Pioneer plants enhance soil multifunctionality by reshaping underground multitrophic community during natural succession of an abandoned rare earth mine tailing

Spontaneous natural succession in metal mine tailings is fundamental to the rehabilitation of bare tailing. Here, an abandoned rare earth element (REE) mine tailing with spontaneous colonisation by pioneer plants with different functional traits was selected. Soil nutrient cycling, fertility, organic matter decomposition as well as underground organismal communities and their multitrophic networks were investigated. Compared with the bare tailing, the colonisation with Lycopodium japonicum, Miscanthus sinensis, and Dicranopteris dichotoma increased soil multifunction by 222%, 293%, and 525%, respectively. This was accompanied by significant changes in soil bacterial and protistan community composition and increased soil multitrophic network complexity. Rhizospheres of different plant species showed distinct microbial community composition compared to that of bare tailing. Some WPS-2, Chloroflexi, and Chlorophyta were mainly present in the bare tailing, while some Proteobacteria and Cercozoa were predominantly seen in the rhizosphere. Pearson correlation and Random Forest revealed the biotic factors driving soil multifunction. Structural equation modelling further revealed that pioneer plants improved soil multifunction primarily by decreasing the microbial biodiversity and increasing the multitrophic network complexity. Overall, this highlights the importance of subterrestrial organisms in accelerating soil rehabilitation during natural succession and provides options for the ecological restoration of degraded REE mining areas.

Phytoremediation with application of anaerobic fermentation residues regulate the assembly of ecological clusters within co-occurrence network in ionic rare earth tailings soil: A pot experiment

The cultivation of energy plants (Pennisetum hybrid) with anaerobic fermentation residues has become an important phytoremediation approach in ionic rare earth elements (REEs) tailings because of its advantages in low cost and sustainability recently. In this study, a comparative pot experiment was carried out to determine the interaction pattern and key ecological clusters in microbial community respond to phytoremediation. Results showed that the application of biogas residues or slurry could effectively mitigate soil acidification, increase soil nutrients, alter REEs bioavailability and promote plant growth. Without fertilization, plant growth was restricted and soil acidification and nutrient-deficiency would be further aggravated. This difference in phytoremediation effect was associated with the assembly of seven key ecological clusters in co-occurrence network of rhizosphere soil. And such assembly pattern of cluster, determined by the environmental preference (e.g. pH, REEs), nutrient demand and interaction among clusters, could alter the microbial communities in response to the changes in soil context rapidly and exert corresponding ecological function during phytoremediation, such as participating in soil nutrient cycling, affecting plant biomass and altering REEs bioavailability. These findings provided new insights for anaerobic fermentation residues application, and can be beneficial to support for studying microbe-plant combined remediation in the future.

Co-occurrence network of microbial communities affected by application of anaerobic fermentation residues during phytoremediation of ionic rare earth tailings area

The long-term exploitation of ionic rare earth elements (REEs) in southern China has produced a large-scale of abandoned tailings area. While the application of anaerobic fermentation residues to cultivate economically valuable remediation plants (e.g. energy plant) has become a hotspot due to their merits in low-cost and sustainability in recent years, the succession and co-occurrence patterns of these microbial communities remain unclear. In this study, soil samples were collected from the sustainable restoration area, natural restoration area and tailings area. The composition and diversity of bacterial and fungal communities on five soil samples were evaluated using high-throughput sequencing technology. The results shown that the phytoremediation with anaerobic fermentation residues could significantly improve the physicochemical properties (especially for soil nutrients) and microbial diversity of soil within 3 years, while these parameters in natural restoration area were lower. The nonmetric multidimensional scaling (NMDS) ordinations revealed the shifts of microbial communities depending on soil physicochemical properties and plant species, and soil nutrients were the main factors affecting the microbial variation explained by the variation partition analysis (VPA). The soil nutrient accumulation obviously changed the proportion of oligotrophic and copiotrophic groups, among which the copiotrophic groups were significantly increased, such as Proteobacteria, Bacteroidetes, Gemmatimonadetes and Glomeromycota. The microbial co-occurrence network analysis indicated that application of anaerobic fermentation residues could significantly improve the topological properties and the stability of microbial network. The copiotrophic groups (e.g. Proteobacteria, Ascomycota) became the key to assemble stable network structure. Moreover, herbaceous plants could increase the proportion of fungi (e.g. Ascomycota) in microbial network, which improved the topological properties with bacteria synergistically. Therefore, the soil environment of REEs tailings area was effectively optimized by anaerobic fermentation residues and herbaceous plants, which furthered understanding of co-occurrence pattern and mutualistic relationships of microbial communities during sustainable restoration.

Nutrients Changed the Assembly Processes of Profuse and Rare Microbial Communities in Coals

Nutrient stimulation is considered effective for improving biogenic coalbed methane production potential. However, our knowledge of the microbial assembly process for profuse and rare microbial communities in coals under nutrient stimulation is still limited. This study collected 16S rRNA gene data from 59 microbial communities in coals for a meta-analysis. Among these communities, 116 genera were identified as profuse taxa, and the remaining 1,637 genera were identified as rare taxa. Nutrient stimulation increased the Chao1 richness of profuse and rare genera and changed the compositions of profuse and rare genera based on nonmetric multidimensional scaling with Bray-Curtis dissimilarities. In addition, many profuse and rare genera belonging to Proteobacteria and Acidobacteria were reduced, whereas those belonging to Euryarchaeota and Firmicutes were increased under nutrient stimulation. Concomitantly, the microbial co-occurrence relationship network was also altered by nutrient addition, and many rare genera mainly belonging to Firmicutes, Bacteroides, and Euryarchaeota also comprised the key microorganisms. In addition, the compositions of most of the profuse and rare genera in communities were driven by stochastic processes, and nutrient stimulation increased the relative contribution of dispersal limitation for both profuse and rare microbial community assemblages and that of variable selection for rare microbial community assemblages. In summary, this study strengthened our knowledge regarding the mechanistic responses of coal microbial diversity and community composition to nutrient stimulation, which are of great importance for understanding the microbial ecology of coals and the sustainability of methane production stimulated by nutrients.

Biogeochemical dynamics of nutrients and rare earth elements (REEs) during natural succession from biocrusts to pioneer plants in REE mine tailings in southern China

The exploitation of ion-adsorption rare earth element (REE) deposits has resulted in large quantities of abandoned mine tailings, which pose significant risks to the surrounding environment. However, the natural evolutional patterns at early successional stages and related biogeochemical dynamics (e.g. nutrient and REE cycling) on such mine tailings remains poorly understood. To this end, a chronosequence of REE mine tailings abandoned for up to 15 years was investigated in a post-mining site in south China. Our results showed that biocrusts were the earliest colonizers on these tailings, reaching a peak of 10% of surface coverage after 10 years of abandonment. Later on, after 15 years, the biocrusts began to be replaced by pioneer plants (e.g. Miscanthus sinensis), suggesting a rather rapid succession. This ecological succession was accompanied by obvious changes in soil nutrients and microbial community structure. Compared to bulk soils, both the biocrusts and rhizospheric soils favored an accumulation of nutrients (e.g. P, S, N, C). Notably, the autotrophic bacteria (e.g. Chloroflexi and Cyanobacteria) with C and N fixation abilities were preferentially enriched in biocrusts, while heterotrophic plant growth promoting bacteria (e.g. Pseudoocardiaceae and Acidobacteriales) were mainly present in the rhizosphere. Moreover, the biocrusts showed a remarkably high concentration of REEs (up to 1820 mg kg^-1), while the rhizospheric soils tended to decrease REE concentrations (~400 mg kg^-1) in comparison with bulk soils, indicating that the REEs could be redistributed by biological processes. Principal component analysis and mantel tests showed that the concentrations of nutrients and REEs were the most important factors affecting the microbial communities in biocrusts, rhizospheric and bulk soils. In sum, based on the observation of nutrient accumulation and pollutant (i.e. REE) dynamics in the initial successional stages, this work provides a feasible theoretical basis for future restoration practices on REE mine tailings.

Microorganisms Accelerate REE Mineralization in Supergene Environments

Exogenic deposits are an important source of rare earth elements (REEs), especially heavy REEs (HREEs). It is generally accepted that microorganisms are able to dissolve minerals and mobilize elements in supergene environments. However, little is known about the roles of microorganisms in the formation of exogenic deposits such as regolith-hosted REE deposits that are of HREE enrichment and provide over 90% of global HREE demand. In this study, we characterized the microbial community composition and diversity along a complete weathering profile drilled from a regolith-hosted REE deposit in Southeastern China and report the striking contributions of microorganisms to the enrichment of REEs and fractionation between HREEs and light REEs (LREEs). Our results provide evidence that the variations in REE contents are correlated with microbial community along the profile. Both fungi and bacteria contributed to the accumulation of REEs, whereas bacteria played a key role in the fractionation between HREEs and LREEs. Taking advantage of bacteria strains isolated from the profile, Gram-positive bacteria affiliated with Bacillus and Micrococcus preferentially adsorbed HREEs, and teichoic acids in the cell wall served as the main sites for HREE adsorption, leading to an enrichment of HREEs in the deposit. The present study provides the first database of microbial community in regolith-hosted REE deposits. These findings not only elucidate the crucial contribution of fungi and bacteria in the supergene REE mineralization but also provide insights into efficient utilization of mineral resources via a biological pathway.

IMPORTANCE Understanding the role of microorganisms in the formation of regolith-hosted rare earth element (REE) deposits is beneficial for improving the metallogenic theory and deposit exploitation, given that such deposits absolutely exist in subtropical regions with strong microbial activities. Little is known of the microbial community composition and its contribution to REE mineralization in this kind of deposit. Using a combination of high-throughput sequencing, batch adsorption experiments, and spectroscopic characterization, the functional microorganisms contributing to REE enrichment and fractionation are disclosed. For bacteria, the surface carboxyl and phosphate groups are active sites for REE adsorption, while teichoic acids in the cell walls of G⁺ bacteria lead to REE fractionation. The above-mentioned findings not only unravel the importance of microorganisms in the formation of supergene REE deposits but also provide experimental evidence for the bioutilization of REE resources.

Soil characteristics and microbial community response in rare earth mining areas in southern Jiangxi Province, China

The microbial community and functional flora in rare earth mining areas are correlated, but the characteristics and metabolic pathways of pollutant in such mining areas are still poorly known. The heavy metals, rare earth elements, and microorganisms present after mining of rare earth mine sites were analyzed. After mining, all sampling sites exhibited low pH and low total organic carbon levels, accompanied by high iron and aluminum concentrations. The development of vegetation is closely related to the development of microorganisms. In the complex environment of rare earth mining areas, Proteobacteria exhibit an absolute competitive advantage. During mine environmental recovery, the relative abundances of Acidobacteria and Chloroflexi will increase markedly, and with further restoration the relative abundance of Firmicutes will gradually decrease. Many genera of bacteria related to the N cycle and heavy metal metabolism were detected in the study area, indicating the important metabolic pathways for ammonia nitrogen and heavy metals in rare earth mining areas. Bacterial genera that promote plant nitrogen fixation also occur in the area, further revealing the nitrogen cycle. This research is important for health assessment and recovery of rare earth mines.