Shifts in composition and function of soil fungal communities and edaphic properties during the reclamation chronosequence of an open-cast coal mining dump

Distribution Pattern and Assembly Process of Fungal Communities Along Altitude Gradient in Sediments of the Yellow River Basin

Microorganisms have a profound impact on the stability and ecological health of aquatic environments. Fungi, as important components of river ecosystems, play critical roles as decomposers and symbionts. A comprehensive understanding of the mechanisms underlying fungal community assembly is essential for the effective conservation and management of river ecosystems. However, the distribution patterns and assembly process of fungal communities along elevation gradients in river sediments remain poorly understood. In this study, ITS amplicon sequencing, a neutral community model, and a null model were employed to analyze the distribution patterns and assembly processes of fungal communities in sediments along the altitudinal gradient of the Yellow River. The results indicated that Ascomycota (47.79%) and Basidiomycota (15.68%) were identified as the dominant phyla in the sediments, collectively accounting for 63.47% of the total relative abundance of the community. In the three different altitudinal gradients, the fungal community diversity (Shannon) showed a gradually decreasing trend with increasing altitude. The co-line networks of fungal communities exhibited positive interactions and had more complex and compact networks in the sediments of the Tibetan Plateau area (YRA). Environmental factors in the sediments played an important role in shaping the structure of fungal communities, with lead (Pb), total nitrogen (TN), silt, and total organic carbon (TOC) being the main factors driving changes in community structure, contributing 15.5%, 12.3%, 10.7%, and 10.2%, respectively. In the community assembly process, deterministic processes were found to dominate, with homogenizing selection contributing the most (69.66%). These research results help us understand the distribution patterns of fungal communities along altitudinal gradients and the mechanisms of community assembly, and also provide a scientific basis for biodiversity conservation and the rational use of biological resources.

The Diversity and Community Composition of Three Plants' Rhizosphere Fungi in Kaolin Mining Areas

Mining activities in the kaolin mining area have led to the disruption of the ecological health of the mining area and nearby soils, but the effects on the fungal communities in the rhizosphere soils of the plants are not clear. Three common plants (Conyza bonariensis, Artemisia annua, and Dodonaea viscosa) in kaolin mining areas were selected and analyzed their rhizosphere soil fungal communities using ITS sequencing. The alpha diversity indices (Chao1, Shannon, Simpson, observed-species, pielou-e) of the fungal communities decreased to different extents in different plants compared to the non-kauri mining area. The β-diversity (PCoA, NMDS) analysis showed that the rhizosphere soil fungal communities of the three plants in the kaolin mine area were significantly differentiated from those of the control plants grown in the non-kaolin mine area, and the extent of this differentiation varied among the plants. The analysis of fungal community composition showed that the dominant fungi in the rhizosphere fungi of C. bonariensis and A. annua changed, with an increase in the proportion of Mycosphaerella (genus) by about 20% in C. bonariensis and A. annua. An increase in the proportion of Didymella (genus) by 40% in D. viscosa was observed. At the same time, three plant rhizosphere soils were affected by kaolin mining activities with the appearance of new fungal genera Ochrocladosporium and Plenodomus. Predictive functional potential analysis of the samples revealed that a significant decrease in the potential of functions such as biosynthesis and glycolysis occurred in the rhizosphere fungal communities of kaolin-mined plants compared to non-kaolin-mined areas. The results show that heavy metals and plant species are the key factors influencing these changes, which suggests that selecting plants that can bring more abundant fungi can adapt to heavy metal contamination to restore soil ecology in the kaolin mining area.

The Changes, Aggregation Processes, and Driving Factors for Soil Fungal Communities during Tropical Forest Restoration

Soil fungal communities play crucial roles in mediating the functional associations between above- and belowground components during forest restoration. Forest restoration shapes the alterations in plant and soil environments, which exerts a crucial effect on soil fungal assemblages. However, the changes, assembly processes, and driving factors of soil fungi communities during tropical forest restoration are still uncertain. We used Illumina high-throughput sequencing to identify the changes of soil fungal communities across a tropical secondary forest succession chronosequence (i.e., 12-, 42-, and 53-yr stages) in Xishuangbanna. During forest restoration, the dominant taxa of soil fungi communities shifted from r- to K-strategists. The relative abundance of Ascomycota (r-strategists) decreased by 10.0% and that of Basidiomycota (K-strategists) increased by 4.9% at the 53-yr restoration stage compared with the 12-yr stage. From the 12-yr to 53-yr stage, the operational taxonomic unit (OTU), abundance-based coverage estimator (ACE), Chao1, and Shannon index of fungal communities declined by 14.5-57.4%. Although the stochastic processes were relatively important in determining fungal assemblages at the late stage, the fungal community assembly was dominated by deterministic processes rather than stochastic processes. The shifts in soil properties resulting from tropical forest restoration exerted significant effects on fungal composition and diversity. The positive effects of microbial biomass carbon, readily oxidizable carbon, and soil water content explained 11.5%, 9.6%, and 9.1% of the variations in fungal community composition, respectively. In contrast, microbial biomass carbon (40.0%), readily oxidizable carbon (14.0%), and total nitrogen (13.6%) negatively contributed to the variations in fungal community diversity. Our data suggested that the changes in fungal composition and diversity during tropical forest restoration were primarily mediated by the positive or negative impacts of soil carbon and nitrogen pools.

The relationships between heavy metals and bacterial communities in a coal gangue site

Coal is the main source of energy for China's economic development, but coal gangue dumps are a major source of heavy metal pollution. Bacterial communities have a major effect on the bioremediation of heavy metals in coal gangue dumps. The effects of different concentrations of heavy metals on the composition of bacterial communities in coal gangue sites remain unclear. Soil bacterial communities from four gangue sites that vary in natural heavy metal concentrations were investigated using high-throughput sequencing in this study. Correlations among bacterial communities, heavy metal concentrations, physicochemical properties of the soil, and the composition of dissolved organic matter of soil in coal gangue dumps were also analyzed. Our results indicated that Actinobacteriota, Proteobacteria, Chloroflexi, Acidobacteriota, and Gemmatimonadota were the bacterial taxa most resistant to heavy metal stress at gangue sites. Heavy metal contamination may be the main cause of changes in bacterial communities. Heavy metal pollution can foster mutually beneficial symbioses between microbial species. Microbial-derived organic matter was the main source of soil organic matter in unvegetated mining areas, and this could affect the toxicity and transport of heavy metals in soil. Polar functional groups such as hydroxyl and ester groups (A_226-400) play an important role in the reaction of cadmium (Cd) and lead (Pb), and organic matter with low molecular weight (S_R) tends to bind more to mercury (Hg). In addition to heavy metals, the content of nitrogen (N), phosphorus (P), and total organic carbon (TOC) also affected the composition of the bacterial communities; TOC had the strongest effect, followed by N, SOM, and P. Our findings have implications for the microbial remediation of heavy metal-contaminated soils in coal gangue sites and sustainable development.

AMF Inoculum Enhances Crop Yields of Zea mays L. 'Chenghai No. 618' and Glycine max L. 'Zhonghuang No. 17' without Disturbing Native Fugal Communities in Coal Mine Dump

For the agricultural development of dumps, increase in land use efficiency and protection of food security, to verify the safety, efficacy and sustainability of field-applied arbuscular mycorrhizal fungi (AMF) inoculum, and to exclude the risk of potential biological invasion, in this study, we determined the effect of AMF inoculation and intercropping patterns (maize-soybean) on the temporal dynamics of soil parameters, native AMF communities and crop yields. AMF communities were analyzed using Illumina MiSeq. A total of 448 AMF operational taxonomic units (OTUs) belonging to six genera and nine families were identified. AMF inoculation treatment significantly improved the yield of intercropping maize and increased the content of available phosphorus. AMF diversity was significantly influenced by cropping pattern and growth stage, but not by the inoculation treatment. Inoculation altered the AMF community composition in the early growth stage and facilitated a more complex AMF network in the early and late growth stages. These results indicate that AMF inoculation affects native AMF only in the early stage, and its impact on yield may be the consequence of cumulative effects due to the advantages of plant growth and nutrient uptake in the early stage.

Occurrence of polycyclic aromatic compounds and potentially toxic elements contamination and corresponding interdomain microbial community assembly in soil of an abandoned gas station

Bacteria, archaea and fungi usually coexist in various soil habitats and play important roles in biogeochemical cycle and remediation of contamination. Despite their significance, their combined bioassembly pattern, ecological interactions and driving factors in contaminated soils still remain obscure. To fill the gap, a systemic investigation on the characteristics of microbial community including bacteria, archaea and fungi, assembly patterns and environmental driving factors was conducted in an abandoned gas station soils which were contaminated by polycyclic aromatic compounds and potentially toxic elements for decades. The results showed that the soils were contaminated excessively by benzo[a]pyrene (0.46-2.00 mg/kg) and Dibenz[a,h]anthracene (0.37-1.30 mg/kg). Multitudinous contaminant-degrading/resistant microorganisms and unigenes were detected, indicating potential of the soils to mitigate the pollution. Compared with fungi and archaea, the bacteria had higher community diversity and were more responsive to seasonal shifts. Functional genes (nidB, nahAb, nahAa, adhP, adh, adhC, etc.) involved in biodegradation were highly enriched in summer (1.96% vs 1.80%). The co-occurrence network analysis showed summer communities exhibit a more robust network structure and positive interactions than winter communities. The fungi Neocucurbitaria, Penicillium, Fusarium, Chrysosporium, Knufia, Filobasidium, Wallemia and Rhodotorula were identified as the keystone taxa, indicating that fungi also had important positions in the interdomain molecular ecological networks of both seasons. The network topological properties and |βNTI| (66.7%-93.3% greater than 2) results indicated the deterministic assembly processes of the microbial communities in the contaminated soil. Acenaphthylene, benzo[b]fluoranthene, indeno[1,2,3-cd]perylene, benzo[g,h,i]pyrene and 9-fluorenone were the key environmental factors driving the deterministic assembly processes of the interdomain microbial community in the contaminated soil. These findings extended our knowledge of interdomain microbial community assembly mechanisms and ecological patterns in natural attenuation and provide valuable guidance in associated bioremediation strategies.

Do the Reclaimed Fungal Communities Succeed Toward the Original Structure in Eco-Fragile Regions of Coal Mining Disturbances? A Case Study in North China Loess—Aeolian Sand Area

Mining activity has caused serious environmental damage, particularly for soil ecosystems. How the soil fungal community evolves in mine reclamation and what are the succession patterns of molecular ecological networks still needs to be studied in depth. We used high-throughput sequencing to explore the changes in soil fungal communities, molecular ecological networks, and interactions with soil environmental factors in five different ages (the including control group) during 14 years of reclamation in eco-fragile mines. The results showed that the abundance and diversity of soil fungi after 14 years of reclamation were close to, but still lower than, those in the undisturbed control area, but the dominant phylum was Ascomycota. Soil nitrate-N, C/N ratio, pH, and water content significantly affected the fungal community with increasing reclamation ages. Moreover, we found that Mortierellomycota, despite its high relative abundance, had little significant connectivity with other species in the molecular ecological network. Fungal molecular ecological networks evolve with increasing ages of reclamation, with larger modules, more positive connections, and tighter networks, forming large modules of more than 60 nodes by age 9. The large modules were composed mainly of Ascomycota and Basidiomycota, which can form mycorrhiza with plant roots, and are not only capable of degrading pollution but are also “encouraged” by most (more than 64%) physicochemical factors in the soil environment. The results can provide a basis for scientific mine ecological restoration, especially for eco-fragile regions.

Alterations in Arbuscular Mycorrhizal Community Along a Chronosequence of Teak (Tectona grandis) Plantations in Tropical Forests of China

Arbuscular mycorrhizal (AM) fungi play a crucial role in promoting plant growth, enhancing plant stress resistance, and sustaining a healthy ecosystem. However, little is known about the mycorrhizal status of teak plantations. Here, we evaluated how the AM fungal communities of rhizosphere soils and roots respond to different stand ages of teak: 22, 35, 45, and 55-year-old from the adjacent native grassland (CK). A high-throughput sequencing method was used to compare the differences in soil and root AM fungal community structures. In combination with soil parameters, mechanisms driving the AM fungal community were revealed by redundancy analysis and the Mantel test. Additionally, spore density and colonization rates were analyzed. With increasing stand age, the AM fungal colonization rates and spore density increased linearly. Catalase activity and ammonium nitrogen content also increased, and soil organic carbon, total phosphorous, acid phosphatase activity, available potassium, and available phosphorus first increased and then decreased. Stand age significantly changed the structure of the AM fungal community but had no significant impact on the diversity of the AM fungal community. However, the diversity of the AM fungal community in soils was statistically higher than that in the roots. In total, nine and seven AM fungal genera were detected in the soil and root samples, respectively. The majority of sequences in soils and roots belonged to Glomus. Age-induced changes in soil properties could largely explain the alterations in the structure of the AM fungal community along a chronosequence, which included total potassium, carbon-nitrogen ratio, ammonium nitrogen, catalase, and acid phosphatase levels in soils and catalase, acid phosphatase, pH, and total potassium levels in roots. Soil nutrient availability and enzyme activity were the main driving factors regulating the shift in the AM fungal community structure along a chronosequence of the teak plantations.