Rhizosphere Microbial Response to Multiple Metal(loid)s in Different Contaminated Arable Soils Indicates Crop-Specific Metal-Microbe Interactions

Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review

Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.

The Diverse Mycorrizal Morphology of Rhododendron dauricum, the Fungal Communities Structure and Dynamics from the Mycorrhizosphere

It is generally believed that mycorrhiza is a microecosystem composed of mycorrhizal fungi, host plants and other microscopic organisms. The mycorrhiza of Rhododendron dauricum is more complex and the diverse morphology of our investigated results displays both typical ericoid mycorrhizal characteristics and ectomycorrhizal traits. The characteristics of ectendoomycorrhiza, where mycelial invade from the outside into the root cells, have also been observed. In order to further clarify the mycorrhizal fungi members and other fungal communities of R. dauricum mycorrhiza, and explore the effects of vegetation and soil biological factors on their community structure, we selected two woodlands in the northeast of China as samples-one is a mixed forest of R. dauricum and Quercus mongolica, and the other a mixed forest of R. dauricum, Q. mongolica, and Pinus densiflor. The sampling time was during the local growing season, from June to September. High-throughput sequencing yielded a total of 3020 fungal amplicon sequence variants (ASVs), which were based on sequencing of the internal transcribed spacer ribosomal RNA (ITS rRNA) via the Illumina NovaSeq platform. In the different habitats of R. dauricum, there are differences in the diversity of fungi obtained from mycorrhizal niches, and specifically the mycorrhizal fungal community structure in the complex vegetation of mixed forests, where R. dauricum is found, exhibits greater stability, with relatively minor changes over time. Soil fungi are identified as the primary source of fungi within the mycorrhizal niche, and the abundance of mycorrhizal fungi from mycorrhizal niches in R. dauricum is significantly influenced by soil pH, organic matter, and available nitrogen. The relationship between soil fungi and mycorrhizal fungi from mycorrhizal niches is simultaneously found to be intricate, while the genus Hydnellum emerges as a central genus among mycorrhizal fungi from mycorrhizal niches. However, there is currently a substantial gap in the foundational research of this genus, including the fact that mycorrhizal fungi from mycorrhizal niches have, compared to fungi present in the soil, proven to be more sensitive to changes in soil moisture.

Root-associated bacterial microbiome shaped by root selective effects benefits phytostabilization by Athyrium wardii (Hook.)

The root-associated microbiome assembly substantially promotes (hyper)accumulator plant growth and metal accumulation and is influenced by multiple factors, especially host species and environmental stress. Athyrium wardii (Hook.) is a phytostabilizer that grows in lead (Pb)-zinc (Zn) mine tailings and shows high root Pb accumulation. However, there remains little information on the assembly of the root-associated microbiome of A. wardii and its role in phytostabilization. A field study investigated the structural and functional variation in the root-associated bacterial microbiome of Athyrium wardii (Hook.) exposed to different levels of contamination in Pb-Zn mine tailings. The root compartment dominated the variation in the root-associated bacterial microbiome but the levels of contaminants showed less impact. Bacterial co-occurrence was enhanced in the rhizosphere soil and rhizoplane but tended to be much simpler in the endosphere in terms of network complexity and connectivity. This indicates that the microbial community assembly of A. wardii was non-random and shaped by root selective effects. Proteobacteria, Chloroflexi, Actinobacteria, Cyanobacteria, and Acidobacteriota were generally the dominant bacterial phyla. The genera Crossiella and Bradyrhizobium were enriched in the rhizosphere and cyanobacterial genera were enriched in the endosphere, demonstrating substantial advantages to plant survival and adaptation in the harsh mine environment. Functional categories involved in amino acid and carbohydrate metabolism were abundant in the rhizosphere soil, thus contributing to metal solubility and bioavailability in the rhizosphere. Membrane transporters, especially ATP-binding cassette transporters, were enriched in the endosphere, indicating a potential role in metal tolerance and transportation in A. wardii. The study shows substantial variation in the structure and function of microbiomes colonizing different compartments, with the rhizosphere and endophytic microbiota potentially involved in plant metal tolerance and accumulation during phytostabilization.

Responses of Soil Microbial Survival Strategies and Functional Changes to Wet-Dry Cycle Events

Soil microbial taxa have different functional ecological characteristics that influence the direction and intensity of plant-soil feedback responses to changes in the soil environment. However, the responses of soil microbial survival strategies to wet and dry events are poorly understood. In this study, soil physicochemical properties, enzyme activity, and high-throughput sequencing results were comprehensively anal0079zed in the irrigated cropland ecological zone of the northern plains of the Yellow River floodplain of China, where Oryza sativa was grown for a long period of time, converted to Zea mays after a year, and then Glycine max was planted. The results showed that different plant cultivations in a paddy-dryland rotation system affected soil physicochemical properties and enzyme activity, and G. max field cultivation resulted in higher total carbon, total nitrogen, soil total organic carbon, and available nitrogen content while significantly increasing α-glucosidase, β-glucosidase, and alkaline phosphatase activities in the soil. In addition, crop rotation altered the r/K-strategist bacteria, and the soil environment was the main factor affecting the community structure of r/K-strategist bacteria. The co-occurrence network revealed the inter-relationship between r/K-strategist bacteria and fungi, and with the succession of land rotation, the G. max sample plot exhibited more stable network relationships. Random forest analysis further indicated the importance of soil electrical conductivity, total carbon, total nitrogen, soil total organic carbon, available nitrogen, and α-glucosidase in the composition of soil microbial communities under wet-dry events and revealed significant correlations with r/K-strategist bacteria. Based on the functional predictions of microorganisms, wet-dry conversion altered the functions of bacteria and fungi and led to a more significant correlation between soil nutrient cycling taxa and environmental changes. This study contributes to a deeper understanding of microbial functional groups while helping to further our understanding of the potential functions of soil microbial functional groups in soil ecosystems.

Field-scale differences in rhizosphere micro-characteristics of Cichorium intybus, Ixeris polycephala, sunflower, and Sedum alfredii in the phytoremediation of Cd-contaminated soil

Understanding the intricate interplay between Cd accumulation in plants and their rhizosphere micro-characteristics is important for the selection of plant species with profitable Cd phytoextraction and soil remediation efficiencies. This study investigated the differences in rhizosphere micro-ecological characteristics and Cd accumulation in chicory, Ixeris polycephala, sunflower, and Sedum alfredii in low-moderate Cd-contaminated soil. Data reveal that the dominant organic acids in rhizosphere soil that responded to Cd were oxalic and lactic acids in chicory and Ixeris polycephala, tartaric acid in sunflower, and succinic acid in Sedum alfredii. These unique organic acids could also influence the abundance of specific rhizobacterial communities in rhizosphere soil that were Sphingomonadaceae and Bradyrhizobiaceae in both Sedum alfredii (9.75 % and 2.56 %, respectively) and chicory (8.98 % and 2.82 %, respectively) rhizosphere soil, Xanthomonadaceae in both Sedum alfredii and Ixeris polycephala rhizosphere soil, and Gaiellaceae in chicory rhizosphere soil. In this case, the combined effects of the organic acids and unique rhizobacterial communities by plant species increased the bioavailable concentration of Cd in Sedum alfredii, Ixeris polycephala, and sunflower rhizosphere soil, while decreasing the Cd-DOM concentrations in chicory rhizosphere soil and the water-extractable Cd reduced by 88.02 % compared to the control. Though the capacity for Cd accumulation in the shoots of chicory was weaker than of Sedum alfredii but better than either Ixeris polycephala or sunflower, chicory presented better Cd translocation and harbored Cd mainly as the low toxic chemical form of pectates and proteins-bound Cd and Cd oxalate in its shoot. Generally, chicory, as an economic plant, is suitable for phytoremediation of low-moderate Cd-contaminated soil after Sedum alfredii.

Indigenous rhizosphere microbial community characteristics of the phytostabilizer Athyrium wardii (Hook.) grown in a Pb/Zn mine tailing

Plant rhizosphere microbiome usually changes dramatically in adaptation to the mine environment to endure high heavy metal concentration, which in turn improves the process of revegetation and phytostabilization of mine tailing and deserves deep investigation. A field study was conducted to investigate the indigenous microbial community of a mining ecotype (ME) of the phytostabilizer Athyrium wardii (Hook.) grown in a Pb/Zn mine tailing and a corresponding non-mining ecotype (NME) grown in an uncontaminated adjacent site. Our study found a slight difference in microbial α-diversity between the ME and NME, and no significant difference between the rhizosphere and bulk soil. Both bacterial and fungal community compositions differed between the ME and NME, for which the differences were mainly driven by pH and metal contaminants. The ME harbored a unique microbial community in the rhizosphere soils different from the bulk soil and NME counterparts. The dominant phyla in the ME rhizosphere were Proteobacteria, Chloroflexi, Actinobacteria, Nitrospirae, and Ascomycota. Several genera from Proteobacteria, Acidobacteria, and Ascomycota were more abundant in the ME rhizosphere than in the NME rhizosphere. Network analysis revealed that keystone taxa were different in the two sites. Some keystone taxa from Gemmatimonadaceae, and Burkholderiaceae and Ascomycota played a critical role in microbial interactions within the mine tailing network. The unique microbial community with high tolerance in the rhizosphere soils of ME may show great benefit for plant growth and metal tolerance of the ME and thereby contributing to the process of revegetation and phytostabilization of mine tailings.

Soil bacterial community response to cover crop introduction in a wheat-based dryland cropping system

The incorporation of cover crops into cropping systems is important for enhancing soil health in agricultural systems. Soil microbes contribute to soil health by supplying key nutrients and providing protection against plant pests, diseases, and abiotic stress. While research has demonstrated the connection between cover crops and the soil microbiology, less is known regarding the impact of cover crops on the soil microbial community in semi-arid regions of the Northern Great Plains. Our objectives were to evaluate changes in the soil bacterial community composition and community networks in wheat grown after multi-species cover crops. Cover crops were compared to continuous cropping and crop/fallow systems and the effects of cover crop termination methods were also evaluated. Cover crops consisted of a cool season multispecies mix, mid-season multispecies mix, and a warm season multispecies mix, which were grown in rotation with winter wheat. A continuous cropping (wheat/barley) and wheat/fallow system were also included along with cover crop termination by grazing, herbicide application, and haying. Cover crop treatments and termination methods had no significant impact on microbial community alpha diversity. Cover crop termination methods also had no significant impact on microbial community beta diversity. Families belonging to the phyla Actinobacteria, Bacterioidota, and Proteobacteria were more abundant in the cool season cover crop treatment compared to the warm season cover crop treatment. Co-occurrence network analysis indicated that incorporation of cool season cover crops or mid-season mixes in a wheat-based cropping system led to greater complexity and connectivity within these microbial networks compared to the other treatments which suggests these communities may be more resilient to environmental disturbances.

Responsive change of crop-specific soil bacterial community to cadmium in farmlands surrounding mine area of Southeast China

In arable soils co-influenced by mining and farming, soil bacteria significantly affect metal (Cadmium, Cd) bioavailability and accumulation. To reveal the soil microecology response under this co-influence, three intersection areas (cornfield, vegetable field, and paddy field) were investigated. With a similar nutrient condition, the soils showed varied Cd levels (0.31-7.70 mg/kg), which was negatively related to the distance from mining water flow. Different soils showed varied microbial community structures, which were dominated by Chloroflexi (19.64-24.82%), Actinobacteria (15.49-31.96%), Acidobacteriota (9.46-20.31%), and Proteobacteria (11.88-14.57%) phyla. A strong correlation was observed between functional microbial taxon (e. g. Acidobacteriota), soil physicochemical properties, and Cd contents. The relative abundance of tolerant bacteria including Vicinamibacteraceae, Knoellia, Ardenticatenales, Lysobacter, etc. elevated with the increase of Cd, which contributed to the enrichment of heavy metal resistance genes (HRGs) and integration genes (intlI), thus enhancing the resistance to heavy metal pollution. Cd content rather than crop species was identified as the dominant factor that influenced the bacterial community. Nevertheless, the peculiar agrotype of the paddy field contributed to its higher HRGs and intlI abundance. These results provided fundamental information about the crop-specific physiochemical-bacterial interaction, which was helpful to evaluate agricultural environmental risk around the intersection of farmland and pollution sources.

Diversity, function and assembly of the Trifolium repens L. root-associated microbiome under lead stress

Root-associated microbial layers provide unique niches that drive specific microbe assemblies. While the rhizosphere microbiome has long received much attention, endophytic microbes remain largely elusive. Characterizing metal-tolerant plants' strategies for assembling different root-associated microbial layers is important for optimizing phytoremediation. Here, a pre-stratified rhizo-box assay was conducted with Trifolium repens L. under greenhouse conditions with artificial Pb-contaminated soil. Cultivation compensated for the pollution-driven loss of soil microbial biomass carbon, enzyme activities and abundance. The acid-soluble Pb proportion increased in the rhizosphere (from 6.5-13.7% to 7.1-18.0%) compared with bulk soil. Under stress, root-layer variants were a considerable source of variation in the microbiome, with the endosphere representing a unique and independent niche. A core set of root microbes were selected by T. repens, with Proteobacteria and Actinobacteria composed of diverse plant-growth-promoting bacteria (PGPBs) and metal-tolerant members. Cluster analysis revealed endosphere-enriched genera, with Rhizobium, Nocardioides, Novosphingobium, Phyllobacterium, and Sphingomonas being the most dominant. Finally, inferred microbial metabolic pathways suggested that these potential metal-tolerant PGPB species provide critical services to hosts, enabling them to tolerate and even flourish in contaminated soil. Our results provide novel insights for understanding how root-associated microbes help metal-tolerant plants cope with abiotic stress.

Assessment about bioindicator capacity of acrocarpous moss Campylopus schmidii exposed to abandoned pyritic tailings

Terrestrial mosses are promising species to study concerning metal deposition, absorption, and soil fertility as moss biocrusts. However, acrocarpous moss, as a kind of terrestrial mosses, has not yet been well understood, both in environmental monitoring and ecological application, especially exposed to an abandoned pyrite mining. Herein, we investigated the concentrations of different heavy metals in soil underlying acrocarpous moss Campylopus schmidii at three distances from an abandoned pyrite mine tailings (0.5, 1, 2 km) by sampling analysis, as well as the accumulation properties of heavy metals in different parts of mosses and soil nutrients under intact mosses and moss-free layers. The results indicated that the soil we researched was heavily polluted by Cr, Cu, and Cd, which was 4.46, 4.18, and 1.77 times higher than the standard of risk screening values for soil environment quality in China. And there was a marked difference in the concentrations and distribution of heavy metals in mosses, with higher concentrations of Cr, Cu, Ni and Pb mainly in the ageing parts. In addition, mosses can effectively promote soil fertility. Compared with the bare soil without the moss layer, the total organic matter and total potassium concentrations of the soil covered by the intact moss layer were significantly increased, by 113.91% and 186.08% respectively. Correlation analysis indicated that similar pollution sources for Zn, Cd, Cu, and Pb, and the concentrations of these heavy metals in soil connected with the distance from the source of pollution. Overall, we expected that these findings could assess the greater potential of single native dominant moss species C.schmidii to act as biomonitors in specific pyrite mine tailings characterized by barren soil with strong acids (pH < 4.0) and polymetallic pollution. Meanwhile, our results revealed may serve as a possibility reference for similar areas and is recommended for developing a vegetative cover utilizing local acrocarpous mosses to achieve greening of degraded tailings in the future, as well as environmental management and protection.

Selective and simultaneous high resolution 2-D imaging of AsIII, CrIII and SbIII and dissolved oxygen by developing a new DGT technique comprising a hybrid sensor

A new diffusive gradients in thin films technique (HR-MPTS DGT) with mercapto-functionalized attapulgite in a binding gel was developed for simultaneous two-dimensional (2-D) chemical imaging of As^III, Cr^III and Sb^III selectively at the submillimeter scale, combined with laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) analysis. The HR-MPTS DGT exhibited selective accumulation of As^III, Sb^III and Cr^III (> 97%), yet negligible accumulation of As^V, Sb^V and Cr^VI (< 2%). Accumulation of As^III, Cr^III and Sb^III on the binding gel had a linear relationship (R² > 0.99) with the corresponding standardized laser ablation signals, proving the feasibility of LA-ICP-MS analysis. Analysis for As^III, Cr^III and Sb^III was provided with favorable analytical precision (relative standard deviation <10%). With the purpose of evaluating the dynamics of As^III, Cr^III, Sb^III and O₂ in the rooting zone, a hybrid sensor, which comprises the HR-MPTS gel overlying an O₂ planar optode, was deployed in rhizosphere sediments. Results showed that the consumption of both As^III and Sb^III due to the oxidation extended ~4.48 mm into the sediments, which was consistent with the extension length of the oxidized sediment layers around the roots created by O₂ leakage.

Characterization of the rare microbiome of rice paddy soil from arsenic contaminated hotspot of West Bengal and their interrelation with arsenic and other geochemical parameters

Rare microbial taxa [bacterial and archaeal operational taxonomic units (OTUs) with mean relative abundance ≤ 0.001%] were critical for ecosystem function, yet, their identity and function remained incompletely understood, particularly in arsenic (As) contaminated rice soils. In the present study we have characterized the rare populations of the As-contaminated rice soil microbiomes from West Bengal (India) in terms of their identity, interaction and potential function. Major proportion of the OTUs (73% of total 38,289 OTUs) was represented by rare microbial taxa (henceforth mentioned as rare taxa), which covered 4.5-15.7% of the different communities. Taxonomic assignment of the rare taxa showed their affiliation to members of Gamma-, Alpha-, Delta- Proteobacteria, Actinobacteria, and Acidobacteria. SO₄^2-, NO₃^-, NH₄⁺and pH significantly impacted the distribution of rare taxa. Rare taxa positively correlated with As were found to be more frequent in relatively high As soil while the rare taxa negatively correlated with As were found to be more frequent in relatively low As soil. Co-occurrence-network analysis indicated that rare taxa whose abundance were correlated strongly (R > 0.8) with As also had strong association (R > 0.8) with PO₄^2-, NO₃^-, and NH₄⁺. Correlation analysis indicated that the rare taxa were likely to involved in two major guilds one, involved in N-metabolism and the second involved in As/Fe as well as other metabolisms. Role of the rare taxa in denitrification and dissimilatory NO₃^- reduction (DNRA), As biotransformation, S-, H-, C- and Fe-, metabolism was highlighted from 16S rRNA gene-based predictive analysis. Phylogenetic analysis of rare taxa indicated signatures of inhabitant rice soil microorganisms having significant roles in nitrogen (N) cycle and As-Fe metabolism. This study provided critical insights into the taxonomic identity, metabolic potentials and importance of the rare taxa in As biotransformation and biogeochemical cycling of essential nutrients in As-impacted rice soils.

Harnessing plant microbiome for mitigating arsenic toxicity in sustainable agriculture

Heavy metal toxicity has become an impediment to agricultural productivity, which presents major human health concerns in terms of food safety. Among them, arsenic (As) a non-essential heavy metal has gained worldwide attention because of its noxious effects on agriculture and public health. The increasing rate of global warming and anthropogenic activities have promptly exacerbated As levels in the agricultural soil, thereby causing adverse effects to crop genetic and phenotypic traits and rendering them vulnerable to other stresses. Conventional breeding and transgenic approaches have been widely adapted for producing heavy metal resilient crops; however, they are time-consuming and labor-intensive. Hence, finding new mitigation strategies for As toxicity would be a game-changer for sustainable agriculture. One such promising approach is harnessing plant microbiome in the era of 'omics' which is gaining prominence in recent years. The use of plant microbiome and their cocktails to combat As metal toxicity has gained widespread attention, because of their ability to metabolize toxic elements and offer an array of perquisites to host plants such as increased nutrient availability, stress resilience, soil fertility, and yield. A comprehensive understanding of below-ground plant-microbiome interactions and their underlying molecular mechanisms in exhibiting resilience towards As toxicity will help in identifying elite microbial communities for As mitigation. In this review, we have discussed the effect of As, their accumulation, transportation, signaling, and detoxification in plants. We have also discussed the role of the plant microbiome in mitigating As toxicity which has become an intriguing research frontier in phytoremediation. This review also provides insights on the advancements in constructing the beneficial synthetic microbial communities (SynComs) using microbiome engineering that will facilitate the development of the most advanced As remedial tool kit in sustainable agriculture.

Prospects for the Use of Echinochloa frumentacea for Phytoremediation of Soils with Multielement Anomalies

In a model experiment, some adaptive characteristics, the bioaccumulation of toxic elements from technogenically-contaminated soils with polyelement anomalies, and rhizosphere microflora of Japanese millet, Echinochloa frumentacea, were studied using biochemical, microbiological, physicochemical (AAS, ICP-MS, INAA), and metagenomic (16S rRNA) methods of analysis. Good adaptive characteristics (the content of photosynthetic pigments, low molecular weight antioxidants) of E. frumentacea grown on the soils of metallurgical enterprises were revealed. The toxic effect of soils with strong polyelement anomalies (multiple excesses of MPC for Cr, Ni, Zn, As, petroleum products) on biometric parameters and adaptive characteristics of Japanese millet were shown. The rhizosphere populations of E. frumentacea grown in the background soil were characterized by the lowest taxonomic diversity compared to the rhizobiomes of plants grown in contaminated urban soils. The minimal number of all groups of microorganisms studied was noted in the soils, which contain the highest concentrations of both inorganic (heavy metals) and organic (oil products) pollutants. The taxonomic structure of the rhizospheric microbiomes of E. frumentacea was characterized. It has been established that E. frumentacea accumulated Mn, Co, As, and Cd from soils with polyelement pollution within the average values. V was accumulated mainly in the root system (transfer factor from roots to shoots 0.01–0.05) and its absorption mechanism is rhizofiltration. The removal of Zn by shoots of E. frumentacea increased on soils where the content of the element exceeded the MPC and was 100–454 mg/kg of dry weight (168–508 g/ha). Analysis of the obtained data makes it possible to recommend E. frumentacea for phytoremediation of soil from Cu and Zn at a low level of soil polyelement contamination using grass mixtures.

Plant-Soil Feedbacks for the Restoration of Degraded Mine Lands: A Review

Much effort has been made to remediate the degraded mine lands that bring severe impacts to the natural environments. However, it remains unclear what drives the recovery of biodiversity and ecosystem functions, making the restoration of these fragile ecosystems a big challenge. The interactions among plant species, soil communities, and abiotic conditions, i.e., plant-soil feedbacks (PSFs), significantly influence vegetation development, plant community structure, and ultimately regulate the recovery of ecosystem multi-functionality. Here, we present a conceptual framework concerning PSFs patterns and potential mechanisms in degraded mine lands. Different from healthy ecosystems, mine lands are generally featured with harsh physical and chemical properties, which may have different PSFs and should be considered during the restoration. Usually, pioneer plants colonized in the mine lands can adapt to the stressful environment by forming tolerant functional traits and gathering specific soil microbial communities. Understanding the mechanisms of PSFs would enhance our ability to predict and alter both the composition of above- and below-ground communities, and improve the recovery of ecosystem functions in degraded mine lands. Finally, we put forward some challenges of the current PSFs study and discuss avenues for further research in the ecological restoration of degraded mine lands.

Deciphering Cadmium (Cd) Tolerance in Newly Isolated Bacterial Strain, Ochrobactrum intermedium BB12, and Its Role in Alleviation of Cd Stress in Spinach Plant (Spinacia oleracea L.)

A cadmium (Cd)-tolerant bacterium Ochrobactrum intermedium BB12 was isolated from sewage waste collected from the municipal sewage dumping site of Bhopal, India. The bacterium showed multiple heavy metal tolerance ability and had the highest minimum inhibitory concentration of 150 mg L-1 of Cd. Growth kinetics, biosorption, scanning electron microscopy (SEM), transmission electron microscopy (TEM), and Fourier transform infrared (FTIR) spectroscopy studies on BB12 in the presence of Cd suggested biosorption as primary mode of interaction. SEM and TEM studies revealed surface deposition of Cd. FTIR spectra indicated nitrogen atom in exopolysaccharides secreted by BB12 to be the main site for Cd attachment. The potential of BB12 to alleviate the impact of Cd toxicity in spinach plants (Spinacia oleracea L.) var. F1-MULAYAM grown in the soil containing Cd at 25, 50, and 75 mg kg-1 was evaluated. Without bacterial inoculation, plants showed delayed germination, decrease in the chlorophyll content, and stunted growth at 50 and 75 mg kg-1 Cd content. Bacterial inoculation, however, resulted in the early germination, increased chlorophyll, and increase in shoot (28.33%) and root fresh weight (72.60%) at 50 mg kg-1 of Cd concentration after 75 days of sowing. Due to bacterial inoculation, elevated proline accumulation and lowered down superoxide dismutase (SOD) enzyme activity was observed in the Cd-stressed plants. The isolate BB12 was capable of alleviating Cd from the soil by biosorption as evident from significant reduction in the uptake/translocation and bioaccumulation of Cd in bacteria itself and in the plant parts of treated spinach. Potential PGP prospects and heavy metal bioremediation capability of BB12 can make the environmental application of the organism a promising approach to reduce Cd toxicity in the crops grown in metal-contaminated soils.

"Breeding on Mountains" Resulted in the Reorganization of Endophytic Fungi in Asexually Propagated Plants (Ligusticum chuanxiong Hort.)

"Breeding on mountains, cultivation in dam areas" is a unique propagation method for the vegetatively propagated plant Ligusticum chuanxiong, including two transplants between the mountain and the dam area. It is well known that the environment can influence the endophytic community structure of plants. However, the change of host endophytic flora caused by transplanting in different places and its influence on asexual reproduction are still poorly understood. We carried out three cycles of cultivation experiments on L. chuanxiong and collected stem nodes (LZ), immature rhizomes (PX), medicinal rhizomes (CX), and rhizosphere. High-throughput sequencing was performed to analyze the endophytic fungi in all samples. We observed that the diversity and richness of endophytic fungi in L. chuanxiong increased as a result of transplanting cultivation from dam areas to mountains. Local transplantation caused minor changes in the endophytic fungus structure of L. chuanxiong, while remote transplantation caused significant changes. Compared with LZ after breeding in the dam area, the LZ after breeding on mountains has more abundant Gibberella, Phoma, Pericona, Paraphoma, and Neocosmospora. The regular pattern of the relative abundance of endophytic fungi is consistent with that of the fungus in the soil, while there are also some cases that the relative abundance of endophytic fungi is the opposite of that of soil fungi. In addition, there is a significant correlation among certain kinds of endophytic fungi whether in the soil or the plants. We have isolated more gibberellin-producing and auxin-producing fungi in the LZ cultivated in the mountains than that in the LZ cultivated in the dam area. The results of pot experiments showed that the three fungi isolated from LZ cultivated in mountainous areas can promote the development of shoots, stem nodes, and internodes of LZ, and increase the activity of plant peroxidase, catalase, phenylalanine ammonia lyase, and other enzymes. We can conclude that transplantation leads to the recombination of the host endophytic fungus, the more significant the difference in the environment is, the greater the reorganization caused by transplanting. Reorganization is determined by the soil environment, hosts, and the interaction of microorganisms. Remote transplantation is a crucial opportunity to reshuffle the micro-ecological structure of the asexual reproduction of plants, and regulate the growth, development, and resistance of plants, and prevent germplasm degradation caused by asexual reproduction.

Structure and variation of root-associated bacterial communities of Cyperus rotundus L. in the contaminated soils around Pb/Zn mine sites

Soil contamination due to mining activities is a great concern in China. Although the effects of mining pollution resulting in changes of soil characteristics and the microbiome have been documented, studies on the responses of plant root-associated microbial assemblages remain scarce. In this work, we collected bulk soil, rhizosphere soil, and root endosphere samples of Cyperus rotundus L (Cyp) plants from two Pb/Zn mines, of which, one was abandoned (SL) and the other was active (GD), to investigate the bacterial community responses across different site contamination levels and Cyp plant compartments. For comparison, one unpolluted site (SD) was included. Results revealed that soils from the SL and GD sites were seriously contaminated by metal(loid)s, including Pb, Zn, As, and Sb. Bacterial richness and diversity depended on the sampling site and plant compartment. All sample types from the SL site had the lowest bacterial diversities and their bacterial communities also exhibited distinct patterns compared to GD and SD samples. As for the specific sampling site, bacterial communities from the root endosphere exhibited different patterns from those in bulk and rhizosphere soil. Compared to the GD and SD sites, the root endosphere and the rhizosphere soil from the SL site shared core microbes, including Halomonas, Pelagibacterium, and Chelativorans, suggesting that they play key roles in Cyp plant survival in such harsh environments.

Identification of Antimonate Reducing Bacteria and Their Potential Metabolic Traits by the Combination of Stable Isotope Probing and Metagenomic-Pangenomic Analysis

Microorganisms play an important role in altering antimony (Sb) speciation, mobility, and bioavailability, but the understanding of the microorganisms responsible for Sb(V) reduction has been limited. In this study, DNA-stable isotope probing (DNA-SIP) and metagenomics analysis were combined to identify potential Sb(V)-reducing bacteria (SbRB) and predict their metabolic pathways for Sb(V) reduction. Soil slurry cultures inoculated with Sb-contaminated paddy soils from two Sb-contaminated sites demonstrated the capability to reduce Sb(V). DNA-SIP identified bacteria belonging to the genera Pseudomonas and Geobacter as putative SbRB in these two Sb-contaminated sites. In addition, bacteria such as Lysinibacillus and Dechloromonas may potentially participate in Sb(V) reduction. Nearly complete draft genomes of putative SbRB (i.e., Pseudomonas and Geobacter) were obtained, and the genes potentially responsible for arsenic (As) and Sb reduction (i.e., respiratory arsenate reductase (arrA) and antimonate reductase (anrA)) were examined. Notably, bins affiliated with Geobacter contained arrA and anrA genes, supporting our hypothesis that they are putative SbRB. Further, pangenomic analysis indicated that various Geobacter-associated genomes obtained from diverse habitats also contained arrA and anrA genes. In contrast, Pseudomonas may use a predicted DMSO reductase closely related to sbrA (Sb(V) reductase gene) clade II to reduce Sb(V), which may need further experiments to verify. This current work represents a demonstration of using DNA-SIP and metagenomic-binning to identify SbRB and their key genes involved in Sb(V) reduction and provides valuable data sets to link bacterial identities with Sb(V) reduction.

Rhizosphere Microbial Communities and Heavy Metals

The rhizosphere is a microhabitat where there is an intense chemical dialogue between plants and microorganisms. The two coexist and develop synergistic actions, which can promote plants’ functions and productivity, but also their capacity to respond to stress conditions, including heavy metal (HM) contamination. If HMs are present in soils used for agriculture, there is a risk of metal uptake by edible plants with subsequent bioaccumulation in humans and animals and detrimental consequences for their health. Plant productivity can also be negatively affected. Many bacteria have defensive mechanisms for resisting heavy metals and, through various complex processes, can improve plant response to HM stress. Bacteria-plant synergic interactions in the rhizosphere, as a homeostatic ecosystem response to HM disturbance, are common in soil. However, this is hard to achieve in agroecosystems managed with traditional practices, because concentrating on maximizing crop yield does not make it possible to establish rhizosphere interactions. Improving knowledge of the complex interactions mediated by plant exudates and secondary metabolites can lead to nature-based solutions for plant health in HM contaminated soils. This paper reports the main ecotoxicological effects of HMs and the various compounds (including several secondary metabolites) produced by plant-microorganism holobionts for removing, immobilizing and containing toxic elements.

Bioaccumulation and potential ecotoxicological effects of trace metals along a management intensity gradient in volcanic pasturelands

The particularities of volcanic soils raise the need to better understand the link between soil agricultural management intensity and trace metal bioaccumulation. The Azores are a region characterized by volcanic soils, which were changed in different degrees according to the intensity of the agricultural practices. The main objective of this study was to assess the potential ecotoxicological effects of the trace metals present in volcanic pastureland soils along a gradient of management intensity (i.e., semi-natural, permanent and reseeded), using earthworms (Eisenia fetida) as biological indicators. For this purpose earthworms were exposed during 7, 14, 28 and 56 days to soils from the three types of pastures. At each exposure time, we quantified trace element bioaccumulation (As, Cd, Co, Cr, Cu, Hg, Li, Mn, Mo, Ni, Pb, Rb, U, V and Zn) and the activities of superoxide dismutase and acetylcholinesterase in earthworm tissues. Overall, the results showed that the type of pastureland management significantly increased the soil contents in trace metals: V, Co, Ni and Zn in semi-natural pasturelands; As, Cd and Hg in reseeded pasturelands; and, Rb and U in both permanent and reseeded pasturelands. The soil physicochemical properties observed in the reseeded pastureland systems (higher electric conductivity values associated with a moderately acid pH value) modulated the metal bioavailability, from soil to biota, leading to a greater Hg bioaccumulation in earthworm tissues. The long-term exposure (56 days) of earthworms to reseeded pastureland soil was associated with adverse biological effects (intensification of AChE activity and decrease of SOD activity), encompassing key processes such as neurotransmission and antioxidant defence mechanisms in resident soil biota (earthworms). This study point towards the increased importance of semi-natural and permanent pastureland management, over the intensive management (reseeded pasturelands), in favour of more sustainable ecosystems.

Rhizodegradation of Pyrene by a Non-pathogenic Klebsiella pneumoniae Isolate Applied With Tagetes erecta L. and Changes in the Rhizobacterial Community

The non-clinical Klebsiella pneumoniae variants, isolated from different environments, are now well acknowledged for their role in plant-growth promotion and biodegradation of pollutants. In the present study, a non-clinical environmental isolate K. pneumoniae AWD5 is being described for rhizoremediation of pyrene, applied through the rhizosphere of an ornamental plant, Tagetes erecta L (marigold). The non-pathogenic nature of AWD5 was established using an in vivo mouse model experiment, where AWD5 was unable to cause lung infection in tested mice. Degradation of pyrene, in the presence of succinate as co-substrate, was observed to be 87.5% by AWD5, after 21 days of incubation in minimal (Bushnell–Hass) medium in vitro conditions. Consequently, the bacterial inoculation through the rhizosphere of T. erecta L. plants resulted in 68.61% degradation of pyrene, which was significantly higher than control soil. Inoculation of AWD5 also improved plant growth and exhibited an increase in root length (14.64%), dry root weight (80.56%), shoot length (3.26%), and dry shoot weight (45.35%) after 60 days of incubation. T. erecta L., an ornamental plant, was also found to be suitable for bioremediation of pyrene. The effect of AWD5 application, and rhizoremediation process, on rhizosphere bacterial diversity and community structure has been studied using the metagenomic analysis of the 16S (V3–V4) region of rRNA. 37 bacterial phyla constituted the core microbiome, which was dominated by Proteobacteria followed by Actinobacteria, Actinobacteria, and Planctomycetes for all the treatments. AWD5 inoculation enhanced the relative abundance of Firmicutes and Acidobacteria as compared with other treatments. Genus Kaistobacter and Verrucomicrobia were found to be an abundant indigenous population in pyrene-spiked soils. Bacterial richness and diversity were analyzed using the Shannon–Wiener (H) index. A lower diversity index was observed in pyrene-spiked soils. Canonical correspondence analysis (CCA) showed a possible linkage with plant growth attributes and available nitrogen content that influences diversity and abundance of the bacterial community.

Responses of soil microbiome to steel corrosion

The process of microbiologically influenced corrosion (MIC) in soils has received widespread attention. Herein, long-term outdoor soil burial experiments were conducted to elucidate the community composition and functional interaction of soil microorganisms associated with metal corrosion. The results indicated that iron-oxidizing (e.g., Gallionella), nitrifying (e.g., Nitrospira), and denitrifying (e.g., Hydrogenophaga) microorganisms were significantly enriched in response to metal corrosion and were positively correlated with the metal mass loss. Corrosion process may promote the preferential growth of the abundant microbes. The functional annotation revealed that the metabolic processes of nitrogen cycling and electron transfer pathways were strengthened, and also that the corrosion of metals in soil was closely associated with the biogeochemical cycling of iron and nitrogen elements and extracellular electron transfer. Niche disturbance of microbial communities induced by the buried metals facilitated the synergetic effect of the major MIC participants. The co-occurrence network analysis suggested possible niche correlations among corrosion related bioindicators.

Microbiome-environment interactions in antimony-contaminated rice paddies and the correlation of core microbiome with arsenic and antimony contamination

Mining activities of antimony (Sb) and arsenic (As) typically result in severe environmental contamination. These contaminants accumulate in rice and thus threaten the health of local residents, who consume Sb- and As-enriched rice grains. Microorganisms play a critical role in the transformation and transportation of Sb and As in paddy soil. Thus, an understanding of the microbiology of contaminated sites would promote the production of safe agricultural products. In this study, six Sb- and As-contaminated rice fields near an active Sb-mining area were investigated. The Sb and As concentrations of all samples were elevated compared to the background level in China. Nitrate, total As, total Sb, and Fe(III) were the major determinants of the microbial community structure. Seven bacterial taxa (i.e. Bradyrhizobium, Bryobacter, Candidatus Solibacter, Geobacter, Gemmatimonas, Halingium, and Sphingomonas) were identified as the core microbiome. These taxa were strongly correlated with the As and Sb contaminant fractions and likely to metabolize As and Sb. Results imply that many soil microbes can survival in the Sb/As contaminated sites.

Disentangling the drivers of Microcystis decomposition: Metabolic profile and co-occurrence of bacterial community

In aquatic ecosystems, water microbial communities can trigger the outbreak or decline of cyanobacterial blooms. However, the microbiological drivers of Microcystis decomposition in reservoirs remain unclear. Here, we explored the bacterial community metabolic profile and co-occurrence dynamics during Microcystis decomposition. The results showed that the decomposition of Microcystis greatly altered the metabolic characteristics and composition of the water bacterial community. Significant variations in bacterial community composition were observed: the bacterial community was mainly dominated by Proteobacteria, Actinobacteria, Planctomycetes, and Bacteroidetes during Microcystis decomposition. Additionally, members of Exiguobacterium, Rhodobacter, and Stenotrophomonas significantly increased during the terminal stages. Dissolved organic matters (DOM) primarily composed of fulvic-like, humic acid-like, and tryptophan-like components, which varied distinctly during Microcystis decomposition. Additionally, the metabolic activity of the bacterial community showed a continuous decrease during Microcystis decomposition. Functional prediction showed a sharp increase in the cell communication and sensory systems of the bacterial communities from day 12 to day 22. Co-occurrence networks showed that bacteria responded significantly to variations in the dynamics of Microcystis decomposition through close interactions between each other. Redundancy analysis (RDA) indicated that Chlorophyll a, nitrate nitrogen (NO₃^--N), dissolved oxygen (DO), and dissolved organic carbon (DOC) were crucial drivers for shaping the bacterial community structure. Taken together, these findings highlight the dynamics of the water bacterial community during Microcystis decomposition from the perspective of metabolism and community composition, however, further studies are needed to understand the algal degradation process associated with bacteria.

Bioremediation of Hexavalent Chromium by Chromium Resistant Bacteria Reduces Phytotoxicity

Chromium (Cr) (VI) has long been known as an environmental hazard that can be reduced from aqueous solutions through bioremediation by living cells. In this study, we investigated the efficiency of reduction and biosorption of Cr(VI) by chromate resistant bacteria isolated from tannery effluent. From 28 screened Cr(VI) resistant isolates, selected bacterial strain SH-1 was identified as Klebsiella sp. via 16S rRNA sequencing. In Luria–Bertani broth, the relative reduction level of Cr(VI) was 95%, but in tannery effluent, it was 63.08% after 72 h of incubation. The cell-free extract of SH-1 showed a 72.2% reduction of Cr(VI), which indicated a higher activity of Cr(VI) reducing enzyme than the control. Live and dead biomass of SH-1 adsorbed 51.25 mg and 29.03 mg Cr(VI) per gram of dry weight, respectively. Two adsorption isotherm models—Langmuir and Freundlich—were used for the illustration of Cr(VI) biosorption using SH-1 live biomass. Scanning electron microscopy (SEM) analysis showed an increased cell size of the treated biomass when compared to the controlled biomass, which supports the adsorption of reduced Cr on the biomass cell surface. Fourier-transform infrared analysis indicated that Cr(VI) had an effect on bacterial biomass, including quantitative and structural modifications. Moreover, the chickpea seed germination study showed beneficial environmental effects that suggest possible application of the isolate for the bioremediation of toxic Cr(VI).

Uncovering microbial responses to sharp geochemical gradients in a terrace contaminated by acid mine drainage

Acid mine drainage (AMD) is harmful to the environment and human health. Microorganisms-mineral interactions are responsible for AMD generation but can also remediate AMD contamination. Understanding the microbial response to AMD irrigation will reveal microbial survival strategies and provide approaches for AMD remediation. A terrace with sharp geochemical gradients caused by AMD flooding were selected to study the microbial response to changes in environmental parameters related to AMD contamination. AMD intrusion reduced soil microbial community diversity and further changed phylogenetic clustering patterns along the terrace gradient. We observed several genera seldom reported in AMD-related environments (i.e., Corynebacterium, Ochrobactrum, Natronomonas), suggesting flexible survival strategies such as nitrogen fixation, despite the poor nutritional environment. A co-occurrence network of heavily-contaminated fields was densely connected. The phyla Proteobacteria, Acidobacteria, Chloroflexi, and Euryarchaeota were all highly interconnected members, which may affect the formation of AMD. Detailed microbial response to different soil characterizations were highlighted by random forest model. Results revealed the top three parameters influencing the microbial diversity and interactions were pH, Fe(III), and sulfate. Various acidophilic Fe- and S-metabolizing bacteria were enriched in the lower fields, which were heavily contaminated by AMD, and more neutrophiles prevailed in the less-contaminated upper fields. Many indicator species in the lower fields were identified, including Desulfosporosinus, Thermogymnomonas, Corynebacterium, Shewanella, Acidiphilium, Ochrobactrum, Leptospirillum, and Allobaculum, representing acid-tolerant bacteria community in relevant environment. The detection of one known sulfate-reducing bacteria (i.e., Desulfosporosinus) suggested that biotic sulfate reduction may occur in acidic samples, which offers multiple advantages to AMD contamination treatment. Collectively, results suggested that the geochemical gradients substantially altered the soil microbiota and enriched the relevant microorganisms adapted to the different conditions. These findings provide mechanistic insights into the effects of contamination on the soil microbiota and establish a basis for in situ AMD bioremediation strategies.

Recovery of the biological function of ethylenediaminetetraacetic acid-washed soils: Roles of environmental variations and microbes

To understand the recovery of the biological functions of washed soil, we studied changes in the microbial communities of soils washed with 10 or 60 mmol kg^-1 ethylenediaminetetraacetic acid (EDTA) for 90 d of incubation. The relative abundance of tolerant or degrading species decreased, while that of microorganisms with chemical autotrophic ability increased as the incubation time increased. The changes in the enzyme activity followed different trends. As an intracellular enzyme, dehydrogenase was initially most severely damaged by the washing process but could recover over time, while the activity of urease increased after washing with EDTA, which may be related to the use of N as a nutrient source by microorganisms. Phosphatase did not significantly change over time. The redundancy discriminant analyses indicated that there were distinct factors driving such changes in the soils washed with different EDTA dosages. For the soil washed with 10 mmol kg^-1 EDTA, bacteria with tolerance or degradation capacity of toxic pollutants, such as Nocardioidaceae, played a more important role in the recovery of soil functions; therefore, the EDTA stress indicator was the main driving factor. However, in the soil washed with 60 mmol kg^-1 EDTA, chemolithoautotrophic bacteria, such as Nitrososphaeraceae, exerted a greater influence on the recovery of biological functions due to the higher loss of nutrients and EDTA residue; therefore, the main driving factor was the nutrients supply.

Comparative Analysis of Rhizosphere Microbiomes of Southern Highbush Blueberry (Vaccinium corymbosum L.), Darrow's Blueberry (V. darrowii Camp), and Rabbiteye Blueberry (V. virgatum Aiton)

Plants are inhabited by millions of parasitic, commensal, and mutualistic microorganisms that coexist in complex ecological communities, and profoundly affect the plant’s productivity, health, and capacity to cope with environmental stress. Therefore, a better understanding of the rhizosphere microbiome may open a yet untapped avenue for the rational exploitation of beneficial plant–microbe interactions in modern agriculture. Blueberries encompass several wild and cultivated species of shrubs of the genus Vaccinium that are native to North America. They are grown commercially for the production of fruits, which are considered a health food due to the rich content of minerals, trace elements, and phenolic compounds with antioxidant, antitumor, and anti-inflammatory properties. Despite a long history of breeding and extensive commercial use, remarkably little is known about the composition and function of the blueberry root microbiome. To address this gap, we employed molecular approaches to characterize and compare microbial communities inhabiting the roots of rabbiteye blueberry (Vaccinium virgatum), Darrow’s blueberry (Vaccinium darrowii), and southern highbush blueberry (SHB; an interspecific hybrid of Vaccinium corymbosum and V. darrowii). Our results revealed that these plant species share a common core rhizobiome, but at the same time differ significantly in the diversity, relative abundance, richness, and evenness of multiple groups of prokaryotic and eukaryotic microorganisms. Although the host signature effects were especially pronounced at the plant species level, we also observed genotype-level variations in the distribution of specific microbial taxa, which suggests that the assembly of the blueberry microbiome is shaped by the plant genotype and modifications associated with the domestication and breeding of members of the Vaccinium genus. We also demonstrated that the studied Vaccinium species differ in the abundance of beneficial rhizobacteria and ericoid mycorrhizal fungi, which play a vital role in their adaptation to soils with low pH and slow turnover of organic matter.

Community Compositions of Phytoplankton and Eukaryotes during the Mixing Periods of a Drinking Water Reservoir: Dynamics and Interactions

In deep drinking water reservoir ecosystems, the dynamics and interactions of community compositions of phytoplankton and eukaryotes during the mixing periods are still unclear. Here, morphological characteristics combined with high-throughput DNA sequencing (HTS) were used to investigate the variations of phytoplankton and the eukaryotic community in a large canyon-shaped, stratified reservoir located at the Heihe River in Shaanxi Province for three months. The results showed that Bacillariophyta and Chlorophyta were the dominant taxa of the phytoplankton community, accounting for more than 97% of total phytoplankton abundance, which mainly consisted of Melosira sp., Cyclotella sp., and Chlorella sp., respectively. Illumina Miseq sequencing suggested that the biodiversity of eukaryotes increased over time and thatspecies distribution was more even. Arthropoda (6.63% to 79.19%), Ochrophyta (5.60% to 35.16%), Ciliophora (1.81% to 10.93%) and Cryptomonadales (0.25% to 11.48%) were the keystone taxa in common, contributing over 50% of the total eukaryotic community. Cryptomycota as a unique fungus was observed to possess significant synchronization with algal density, reaching a maximum of 10.70% in December (when the algal density distinctly decreased) and suggesting that it might affect the growth of algae through parasitism. Co-occurrence network patterns revealed the complicated and diverse interactions between eukaryotes and phytoplankton, suggesting that eukaryotes respond to variations in dynamic structure of the phytoplankton community, although there might be antagonistic or mutualistic interactions between them. Redundancy analysis (RDA) results showed that environmental variables collectively explained a 96.7% variance of phytoplankton and 96.3% variance of eukaryotic microorganisms, indicating that the temporal variations of phytoplankton and eukaryotic microorganisms were significantly affected by environmental conditions. This study shows that potential interactions exist between phytoplankton and eukaryotic microorganism communities, andcould improve our understanding of the ecological roles of phytoplankton and eukaryotic microorganisms in changing aquatic ecosystems. However, long-term investigations are necessary in order to obtain comprehensive understandings of their complicated associations.

Variation in rhizosphere microbiota correlates with edaphic factor in an abandoned antimony tailing dump

The distribution pattern of root-associated bacteria in native plant growth in tailing dumps with extreme conditions remains poorly understood and largely unexplored. Herein we chose a native plant, Bidens bipinnata, growing on both an Sb tailing dump (WKA) and adjacent normal soils (WKC) to in-depth understand the distribution pattern of root-associated bacteria and their responses on environmental factors. We found that the rhizosphere microbial diversity indices in the tailing dump were significantly different from that in the adjacent soil, and that such variation was significantly related with soil nutrients (TC, TOC, TN) and metal(loid) concentrations (Sb and As). Some dominant genera were significant enriched in WKA, suggesting their adaption to harsh environments. Notably, these genera are proposed to be involved in nutrient and metal(liod) cycling, such as nitrogen fixing (Devosia, Cellvibrio, Lysobacter, and Cohnella), P solubilizing (Flavobacterium), and Sb and As oxidation (Paenibacillus, Bacillus, Pseudomonas, and Thiobacillus). Our results suggest that certain root-associated bacteria in tailing dump were governed by soil edaphic factors and play important ecological roles in nutrient amendments and metal cycling for the successful colonization of Bidens bipinnata in this tailing dump.

Impacts of Arsenic and Antimony Co-Contamination on Sedimentary Microbial Communities in Rivers with Different Pollution Gradients

Arsenic (As) and antimony (Sb) are both toxic metalloids that are of primary concern for human health. Mining activity has introduced elevated levels of arsenic and antimony into the rivers and has increased the risks of drinking water contamination in China. Due to their mobility, the majority of the metalloids originating from mining activities are deposited in the river sediments. Thus, depending on various geochemical conditions, sediment could either be a sink or source for As and Sb in the water column. Microbes are key mediators for biogeochemical transformation and can both mobilize or precipitate As and Sb. To further understand the microbial community responses to As and Sb contamination, sediment samples with different contamination levels were collected from three rivers. The result of the study suggested that the major portions of As and Sb were in strong association with the sediment matrix and considered nonbioavailable. These fractions, however, were also suggested to have profound influences on the microbial community composition. As and Sb contamination caused strong reductions in microbial diversity in the heavily contaminated river sediments. Microorganisms were more sensitive to As comparing to Sb, as revealed by the co-occurrence network and random forest predictions. Operational taxonomic units (OTUs) that were potentially involved in As and Sb metabolism, such as Anaerolinea, Sphingomonas, and Opitutus, were enriched in the heavily contaminated samples. In contrast, many keystone taxa, including members of the Hyphomicrobiaceae and Bradyrhizobiaceae families, were inhibited by metalloid contamination, which could further impair crucial environmental services provided by these members.

Comparative Analyses of the Microbial Communities Inhabiting Coal Mining Waste Dump and an Adjacent Acid Mine Drainage Creek

Microbial communities inhabiting the acid mine drainage (AMD) have been extensively studied, but the microbial communities in the coal mining waste dump that may generate the AMD are still relatively under-explored. In this study, we characterized the microbial communities within these under-explored extreme habitats and compared with those in the downstream AMD creek. In addition, the interplay between the microbiota and the environmental parameters was statistically investigated. A Random Forest ensemble model indicated that pH was the most important environmental parameter influencing microbial community and diversity. Parameters associated with nitrogen cycling were also critical factors, with positive effects on microbial diversity, while S-related parameters had negative effects. The microbial community analysis also indicated that the microbial assemblage was driven by pH. Various taxa were enriched in different pH ranges: Sulfobacillus was the indicator genus in samples with pH < 3 while Acidobacteriaceae-affiliated bacteria prevailed in samples with 3 < pH < 3.5. The detection of some lineages that are seldom reported in mining areas suggested the coal mining dumps may be a reservoir of phylogenetic novelty. For example, potential nitrogen fixers, autotrophs, and heterotrophs may form diverse communities that actively self-perpetuate pyrite dissolution and acidic waste generation, suggesting unique ecological strategies adopted by these innate microorganisms. In addition, co-occurrence network analyses suggest that members of Acidimicrobiales play important roles in interactions with other taxa, especially Fe- and S-oxidizing bacteria such as Sulfobacillus spp.

Characterization of iron-metabolizing communities in soils contaminated by acid mine drainage from an abandoned coal mine in Southwest China

Acid mine discharge (AMD) has been demonstrated to have significant impacts on microbial community composition in the surrounding soil environment. However, their effect on adjacent soil has not been extensively studied. In this study, microbial community composition of 20 AMD-contaminated soil samples collected from an abandoned coal mine along an AMD creek was characterized using high-throughput sequencing. All samples were characterized as extremely low in pH (< 3) and relatively enriched in HCl-extractable Fe species. The dominant phylotypes were belonging to genera Ochrobactrum, Acidiphilium, Staphylococcus, Brevibacterium, and Corynebacterium. Canonical correspondence analysis results revealed that the HCl-extractable Fe(III) had a strong impact on the soil microbial assemblage. Co-occurrence network analysis revealed that Aquicella, Acidobacteriaceae, Ochrobactrum, Enhydrobacter, Sphingomonas, and Legionellales were actively correlated with other taxa. As expected, most of the abundant taxa have been reported as acidophilic Fe-metabolizing bacteria. Hence, a co-occurring sub-network and a phylogenetic tree related to microbial taxa responsible for Fe metabolism were constructed and described. The biotic interaction showed that Dechloromonas exhibited densely connections with Fe(III)-reducing bacteria of Comamonas, Burkholderia, Shewanella, Stenotrophomonas, Acidithiobacillus, and Pseudomonas. These results demonstrated that Fe-metabolizing bacteria could have an important role in the Fe biogeochemical cycling.