Illumina MiSeq sequencing investigation on the contrasting soil bacterial community structures in different iron mining areas

Actinomycetota bioprospecting from ore-forming environments

Natural products from Actinomycetota have served as inspiration for many clinically relevant therapeutics. Despite early triumphs in natural product discovery, the rate of unearthing new compounds has decreased, necessitating inventive approaches. One promising strategy is to explore environments where survival is challenging. These harsh environments are hypothesized to lead to bacteria developing chemical adaptations (e.g. natural products) to enable their survival. This investigation focuses on ore-forming environments, particularly fluoride mines, which typically have extreme pH, salinity and nutrient scarcity. Herein, we have utilized metagenomics, metabolomics and evolutionary genome mining to dissect the biodiversity and metabolism in these harsh environments. This work has unveiled the promising biosynthetic potential of these bacteria and has demonstrated their ability to produce bioactive secondary metabolites. This research constitutes a pioneering endeavour in bioprospection within fluoride mining regions, providing insights into uncharted microbial ecosystems and their previously unexplored natural products.

Shifts in bacterial diversity, interactions and microbial elemental cycling genes under cadmium contamination in paddy soil: Implications for altered ecological function

Cadmium (Cd) contamination has become an emergent environmental issue in agroecosystems worldwide. The impacts of Cd on microbial community and their ecological functional remain unrevealed. This study investigated the response of bacterial community and microbial ecological functions to Cd contamination in paddy soil of East China. Bacterial diversity and community structure significantly changed under Cd contamination. Proteobacteria and Acidobacteria were identified as biomarkers to indicate Cd contamination. The overall elemental cycling genes abundance was negatively correlated to soil Cd content. Acetyl-CoA synthesis, organic N mineralization, N fixation and nitrous reduction genes were especially sensitive to elevated Cd stress, resulting in loss of microbial derived soil C and N pool and increase in N2O emission potential. Bacteria interactions were sparser yet more competitive under Cd contamination. Cd resistant genera Massilia, Burkholderia, Streptomyces and Methylobacterium were essential to bacterial interactions via building connections with non-resistant species. Microbial Cd immobilization potential by urea hydrolysis was enhanced under Cd contamination, with Massilia being the keystone functional taxa involved in this process. Our study elucidated the ecological risks of altered microbial functions under Cd contamination in paddy soil, as well as the significance of Cd resistant bacteria to microbial community and ecological functionality.

Shift in the rhizosphere soil fungal community associated with root rot infection of Plukenetia volubilis Linneo caused by Fusarium and Rhizopus species

BACKGROUND

Plukenetia volubilis Linneo is an oleaginous plant belonging to the family Euphorbiaceae. Due to its seeds containing a high content of edible oil and rich in vitamins, P. volubilis is cultivated as an economical plant worldwide. However, the cultivation and growth of P. volubilis is challenged by phytopathogen invasion leading to production loss.

METHODS

In the current study, we tested the pathogenicity of fungal pathogens isolated from root rot infected P. volubilis plant tissues by inoculating them into healthy P. volubilis seedlings. Metagenomic sequencing was used to assess the shift in the fungal community of P. volubilis rhizosphere soil after root rot infection.

RESULTS

Four Fusarium isolates and two Rhizopus isolates were found to be root rot causative agents of P. volubilis as they induced typical root rot symptoms in healthy seedlings. The metagenomic sequencing data showed that root rot infection altered the rhizosphere fungal community. In root rot infected soil, the richness and diversity indices increased or decreased depending on pathogens. The four most abundant phyla across all samples were Ascomycota, Glomeromycota, Basidiomycota, and Mortierellomycota. In infected soil, the relative abundance of each phylum increased or decreased depending on the pathogen and functional taxonomic classification.

CONCLUSIONS

Based on our results, we concluded that Fusarium and Rhizopus species cause root rot infection of P. volubilis. In root rot infected P. volubilis, the shift in the rhizosphere fungal community was pathogen-dependent. These findings may serve as a key point for a future study on the biocontrol of root rot of P. volubilis.

pH-Related Changes in Soil Bacterial Communities in the Sanjiang Plain, Northeast China

Soil bacteria are crucial components of terrestrial ecosystems, playing an important role in soil biogeochemical cycles. Although bacterial community diversity and composition are regulated by many abiotic and biotic factors, how soil physiochemical properties impact the soil bacteria community diversity and composition in wetland ecosystems remains largely unknown. In this study, we used high-throughput sequencing technology to investigate the diversity and composition of a soil bacterial community, as well as used the structural equation modeling (SEM) method to investigate the relationships of the soil's physicochemical properties (i.e., soil pH, soil organic carbon (SOC), total nitrogen (TN), ammonium nitrogen (NH4+N), electrical conductivity (EC) and nitrate nitrogen (NO3-N)), and soil bacterial community structures in three typical wetland sites in the Sanjiang Plain wetland. Our results showed that the soil physicochemical properties significantly changed the α and β-diversity of the soil bacteria communities, e.g., soil TN, NH4+N, NO3-N, and SOC were the main soil factors affecting the soil bacterial α-diversity. The soil TN and pH were the key soil factors affecting the soil bacterial community. Our results suggest that changes in soil pH indirectly affect soil bacterial communities by altering the soil nitrogenous nutrient content.

Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review

Continuous improvement in the living standards of developing countries, calls for an urgent need of high quality meat and dairy products. The farm animals have a micro-ecosystem in gastro-intestinal tract, comprising of a wide variety of flora and fauna which converts roughages and agricultural byproducts as well as nutrient rich concentrate sources into the useful products such as volatile fatty acids and microbial crude proteins. The microbial diversity changes according to composition of the feed, host species/breed and host's individual genetic makeup. From culture methods to next-generation sequencing technologies, the knowledge has emerged a lot to know-how of microbial world viz. their identification, enzymatic activities and metabolites which are the keys of ruminant's successful existence. The structural composition of ruminal community revealed through metagenomics can be elaborated by metatranscriptomics and metabolomics through deciphering their functional role in metabolism and their responses to the external and internal stimuli. These highly sophisticated analytical tools have made possible to correlate the differences in the feed efficiency, nutrients utilization and methane emissions to their rumen microbiome. The comprehensively understood rumen microbiome will enhance the knowledge in the fields of animal nutrition, biotechnology and climatology through deciphering the significance of each and every domain of residing microbial entity. The present review undertakes the recent investigations regarding rumen multi-omics viz. taxonomic and functional potential of microbial populations, host-diet-microbiome interactions and correlation with metabolic dynamics.

Microbial electrochemical system: an emerging technology for remediation of polycyclic aromatic hydrocarbons from soil and sediments

Worldwide industrialization and other human activities have led to a frightening stage of release of hazardous, highly persistent, toxic, insoluble, strongly adsorbed to the soil and high molecular weight ubiquitous polycyclic aromatic hydrocarbons (PAHs) in soils and sediments. The various conventional remediation methods are being used to remediate PAHs with certain drawbacks. Time taking process, high expenditure, excessive quantities of sludge generation, and various chemical requirements do not only make these methods outdated but produce yet much resistant and toxic intermediate metabolites. These disadvantages may be overcome by using a microbial electrochemical system (MES), a booming technology in the field of bioremediation. MES is a green remediation approach that is regulated by electrochemically active microorganisms at the electrode in the system. The key advantage of the system over the conventional methods is it does not involve any additional chemicals, takes less time, and generates minimal sludge or waste during the remediation of PAHs in soils. However, a comprehensive review of the MES towards bioremediation of PAHs adsorbed in soil and sediment is still lacking. Therefore, the present review intended to summarize the recent information on PAHs bioremediation, application, risks, benefits, and challenges based on sediment microbial fuel cell and microbial fuel cell to remediate mount-up industrial sludge, soil, and sediment rich in PAHs. Additionally, bio-electrochemically active microbes, mechanisms, and future perspectives of MES have been discussed.

Synergistic improvement of nitrogen and phosphorus removal in constructed wetlands by the addition of solid iron substrates and ferrous irons

Sanjiang Plain is intensively used for rice production, and ditch drainage diffuse pollution prevention is crucial. Groundwater, rich in Fe ions, is the main source of irrigation water in this region. In this study, pyrite and zero-valent iron (ZVI) (sponge iron and iron scraps) were used as substrates to identify the synergistic influence of exogenous Fe2+ addition and solid iron substrates on pollutant removal in constructed wetlands. Based on the results, iron substrates hardly improved the ammonia removal, mainly because of the physical structure and oxidation activity. At a hydraulic retention time longer than 8 h, the pollution removal efficiency in the zero-valent iron (ZVI) substrate treatment increased significantly, and the removal of nitrate (NO3 --N) and total phosphorus (TP) in the iron scrap substrate treatment reached about 60% and 70%, respectively. The high-throughput sequencing results showed a significant increase in the abundance of microorganisms involved in denitrification and phosphate accumulation in biofilms on ZVI substrates. The highest diversities of such microorganisms in biofilms on iron scraps were found for denitrifying bacteria (Pseudomonas), nitrate-reducing Fe (II)-oxidizing bacteria (Acidovorax), and Dechloromonas with autotrophic denitrification and phosphate accumulation, with a 43% cumulative abundance. Dechloromonas dominated in the iron sponge substrate treatment. The highest relative abundance of Acidovorax was found in the mixed iron substrate (pyrite, sponge iron, and iron scraps) treatment. The addition of ZVI substrate significantly improved the removal of NO3 --N and TP and reduced the hydraulic retention time through the continuous release of Fe2+ and the promotion of microbial growth. When designing constructed wetlands for treating paddy field drainage, the appropriate addition of iron scrap substrates is recommended to enhance the pollutant removal efficiency and shock load resistance of CWs.

Rhizosphere interface microbiome reassembly by arbuscular mycorrhizal fungi weakens cadmium migration dynamics

The prevalence of cadmium (Cd)-polluted agricultural soils is increasing globally, and arbuscular mycorrhizal fungi (AMF) can reduce the absorption of heavy metals by plants and improve mineral nutrition. However, the immobilization of the rhizosphere on cadmium is often overlooked. In this study, Glomus mosseae and Medicago sativa were established as symbiotes, and Cd migration and environmental properties in the rhizosphere were analyzed. AMF reduced Cd migration, and Cd2+ changed to an organic-bound state. AMF symbiosis treatment and Cd exposure resulted in microbial community variation, exhibiting a distinct deterministic process (|βNTI| > 2), which ultimately resulted in a core microbiome function of heavy metal resistance and nutrient cycling. AMF increased available N and P, extracellular enzyme activity (LaC, LiP, and CAT), organic matter content (TOC, EOC, and GRSP), and Eh of the rhizosphere soil, significantly correlating with decreased Cd migration (p < 0.05). Furthermore, AMF significantly affected root metabolism by upregulating 739 metabolites, with flavonoids being the main factor causing microbiome variation. The structural equation model and variance partial analysis revealed that the superposition of the root metabolites, microbial, and soil exhibited the maximum explanation rate for Cd migration reduction (42.4%), and the microbial model had the highest single explanation rate (15.5%). Thus, the AMF in the rhizosphere microenvironment can regulate metabolite-soil-microbial interactions, reducing Cd migration. In summary, the study provides a new scientific explanation for how AMF improves plant Cd tolerance and offers a sustainable solution that could benefit both the environment and human health.

Multi-Omics Analysis Reveals the Gut Microbiota Characteristics of Diarrheal Piglets Treated with Gentamicin

The involvement of alterations in gut microbiota composition due to the use of antibiotics has been widely observed. However, a clear picture of the influences of gentamicin, which is employed for the treatment of bacterial diarrhea in animal production, are largely unknown. Here, we addressed this problem using piglet models susceptible to enterotoxigenic Escherichia coli (ETEC) F4, which were treated with gentamicin. Gentamicin significantly alleviated diarrhea and intestinal injury. Through 16s RNS sequencing, it was found that gentamicin increased species richness but decreased community evenness. Additionally, clear clustering was observed between the gentamicin-treated group and the other groups. More importantly, with the establishment of a completely different microbial structure, a novel metabolite composition profile was formed. KEGG database annotation revealed that arachidonic acid metabolism and vancomycin resistance were the most significantly downregulated and upregulated pathways after gentamicin treatment, respectively. Meanwhile, we identified seven possible targets of gentamicin closely related to these two functional pathways through a comprehensive analysis. Taken together, these findings demonstrate that gentamicin therapy for diarrhea is associated with the downregulation of arachidonic acid metabolism. During this process, intestinal microbiota dysbiosis is induced, leading to increased levels of the vancomycin resistance pathway. An improved understanding of the roles of these processes will advance the conception and realization of new therapeutic and preventive strategies.

Patterns and drivers of microbiome in different rock surface soil under the volcanic extreme environment

Soil microbial communities were investigated under the volcanic extreme environment. Soil bacterial networks exhibited higher stability than fungal networks. Holocene granite had a more complex microbial network than basalt. Soil pH and total protein were key drivers of microbial network stability.

Trajectories of soil microbial recovery in response to restoration strategies in one of the largest and oldest open-pit phosphate mine in Asia

Southwestern China has the largest geological phosphorus-rich mountain in the world, which is seriously degraded by mining activities. Understanding the trajectory of soil microbial recovery and identifying the driving factors behind such restoration, as well as conducting corresponding predictive simulations, can be instrumental in facilitating ecological rehabilitation. Here, high-throughput sequencing and machine learning-based approaches were employed to investigate restoration chronosequences under four restoration strategies (spontaneous re-vegetation with or without topsoil; artificial re-vegetation with or without the addition of topsoil) in one of the largest and oldest open-pit phosphate mines worldwide. Although soil phosphorus (P) is extremely high here (max = 68.3 mg/g), some phosphate solubilizing bacteria and mycorrhiza fungi remain as the predominant functional types. Soil stoichiometry ratios (C:P and N:P) closely relate to the bacterial variation, but soil P content contributes less to microbial dynamics. Meanwhile, as restoration age increases, denitrifying bacteria and mycorrhizal fungi significantly increased. Significantly, based on partial least squares path analysis, it was found that the restoration strategy is the primary factor that drives soil bacterial and fungal composition as well as functional types through both direct and indirect effects. These indirect effects arise from factors such as soil thickness, moisture, nutrient stoichiometry, pH, and plant composition. Moreover, its indirect effects constitute the main driving force towards microbial diversity and functional variation. Using a hierarchical Bayesian model, scenario analysis reveals that the recovery trajectories of soil microbes are contingent upon changes in restoration stage and treatment strategy; inappropriate plant allocation may impede the recovery of the soil microbial community. This study is helpful for understanding the dynamics of the restoration process in degraded phosphorus-rich ecosystems, and subsequently selecting more reasonable recovery strategies.

Linkages between Plant Community Composition and Soil Microbial Diversity in Masson Pine Forests

Plant species identity influences soil microbial communities directly by host specificity and root exudates, and indirectly by changing soil properties. As a native pioneer species common in early successional communities, Masson pine (Pinus massoniana) forests are widely distributed in subtropical China, and play a key role in improving ecosystem productivity. However, how pine forest composition, especially the dominance of plant functional groups, affects soil microbial diversity remains unclear. Here, we investigated linkages among woody plant composition, soil physicochemical properties, and microbial diversity in forests along a dominance gradient of Masson pine. Soil bacterial and fungal communities were mainly explained by woody plant community composition rather than by woody species alpha diversity, with the dominance of tree (without including shrub) species and ectomycorrhizal woody plant species accounting for more of the variation among microbial communities than pine dominance alone. Structural equation modeling revealed that bacterial diversity was associated with woody plant compositional variation via altered soil physicochemical properties, whereas fungal diversity was directly driven by woody plant composition. Bacterial functional groups involved in carbohydrate and amino acid metabolism were negatively correlated with the availability of soil nitrogen and phosphorus, whereas saprotrophic and pathogenic fungal groups showed negative correlations with the dominance of tree species. These findings indicate strong linkages between woody plant composition than soil microbial diversity; meanwhile, the high proportion of unexplained variability indicates great necessity of further definitive demonstration for better understanding of forest-microbe interactions and associated ecosystem processes.

Remedial effect and operating status of a decommissioned uranium mill tailings (UMT) repository: A micro-ecological perspective based on bacterial community

From a radioecological perspective, increasing attention has been paid to the long-term stabilisation of decommissioned uranium mill tailings (UMT) repositories. However, little is known about the evaluation of decommissioning and remedial effects of UMT repositories from a microecological perspective based on bacterial communities. Here, we analysed the distribution and structure of soil community assemblies along different vertical soil profiles in a decommissioned UMT repository and explored the impact of soil properties, including physicochemical parameters, metal(loid)s, and radionuclides, on the bacterial assemblage. We found that the α diversity of the bacterial community was unaffected by variations in different soil profiles and taxa were classified at the phylum level with small significant differences. In contrast, the bacterial community structure in and around the UMT repository showed significant differences; however, this difference was significantly affected by soil metal(loid)s and physicochemical properties rather than soil radionuclides. In addition, seven bacterial genera with significant differences between the inner and surrounding regions of the repository could be used as potential indicators to further investigate the remedial effects on soil environmental quality. These findings provide novel insights into the construction of an assessment system and in situ biomonitoring of UMT repositories from a microecological perspective based on bacterial communities.

Soybean rhizosphere microorganisms alleviate Mo nanomaterials induced stress by improving soil microbial community structure

With the wide application of nanomaterials (NMs) in agriculture, it is particularly important to assess the impact of these NMs on soil microorganisms. In this study, different varieties of soybean rhizosphere microorganisms (RM) were employed to simulate the alleviate effect of molybdenum nanoparticles (Mo NPs) induced stress in presence of soybean plants. Mo NPs caused serious toxic effects on soybean growth and nitrogen fixation at a concentration of 100 mg kg^-1: plant height and biomass were reduced by 56.4% and 82.8%, respectively, and the ability to fix nitrogen was almostly lost. However, after adding different varieties of soybean RM (RM-Williams 82, RM-Youchun 1204, and RM-Zhongdou 41), the stress caused by high concentrations of Mo NPs on soybean plants was significantly reduced. The plant height, root length, biomass, and nitrogen fixation ability were improved by 70.8%, 80.7%, 145.8%, and 349.8%, respectively, following the addition of soybean RM-Williams 82. High-throughput sequencing revealed that Mo NPs treatment affected the microbial community structure. Among them, Flavisolibacter and Caulobacter genera abundance increased significantly, which might be the key factor in relieving Mo NPs-induced stress on soybean growth. These findings suggest a novel mode of RM as a promising strategy to prevent deleterious effects of stress with NPs on plants in the future.

Temporal dynamics of total and active root-associated diazotrophic communities in field-grown rice

Plant-associated nitrogen-fixing microorganisms (diazotrophs) are essential to host nutrient acquisition, productivity and health, but how host growth affects the succession characteristics of crop diazotrophic communities is still poorly understood. Here, Illumina sequencing of DNA- and RNA-derived nifH genes was employed to investigate the dynamics of total and active diazotrophic communities across rhizosphere soil and rice roots under four fertilization regimes during three growth periods (tillering, heading and mature stages) of rice in 2015 and 2016. Our results indicated that 71.9–77.2% of the operational taxonomic units (OTUs) were both detected at the DNA and RNA levels. According to the nonmetric multidimensional scaling ordinations of Bray–Curtis distances, the variations in community composition of active rhizosphere diazotrophs were greater than those of total rhizosphere diazotrophs. The community composition (β-diversity) of total and active root-associated diazotrophs was shaped predominantly by microhabitat (niche; R² ≥ 0.959, p < 0.001), followed by growth period (R² ≥ 0.15, p < 0.001). The growth period had a stronger effect on endophytic diazotrophs than on rhizosphere diazotrophs. From the tillering stage to the heading stage, the α-diversity indices (Chao1, Shannon and phylogenetic diversity) and network topological parameters (edge numbers, average clustering coefficient and average degree values) of total endophytic diazotrophic communities increased. The proportions of OTUs shared by the total rhizosphere and endophytic diazotrophs in rhizosphere diazotrophs gradually increased during rice growth. Moreover, total diazotrophic α-diversity and network complexity decreased from rhizosphere soil to roots. Collectively, compared with total diazotrophic communities, active diazotrophic communities were better indicators of biological response to environmental changes. The host microhabitat profoundly drove the temporal dynamics of total and active root-associated diazotrophic communities, followed by the plant growth period.

Analysis of microbial diversity and community structure of rhizosphere soil of Cistanche salsa from different host plants

Host plants influence rhizosphere microorganism composition through root secretions, and rhizosphere associated microorganisms influence Cistanche seeds germination. At present, little is known about effects of different host plants on soil bacteria and fungi in the rhizosphere of Cistanche salsa. High-throughput sequencing was used here to reveal the similarities and differences in the structural composition of the soil microbial community of C. salsa from six host plants (i.e., Halocnemum strobilaceum, Atriplex patens, Kalidium foliatum, Caroxylon passerinum, Anabasis aphylla, Krascheninnikovia ceratoides). We discovered that Krascheninnikovia ceratoides-parasitizing C. salsa (YRCR6) had the highest diversity of rhizosphere bacterial communities, and Anabasis aphylla -parasitizing C. salsa (YRCR5) had the highest diversity of rhizosphere fungal communities. Fungal communities were more influenced by the host plant than bacterial communities. In addition, we discovered certain rhizosphere microorganisms that may be associated with Cistanche seeds germination, including Mortierella, Aspergillus alliaceus, and Cladosporium, which are account for a relatively high proportion in Halocnemum strobilaceum, Atriplex patens and Anabasis aphylla -parasitizing C. salsa. Redundancy analysis results also revealed that AP, HCO₃^–, pH, Ca²⁺, SO₄^2–, and K⁺ had a highly significant impact on the bacterial community structure (P < 0.01), while pH and SO₄^2– had a significant impact on the fungal community structure (P < 0.05). Conclusively, differences were noted in the structure of rhizosphere bacterial and fungal communities of C. salsa parasitizing different plants in the same habit and the difference may be related to the host plant. This result can provide a new ideas for the selection of host plants and the cultivation of C. salsa.

Pollution and edaphic factors shape bacterial community structure and functionality in historically contaminated soils

Studies about biodegradation potential in soils often refer to artificially contaminated and simplified systems, overlooking the complexity associated with contaminated sites in a real context. This work aims to provide a holistic view on microbiome assembly and functional diversity in the model site SIN Brescia-Caffaro (Italy), characterized by historical and uneven contamination by organic and inorganic compounds. Here, physical and chemical analyses and microbiota characterization were applied on one-hundred-twenty-seven soil samples to unravel the environmental factors driving bacterial community assembly and biodegradation potential in three former agricultural fields. Chemical analyses showed a patchy distribution of metals, metalloids and polychlorinated biphenyls (PCB) and allowed soil categorization according to depth and area of collections. Likewise, the bacterial community structure, described by molecular fingerprinting and 16S rRNA gene analyses, was significantly different according to collection site and depth. Pollutant concentrations (i.e., hexachloro-biphenyls, arsenic and mercury), nitrogen content and parameters related to soil texture were identified as main drivers of microbiota assembly, being significantly correlated to bacterial community composition. Moreover, bacteria putatively involved in the aerobic degradation of PCBs were enriched over the total bacterial community in topsoils, where the highest activity was recorded using fluorescein hydrolysis as proxy. Metataxonomic analyses revealed the presence of bacteria having metabolic pathways related to PCB degradation and tolerance to heavy metals and metalloids in the topsoil samples collected in all areas. Overall, the provided dissection of soil microbiota structure and its degradation potential in the SIN Brescia-Caffaro can contribute to target specific areas for rhizoremediation implementation. Metagenomics studies could be implemented in the future to understand if specific degradative pathways are present in historically polluted sites characterized by the co-occurrence of multiple classes of contaminants.

Grazing Changed Plant Community Composition and Reduced Stochasticity of Soil Microbial Community Assembly of Alpine Grasslands on the Qinghai-Tibetan Plateau

Grazing is a substantial threat to the sustainability of grassland ecosystems, while it is uncertain about the variety of plant and soil microbial community and the linkages between them limit the comprehensive understanding of grazing ecology. We conducted an experiment on the effects of the grazing regimes rotational grazing (RG), continuous grazing (CG), and grazing exclusion (GE) on an alpine meadow in Qinghai-Tibetan Plateau. The differences of plant community composition, soil microbial community assembly mechanism, and taxonomic and functional composition between grazing regimes were examined, and the relationship between plant species and the soil microbes was assessed by constructing a co-occurrence network. The results showed that the plant community composition varied with the grazing regimes, while the soil microbial community composition did not vary with the grazing regimes. The soil bacterial functional composition was similar under RG and CG, while the soil fungal functional composition was similar under GE and RG. The soil microbial community under all grazing regimes was assembled mainly according to stochastic rather than deterministic mechanisms, and RG and CG reduced the relative importance of the stochastic ratio. At the microbial phylum level, CG and GE increased the relative abundance of Acidobacteria and Armatimonadetes and CG and RG increased the relative abundance of Elusimicrobia. In the network of plant species and soil microbial classes, plants and bacteria themselves were mainly positively linked (symbiosis and promotion), while plants and soil microbes were mainly negatively linked (competition). There were five microbial generalists in the network, which connected with many microbes, and four showed no difference in their abundance among the grazing regimes. Overall, the stable key microbes in the network and the fact that many of the plants are unconnected with microbes weakened the impact of grazing-induced changes in the plant community on soil microbes, probably resulting in the stable soil microbial community composition. Moreover, there was still a dominant and tolerant plant species, Kobresia pygmaea, that connected the plant and microbial communities, implying that the dominant plant species not only played a crucial role in the plant community but also acted as a bridge between the plants and soil microbes; thus, its tolerance and dominance might stabilize the soil microbial community.

Different Assembly Patterns of Planktonic and Sedimentary Bacterial Community in a Few Connected Eutrophic Lakes

The mechanism of bacterial community assembly has been the hot spot in the field of microbial ecology and it is difficult to quantitatively estimate the influences of different ecological processes. Here, a total of 23 pairs of planktonic and sedimentary samples were collected from five lakes in Wuhan, China. significant higher α-diversity (p < 0.001) and β-diversity (p < 0.001) of bacterial communities were observed in sediment than those in water. Some phylum had linear relationships with the comprehensive TSI (TSIc) by regression analysis. Non-metric multidimensional scaling (NMDS) and redundancy analysis (RDA) revealed that the depth of water, NO3−-N, NH4+-N, PO43−, and CODcr were the key environmental variables in planktonic bacterial communities, whereas in sediment they were the depth, NO3−-N, and NH4+-N. Furthermore, variation partitioning analysis (VPA) showed that spatial and environmental factors could only explain 40.2% and 27.9% of the variation in planktonic and sedimentary bacterial communities, respectively. More importantly, null model analysis suggested that different assembly mechanisms were found between in water and in sediment with the fact that planktonic bacterial community assembly was mainly driven by dispersal limitation process whereas variable selection process played a vital role in that of sediment.

An Endophytic Strain of Bacillus amyloliquefaciens Suppresses Fusarium oxysporum Infection of Chinese Wolfberry by Altering Its Rhizosphere Bacterial Community

Root rot disease is a serious infection leading to production loss of Chinese wolfberry (Lycium barbarum). This study tested the potential for two bacterial biological control agents, Bacillus amyloliquefaciens HSB1 and FZB42, against five fungal pathogens that frequently cause root rot in Chinese wolfberry. Both HSB1 and FZB42 were found to inhibit fungal mycelial growth, in vitro and in planta, as well as to promote the growth of wolfberry seedlings. In fact, a biocontrol experiment showed efficiency of 100% with at least one treatment involving each biocontrol strain against Fusarium oxysporum. Metagenomic sequencing was used to assess bacterial community shifts in the wolfberry rhizosphere upon introduction of each biocontrol strain. Results showed that HSB1 and FZB42 differentially altered the abundances of different taxa present and positively influenced various functions of inherent wolfberry rhizosphere bacteria. This study highlights the application of biocontrol method in the suppression of fungal pathogens that cause root rot disease in wolfberry, which is useful for agricultural extension agents and commercial growers.

Microbial diversity alteration reveals biomarkers of contamination in soil-river-lake continuum

Microbial communities inhabiting soil-water-sediment continuum in coastal areas provide important ecosystem services. Their adaptation in response to environmental stressors, particularly mitigating the impact of pollutants discharged from human activities, has been considered for the development of microbial biomonitoring tools, but their use is still in the infancy. Here, chemical and molecular (16S rRNA gene metabarcoding) approaches were combined in order to determine the impact of pollutants on microbial assemblages inhabiting the aquatic network of a soil-water-sediment continuum around the Ichkeul Lake (Tunisia), an area highly impacted by human activities. Samples were collected within the soil-river-lake continuum at three stations in dry (summer) and wet (winter) seasons. The contaminant pressure index (PI), which integrates Polycyclic aromatic hydrocarbons (PAHs), alkanes, Organochlorine pesticides (OCPs) and metal contents, and the microbial pressure index microgAMBI, based on bacterial community structure, showed significant correlation with contamination level and differences between seasons. The comparison of prokaryotic communities further revealed specific assemblages for soil, river and lake sediments. Correlation analyses identified potential "specialist" genera for the different compartments, whose abundances were correlated with the pollutant type found. Additionally, PICRUSt analysis revealed the metabolic potential for pollutant transformation or degradation of the identified "specialist" species, providing information to estimate the recovery capacity of the ecosystem. Such findings offer the possibility to define a relevant set of microbial indicators for assessing the effects of human activities on aquatic ecosystems. Microbial indicators, including the detection of "specialist" and sensitive taxa, and their functional capacity, might be useful, in combination with integrative microbial indices, to constitute accurate biomonitoring tools for the management and restoration of complex coastal aquatic systems.

Can moderate heavy metal soil contaminations due to cement production influence the surrounding soil bacterial communities?

Events of soil contamination by heavy metals are mostly related to human activities that release these metals into the environment as emissions or effluents. Among the industrial activities related to heavy metal pollution, cement production plants are considered one of the most common sources. In this work we applied the High-throughput sequencing approach called 16 S rDNA metabarcoding to perform the taxonomic characterization of the prokaryotic communities of the soil surrounding three cement plants as well as two areas outside the influence of the cement plants that represented agricultural production environments free of heavy metal contamination (control areas). We applied the environmental genomics approaches known as "structural community metrics" (α- and β-diversity metrics) and "functional community metrics" (PICRUSt2 approach) to verify whether or not the effects of heavy metal contamination in the study area generated impacts on soil bacterial communities. We found that the impact related to the elevation of heavy metal concentration due to the operation of cement plants in the surrounding soil can be considered smooth according to globally recognized indices such as Igeo. However, we identified that both the taxonomic and functional structures of the communities surrounding cement plants were different from those found in the control areas. We consider that our findings contribute significantly to the general understanding of the effects of heavy metals on the soil ecosystem by showing that light contamination can disturb the dynamics of ecosystem services provided by soil, specifically those associated with microbial metabolism.

Ecological network analysis reveals distinctive microbial modules associated with heavy metal contamination of abandoned mine soils in Korea

Heavy metal pollution in soil around abandoned mine sites is one of the most critical environmental issues worldwide. Soil microbes form complex communities and perform ecological functions individually or in cooperation with other organisms to adapt to harsh environments. In this study, we investigated the distribution patterns of bacterial and fungal communities in non-contaminated and heavy metal-contaminated soil of the abandoned Samkwang mine in Korea to explore microbial interaction mechanisms and their modular structures. As expected, the bacterial and fungal community structures showed large differences depending on the degree of heavy metal contamination. The microbial network was divided into three modules based on the levels of heavy metal pollution: heavy metal-tolerant (HM-Tol), heavy metal-mid-tolerant (HM-mTol), and heavy metal-sensitive (HM-Sens) modules. Taxonomically, microbes assigned to Vicinamibacterales, Pedosphaeraceae, Nitrosomonadaceae, and Gemmatimonadales were the major groups constituting the HM-Tol module. Among the detected heavy metals (As, Pb, Cd, Cu, and Zn), copper concentrations played a key role in the formation of the HM-Tol module. In addition, filamentous fungi (Fusarium and Mortierella) showed potential interactions with bacteria (Nitrosomonadaceae) that could contribute to module stability in heavy metal-contaminated areas. Overall, heavy metal contamination was accompanied by distinct microbial communities, which could participate in the bioremediation of heavy metals. Analysis of the microbial interactions among bacteria and fungi in the presence of heavy metals could provide fundamental information for developing bioremediation mechanisms for the recovery of heavy metal-contaminated soil.

Exploitation of extracellular organic matter from Micrococcus luteus to enhance ex situ bioremediation of soils polluted with used lubricants

Chronic pollution by used lubricant oils (ULOs) poses a serious challenge to the environment. Under stress conditions, microorganisms, including potential degraders, can enter a viable but non-culturable (VBNC) state, complicating the bioremediation of ULO-polluted areas. Resuscitation-promoting factors (Rpfs) can reverse this transition and/or enhance the biodegradation performance of both native and augmented strains. Here, Rpf-containing extracellular organic matter (EOM) from Micrococcus luteus was used to enhance the ex situ ULO removal in biostimulated and bioaugmented (with Rhodococcus qingshengii KAG C, R. erythropolis PR4) soils. ULO bioconversion, microbial activity, and CFUs were significantly higher in EOM-treated soils compared to corresponding control soils. After 60 days, the initial ULO concentration (52,500 mg kg^-1) was reduced by 37% and 45% with EOM-supplemented biostimulation and bioaugmentation, respectively. Based on high-throughput 16S rRNA analysis, the enhancement was attributable both to the reactivation of EOM-responsive hydrocarbonoclastic bacterial genera (e.g., Pseudomonas, Comamonas, Stenotrophomonas, Gordonia) and to the long-term positive effect of EOM on the degradative efficacy of the introduced rhodococci. Ecotoxicological responses revealed that reduced ULO concentration did not correlate with decreased soil toxicity. Our findings provide an insight into the applicability of EOM in bioremediation and its effects on the soil microbial activity and community composition.

Effect of Fe-Mn-La-modified biochar composites on arsenic volatilization in flooded paddy soil

As can be volatilized naturally; however, this has adverse environmental effects. In this study, we investigated As volatilization in flooded paddy soil with the addition of biochar (BC) and Fe-Mn-La-modified BC composites (FMLBCs). The addition of BC and FMLBCs caused decreases in total As volatilization in the soil over 7 weeks. Maximum volatilization was achieved in the third week followed by stabilization. Volatilization decreased by 21.9%, 18.8%, 20.8%, and 31.1% with the addition of BC, FMLBC₁, FMLBC₂, and FMLBC₃ (BC/Fe/Mn/La weight ratios different), respectively, in lightly contaminated soil, and by 15.2%, 20.5%, 17.6%, and 25.4%, respectively, in highly contaminated soil. The FMLBCs decreased the exchangeable As fractions and increased the non-swappable As in the soil. Furthermore, the addition of FMLBCs significantly reduced the As(III) concentration in a suspended solution (P < 0.05), whereas no significant changes were observed in the As(V) or methyl arsenic acid concentrations. Soil enzyme activity increased and the relative abundances of Proteobacteria and Actinobacteria changed with the addition of FMLBCs. Therefore, the mechanism by which FMLBCs affected As volatilization likely included the following two aspects: (1) FMLBCs affected the transformation and distribution of soil As and decreased As dissolution, crystallization, and methylation; (2) FMLBCs influenced soil properties, which directly affected microorganism activity, thereby affecting As volatilization. FMLBCs therefore can decrease As volatilization properties and be used to control As volatilization in As-contaminated paddy soils.

Characteristics of size-segregated aerosols emitted from an aerobic moving bed biofilm reactor at a full-scale wastewater treatment plant

Aerosol emissions from wastewater treatment plants (WWTPs) have been associated with health reverberation but studies about characteristics of size-segregated aerosol particulate matter (PM) are scarce. In this study, the measurement of particulate number size distribution in the range of < 10 µm, and the collection of PM_10-2.5, PM_2.5-1.0 and PM_1.0, were conducted from an aerobic moving bed biofilm reactor (MBBR) at a full-scale WWTP. MBBR aerosols showed a unimodal number size distribution, with the majority of particles (>94%) in the ultrafine size range (<100 nm). For toxic metal(loid)s or potential pathogens, significant differences were found within MBBR aerosols (PM_10-2.5, PM_2.5-1.0, and PM_1.0), and also between MBBR aerosols and wastewater. Both wastewater and ambient air had important source contributions for MBBR aerosols. The compositions of toxic metal(loid)s in PM_1.0, and the populations of potential bacterial or fungal pathogens in PM_10-2.5 and PM_2.5-1.0, were dominated by that from wastewater. Compared to PM_10-2.5 and PM_2.5-1.0, PM_1.0 had the highest aerosolization potential for the toxic metal(loid)s of As, Cd, Co, Cr, Li, Mn, Ni, U, and Zn, and the genera of Acinetobacter, Pseudomonas and Fusarium. Due to the size-segregated specialty, targeted measures should be employed to reduce the health risks. CAPSULE: The compositions of toxic metal(loid)s in PM_1.0, and the populations of potential pathogens in PM_10-2.5 and PM_2.5-1.0, were dominated by that from wastewater.

Metagenomics of two gnotobiotically grown aromatic rice cultivars reveals genotype-dependent and tissue-specific colonization of endophytic bacterial communities attributing multiple plant growth promoting traits

Exploration of community structures, habitations, and potential plant growth promoting (PGP) attributes of endophytic bacteria through next generation sequencing (NGS) is a prerequisite to culturing PGP endophytic bacteria for their application in sustainable agriculture. The present study unravels the taxonomic abundance and diversity of endophytic bacteria inhabiting in vitro grown root, shoot and callus tissues of two aromatic rice cultivars through 16S rRNA gene-based Illumina NGS. Wide variability in the number of bacterial operational taxonomic units (OTUs) and genera was observed between the two samples of the root (55, 14 vs. 310, 76) and shoot (26, 12 vs. 276, 73) but not between the two callus samples (251, 61 vs. 259, 51), indicating tissue-specific and genotype-dependent bacterial community distribution in rice plant, even under similar gnotobiotic growth conditions. Sizes of core bacteriomes of the selected two rice genotypes varied from 1 to 15 genera, with Sphingomonas being the only genus detected in all six samples. Functional annotation, based upon the abundance of bacterial OTUs, revealed the presence of several PGP trait-related genes having variable relative abundance in tissue-specific and genotype-dependent manners. In silico study also documented a higher abundance of certain genes in the same biochemical pathway, such as nitrogen fixation, phosphate solubilization and indole acetic acid production; implying their crucial roles in the biosynthesis of metabolites leading to PGP. New insights on utilizing callus cultures for isolation of PGP endophytes aiming to improve rice crop productivity are presented, owing to constancy in bacterial OTUs and genera in callus tissues of both the rice genotypes.

Soil stabilization/solidification (S/S) agent---water-soluble thiourea formaldehyde (WTF) resin: Mechanism and performance with cadmium (Ⅱ)

It is vital for the development and application of heavy metal stabilization/solidification (S/S) agents to reveal the mechanism of the reaction between water-soluble thiourea formaldehyde (WTF) resin and heavy metal and evaluate its repairing effect. Based on the density functional theory analysis of the WTF resin structure, the mechanism analysis and scanning electron microscope (SEM) showed that the three-dimensional network structure with thiocarbonyl and hydroxyl groups is very conducive to the capture of Cd²⁺. The reduction rate of Cd²⁺ in soil added WTF resin could reach 70.6%-86.0%. The result of BCR's sequential extraction also proved that the 86.4%-94.1% of Cd in the soil repaired by WTF resin changed from acid-soluble state to residue state. Enzyme activity analysis and 16sRNA sequencing experiments showed that such a structure does not harm soil health. The urease and phosphatase tests showed the nitrogen and phosphorus cycle of the soil added WTF resin was repaired. Even compared with the remediation agents Na₂S and hydroxyapatite, WTF resin still performed better in repairing soil health. These findings provide valuable insights into the efficient causes of WTF resin and its harmless effects on soil. The results obtained provide a critical reference for the future application of practical and gentle heavy metal S/S agents.

Profiling multiple heavy metal contamination and bacterial communities surrounding an iron tailing pond in Northwest China

Northwest China is abundant in iron ore reserves and has become one of the important iron ore mining bases in China. However, the contamination and microbial community structure of iron tailing ponds in Northwest China have not been extensively investigated. In the present study, we characterized the main physicochemical properties, the multiple heavy metal contamination, and the bacterial community structure of the soils surrounding an iron tailing pond in Linze County, Zhangye city, Gansu Province. The tailing-associated soils were barren, exhibiting alkaline pH and low organic matter (OM), total nitrogen (TN) and total potassium (TK) compared with the control areas. There was considerable multiple heavy metal pollution in the iron tailing pond, mainly including lead (Pb), manganese (Mn), arsenic (As), cadmium (Cd), zinc (Zn), iron (Fe) and copper (Cu). Among the 303 identified core operational taxonomic units (OTUs), Actinobacteria, Proteobacteria and Deinococcus-Thermus were predominant at the phylum level, and Blastococcus, Arthrobacter, Marmoricola, Kocuria, Truepera, and Sphingomonadaceae were prevalent at a finer taxonomic level. The bacterial richness and diversity of the tailing samples were significantly lower than those of the reference samples. RDA, VPA and Spearman correlation analyses showed that the soil pH, CEC, OM, TP, TK, Cd, Pb, Ni, Zn, As and Mn had significant effects on the bacterial community composition and distribution. This work profiles the basic features of the soil physicochemical properties, the multiple heavy metal contamination and the bacterial community structure in an iron tailing pond in Northwest China, thereby providing a foundation for the future ecological remediation of the iron tailing environment in the area.

Effect of Two Different Sugarcane Cultivars on Rhizosphere Bacterial Communities of Sugarcane and Soybean Upon Intercropping

Intercropping of soybean and sugarcane is an important strategy to promote sustainable development of the sugarcane industry. In fact, our understanding of the interaction between the rhizosphere and bacterial communities in the intercropping system is still evolving; particularly, the influence of different sugarcane varieties on rhizosphere bacterial communities in the intercropping process with soybean, still needs further research. Here, we evaluated the response of sugarcane varieties ZZ1 and ZZ9 to the root bacterial community during intercropping with soybean. We found that when ZZ9 was intercropped with soybean, the bacterial diversity increased significantly as compared to that when ZZ1 was used. ZZ9 played a major role in changing the bacterial environment of the root system by affecting the diversity of rhizosphere bacteria, forming a rhizosphere environment more conducive to the growth of sugarcane. In addition, our study found that ZZ1 and ZZ9 had differed significantly in their utilization of nutrients. For example, nutrients were affected by different functional genes in processes such as denitrification, P-uptake and transport, inorganic P-solubilization, and organic P-mineralization. These results are significant in terms of providing guidance to the sugarcane industry, particularly for the intercropping of sugarcane and soybean in Guangxi, China.

Impact of anaerobically digested silver and copper oxide nanoparticles in biosolids on soil characteristics and bacterial community

This study investigated whether 2 and 30 mg AgNPs or CuONPs/g TS present in treated sludge (biosolids) may impact the soil health by monitoring the soil characteristics and soil bacterial community for 105 days after the application of biosolids. AgNPs or CuONPs/g TS were first anaerobically digested with mixed primary and secondary sludge rather than adding pristine nanoparticles to biosolids directly. Both environmentally relevant (under the USEPA ceiling concentration limits) and high concentrations of AgNPs and CuONPs were tested. Soil tests included TOC, TN, TP, pH, cell viability and heterotrophic plate counts (HPC). Metagenomic data was generated by high-throughput sequencing of the 16S rRNA gene to explore bacterial populations and diversity. AgNPs and CuONPs at 2 and 30 mg NPs/g TS of sludge could impact soil health factors such as bacterial diversity, community structure, and the population of plant growth-promoting rhizobacteria (PGPR). The population of the highly abundant bacteria that have important physiological roles in soil decreased, while the less important bacteria for soil function were able to thrive. CuONPs exhibited a higher level of toxicity than the AgNPs at both phylum and genus taxonomic levels, and the HPC decreased with higher concentrations of AgNPs and CuONPs. Initially, most of the studied phyla abundance was affected, but the control and other reactors approached similar levels by the end of the experiments, which may be explained by the decrease in toxicity due to the transformation of nanoparticles and the defence mechanisms of bacteria, and indicates the need for long-term field studies.

Impact of Fe(III) (Oxyhydr)oxides Mineralogy on Iron Solubilization and Associated Microbial Communities

Iron-reducing bacteria (IRB) are strongly involved in Fe cycling in surface environments. Transformation of Fe and associated trace elements is strongly linked to the reactivity of various iron minerals. Mechanisms of Fe (oxyhydr)oxides bio-reduction have been mostly elucidated with pure bacterial strains belonging to Geobacter or Shewanella genera, whereas studies involving mixed IRB populations remain scarce. The present study aimed to evaluate the iron reducing rates of IRB enriched consortia originating from complex environmental samples, when grown in presence of Fe (oxyhydr)oxides of different mineralogy. The abundances of Geobacter and Shewanella were assessed in order to acquire knowledge about the abundance of these two genera in relation to the effects of mixed IRB populations on kinetic control of mineralogical Fe (oxyhydr)oxides reductive dissolution. Laboratory experiments were carried out with two freshly synthetized Fe (oxyhydr)oxides presenting contrasting specific surfaces, and two defined Fe-oxides, i.e., goethite and hematite. Three IRB consortia were enriched from environmental samples from a riverbank subjected to cyclic redox oscillations related to flooding periods (Decize, France): an unsaturated surface soil, a flooded surface soil and an aquatic sediment, with a mixture of organic compounds provided as electron donors. The consortia could all reduce iron-nitrilotriacetate acid (Fe(III)-NTA) in 1–2 days. When grown on Fe (oxyhydr)oxides, Fe solubilization rates decreased as follows: fresh Fe (oxyhydr)oxides > goethite > hematite. Based on a bacterial rrs gene fingerprinting approach (CE-SSCP), bacterial community structure in presence of Fe(III)-minerals was similar to those of the site sample communities from which they originated but differed from that of the Fe(III)-NTA enrichments. Shewanella was more abundant than Geobacter in all cultures. Its abundance was higher in presence of the most efficiently reduced Fe (oxyhydr)oxide than with other Fe(III)-minerals. Geobacter as a proportion of the total community was highest in the presence of the least easily solubilized Fe (oxyhydr)oxides. This study highlights the influence of Fe mineralogy on the abundance of Geobacter and Shewanella in relation to Fe bio-reduction kinetics in presence of a complex mixture of electron donors.

Recent advances in exploring the heavy metal(loid) resistant microbiome

Heavy metal(loid)s exert selective pressure on microbial communities and evolution of metal resistance determinants. Despite increasing knowledge concerning the impact of metal pollution on microbial community and ecological function, it is still a challenge to identify a consistent pattern of microbial community composition along gradients of elevated metal(loid)s in natural environments. Further, our current knowledge of the microbial metal resistome at the community level has been lagging behind compared to the state-of-the-art genetic profiling of bacterial metal resistance mechanisms in a pure culture system. This review provides an overview of the core metal resistant microbiome, development of metal resistance strategies, and potential factors driving the diversity and distribution of metal resistance determinants in natural environments. The impacts of biotic factors regulating the bacterial metal resistome are highlighted. We finally discuss the advances in multiple technologies, research challenges, and future directions to better understand the interface of the environmental microbiome with the metal resistome. This review aims to highlight the diversity and wide distribution of heavy metal(loid)s and their corresponding resistance determinants, helping to better understand the resistance strategy at the community level.

Deciphering the rhizosphere microbiome of a bamboo plant in response to different chromium contamination levels

Bamboo has been considered a potential plant species for phytoremediation due to its high biomass and heavy metal (HM) resistance. However, little is known about the interactions between bamboo and soil microbial activities in HM-contaminated soils. Here, we investigated the characteristics of microbial communities in the rhizosphere soil of Lei bamboo (Phyllostachys praecox) along a chromium (Cr) gradient. We found that the soil Cr content was positively correlated with the total organic carbon (TOC) and HCl-extractable Cr but negatively correlated with the pH and bacterial and fungal Shannon indices. Proteobacteria and Ascomycota predominated in the bamboo rhizosphere under Cr pollution. A co-occurrence network showed that two of the most Cr-sensitive bacterial genera and keystone taxa were from the Acidobacteria, indicating that this phylum can be as an indicator for the studied Cr-polluted soils. Redundancy analysis revealed that both the soil bacterial and fungal community compositions were significantly correlated (p < 0.05) with Cr, pH, TOC, alkali-hydrolysable N (AN), and available phosphorus (AP). The increase in TOC as the Cr content increased can be ascribed to an adverse Cr effect on the soil microflora, probably because the microbial biomass was less effective in mineralizing soil C under Cr-polluted conditions.

Microbial structure and diversity in non-sanitary landfills and association with physicochemical parameters

This study assessed the bacterial populations in a non-sanitary landfill around Guarani Aquifer recharge zone in Brazil. Samples from two different positions (sites 1 and 2) at three different depths were evaluated, totaling six solid waste samples; two samples from an impacted stream were also collected. 16S rRNA sequencing was performed using the Ion S5TM XL platform; 3113 operational taxonomic units (OTUs) and 52 phyla were identified. Proteobacteria (37%) and Firmicutes (28%) were the most abundant phyla in the landfill, whereas Proteobacteria (~ 50%) and Bacteroidetes (~ 10%) were more profuse in surface water samples. Canonical correlation analysis (CCA) enabled us to clearly separate the samples according to their spatial location (site 1 or 2) or environmental matrix (surface water or solid waste samples), showing that microbiological populations are strongly associated with site-specific conditions and the kind of environmental matrix they come from. Environmental factors that mostly influenced the microbial communities were organic matter, oxidation-reduction potential, moisture, alkalinity, nitrogen (TKN), sodium, potassium, and zinc. Exiguobacterium (phylum Firmicutes) was overwhelmingly dominant at site 1 and was associated with higher concentrations of organic matter and potassium. Differently, site 2 did not present such dominant genera and was more diverse having lower concentrations of organic matter and nutrients. Distinct environments co-exist inside the same waste deposit, including zones which are representative of active and closed landfills and the occurrence of considerable physicochemical and microbiological shifts within short distances. Those shifts indicate that microbial populations are well adapted to the heterogeneity typical of urban solid waste, which is possibly beneficial to contaminant degradation. Graphical abstract.

Identification of Bacterial and Fungal Communities in the Roots of Orchids and Surrounding Soil in Heavy Metal Contaminated Area of Mining Heaps

Orchids represent a unique group of plants that are well adapted to extreme conditions. In our study, we aimed to determine if different soil contamination and pH significantly change fungal and bacterial composition. We identified bacterial and fungal communities from the roots and the surrounding soil of the family Orchidaceae growing on different mining sites in Slovakia. These communities were detected from the samples of Cephalanthera longifolia and Epipactis pontica from Fe deposit Sirk, E. atrorubens from Ni-Co deposit Dobšiná and Pb-Zn deposit Jasenie and Platanthera bifolia by 16S rRNA gene and ITS next-generation sequencing method. A total of 171 species of fungi and 30 species of bacteria were detected from five samples of orchids. In summary, slight differences in pH of the initial soils do not significantly affect the presence of fungi and bacteria and thus the presence of the studied orchids in these localities. Similarly, the toxic elements in the studied localities, do not affect the occurrence of fungi, bacteria, and orchids. Moreover, Cortinarius saturatus, as a dominant fungus, and Candidatus Udaeobacter as a dominant bacterium were present in all soil samples and some root samples. Finally, many of these fungal and bacterial communities have the potential to be used in the bioremediation of the mining areas.

Responses of soil and earthworm gut bacterial communities to heavy metal contamination

The large accumulation of heavy metals in the soil surrounding steel factories has become a severe environmental problem. However, few studies have focused on how the earthworm gut microbiota responds to heavy metals in the soil. This study used research sites at a steel factory in Nanjing, China, to investigate how the soil bacterial community and earthworm gut microbiota respond differently to heavy metal contamination using Illumina high-throughput sequencing targeting 16S rRNA genes. The bacterial community of earthworm guts showed a distinct structure compared with that of the soil, featuring a higher relative abundance of Proteobacteria (45.7%) and Bacteroidetes (18.8%). The bacterial community in the earthworm gut appeared more susceptible to heavy metal contamination compared with the soil community. For example, we identified 38 OTUs (Operational taxonomic units) significantly influenced by contamination among 186 abundant OTUs in the soil, whereas 63 out of the 127 abundant OTUs in the earthworm gut were altered significantly under contamination. This susceptibility may be partly explained by the lower alpha diversity and distinct microbial interactions in the gut. In addition, the accumulation of heavy metals also stimulated the growth of potential plant growth promoting bacteria (PGPB) in the earthworm gut, especially those related to indole-3-acetic acid (IAA) and 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD) production, which may potentially benefit the phyto-remediation of heavy metals. These results contribute to our understanding of the soil biota and its interactions under heavy metal contamination and may provide further insights into the phyto-remediation of metal-contaminated soil.

Succession of the bacterial community structure and functional prediction in two composting systems viewed through metatranscriptomics

In this work, Illumina MiSeq sequencing of cDNA from metatranscriptomics RNA reverse transcription were employed in combination with phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) to estimate the dynamic variations of bacterial community structures and metabolic functions in a bioreactor and traditional composting process. Results showed that the change of bacterial α-diversity in the first three stages exhibit opposite trends in the two composting systems. The four most abundant phyla were the same in both systems (Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria), but the most abundant genera were different. The five most abundant genus-level groups in the bioreactor were Psychrobacter, Galbibacter, Pseudomonas, Staphylococcus and Flavobacterium. Within the same phase, the functional bacteria were dramatically different in the two composting processes. In the bioreactor system both bacterial community structure and metabolism function were greatly affected by available phosphorus.

An appropriate technique for treating rural wastewater by a flow step feed system driven by wind-solar hybrid power

Most rural wastewater treatment facilities require aeration equipment to ensure sufficient dissolved oxygen (DO) during processing. Operation and maintenance are costly, and cannot be met in many areas with poor economic levels. This has led to further deterioration of the rural water environment and aroused much attention. This work reports a plug-flow step feed system utilizing wind and solar hybrid energy for rural wastewater treatment. Under certain climatic conditions, the wind energy and solar energy provided complimentary power generation, and an automatic control system (without batteries) was constructed. The corresponding control logic for multi-energy level operation was developed. Furthermore, the power generation efficiency of the system, the pollutant removal, and its mechanism on the bioreactor were also analyzed. According to the monitoring of meteorological conditions, wind and solar resources at the test site were abundant, and the electricity generated by the power generation was sufficient to meet the operational needs of the equipment. Energy efficiency can reach 80.0%. The characteristics of pollutant removal in each process section were studied on spatial and temporal dimensions. Results showed that the wastewater treatment process reached mean removal efficiencies of chemical oxygen demand (COD_cr), NH₄⁺-N, total nitrogen (TN) and total phosphorus (TP) were 90.2%, 94.3%, 61.4% and 63.1%, respectively. Analyses of microbial community richness and group changes in each anoxic/aerobic reaction chamber in the biofilm reactor showed that the population structure was relatively stable and that there were abundant functional bacteria capable of degrading pollutants in each aerobic and anoxic unit. This system can thus be a more sustainable treatment process than traditional techniques used for rural wastewater treatment, providing a new design approach for low-energy consumption and unattended rural wastewater treatment.

The limits of lead (Pb) phytoextraction and possibilities of phytostabilization in contaminated soil: a critical review

This review article focuses on lead (Pb), one of the most ubiquitous and harmful toxicants found in soil. Our objective is to address misconceptions regarding the ability of plants to uptake Pb through their roots and translocate it to above-ground tissues, and their ability to act as hyperaccumulators and thereby phytoextract Pb. In accordance with a number of cited definitions, we suggest that species capable of Pb phytoextraction can be rated with the following three criteria: (1) root uptake above a nominal threshold of 1,000 mg Pb/kg, (2) bioconcentration factor (BCF or shoot/soil concentration) >1, and (3) translocation factor (TF or shoot/root concentration) > 1. We review the literature in the updated USDA Phytoremediation Database and conclude that without amendments: no plant has met all three criteria; no plant has been confirmed as a Pb hyperaccumulator. Our analysis suggests that Pb phytoextraction is not a viable remediation option. Pb phytostabilization, however, may be an effective remediation tool in a variety of settings. Planting some of the many species capable of tolerating soil Pb exposure and sequestering it in or around the root zone will limit Pb movement into other ecosystems, prevent resuspended dusts, and mitigate Pb exposure.

Effect of Fe-Mn-Ce modified biochar composite on microbial diversity and properties of arsenic-contaminated paddy soils

In this study, we investigated the mechanism of decrease in arsenic (As) bioavailability after addition of biochar (BC) supplemented with iron (Fe)- manganese (Mn)- cerium (Ce) oxide (FMCBC) to As-contaminated paddy soil. We explored the effects of these composites on the oxidation, reduction, microbial community, and soil enzyme activity of As-contaminated paddy soil. Results showed that FMCBCs improve soil pH, significantly improve the redox capacity of soil, and reduce bioavailable forms of As. FMCBCs can convert As from a specifically or non-specifically bound form into amorphous hydrous oxide bound- and crystalline hydrous oxide bound form. The application of FMCBCs increased soil enzyme activity (urease, catalase, alkaline phosphatase, and peroxidase), and greatly influenced the relative abundance of certain microorganisms (Proteobacteria, Acidobacteria, and Gemmatimonadetes), which improved soil enzyme heavy metal tolerance and prevented their denaturation. Thus, FMCBCs can not only change the form and distribution of As in soil but also create an environment suitable for microbial growth, consequently affecting the geochemical cycling of As in soil.

Mobility and potential bioavailability of antimony in contaminated soils: Short-term impact on microbial community and soil biochemical functioning

Antimony (Sb) and its compounds are emerging priority pollutants which pose a serious threat to the environment. The aim of this study was to evaluate the short-term fate of antimonate added to different soils (S1 and S2) with respect to its mobility and impact on soil microbial communities and soil biochemical functioning. To this end, S1 (sandy clay loam, pH 8.2) and S2 (loamy coarse sand, pH 4.9) soils were spiked with 100 and 1000 mg Sb(V) kg^-1 soil and left in contact for three months. Sequential extractions carried out after this contact time indicated a higher percentage of labile antimony in the Sb-spiked S1 soils than S2 (e.g. ~13 and 4% in S1 and S2 treated with 1000 mg Sb(V) kg^-1 respectively), while the opposite was found for residual (hardly bioavailable) Sb. Also, a reduced number of culturable heterotrophic bacteria was recorded in Sb-spiked S1 soil (compared to the unpolluted S1), while an increased one was found in S2. Heterotrophic fungi followed the opposite trend. Actinomycetes and heat-resistant aerobic bacterial spores showed a variable trend depending on the soil type and Sb(V) treatment. The Biolog community level physiological profile indicated a reduced metabolic activity potential of microbial communities from the Sb-spiked S1 soils (e.g. <50% for Sb-1000 compared to the unpolluted S1), while an increase was recorded for those extracted from the Sb-spiked S2 soils (e.g. >2-fold for Sb-1000). The soil dehydrogenase activity followed the same trend. High-throughput 16S rRNA amplicon sequencing analysis revealed that Sb did not influence the bacterial α-diversity in both soils, while significantly affected the composition of the respective soil bacterial communities. Several phyla (e.g. Nitrosospira Nitrososphaeraceae, Adheribacter) were found positively correlated with the concentration of water-soluble Sb in soil. Overall, the results obtained suggest that the risk assessment in soils polluted with antimony should be a priority especially for alkaline soils where the high mobility of the anionic Sb(OH)₆- species can pose, at least in the short-term, a serious threat for soil microbial abundance, diversity and functionality, soil fertility and eventually human health.

Characteristics and interactions of bioaerosol microorganisms from wastewater treatment plants

Bacteria and fungi are abundant and ubiquitous in bioaerosols from wastewater treatment plants (WWTPs). However, the specificity and interactions of bioaerosol microorganism, particularly of potential pathogens, from WWTPs are still poorly understood. In this study, we investigated 9 full-scale WWTPs in different areas of China for 3 years, and found microbial variations in bioaerosols to be associated with regions, seasons, and processes. Relative humidity, total suspended particulates, wind speed, temperature, total organic carbon, NH₄⁺, Cl^- and Ca²⁺ were the major factors influencing this variation, and meteorological factors were more strongly associated with the variation than chemical composition. In total, 95 and 22 potential bacterial and fungal pathogens were detected in bioaerosols, respectively. The linear discriminant analysis effect size method suggested that Serratia, Yersinia, Klebsiella, and Bacillus were discriminative genera in bioaerosols on the whole, and were also hub niches in the interactions within potential bacterial pathogens, based on network analysis. Strong co-occurrences such as Serratia-Bacillus and Staphylococcus-Candida, and co-exclusions such as Rhodotorula-Cladosporium and Pseudomonas-Candida, were found within and between potential bacterial and fungal pathogens in bioaerosols from WWTPs. This study furthers understanding of the biology and ecology of bioaerosols from WWTPs, and offers a theoretical basis for determining bioaerosol control.

Influence of the application of Fe-Mn-La ternary oxide-biochar composites on the properties of arsenic-polluted paddy soil

Arsenic exists ubiquitously in the soil and has been proved to be of significant hazard to human health upon transmission through food chain. Herein, we determined the effects of Fe-Mn-La ternary oxide-biochar composites (FMLBCs) on arsenic (As) fractionation, soil enzyme activities, and microbial communities in arsenic-polluted soils. The results demonstrated that the proportion of non-swappable As fractions reduced and that of the exchangeable As fractions increased with the addition of FMLBCs. Furthermore, the addition of FMLBCs significantly increased the catalase (CAT) activity (P < 0.05), and an increase of 69.2-268% was observed when 2 wt% FMLBCs were added. Supplementation with biochar or FMLBCs increased the relative abundance of Proteobacteria and Acidobacteria and decreased the relative abundance of Firmicutes; moreover, the effect was more obvious as the addition amount of biochar or FMLBCs increased. In addition, the FMLBCs, except for FMLBC3, increased the content of available phosphorus. Moreover, amendments of FMLBCs led to an increase in the available potassium content by an average of 212%, 113%, and 62.1% in highly polluted soil. Therefore, the FMLBCs affected the physical and chemical properties of soil in different manners. The results suggested that the addition of FMLBCs changed the distribution and increased the immobilization of As in the soil; this could indirectly reduce the risk of the transport of As to rice. The amendment mechanism of FMLBCs may include changes to the physicochemical soil properties and consequently, the soil enzyme activities are affected, which can influence the microbial communities in soils.

Assessing Chromium Contamination in Red Soil: Monitoring the Migration of Fractions and the Change of Related Microorganisms

The improper stacking of chromium (Cr) slag poses a great threat to the environment and human health. The toxicity of Cr in soil is not only related to its total amount, but also to its fractions. A simulated experiment was conducted in laboratory to assess the environmental risk of Cr fractions migration and distribution in red soil. The results showed the content of acid-soluble and reducible Cr significantly decreased (P < 0.05) in top layer but increased in middle and substratum layers over time. This indicated that acid-soluble and reducible Cr migrated downward with time and the relative mobility of acid-soluble Cr (0.038 mg/kg·d·m) was higher than that of reducible Cr (0.028 mg/kg·d·m). Furthermore, correlation analysis between microbial community and chromium fraction showed the relative abundance of Lysobacter, Flavihumibacter, Flavisolbacter, and Altererythrobacter was significantly (P < 0.05) correlated with acid-soluble and reducible fractions. Thus, these microorganisms might be evaluators to assess the migration of acid-soluble and reducible fractions in red soil. In summary, this study provided a new comprehension on remediation of Cr-contaminated soil by monitoring the migration of acid-soluble and reducible fractions and the changes of related microbial groups.

Soil Biodiversity Integrates Solutions for a Sustainable Future

Soils are home to more than 25% of the earth’s total biodiversity and supports life on land and water, nutrient cycling and retention, food production, pollution remediation, and climate regulation. Accumulating evidence demonstrates that multiple sustainability goals can be simultaneously addressed when soil biota are put at the center of land management assessments; this is because the activity and interactions of soil organisms are intimately tied to multiple processes that ecosystems and society rely on. With soil biodiversity at the center of multiple globally relevant sustainability programs, we will be able to more efficiently and holistically achieve the Sustainable Development Goals and Aichi Biodiversity Targets. Here we review scenarios where soil biota can clearly support global sustainability targets, global changes and pressures that threaten soil biodiversity, and actions to conserve soil biodiversity and advance sustainability goals. This synthesis shows how the latest empirical evidence from soil biological research can shape tangible actions around the world for a sustainable future.

Bioremediation of Historically Chlorimuron-Ethyl-Contaminated Soil by Co-Culture Chlorimuron-Ethyl-Degrading Bacteria Combined with the Spent Mushroom Substrate

In this study, a novel chlorimuron-ethyl-degrading Pleurotus eryngiu-SMS-CB was successfully constructed for remediation of soil historically contaminated with chlorimuron-ethyl. The P. eryngiu-SMS-CB was prepared using efficient chlorimuron-ethyl-degrading cocultured bacteria, Rhodococcus sp. D310-1 and Enterobacter sp. D310-5, with spent mushroom substrate (SMS, a type of agricultural waste containing laccase) of Pleurotus eryngiu as a carrier. The chlorimuron-ethyl degradation efficiency in historically chlorimuron-ethyl-contaminated soil reached 93.1% at the end of 80 days of treatment with the P. eryngiu-SMS-CB. Although the P. eryngiu-SMS-CB altered the microbial community structure at the beginning of the 80 days, the bacterial population slowly recovered after 180 days; thus, the P. eryngiu-SMS-CB does not have an excessive effect on the long-term microbial community structure of the soil. Pot experiments indicated that contaminated soil remediation with P. eryngiu-SMS-CB reduced the toxic effects of chlorimuron-ethyl on wheat. This paper is the first to attempt to use chlorimuron-ethyl-degrading bacterial strains adhering to P. eryngiu-SMS to remediate historically chlorimuron-ethyl-contaminated soil, and the microbial community structure and P. eryngiu-SMS-CB activity in chlorimuron-ethyl-contaminated soil were traced in situ to evaluate the long-term effects of this remediation.

Ganoderma lucidum cultivation affect microbial community structure of soil, wood segments and tree roots

The popular medicinal mushroom Ganoderma lucidum (Fr.) Karst. [Ling Zhi] has been widely used for the general promotion of health and longevity in Asian countries. Continuous cultivation may affect soil microbe and soil properties. However, the effect of G. lucidum cultivation on related wood segments, soil and tree roots microbial communities and soil properties is remain unknown. In our study, the microbial communities of soils, wood segments, and tree roots before and after G. lucidum cultivation were investigated by Illumina Miseq sequencing of both ITS and 16S rDNA, and taxonomic composition of eukaryotic and prokaryotic microorganisms were observed. Indices of microbial richness, diversity and evenness significantly differed between before and after G. lucidum cultivation. Each of the investigated sampling type harbored a distinctive microbial community and differed remarkably before and after G. lucidum cultivation. Ascomycota and Basidiomycota (fungi), Proteobacteria and Actinobacteria (bacteria) showed significant differences after Ling Zhi cultivation. The soil property values also changed after cultivation. The redundancy analysis (RDA) showed that both the fungal and bacterial community structure significantly correlated with soil humus, pH, nitrogen, carbon and trace elements (Fe, Zn, Mn, Cu) contents. The results indicated that G. lucidum cultivation may have significant differed the associated microbial community structures and soil properties. The study will provide useful information for G. lucidum cultivation and under-forest economic development.

Advances in monitoring soil microbial community dynamic and function

Microorganisms are vital to the overall ecosystem functioning, stability, and sustainability. Soil fertility and health depend on chemical composition and also on the qualitative and quantitative nature of microorganisms inhabiting it. Historically, denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE), single-strand conformation polymorphism, DNA amplification fingerprinting, amplified ribosomal DNA restriction analysis, terminal restriction fragment length polymorphism, length heterogeneity PCR, and ribosomal intergenic spacer analysis were used to assess soil microbial community structure (SMCS), abundance, and diversity. However, these methods had significant shortcomings and limitations for application in land reclamation monitoring. SMCS has been primarily determined by phospholipid fatty acid (PLFA) analysis. This method provides a direct measure of viable biomass in addition to a biochemical profile of the microbial community. PLFA has limitations such as overlap in the composition of microorganisms and the specificity of PLFAs signature. In recent years, high-throughput next-generation sequencing has dramatically increased the resolution and detectable spectrum of diverse microbial phylotypes from environmental samples and it plays a significant role in microbial ecology studies. Next-generation sequencings using 454, Illumina, SOLiD, and Ion Torrent platforms are rapid and flexible. The two methods, PLFA and next-generation sequencing, are useful in detecting changes in microbial community diversity and structure in different ecosystems. Single-molecule real-time (SMRT) and nanopore sequencing technologies represent third-generation sequencing (TGS) platforms that have been developed to address the shortcomings of second-generation sequencing (SGS). Enzymatic and soil respiration analyses are performed to further determine soil quality and microbial activities. Other valuable methods that are being recently applied to microbial function and structures include NanoSIM, GeoChip, and DNA stable staple isotope probing (DNA-SIP) technologies. They are powerful metagenomics tool for analyzing microbial communities, including their structure, metabolic potential, diversity, and their impact on ecosystem functions. This review is a critical analysis of current methods used in monitoring soil microbial community dynamic and functions.