Response of Soil Microbial Community to Vegetation Reconstruction Modes in Mining Areas of the Loess Plateau, China

Integrating Cover Crops and Manure to Boost Goji Berry Yield: Responses of Soil Physicochemical Properties and Microbial Communities

A sustainable Goji berry (Lycium barbarum L.) planting system that integrates forage radish cover crops (Raphanus sativus L.) and animal manure has been established in northwestern China. This study investigated the effects of different cropping systems and manure application levels on soil physicochemical properties, microbial community structure, and L. barbarum yield under field conditions. A split-plot design was used, with the main-plot treatments consisting of two cropping systems and the sub-plot treatments involving three manure application levels. The results showed that compared to L. barbarum monocropping, cover cropping with R. sativus led to a decrease in soil bulk density (1.90%) and increase in soil electrical conductivity (11.5%), nutrient contents (total N and available N, P, and K: 30.3-138%), and microbial biomass (C: 79.0%; N: 184%). Cover cropping additionally enhanced the community diversity and richness of soil bacteria. Beta-diversity analysis revealed significant differences in bacterial rather than fungal community composition among various treatments. The bacterial network showed a lower ratio of positive to negative correlations and reduced complexity in response to cover cropping, which contrasted with fungal network patterns. Integration of cover cropping and medium manure application increased fruit yield by 8.71%. Cover crops and manure influenced soil microbial diversity mainly through their positive effects on soil total and available N contents.

Characteristics and driving forces of the soil microbial community during 35 years of natural restoration in abandoned areas of the Daxin manganese mine, China

The restoration of mining wastelands, particularly in karst regions contaminated by heavy metals, is an environmental challenge in need of urgent attention. Soil microbes play a vital role in nutrient cycling and ecosystem recovery, yet the long-term evolution of soil microbial communities in such settings remains poorly understood. This study explored the dynamics and influencing factors of soil microbial communities during 35 years of natural restoration in abandoned manganese (Mn) mine areas in Guangxi Province, China. The results revealed that the concentrations of Mn, Cd, Zn, and Cu were significantly (p < 0.05) reduced by 80.4-85.3%, 55.3-70.0%, 21.0-38.1%, and 29.4-49.4%, respectively, in the mid-late restoration periods (R19 and R35) compared with R1. The α diversities of the bacterial and fungal communities significantly increased in the middle-late restoration periods (R19 and R35), indicating increased microbial diversity as restoration progressed. The bacterial community structure exhibited more pronounced changes than did the fungal community structure, with significant shifts observed in dominant phyla such as Proteobacteria, Actinobacteria, Acidobacteriota, and Ascomycota. Notably, the relative abundances of Rhizobiales, Burkholderiales, and Hypocreales increased gradually with succession. Co-occurrence network analysis revealed that bacterial interactions became stronger over time, whereas interactions between bacteria and fungi weakened. Mantel tests and partial least squares path modeling (PLS‒PM) identified soil pH, heavy metals (Mn, Cd, Zn, and Cu), and nutrients (SOM and TN) as key drivers shaping the microbial community composition. These factors were more strongly correlated with bacterial communities than with fungal communities, underscoring the different responses of microbial groups to environmental changes during natural restoration. These findings enhance our understanding of the ecological processes governing microbial community succession in heavy metal-contaminated soils undergoing natural restoration.

Seed endophytes and rhizosphere microbiome of Imperata cylindrica, a pioneer plant of abandoned mine lands

Some plant-associated microorganisms could improve host plants biotic and abiotic stress tolerance. Imperata cylindrica is a dominant pioneer plant in some abandoned mine lands with higher concentrations of heavy metal (HM). To discover the specific microbiome of I. cylindrica in this extreme environment and evaluate its role, the microbiome of I. cylindrica's seeds and rhizosphere soils from HM heavily contaminated (H) and lightly contaminated (L) sites were studied. It was found that HM-contamination significantly reduced the richness of endophytic bacteria in seeds, but increased the abundance of resistant species, such as Massilia sp. and Duganella sp. Spearman's rank correlation coefficient analysis showed that both Massilia sp. and Duganella sp. showed a significant positive correlation with Zn concentration, indicating that it may have a strong tolerance to Zn. A comparison of the microbiome of rhizosphere soils (RS) and adjacent bare soils (BS) of site H showed that I. cylindrica colonization significantly increased the diversity of fungi in rhizosphere soil and the abundance of Ascomycota associated with soil nutrient cycling. Spearman's rank correlation coefficient analysis showed that Ascomycota was positively correlated with the total nitrogen. Combined with the fact that the total nitrogen content of RS was significantly higher than that of BS, we suppose that Ascomycota may enhance the nitrogen fixation of I. cylindrica, thereby promoting its growth in such an extreme environment. In conclusion, the concentration of HM and nutrient contents in the soil significantly affected the microbial community of rhizosphere soils and seeds of I. cylindrica, in turn, the different microbiomes further affected soil HM concentration and nutrient contents. The survival of I. cylindrica in HM severely contaminated environment may mainly be through recruiting more microorganisms that can enhance its nutrition supply.

Bacteria-loaded biochar for the immobilization of cadmium in an alkaline-polluted soil

The combination of biochar and bacteria is a promising strategy for the remediation of Cd-polluted soils. However, the synergistic mechanisms of biochar and bacteria for Cd immobilization remain unclear. In this study, the experiments were conducted to evaluate the effects of the combination of biochar and Pseudomonas sp. AN-B15, on Cd immobilization, soil enzyme activity, and soil microbiome. The results showed that biochar could directly reduce the motility of Cd through adsorption and formation of CdCO3 precipitates, thereby protecting bacteria from Cd toxicity in the solution. In addition, bacterial growth further induces the formation of CdCO3 and CdS and enhances Cd adsorption by bacterial cells, resulting in a higher Cd removal rate. Thus, bacterial inoculation significantly enhances Cd removal in the presence of biochar in the solution. Moreover, soil incubation experiments showed that bacteria-loaded biochar significantly reduced soil exchangeable Cd in comparison with other treatments by impacting soil microbiome. In particular, bacteria-loaded biochar increased the relative abundance of Bacillus, Lysobacter, and Pontibacter, causing an increase in pH, urease, and arylsulfatase, thereby passivating soil exchangeable Cd and improving soil environmental quality in the natural alkaline Cd-contaminated soil. Overall, this study provides a systematic understanding of the synergistic mechanisms of biochar and bacteria for Cd immobilization in soil and new insights into the selection of functional strain for the efficient remediation of the contaminated environments by bacterial biochar composite.

Driving Factors Influencing Soil Microbial Community Succession of Coal Mining Subsidence Areas during Natural Recovery in Inner Mongolia Grasslands

Soil microorganisms significantly influence the energy flow and material cycle of soil ecosystems, making them highly susceptible to environmental changes, such as those induced by mining activities. Studying the succession of soil microbial communities after mining subsidence is crucial for comprehending the significance of soil microbes in the natural recovery process following subsidence. Therefore, the soil properties, vegetation communities, and soil microbial communities of the subsidence area, as well as unexploited areas, were analyzed during the natural restoration process (1, 2, 5, 10, and 15 years). The results demonstrate that mining subsidence has a significant impact on the aboveground vegetation community, soil properties, and microbiological community. Following an extended period of natural recovery, a new stable state has emerged, which differs from that observed in non-subsidence areas. The total nitrogen, nitrate nitrogen, and ammonium nitrogen amounts may be key factors driving the natural recovery of bacterial communities, and total potassium and available potassium may be key factors driving the natural recovery of fungal communities. The natural recovery mechanism of soil microorganisms was analyzed along with the changes related to vegetation and soil physicochemical properties. The mechanism was explained from three perspectives, namely, plant-led, soil-led, and soil-microbial-led, which could provide a theoretical basis for the natural restoration of grassland ecosystems and provide guidance for the treatment of coal mining subsidence areas.

Different bacterial and fungal community patterns in restored habitats in coal-mining subsidence areas

Soil microbiota, which plays a fundamental role in ecosystem functioning, is sensitive to environmental changes. Studying soil microbial ecological patterns can help to understand the consequences of environmental disturbances on soil microbiota and hence ecosystem services. The different habitats with critical environmental gradients generated through the restoration of coal-mining subsidence areas provide an ideal area to explore the response of soil microbiota to environmental changes. Here, based on high-throughput sequencing, we revealed the patterns of soil bacterial and fungal communities in habitats with different land-use types (wetland, farmland, and grassland) and with different restored times which were generated during the ecological restoration of a typical coal-mining subsidence area in Jining City, China. The α-diversity of bacterial was higher in wetland than in farmland and grassland, while that of fungi had no discrepancy among the three habitats. The β-diversity of bacterial community in the grassland was lower than in the farmland, and fungal community was significant different in all three habitats, showing wetland, grassland, and farmland from high to low. The β-diversity of the bacterial community decreased with restoration time while that of the fungal community had no significant change in the longer-restoration-time area. Furthermore, soil electrical conductivity was the most important driver for both bacterial and fungal communities. Based on the taxonomic difference among different habitats, we identified a group of biomarkers for each habitat. The study contributes to understand the microbial patterns during the ecological restoration of coal-mining subsidence areas, which has implications for the efficient ecological restoration of subsidence areas.

Fertilization treatments affect soil CO2 emission through regulating soil bacterial community composition in the semiarid Loess Plateau

A growing body of literature have emphasized the effects of fertilization regimes on soil respiration and microbial community in the semiarid region, however, fertilization treatment effects on the soil CO2 emission, soil bacterial community, and their relationships from long-term experiments is lacking. In the present study, we investigated the effects of long-term fertilization regimes on soil bacterial community and thereafter on soil CO2 emission. A 9-year field experiment was conducted with five treatments, including no fertilizer (NA) and four fertilization treatments (inorganic fertilizer (CF), inorganic plus organic fertilizer (SC), organic fertilizer (SM), and maize straw (MS)) with equal N input as N 200 kg hm-2. The results indicated that CO2 emission was significantly increased under fertilization treatments compared to NA treatment. The bacterial abundance was higher under MS treatment than under NA treatment, while the Chao1 richness showed opposite trend. MS treatment significantly change soil bacterial community composition compared to NA treatment, the phyla (Alphaproteobacteria and Gammaproteobacteria) and potential keystone taxa (Nitrosomonadaceae and Beijerinckiaceae) were higher, while the Acidobacteriota was lower under MS treatment than under NA treatment. CO2 emission was positively correlated with the abundance of Alphaproteobacteria, Gammaproteobacteria, and keystone taxa, negatively correlated with these of Acidobacteriota. Random forest modeling and structural equation modeling determined soil organic carbon, total nitrogen, and the composition and network module III of the bacterial community are the main factors contribute to CO2 emission. In conclusion, our results suggest that the increased CO2 emission was affected by the varied of soil bacterial community composition derived from fertilization treatments, which was related to Alphaproteobacteria, Gammaproteobacteria, Acidobacteriota, and potential keystone taxa (Nitrosomonadaceae and Beijerinckiaceae), and highlight that the ecological importance of the bacterial community in mediating carbon cycling in the semiarid Loess Plateau.

Review on Eco-Environment Research in the Yellow River Basin: A Bibliometric Perspective

The Yellow River Basin (YRB) is an important economic zone and ecological barrier in China. The analysis of its research characteristics and hotspots has been helpful to grasping the future research direction. This work carried out text mining and analysis on scientific papers related to eco-environment research in the YRB from English and Chinese publications. It showed that: there was a fluctuating upward trend over the past 30 years, which was closely related to major events in the YRB during the same period. Chinese research institutions have a closer cooperation with the USA, Australia and other developed countries. More articles were from high-quality journals in ecology, the environment, and others. Interestingly, research institutions with more Chinese articles were mainly located around Beijing or the YRB. Additionally, from a research object perspective, both the English and Chinese articles have mainly focused on large areas such as the lower Yellow River, the middle reaches of the Yellow River, and the upper reaches of the Yellow River, then turning to small areas such as the Yellow River estuary and the source area of the Yellow River. Eco-environment research in the YRB has involved multiple disciplines, and "water-soil-vegetation-ecological protection" has been widely concerned. From the evolution law of hot topics, it has shown a transformation from quantity to quality, from utilization to management, from macro to micro, from construction to high-quality development. It suggests that future research should focus on water, soil, the ecological environment and local high-quality development in small regions and small watersheds.

Biotechnology of Microorganisms from Coal Environments: From Environmental Remediation to Energy Production

Simple Summary

Despite the wide perception that coal environments are extreme habitats, they harbor resident microbial communities. Coal-associated habitats, such as coal mine areas/drainages, spoil heaps, and coalbeds, are defined as complex ecosystems with indigenous microbial groups and native microecological networks. Resident microorganisms possess rich functional potentials and profoundly shape a range of biotechnological processes in the coal industry, from production to remediation.

Abstract

It was generally believed that coal sources are not favorable as live-in habitats for microorganisms due to their recalcitrant chemical nature and negligible decomposition. However, accumulating evidence has revealed the presence of diverse microbial groups in coal environments and their significant metabolic role in coal biogeochemical dynamics and ecosystem functioning. The high oxygen content, organic fractions, and lignin-like structures of lower-rank coals may provide effective means for microbial attack, still representing a greatly unexplored frontier in microbiology. Coal degradation/conversion technology by native bacterial and fungal species has great potential in agricultural development, chemical industry production, and environmental rehabilitation. Furthermore, native microalgal species can offer a sustainable energy source and an excellent bioremediation strategy applicable to coal spill/seam waters. Additionally, the measures of the fate of the microbial community would serve as an indicator of restoration progress on post-coal-mining sites. This review puts forward a comprehensive vision of coal biodegradation and bioprocessing by microorganisms native to coal environments for determining their biotechnological potential and possible applications.

Bioinformatics approaches and applications in plant biotechnology

BACKGROUND

In recent years, major advance in molecular biology and genomic technologies have led to an exponential growth in biological information. As the deluge of genomic information, there is a parallel growth in the demands of tools in the storage and management of data, and the development of software for analysis, visualization, modelling, and prediction of large data set.

MAIN BODY

Particularly in plant biotechnology, the amount of information has multiplied exponentially with a large number of databases available from many individual plant species. Efficient bioinformatics tools and methodologies are also developed to allow rapid genome sequence and the study of plant genome in the 'omics' approach. This review focuses on the various bioinformatic applications in plant biotechnology, and their advantages in improving the outcome in agriculture. The challenges or limitations faced in plant biotechnology in the aspect of bioinformatics approach that explained the low progression in plant genomics than in animal genomics are also reviewed and assessed.

CONCLUSION

There is a critical need for effective bioinformatic tools, which are able to provide longer reads with unbiased coverage in order to overcome the complexity of the plant's genome. The advancement in bioinformatics is not only beneficial to the field of plant biotechnology and agriculture sectors, but will also contribute enormously to the future of humanity.

Influence of revegetation on soil microbial community and its assembly process in the open-pit mining area of the Loess Plateau, China

Vegetation recovery is an important marker of ecosystem health in the mining area. Clarifying the influence of vegetation recovery on the characteristics of soil microbial community and its assembly process can improve our understanding of the ecological resilience and self-maintaining mechanism in the open-pit mining area. For this purpose, we employed MiSeq high-throughput sequencing coupled with null model analysis to determine the composition, molecular ecological network characteristics, key bacterial and fungal clusters, and the assembly mechanism of the soil microbial communities in shrubs (BL), coniferous forest (CF), broad-leaved forests (BF), mixed forest (MF), and the control plot (CK, the poplar plantation nearby that had been continuously grown for over 30 a without disturbance). The results showed that the vegetation restoration model had a significant influence on the α-diversity of the microbial community (p < 0.05). Compared with CK, Sobs and Shannon index of MF and CF have increased by 35.29, 3.50, and 25.18%, 1.05%, respectively, whereas there was no significant difference in the α-diversity of fungal community among different vegetation restoration types, Actinobacteria, Chloroflexi, Proteobacteria, and Acidobacteria were the dominant phyla. The diversity of the first two phyla was significantly higher than those of CK. However, the diversity of the last two phyla was dramatically lower than those of CK (p < 0.05). Ascomycota and Basidiomycota were dominant phyla in the fungal community. The abundance and diversity of Ascomycota were significantly higher than those of CK, while the abundance and diversity of the latter were considerably lower than those of CK (p < 0.05). The stochastic process governed the assembly of the soil microbial community, and the contribution rate to the bacterial community construction of CK, CF, BF, and MF was 100.0%. Except for MF, where the soil fungal community assembly was governed by the deterministic process, all other fungal communities were governed by the stochastic process. Proteobacteria and Acidobacteria are key taxa of the bacterial network, while Mortierellales, Thelebolales, Chaetothyriales, and Hypocreales are the key taxa of the fungal network. All these results might provide the theoretical foundation for restoring the fragile ecosystem in the global mining region.