distribution of soil bacterial communities' structure; however, SOC, TN, and NO3-N were the primary factors influencing the soil distribution of fungal communities. The results of this study indicate that different degrees of vegetation restoration in alpine mining areas can significantly affect soil bacterial and fungal communities, and the degree of restoration has varying effects on the soil bacteria and fungi community structure in alpine mining areas.

Changes in soil organic carbon status and microbial community structure following biogas slurry application in a wheat-rice rotation

Effects of different long-term farmland mulching practices on the loessial soil fungal community in a semiarid region of China

The effects of Chinese pine (Pinus tabuliformis) on soil variables after afforestation have been established, but microbial community changes still need to be explored. Using high-throughput sequencing technology, we analyzed bacterial and fungal community composition and diversity in soils from three stands of different-aged, designated 12-year-old (PF1), 29-year-old (PF2), and 53-year-old (PF3), on a Chinese pine plantation and from a natural secondary forest (NSF) stand that was almost 80 years old. Abandoned farmland (BL) was also analyzed. Shannon index values of both bacterial and fungal community in PF1 were greater than those in PF2, PF3 and NSF. Proteobacteria had the lowest abundance in BL, and the abundance increased with stand age. The abundance of Actinobacteria was greater in BL and PF1 soils than those in other sites. Among fungal communities, the dominant taxa were Ascomycota in BL and PF1 and Basidiomycota in PF2, PF3 and NSF, which reflected the successional patterns of fungal communities during the development of Chinese pine plantations. Therefore, the diversity and dominant taxa of soil microbial community in stands 12 and 29 years of age appear to have undergone significant changes; afterward, the soil microbial community achieved a relatively stable state. Furthermore, the abundances of the most dominant bacterial and fungal communities correlated significantly with organic C, total N, C:N, available N, and available P, indicating the dependence of these microbes on soil nutrients. Overall, our findings suggest that the large changes in the soil microbial community structure of Chinese pine plantation forests may be attributed to the phyla present (e.g., Proteobacteria, Actinobacteria, Ascomycota and Basidiomycota) which were affected by soil carbon and nutrients in the Loess Plateau.

Soil microbial communities under wheat and maize straw incorporation are closely associated with soil organic carbon fractions and chemical structure