Paddy soil microbial communities driven by environment- and microbe-microbe interactions: A case study of elevation-resolved microbial communities in a rice terrace

Microbial Sulfur and Arsenic Oxidation Facilitate the Establishment of Biocrusts during Reclamation of Degraded Mine Tailings

Degraded tailings generated by the mining of metal ores are major environmental threats to the surrounding ecosystems. Tailing reclamation, however, is often impeded due to adverse environmental conditions, with depleted key nutrients (i.e., nitrogen (N) and phosphorus (P)) and elevated sulfur and metal(loid) concentrations. Formation of biocrusts may significantly accelerate nutrient accumulation and is therefore an essential stage for tailing reclamation. Although suggested to play an important role, the microbial community composition and key metabolisms in biocrusts remain largely unknown and are therefore investigated in the current study. The results suggested that sulfur and arsenic oxidation are potential energy sources utilized by members of predominant biocrust bacterial families, including Beijerinckiaceae, Burkholderiaceae, Hyphomicrobiaceae, and Rhizobiaceae. Accordingly, the S and As oxidation potentials are elevated in biocrusts compared to those in their adjacent tailings. Biocrust growth, as proxied by chlorophyll concentrations, is enhanced in treatments supplemented with S and As. The elevated biocrust growth might benefit from nutrient acquisition services (i.e., nitrogen fixation and phosphorus solubilization) fueled by microbial sulfur and arsenic oxidation. The current study suggests that sulfur- and arsenic-oxidizing microorganisms may play important ecological roles in promoting biocrust formation and facilitating tailing reclamation.

Combined effects of cadmium and simulated acid rain on soil microbial communities in the early cultivation of Populus beijingensis seedlings

The combined cadmium (Cd) and acid rain pollution poses a significant threat to the global ecological environment. Previous studies on the combined adverse effects have predominantly focused on the aboveground plant physiological responses, with limited reports on the microbial response in the rhizosphere soil. This study employed Populus beijingensis seedlings and potting experiments to simulate the impacts of combined mild acid rain (pH=4.5, MA) or highly strong acid rain (pH=3.0, HA), and soil Cd pollution on the composition and diversity of microbial communities, as well as the physiochemical properties in the rhizosphere soil. The results showed that Cd decreased the content of inorganic nitrogen, resulting in an overall decrease of 49.10 % and 46.67 % in ammonium nitrogen and nitrate nitrogen, respectively. Conversely, acid rain was found to elevate the content of total potassium and soil organic carbon by 4.68 %-6.18 % and 8.64-19.16 %, respectively. Additionally, simulated acid rain was observed to decrease the pH level by 0.29-0.35, while Cd increased the pH level by 0.11. Moreover, Cd alone reduced the rhizosphere bacterial diversity, however, when combined with acid rain, regardless of its intensity, Cd was observed to increase the diversity. Fungal diversity was not influenced by the acid rain, but Cd increased fungal diversity to some extend under HA as observed in bacterial diversity. In addition, composition of the rhizosphere bacterial community was primarily influenced by the inorganic nitrogen components, while the fungal community was driven mainly by soil pH. Furthermore, "Metabolism" was emerged as the most significant bacterial function, which was markedly affected by the combined pollution, while Cd pollution led to a shift from symbiotroph to other trophic types for fungi. These findings suggest that simulated acid rain has a mitigating effect on the diversity of rhizosphere bacteria affected by Cd pollution, and also alters the trophic type of these microorganisms. This can be attributed to the acid rain-induced direct acidic environment, as well as the indirect changes in the availability or sources of carbon, nitrogen, or potassium.

Impacts of multiple environmental factors on soil bacterial community assembly in heavy metal polluted paddy fields

Soil microorganisms play pivotal roles in driving essential biogeochemical processes in terrestrial ecosystems, and they are sensitive to heavy metal pollution. However, our understanding of multiple environmental factors interaction in heavy metal polluted paddy fields to shape microbial community assembly remain limited. In the current study, we used 16S rRNA amplicon sequencing to characterize the microbial community composition in paddy soils collected from a typical industry town in Taihu region, eastern China. The results revealed that Cd and Pb were the major pollutant, and Proteobacteria, Acidobacteria and Chloroflexi were the dominate indigenous bacterial phyla. Linear regression and random forest analysis demonstrated that soil pH was the most important predictor of bacterial diversity. Mantel analysis showed that bacterial community structure was mainly driven by pH, CEC, silt, sand, AK, total Cd and DTPA-Cd. The constructed bacterial co-occurrence network, utilizing a random matrix theory-based approach, exhibited non-random with scale-free and modularity features. The major modules within the networks also showed significant correlations with soil pH. Overall, our study indicated that soil physiochemical properties made predominant contribution to bacterial community diversity, structure and their association in Cd/Pb polluted paddy fields. These findings expand our knowledge of the key environmental drivers and co-occurrence patterns of bacterial community in polluted paddy fields.

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome

BACKGROUND

Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome.

RESULTS

After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments).

CONCLUSION

Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.

Comparative analysis of root associated microbes in tropical cultivated and weedy rice (Oryza spp.) and temperate cultivated rice

Weedy rice is a major problem in paddy fields around the world. It is well known that weedy rice appears to grow faster and mature earlier than cultivated rice. It is possible that differences in the root microbial genetics are correlated with this characteristic. This study incorporated 16S rRNA amplicon sequencing to study the microbial composition in the rhizosphere and endosphere of rice root. No significant difference was found between the microbiota associated with weedy and cultivated rice lines grown in the same field. It was found that the endosphere had less microbial diversity compared to the rhizosphere. The major groups of bacteria found in the endosphere are from the phylum Proteobacteria, Myxococcota, Chloroflexota, and Actinobacteria. In addition, by analyzing the microbiome of japonica rice grown in the field in a temperate climate, we found that despite differences in genotype and location, some bacterial taxa were found to be common and these members of the putative rice core microbiome can also be detected by in situ hybridization. The delineation of a core microbiome in the endosphere of rice suggests that these bacterial taxa might be important in the life cycle of a wide range of rice types.

Stability and Assembly Mechanisms of Butterfly Communities across Environmental Gradients of a Subtropical Mountain

Mountain ecosystems harbor evolutionarily unique and exceptionally rich biodiversity, particularly in insects. In this study, we characterized the diversity, community stability, and assembly mechanisms of butterflies on a subtropical mountain in the Chebaling National Nature Reserve, Guangdong Province, China, using grid-based monitoring across the entire region for two years. The results showed that species richness, abundance, and Faith's phylogenetic diversity decreased with increasing elevation; taxonomic diversity played a considerable role in mediating the effects of environmental changes on stability. Moreover, our results showed that stochastic processes are dominant in governing the assembly of butterfly communities across all elevational gradients, with habitats at an elevation of 416-580 m subjected to the strongest stochastic processes, whereas heterogeneous selection processes displayed stronger effects on the assembly of butterfly communities at 744-908 m, 580-744 m, and 908-1072 m, with abiotic factors inferred as the main driving forces. In addition, significant differences were detected between the barcode tree and the placement tree for the calculated β-NTI values at 416-580 m. Overall, this study provides new insights into the effects of environmental change on the stability and assembly of butterflies in Chebaling, which will be beneficial for biodiversity conservation and policy development.

Fate of carbon influenced by the in-situ growth of phototrophic biofilms at the soil-water interface of paddy soil

Phototrophic biofilms (PBs) are commonly found in the sediment/soil-water interface of paddy soils and have a significant impact on carbon cycles. However, the specific carbon fate influenced by the in-situ growth of PBs in paddy soil remains unclear. In this study, we investigated the effect of in situ PBs growth on methane and carbon dioxide emissions, as well as dissolved organic matter (DOM) transformation. Our findings demonstrated a negative correlation between PBs growth and methane and carbon dioxide emissions, while showing a positive correlation with DOM composition. The in-situ growth of PBs reduced methane emissions by approximately 79 % and carbon dioxide emissions by approximately 33 % in the daytime, and also slowed down the degradation rate of dissolved organic matter from over 30.4 % to <16 %. Microsensor measurements revealed that these changes were attributed to the increased concentration and penetration depth of oxygen, as well as variations in pH caused by the growth of in situ PBs. Co-occurrence analysis indicated a robust correlation between DOM transformation and the significantly suppressed methanogenesis by methanogens such as Methanosaeta, Methanomassiliicoccus and Methanosarcina, and also the notably enhanced methane oxidation by methanotrophs including Methylobacterium, Methyloversatilis and Methylomonas, in response to the growth of PBs. These findings shed light on the impact of in situ PBs on methane and carbon dioxide emissions and DOM transformation, providing new insights for understanding carbon cycling in paddy soils.

Preliminary analysis of mucosal and salivary bacterial communities in oral lichen planus

OBJECTIVE

To characterize the bacterial community from different oral niches (buccal mucosa and saliva) in oral lichen planus (OLP) patients.

SUBJECTS AND METHODS

This preliminary study analyzed site-specific (mucosa and saliva) microbial landscape of 20 OLP patients and 10 healthy controls.

RESULTS

The microbial diversity was similar between OLP patients and healthy controls in both salivary and mucosal communities. However, the topological properties of co-occurrence networks of salivary and mucosal microbiome were different between healthy controls and OLP patients. SparCC analysis inferred three and five keystone taxa in the salivary and mucosal microbial networks of healthy controls, respectively. However, in the salivary and mucosal bacterial networks of OLP patients, only one hub OTU and three OTUs were identified as keystone taxa, respectively. In addition, analysis of community cohesion revealed that mucosal microbial community in OLP patients had lower stability than that in healthy controls. In final, correlation assay showed that the clinical severity of OLP was positively associated with the relative abundance of Rothia in saliva but negatively associated with that of Porphyromonas on mucosa.

CONCLUSIONS

The salivary and mucosal bacterial communities of OLP patients differ in terms of composition, the genera associated with OLP severity, and co-occurrence patterns.

Reciprocal Interactions of Abiotic and Biotic Dechlorination of Chloroethenes in Soil

Chloroethenes (CEs) as common organic pollutants in soil could be attenuated via abiotic and biotic dechlorination. Nonetheless, information on the key catalyzing matter and their reciprocal interactions remains scarce. In this study, FeS was identified as a major catalyzing matter in soil for the abiotic dechlorination of CEs, and acetylene could be employed as an indicator of the FeS-mediated abiotic CE-dechlorination. Organohalide-respiring bacteria (OHRB)-mediated dechlorination enhanced abiotic CEs-to-acetylene potential by providing dichloroethenes (DCEs) and trichloroethene (TCE) since chlorination extent determined CEs-to-acetylene potential with an order of trans-DCE > cis-DCE > TCE > tetrachloroethene/PCE. In contrast, FeS was shown to inhibit OHRB-mediated dechlorination, inhibition of which could be alleviated by the addition of soil humic substances. Moreover, sulfate-reducing bacteria and fermenting microorganisms affected FeS-mediated abiotic dechlorination by re-generation of FeS and providing short chain fatty acids, respectively. A new scenario was proposed to elucidate major abiotic and biotic processes and their reciprocal interactions in determining the fate of CEs in soil. Our results may guide the sustainable management of CE-contaminated sites by providing insights into interactions of the abiotic and biotic dechlorination in soil.

Hydrochemical characteristics and microbial community evolution of Pinglu River affected by regional abandoned coal mine drainage, Guizhou Province, China

Pinglu River in southwestern China was continuously polluted by acid mine drainage (AMD) from abandoned coal mines, and AMD has become a major source of recharge to the river (43.26% of total flow), resulting in structural changes in the physicochemical properties and microbial communities of river water and sediments. In this study, we collected abandoned coal mine drainage, river water, and river sediment samples for comprehensive analysis. Results indicated that the hydrochemical types of AMD from abandoned coal mines were mainly SO₄-Ca·Mg. The pH of river water in Pinglu River decreased from upstream to downstream due to AMD, with the hydrochemical type gradually changing from SO₄·HCO₃-Ca·Mg to SO₄-Ca·Mg. The variation of pH along the river sediments was less than that of water samples, which remained weakly alkaline. However, high-throughput sequencing revealed a gradual decrease in microbial diversity in river sediments from upstream to downstream. The core bacteria groups in the upstream sediments were mainly attributed to the phylum Proteobacteria and Actinobacteriota, mainly including Geobacter, Anaeromyxobacter, Marmoricola, and Phycicoccus. The relative abundance of Gaiella, MND1, and Pseudolabrys in sediment samples gradually increased with the confluence of AMD, and the differences in microbial communities may be attributed to pH, TOC, and TP. Results of phenotype prediction demonstrated that the relative abundance of anaerobic microorganisms in river sediment gradually decreased from upstream to downstream (from 24.77 to 12.46%), presumably due to the large amount of oligotrophic AMD converge.

Enrichment and response of iron-metabolizing microorganisms and metabolic genes in the contaminated area of stratified stacking coal gangue dumps, Northern China

In the Xishan coalfield of northern China, the stratified stacking of soil and gangue was applied to limit the acid pollution from high-sulfur coal gangue. In this study, we found that stratified stacking can effectively neutralize the acidity, with the pH value of gangue-leaching water being 6.02-8.13. In contrast to the acidic contaminated area, most of the microorganisms in the study area sediment were neutrophilic, with the main genera being Arthrobacter, Pseudorhodobacter, Pseudomonas, and Rhodoferax. A variety of iron- and sulfur-metabolizing bacteria was discovered in the gangue-leaching sediment, with the total relative abundance ranging from 4.20 to 23.75%, of which the iron-reducing bacteria (FeRB) accounted for the highest percentage. The distributions of these functional microorganisms in the samples were significantly influenced by Fe and S. The co-occurrence network analysis revealed a significant positive correlation between the iron- and sulfur-metabolizing bacteria in the sediment (93.75%), indicating a strong reciprocal symbiotic relationship between these bacteria. The iron and sulfur metabolism genes in the sediment were predicted and compared based on the Tax4Fun functional prediction method. Results showed that functional genes related to iron metabolism were highly expressed in the gangue-leaching sediment. This study enhances the understanding of iron and sulfur metabolism in gangue-leaching contaminated areas.

Evolution of livelihood vulnerability in rice terrace systems: Evidence from households in the Ziquejie terrace system in China

Introduction

Globally, terraces, and rice terrace systems face problems that affect their sustainability, such as terrace degradation, abandonment, de-agriculturalization, labor migration, etc. The implementation of development projects such as reforestation, poverty alleviation, and tourism development have changed traditional smallholder livelihood patterns. It is not clear whether farmers' livelihoods have become more resilient or vulnerable as a result.

Methods

Using survey data on households' livelihoods in a rice terrace system in Southern China, we evaluated the livelihood impacts of multiple changes.

Results

The results show that development projects are not entirely beneficial. The attributes and intensity of the disturbance of projects (e.g., tourism) on land functions, and differentiated farmer strategies jointly drive the hierarchical evolution of livelihood vulnerability. In detail, underdeveloped tourism increased rather than reduced livelihood vulnerability; the role of agriculture in livelihood directly exacerbated the variation in vulnerability levels; this resulted in the most vulnerable livelihood for households that are exogenously dependent or located in the core tourism area.

Discussion

Subsequently, an evolutionary model of livelihood vulnerability is proposed in this study. Based on this, we judged that the livelihood vulnerability of rice terrace systems has entered a chaotic stage of adaptation. Reducing livelihood vulnerability will require the support of a tangible and circular pathway of benefits between farmers and the land. Policies should focus on the heterogeneity of farmers and the “negative effects” of development projects on livelihood. This household-level farmer livelihood vulnerability dynamics study goes beyond anti-poverty to provide science-based practical guidance to promote the sustainable development of rice terrace systems.

Novel insights in seasonal dynamics and co-existence patterns of phytoplankton and micro-eukaryotes in drinking water reservoir, Northwest China: DNA data and ecological model

Although associations between phytoplankton and micro-eukaryotes have been studied in aquatic ecosystems, there are still knowledge gaps in comprehending their dynamics and interactions in drinking water reservoirs. Here, the seasonal dynamics of phytoplankton and micro-eukaryotic diversities and their co-existence patterns were studied in a drinking water reservoir, Northwest China. The highest phytoplankton diversity was observed in summer, and Chlorella sp. that belongs to Chlorophyta was the most abundant genus. The highest eukaryotic diversity was also detected in summer, and Rimostrombidium sp. that belongs to Ciliophora was the most dominant genus. Mantel test showed that the phytoplankton diversity was significantly correlated with ammonia nitrogen (r = 0.561, p = 0.001) and dissolved organic carbon (r = 0.267, p = 0.017), while the eukaryotic diversity was significantly associated with ammonia nitrogen (r = 0.265, p = 0.034) and temperature (r = 0.208, p = 0.046). PLS-PM (Partial Least Squares Path Modeling) further revealed that nutrients (P < 0.01) significantly affected the phytoplankton diversity, while nutrients (P < 0.01) and temperature (P < 0.01) significantly influenced the eukaryotic diversity. Co-occurrence network displayed the primarily positive interactions (77.66% positive and 22.34% negative) between phytoplankton and micro-eukaryotes. These findings could deepen our understanding of interactions between phytoplankton and micro-eukaryotes and their driving factors under changing aquatic environments of drinking water reservoirs.

Response of soil microbial communities and rice yield to nitrogen reduction with green manure application in karst paddy areas

Fertilizer application practices are one of the major challenges facing agroecology. The agrobenefits of combined application of green manure and chemical fertilizers, and the potential of green manure to replace chemical fertilizers are now well documented. However, little is known about the impact of fertilization practices on microbial communities and tice yield. In this study, the diversity of bacterial and fungal communities, symbiotic networks and their relationship with soil function were analyzed in five fertilization treatments (N: 100% nitrogen fertilizer alone; M: green manure alone; MN₆₀: green manure couple with 60% nitrogen fertilizer, MN₈₀: green manure couple with 80% nitrogen fertilizer; and MN₁₀₀: green manure couple with 100% nitrogen fertilizer). First, early rice yield was significantly higher by 12.6% in MN₁₀₀ treatment in 2021 compared with N. Secondly, soil bacterial diversity showed an increasing trend with increasing N fertilizer application after green manure input, however, the opposite was true for fungal diversity. Microbial interaction analysis showed that different fertilizer applications changed soil microbial network complexity and fertilizer-induced changes in soil microbial interactions were closely related to soil environmental changes. Random forest models further predicted the importance of soil environment, microorganisms and rice yield. Overall, nitrogen fertilizer green manure altered rice yield due to its effects on soil environment and microbial communities. In the case of combined green manure and N fertilizer application, bacteria and fungi showed different responses to fertilization method, and the full amount of N fertilizer in combination with green manure reduced the complexity of soil microbial network. In contrast, for more ecologically sensitive karst areas, we recommend fertilization practices with reduced N by 20-40% for rice production. Graphical Abstract.

Divergent prokaryotic microbial assembly, co-existence patterns and functions in surrounding river sediments of a Cu-polymetallic deposit in Tibet

The exploitation of polymetallic deposits produces large amounts of mine drainage, which poses great challenges to the surrounding aquatic ecosystem. However, the prokaryotic microbial community assembly and co-existence patterns in the polluted area are poorly understood, especially in high-altitude localities. Herein, we investigated the prokaryotic microbial assembly, co-existence patterns and their potential functional responses in surrounding river sediments of a Cu-polymetallic deposit in Tibet. The sediments from mine drainage and surrounding tributaries exhibited distinct geochemical gradients, especially the changes in Cu content. The microbial community structure changed significantly, accompanied by decreased richness and diversity with increased Cu content. Interestingly, the relative abundances of some potential functional bacteria (e.g., Planctomycetota) actually increased as the Cu levels raised. In low contaminated area, ecological drift was the most important assembly process, whereas deterministic processes gained importance with pollution levels. Meanwhile, negative interactions in co-occurrence networks were more frequent with higher modularity and reduced keystone taxa in high contaminated area. Notably, the functions related to ABC transporters and quorum sensing (QS) were more abundant with high Cu content, which helped bacteria work together to cope with the stressful environment. Taken together, the physicochemical gradients dominated by Cu content drove the distribution, assembly and co-existence patterns of microbial communities in surrounding river sediments of a Cu-polymetallic deposit. These findings provide new insights into the maintenance mechanisms of prokaryotic microbial communities in response to heavy metal stress at high altitudes.

The Biosorption of Copper(II) Using a Natural Biofilm Formed on the Stones from the Metro River, Malang City, Indonesia

Biofilm is the predominant habitat of microbes in aquatic ecosystems. Microhabitat inside the biofilm matrix is a nutrient-rich environment promoted by the adsorption of nutrient ions from the surrounding water. Biofilms can not only adsorb ions that are nutrients but also other ions, such as heavy metals. The ability of biofilm to attract and retain heavy metals, such as copper(II), makes biofilms a promising biosorbent for water pollution treatment. The present study analyzes the characteristics of copper(II) adsorption by biofilms naturally formed in the river. The biofilms used in this study grow naturally on the stones in the Metro River in Malang City, Indonesia. Methods to analyze the adsorption characteristics of copper(II) by biofilms were kinetics of the adsorption and adsorption isotherm. The maximum adsorption amount and the adsorption equilibrium constant were calculated using a variant of the Langmuir isotherm model. In addition, the presence of the functional groups as suggested binding sites in biofilm polymers was investigated using the Fourier transform infrared (FTIR) analysis. The results indicate that copper(II)’s adsorption to the biofilm is a physicochemical process. The adsorption of copper(II) is fitted well with the Langmuir isotherm model, suggesting that the adsorption of copper(II) to a biofilm is due to the interaction between the adsorption sites on the biofilm and the ions. The biofilm’s maximum absorption capacity for copper(II) is calculated to be 2.14 mg/wet-g of biofilm, with the equilibrium rate constant at 0.05 L/mg. Therefore, the biofilms on the stones from river can be a promising biosorbent of copper(II) pollution in aquatic ecosystems.

Effects of combined applications of straw with industrial and agricultural wastes on greenhouse gases emissions, temperature sensitivity, and rice yield in a subtropical paddy field

The incorporation of post-harvest crop straw and application of industrial and agricultural wastes to paddy soils increase rice crop yields and soil fertility. However, the impacts of combined applications of straw and waste products on greenhouse gas (GHG) emissions and global warming potential (GWP) of paddy soils are unclear. Therefore, we conducted a field experiment in subtropical rice in China to test the effects of applications of straw, straw+biochar, straw+shell slag, straw+gypsum slag, straw+silicon, and straw+steel slag on rice yields, GWP, and greenhouse gas emission intensity (GHGI). The results showed that, compared to the control, cumulative emissions of carbon dioxide (CO₂) from paddy soils were 15.2, 16.9, and 36.6 % lower following application of straw+steel slag, straw+silicon, and straw+gypsum, respectively, and cumulative emissions of methane (CH₄) were 5.0 and 62.1 % lower following application of straw+steel slag and straw+gypsum, respectively. Meanwhile, relative to the addition of straw alone, application of straw+steel slag and straw+gypsum reduced GHG emissions largely due to reductions in CO₂ emissions, further declining the GWP of CO₂ and GHGI. In addition, temperature sensitivity (Q₁₀) of CO₂ emissions was highest following application of straw+silicon and lowest following application of straw+gypsum. There were no treatment effects on mean dissolved porewater concentrations of CO₂, CH₄, or nitrous oxide (N₂O) and soil emissions of CO₂ were negatively correlated with mean dissolved concentrations of CO₂, CH₄, and N₂O. Rice yields were reduced following application of straw+gypsum and unaffected by the other treatments. Thus, relative to the addition of straw alone or control, we suggest the combined application of straw+steel slag may improve the sustainability of paddy rice production, because it reduces GWP, while maintaining yields.

Microbial communities in swamps of four mangrove reserves driven by interactions between physicochemical properties and microbe in the North Beibu Gulf, China

Mangroves are distributed in coastal and estuarine regions and are characterized as a sink for terrestrial pollution. It is believed that complex interactions between environmental factors and microbial communities exist in mangrove swamps. However, little is known about environment-microbe interactions. There is a need to clarify some important environmental factors shaping microbial communities and how environmental factors interact with microbial assemblages in mangrove swamps. In the present study, physicochemical and microbial characteristics in four mangrove reserves (named ZZW, Qin, Bei, and GQ) in the North Beibu Gulf were determined. The interactions between environmental factors and microbial assemblages were analyzed with statistical methods in addition to CCA and RDA. Higher concentrations of sulfate (SO₄^2--S) and Fe but lower concentrations of total phosphorus (TP) and NO₃^--N were detected in ZZW and Qin. Nutrient elements (NO₃^--N, NH₄⁺-N, organic matter (OM), SO₄^2--S, Fe, and TP) were more important than heavy metals for determining the microbial assemblages, and NO₃^--N was the most important factor. NO₃^--N, SO₄^2--S, TP, and Fe formed a significant co-occurrence network in conjunction with some bacterial taxa, most of which were Proteobacteria. Notably, comparatively elevated amounts of sulfate-reducing bacteria (Desulfatibacillum, Desulfomonile, and Desulfatiglans) and sulfur-oxidizing bacteria (Thioprofundum and Thiohalophilus) were found in ZZW and Qin. The co-occurrence network suggested that some bacteria involved in sulfate reduction and sulfur oxidation drive the transformation of P and N, resulting in the reduction of P and N in mangrove swamps. Through the additional utilization of multivariate regression tree (MRT) and co-occurrence network analysis, our research provides a new perspective for understanding the interactions between environmental factors and microbial communities in mangroves.

Dissolved organic carbon drives nutrient cycling via microbial community in paddy soil

Microbial mediated iron cycling drives the biogeochemical cycling of carbon, nitrogen, sulfur, and phosphorus. However, the fate of the microbial community and the relative metabolic pathways in paddy soil after the addition of biogas slurry are poorly understood. In this study, the response of functional genes was investigated by growing one-season rice in paddy soils in a pot experiment. Seven treatments were prepared: 1) control (CK); 2) organic carbon (OC); 3) fertilizer (F); 4) 5% of biogas slurry (B05); 5) 10% of biogas slurry (B10); 6) 15% of biogas slurry (B15); 7) 20% of biogas slurry (B20). In the biogas slurry treatments, Geobacter increased more than in the other treatments during rice growth, which were structured by TOC. Particularly, in the B10 treatment, the relative abundance of Geobacter was 1.6 and 14.8 times higher than that of CK at the heading and mature stages, respectively. At the heading stage, the addition of biogas slurry and OC shifted the microbial phosphorus-transformation communities differently. There were no significant differences in the carbon, nitrogen, and sulfur metabolic pathways between the two treatments. At the mature stage, the carbon: nitrogen: phosphorus balance was significantly influenced by the regulation of functional gene expression and metabolic activities. These findings provide insight into the key factors affecting carbon, nitrogen, sulfur, phosphorus, and iron during rice growth after carbon inputs.

Continental-Scale Paddy Soil Bacterial Community Structure, Function, and Biotic Interaction

Rice paddy soil-associated microbiota participate in biogeochemical processes that underpin rice yield and soil sustainability, yet continental-scale biogeographic patterns of paddy soil microbiota remain elusive. The soil bacteria of four typical Chinese rice-growing regions were characterized and compared to those of nonpaddy soils. The paddy soil bacteria were significantly less diverse, with unique taxonomic and functional composition, and harbored distinct cooccurrence network topology. Both stochastic and deterministic processes shaped soil bacteria assembly, but paddy samples exhibited a stronger deterministic signature than nonpaddy samples. Compared to other environmental factors, climatic factors such as mean monthly precipitation and mean annual temperature described most of the variance in soil bacterial community structure. Cooccurrence network analysis suggests that the continental biogeographic variance in bacterial community structure was described by the competition between two mutually exclusive bacterial modules in the community. Keystone taxa identified in network models (Anaerolineales, Ignavibacteriae, and Deltaproteobacteria) were more sensitive to changes in environmental factors, leading us to conclude that environmental factors may influence paddy soil bacterial communities via these keystone taxa. Characterizing the uniqueness of bacterial community patterns in paddy soil (compared to nonpaddy soils) at continental scales is central to improving crop productivity and resilience and to sustaining agricultural soils.

IMPORTANCE Rice fields provide food for over half of the world’s human population. The ecology of paddy soil microbiomes is shaped by human activities, which can have a profound impact on rice yield, greenhouse gas emissions, and soil health. Investigations of the soil bacteria in four typical Chinese rice-growing regions showed that (i) soil bacterial communities maintain highly modularized species-to-species network structures; (ii) community patterns were shaped by the balance of integrated stochastic and deterministic processes, in which homogenizing selection and dispersal limitation dominate; and (iii) deterministic processes and climatic and edaphic factors influence community patterns mainly by their impact on highly connected nodes (i.e., keystone taxa) in networks. Characterizing the unique ecology of bacterial community patterns in paddy soil at a continental scale may lead to improved crop productivity and resilience, as well as sustaining agricultural soils.

Effects of long-term discharge of acid mine drainage from abandoned coal mines on soil microorganisms: microbial community structure, interaction patterns, and metabolic functions

More than twenty abandoned coal mines in the Yudong River Basin of Guizhou Province have discharged acid mine drainage (AMD) for a long time. The revelation of microbial community composition, interaction patterns, and metabolic functions can contribute to a better understanding of such ecosystems, which in its turn can be helpful in the development of strategies aiming at the ecological remediation of AMD pollution. In this study, reference and contaminated soil samples were collected along the AMD flow path for high-throughput sequencing. Results showed that the long-term AMD pollution promoted the evolution of γ-Proteobacteria, and the acidophilic iron-oxidizing bacteria Ferrovum (relative abundance of 15.50%) and iron-reducing bacteria Metallibacterium (9.87%) belonging to this class became the dominant genera. Co-occurrence analysis revealed that the proportion of positive correlations among bacteria increased from 51.02 (reference soil) to 75.16% (contaminated soil), suggesting that acidic pollution promotes the formation of mutualistic interaction networks of microorganisms. Metabolic function prediction (Tax4Fun) revealed that AMD contamination enhanced microbial functions such as translation, repair, and biosynthesis of peptidoglycan and lipopolysaccharide, etc., which may be an adaptive mechanism for microbial survival in extremely acidic environment. In addition, acidic pollution promoted the high expression of nitrogen-fixing genes in soil, and the discovery of autotrophic nitrogen-fixing bacteria such as Ferrovum highlights the possibility of using this taxon for bioremediation of AMD pollution.

Compositional Shift of Bacterial, Archaeal, and Fungal Communities Is Dependent on Trophic Lifestyles in Rice Paddy Soil

The soil environment determines plants’ health and performance during their life cycle. Therefore, ecological understanding on variations in soil environments, including physical, chemical, and biological properties, is crucial for managing agricultural fields. Here, we present a comprehensive and extensive blueprint of the bacterial, archaeal, and fungal communities in rice paddy soils with differing soil types and chemical properties. We discovered that natural variations of soil nutrients are important factors shaping microbial diversity. The responses of microbial diversity to soil nutrients were related to the distribution of microbial trophic lifestyles (oligotrophy and copiotrophy) in each community. The compositional changes of bacterial and archaeal communities in response to soil nutrients were mainly governed by oligotrophs, whereas copiotrophs were mainly involved in fungal compositional changes. Compositional shift of microbial communities by fertilization is linked to switching of microbial trophic lifestyles. Random forest models demonstrated that depletion of prokaryotic oligotrophs and enrichment of fungal copiotrophs are the dominant responses to fertilization in low-nutrient conditions, whereas enrichment of putative copiotrophs was important in high-nutrient conditions. Network inference also revealed that trophic lifestyle switching appertains to decreases in intra- and inter-kingdom microbial associations, diminished network connectivity, and switching of hub nodes from oligotrophs to copiotrophs. Our work provides ecological insight into how soil nutrient-driven variations in microbial communities affect soil health in modern agricultural systems.

Change in microbial profile and environmental conditions in a constructed wetland system treating greywater

The objective of this work was to verify the relationships between environmental conditions and microbial processes along a raw-light greywater flow in an improved constructed wetland (CW) system. Physicochemical analysis and high-throughput DNA sequencing were performed in the different zones to investigate the environmental conditions and microbial communities. The results showed that the system operated predominantly under anaerobic conditions, with redox potential (Eh) increasing from the inlet (-342.9 mV) to the outlet (-316.4 mV). Conversely, the chemical oxygen demand (COD) decreased along the greywater flow, suggesting negative correlation between these characteristics. The zones of the evapotranspiration and treatment tank (CEvaT) were characterized by lower community diversity and richness and by the presence of specific groups: Proteobacteria and Synergistetes related to the first steps of the conversion of organic carbon, in the bottom layer inside the anaerobic chamber (AnC); methanogens (Methanosaeta and Methanobacterium) and sulphate-reducing bacteria (Desulfovibrio, Desulforhabdus and Desulfomonile) in the middle layer; and microorganisms associated with the nitrogen cycle and oxygen release (Acinetobacter, Novosphingobium, Candidatus Nitrososphaera) in the top layer. On the other hand, the increase of the ORP and decrease of organic matter concentrations were associated with higher community diversity and richness in the middle layer of the CW, which showed higher abundance of microorganisms involved in methane (Methylobacterium and Candidatus Koribacter) and sulphur (Rhodoblastus and Thiobacillus) oxidation.

Exploring the allochthonous pollution influence on bacterial community and co-occurrence dynamics of River Ganga water through 16S rRNA-tagged amplicon metagenome

River Ganga is one of the largest and most sacred rivers of India. This river is largely affected by anthropogenic activities causing significant increase in water pollution. The impact of drains discharging polluted water on the bacterial community dynamics in the river remains unexplored. To elucidate this, the targeted 16S rRNA V3-V4 variable region amplicon sequencing and bioinformatic analysis were performed using water from upstream, drain, and downstream of river Ganga. Analysis revealed significant difference in relative abundances of bacterial communities. The increase in bacterial abundance and alpha diversity was detected in the downstream compared to the upstream. Environmental factors were found significantly different between upstream and downstream water. At the phyla level, highly abundant taxa such as Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, and Verrucomicrobia were observed. Bacterial genera like Prevotella, Bacteroides, Blautia, and Faecalibacterium (fecal indicator) had higher abundance in the downstream site. Network co-occurrence revealed that bacterial communities have a modular profile with reduced interaction in drain and downstream water. The network of co-occurring bacterial communities consists of 283 nodes with edge connectivity of 6900, 7074, and 5294 in upstream, drain, and downstream samples, respectively. Upstream communities exhibited the highest positive interaction followed by the drain and the downstream sites. Additionally, highly abundant pathogenic species such as Acinetobacter baumannii and Prevotella copri were also detected in all samples. This study suggests the drain to be allochthonous pollution vector that significantly contributes to bacterial community enrichment. From the results of this study, it is apparent that the lotic water may be used as the ecological reference to understand and monitor the variations in the bacterial communities and their co-occurrence dynamics in the fresh water ecosystems.

Prokaryotic and microeukaryotic communities in an experimental rice plantation under long-term use of pesticides

Conventional agricultural practices, such as rice plantations, often contaminate the soil and water with xenobiotics. Here we evaluated the microbiota composition in experimental rice planting with a record of prolonged pesticide use, using 16S and 18S rRNA amplicon sequencing. We investigated four components of a complete agricultural system: affluent water (A), rice rhizosphere soil (R), sediment from a storage pond (S), and effluent (E) water (drained from the storage pond). Despite the short spatial distance between our sites, the beta diversity analysis of bacterial communities showed two well-defined clusters, separating the water and sediment/rhizosphere samples; rhizosphere and sediment were richer while the effluent was less diverse. Overall, the site with the highest evenness was the rhizosphere. Unlike the bacterial communities, Shannon diversity of microeukaryotes was significantly different between A and E. The effluent presented the lowest values for all ecological indexes tested and differed significantly from all sampled sites, except on evenness. When mapped the metabolic pathways, genes corresponding to the degradation of aromatic compounds, including genes related to pesticide degradation, were identified. The most abundant genes were related to the degradation of benzoate. Our results indicate that the effluent is a selective environment for fungi. Interestingly, the overall fungal diversity was higher in the affluent, the water that reached the system before pesticide application, and where the prokaryotic diversity was the lowest. The affluent and effluent seem to have the lowest environmental quality, given the presence of bacteria genera previously recorded in environments with high concentrations of pesticide residues. The microbiota, environmental characteristics, and pesticide residues should be further studied and try to elucidate the potential for pesticide degradation by natural consortia. Thus, extensive comparative studies are needed to clarify the microbial composition, diversity, and functioning of rice cultivation environments, and how pesticide use changes may reflect differences in microbial structure.

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.

Reservoir water stratification and mixing affects microbial community structure and functional community composition in a stratified drinking reservoir

To investigate how the aquatic bacterial community of a stratified reservoir drives the evolution of water parameters, the microbial community structure and network characteristics of bacteria in a stratified reservoir were investigated using Illumina MiSeq sequencing technology. A total of 42 phyla and 689 distinct genera were identified, which showed significant seasonal variation. Additionally, stratified variations in the bacterial community strongly reflected the vertical gradient and seasonal changes in water temperature, dissolved oxygen, and nutrition concentration. Furthermore, principal coordinate analysis indicated that most microorganisms were likely influenced by changes in water stratification conditions, exhibiting significant differences during the stratification period and mixing period based on Adonis, MRPP, and Anosim. Compared to the stratification period, 123 enhanced operational taxonomic units (OTUs; 29%) and 226 depleted OTUs (52%) were identified during the mixing period. Linear discriminant analysis effect size results showed that 15 major genera were enriched in the mixing period and 10 major genera were enriched in the stratification period. Importantly, network analysis revealed that the keystone species belonged to hgcI_clade, CL500-29, Acidibacter, Paucimonas, Flavobacterium, Prochlorothrix, Xanthomonadales, Chloroflexia, Burkholderiales, OPB56, KI89A_clade, Synechococcus, Caulobacter or were unclassified. Redundancy analysis showed that temperature, dissolved oxygen, pH, chlorophyll-α, total phosphorus, nitrate, and ammonia were important factors influencing the water bacterial community and function composition, which were consistent with the results of the Mantel test analysis. Furthermore, random forest analysis showed that temperature, dissolved oxygen, ammonia, and total dissolved phosphorous were the most important variables predicting water bacterial community and function community α- and β-diversity (P < 0.05). Overall, these results provide insight into the interactions between the microbial community and water quality evolution mechanism in Zhoucun reservoir.

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.

Chemolithoautotropic Diazotrophy Dominates the Nitrogen Fixation Process in Mine Tailings

Nutrient deficiency, especially bio-available nitrogen deficiency, often impedes the bioremediation efforts of mining generated tailings. Biological nitrogen fixation is a critical process necessary for the initial nitrogen buildup in tailings. Current knowledge regarding the diazotrophs that inhabit tailings is still in its infancy. Therefore, in this study, a comprehensive investigation combining geochemical characterization, sequence analyses, molecular techniques, and activity measurements was conducted to characterize the diazotrophic community residing in tailing environments. Significant differences between tailings and their adjacent soils in prokaryotic and diazotrophic communities were detected. Meanwhile, strong and significant correlations between the absolute abundance of the nitrogen fixation (nifH), carbon fixation (cbbL), sulfur oxidation (soxB), and arsenite oxidation (aioA) genes were observed in the tailings but not in the soils. The reconstructed nif-containing metagenome-assembled genomes (MAGs) suggest that the carbon fixation and sulfur oxidation pathways were important for potential diazotrophs inhabiting the tailings. Activity measurements further confirmed that diazotrophs inhabiting tailings preferentially use inorganic electron donors (e.g., elemental sulfur) compared to organic electron donors (e.g., sucrose), while diazotrophs inhabiting soils preferred organic carbon sources. Collectively, these findings suggest that chemolithoautotrophic diazotrophs may play essential roles in acquiring nutrients and facilitating ecological succession in tailings.

Characteristics and Driving Factors of the Aerobic Denitrifying Microbial Community in Baiyangdian Lake, Xiong'an New Area

Here, the ion-exchangeable form of nitrogen (IEF-N), weak-acid extractable form of nitrogen (WAEF-N), strong-alkali extractable form of nitrogen (SAEF-N), strong-oxidant extractable form of nitrogen (SOEF-N), residue nitrogen (Res-N), and total nitrogen (TN) showed spatial differences, and most of the sediment nitrogen fractions exhibited positive correlations in Baiyangdian Lake. High-throughput sequencing analysis revealed that the aerobic denitrification microbial community was composed of proteobacteria (42.04%–99.08%) and unclassified_bacteria (0.92%–57.92%). Moreover, the microbial community exhibited significant differences (R² = 0.4422, P < 0.05) on the basis of the adonis analysis. T(temperature), Moisture content (MC), sediment total phosphorus (STP), ion-exchangeable form of ammonia (IEF-NH₄⁺-N), weak-acid extractable form of ammonia (WAEF-NH₄⁺-N), weak-acid extractable form of nitrate (WAEF-NO₃⁻-N), and strong-alkali extractable form of ammonia (SAEF-NH₄⁺-N) were the dominant environmental factors and explained 11.1%, 8.2%, 10.7%, 6.9%, 9.3%, 8.1%, 10.5%, 7.5%, and 7% variation, respectively, of the total variation in the microbial community. Furthermore, the network analysis showed that symbiotic relationships accounted for a major percentage of the microbial networks. The keystone aerobic denitrifying bacteria belonged to Comamonas, Rhodobacter, Achromobacter, Aeromonas, Azoarcus, Leptothrix_Burkholderiales, Pseudomonas, Thauera, unclassified_Burkholderiales, and unclassified_bacteria. The composition of the keystone aerobic denitrifying microbial community also exhibited significant differences (R² = 0.4534, P < 0.05) on the basis of the adonis analysis. T, STP, IEF-NH₄⁺-N, ion-exchangeable form of nitrate (IEF-NO₃⁻-N), WAEF-NO₃⁻-N, SAEF-NH₄⁺-N, and TN were the dominant environmental factors that explained 8.4%, 6.2%, 4.6%, 5.9%, 5.9%, 4.5%, and 9.4% variation, respectively, of the total variation in the keystone aerobic denitrifying microbial community. The systematic investigation could provide a theoretical foundation for the evolution mechanism of the aerobic denitrifying microbial community in Baiyangdian Lake.

Pollutant removal performance and microbial enhancement mechanism by water-lifting and aeration technology in a drinking water reservoir ecosystem

Here, the performance and mechanism of pollutant removal in the Zhoucun reservoir by water-lifting and aeration systems (WLAs) were explored. The hypolimnion anoxic layer disappeared and the reservoir was mixed after the WLAs were operated for approximately 35 days, providing a suitable environment for pollutant removal. Operation of the system enhanced the metabolic activity of the water microbes and their capacity for purification, which contributed to the removal of nitrogen, organic carbon, Fe, Mn, P, and S. Specifically, the total N concentration decreased from 2.55 to 0.48 mg/L, showing an 81.18% removal rate. Microbial metabolism and the diversity index increased following the operation of the WLAs in the Zhoucun Reservoir. Furthermore, the water reservoir clearly inhibited the performance of Fe, Mn, P, and S through the WLA operation, meeting the requirements for class III based on the Chinese Surface Water Environmental Quality Standard (GB3838-2002). High-throughput sequencing analysis revealed increased levels of indicator and keystone operational taxonomic units belonging to Flavobacterium, hgcI_clade, Rheinheimera, Dechloromonas, Pseudomonas, and Rhodocyclaceae, which are related to the degradation of organic carbon and removal of nitrogen and phosphorus. Moreover, total N, ammonia, total P, dissolved oxygen, temperature, and pH were the principal factors affecting the microbial community based on redundancy analysis and the Mantel test. Furthermore, network analysis showed that symbiotic relationships accounted for the major proportion of the microbial network. Our results provide a theoretical foundation for the efficiency of N removal and essential technical support for improving the self-repair capacity of water in drinking water reservoirs.

Bacterial networks mediate pentachlorophenol dechlorination across land-use types with citrate addition

Soil microorganisms play a crucial role in the bioremediation of pentachlorophenol (PCP)-contaminated soils. However, whether and how soil bacterial networks with keystone taxa affect PCP dechlorination is not well understood. The present study investigated the effects of citrate on soil bacterial networks mediating PCP dechlorination by direct and indirect transformation in iron-rich upland and paddy soils. The rates of PCP dechlorination and Fe(II) generation were accelerated by citrate addition, particularly in the paddy soils. Network analysis revealed that the topological properties of bacterial networks were changed by citrate addition; more modules and keystone taxa were significantly correlated with PCP dechlorination and Fe(II) generation in the networks. Random forest modeling indicated that Clostridiales was the most important bacterial order; it was significantly involved in both the direct and indirect pathways of PCP dechlorination. Citrate addition had less influence on the balance between the direct and indirect pathways of PCP dechlorination in the upland soils, whereas it enhanced biological PCP dechlorination more directly and efficiently in the paddy soils. Our results suggested that land-use type and citrate addition play a critical role in controlling the biogeochemical mechanisms of PCP dechlorination.

Volatile organic compounds in the salt-lake sediments of the Tibet Plateau influence prokaryotic diversity and community assembly

Volatile organic compounds (VOCs) are important environmental factors because they supply nutrients for microbial cells and mediate intercellular interactions. However, few studies have focused on the effects of VOCs on prokaryotic diversity and community composition. In this study, we examined the relationship between prokaryotic diversity and community composition and the content of VOCs in salt-lake sediments from the Tibet Plateau using amplicon sequencing of the 16S rRNA gene. Results showed that the alpha-diversity indices (Chao1, Shannon, and Simpson) were generally negatively correlated with the content of 36 VOCs (P < 0.05). The prokaryotic communities were significantly driven by multiple VOCs at the lineage-dependent pattern (P < 0.05). Further analysis indicated that VOCs, including 3-methylpyruvate, biuret, isocitric acid, and stearic acid, jointly explained 37.3% of the variations in prokaryotic communities. Supplemental VOCs-pyruvate, biuret, alanine, and aspartic acid-notably decreased the Chao1 and Shannon indices and significantly assembled co-occurrence networks for the bacterial communities in the saline sediments. Together, these results demonstrated that VOCs play a critical role in the regulation of the diversity, compositions, and network structures of prokaryotic communities in saline sediments.

A biophysiological perspective on enhanced nitrate removal from decentralized domestic sewage using gravitational-flow multi-soil-layering systems

Multi-soil-layering (MSL) system with brick-wall pattern structure and gravitational flow can be used for decentralized rural domestic sewage treatment. The capability of soil for contaminant removal is maximized within soil mixture blocks (SMBs). However, the performance of removing nitrate was still not ideal during operation. To improve its performance in MSL system, the relationship between biophysiological characteristics of denitrifying species and operating conditions was studied. Microbial species diversity of activated sludge and soil samples were analyzed. The significant effects of independent factors and their interactions on microbial species diversity and denitrifying species abundance were revealed on the basis of factorial analysis. The results indicated activated sludge in SMBs played a key role in increasing the richness of denitrifying species in MSL system. Slow-release poly (butylene succinate) (PBS) had the most dominant positive effect on increasing denitrifying species abundance. Submersion had significantly positive effect on species richness in SMBs. These three factors, including activated sludge, PBS in SMBs, and submersion condition had different significant effects on microbial responses. They were favorable for denitrification and ensuring a better removal efficiency of nitrate and total nitrogen. The porous zeolites were served as the habitats for most of aerobic bacteria to form biofilms, which could promote the oxygen consumption in both sewage and system to improve denitrification in SMBs. The results could help on the enhancement of denitrification in MSL system from biophysiological insights. It can provide a sound strategy for using MSL system with great performance on contaminant removal.

Industrial wastes: Fly ash, steel slag and phosphogypsum- potential candidates to mitigate greenhouse gas emissions from paddy fields

Waste management and global warming are the two challenging issues of the present global scenario. Increased human population has set the platform for rapid industrialization and modern agriculture. The industries such as energy, steel, and fertilizers play a significant role in improving the social, and economic status of human beings. The industrial production of energy (that involves combustion of coal), production of steel items and diammonium ammonium fertilizer generate a huge amount of wastes such as fly ash (FA), steel slag (SS) and phosphogypsum (PG), respectively. Inappropriate dumping of any kind of waste poses a threat to the environment, therefore, scientific management of waste is required to reduce associated environmental risks. These wastes i.e. SS, FA, and PG being rich sources of oxides of calcium (CaO), silicon (SiO₂), iron (FeO), and aluminum (Al₂O₃), etc. may affect the release of greenhouse gases from the soil. The information associated with the application of FA, SS, and PG onto the paddy fields and their impacts on methane and nitrous oxide emissions are highly fragmented and scarce. The present review extensively and critically explores the available information with respect to the effective utilization of FA, SS, and PG in paddy cultivation, their potential to mitigate greenhouse gases emission and their associated mechanisms. The fine grid assessment of these waste management provides new insight into the next level research and future policy options for industries and farmers.

Risk assessment for and microbial community changes in Farmland soil contaminated with heavy metals and metalloids

Food security and human health can be seriously affected by heavy metal and metalloid (HM) pollution of soil. In this study, the risks posed by HMs and microbial community responses to HM pollution of agricultural soil in southwestern China were investigated. The C, N, P, and S (nutrients) concentrations were 12040.7-15912.7, 1298.06-1832.01, 750.91-2050.35, and 269.17-2115.52 mg/kg, respectively. The As, Cd, Cr, Cu, Hg, Ni, Pb, and Zn concentrations were 3.11-8.20, 1.85-6.56, 22.83-43.96, 11.21-23.30, 0.08-0.81, 11.02-22.97, 24.07-42.96, and 193.63-698.39 mg/kg, respectively. Interpolation analysis indicated that the nutrient and HM concentrations varied spatially rather strongly. The concentrations of all of the elements were higher in soil from the northern sampling sites than in soil from the other sites. HMs in soil were found to pose high levels of risk (RI 898.85, i.e., >600). Cd contributed more than the other HMs to the risk assessment values (Er_Cd 293.72-1031.94), so was the most serious contaminant. Microbial diversity decreased over time in soil with high HM concentrations (plot S2) and was lower than in soil with low HM concentrations (plot S8). The nutrient and HM concentrations correlated with the microbial community characteristics. Proteobacteria, Acidobacteria, and Chloroflexi were (in decreasing order) the dominant bacterial phyla. We speculate that these phyla may be strongly resistant to HMs. The fourth most common phylum was Actinobacteria. Bacteria in this phylum could be used as biological indicators of the HM pollution status. Soil micro-ecosystems can self-regulate. HM stress will affect the evolution of soil microorganisms and relevant functional genes. The spatiotemporal variability in the microbial community responses to HMs and the spatial analysis and ecological risk assessment results will be useful reference data for the remediation of HM-polluted soil.

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.

Bacterial response to antimony and arsenic contamination in rice paddies during different flooding conditions

Rice is more vulnerable to arsenic (As) and antimony (Sb) contamination than other cereals due to the special cultivation methods, during which irrigation conditions are adjusted depending upon the growth stages. The changes in irrigation conditions may alter the oxidation states of Sb and As, which influences their mobility and bioavailability and hence uptake by rice. In this study, bacterial responses to As and Sb contamination in rice fields were investigated during two different stages of rice growth: the vegetative stage (flooded conditions), and the ripening stage (drained conditions). The substantial changes in the irrigation conditions caused a variation in geochemical parameters including the As- and Sb-extractable fractions. As and Sb were more mobile and bioaccessible during the flooded than under drained conditions. The microbial communities varied during two irrigation conditions, suggesting that the geochemical conditions may have different effects on the innate paddy microbiota. Therefore, various statistical tools including co-occurrence network and random forest (RF) were performed to reveal the environment-microbe interactions in two different irrigation conditions. One of the notable findings is that Sb- and As-related parameters exerted more influences during the flooded than under drained conditions. Furthermore, a detailed RF analysis indicated that the individual bacterial taxa may also respond differently to contaminant fractions during the two irrigation conditions. Notably, RF indicated that individual taxa such as Clostridiaceae and Geobacter may be responsible for biotransformation of As and Sb (e.g., As and Sb reduction). The results provided knowledge for As and Sb transformation during contrasting irrigation conditions and the potential mitigation strategy for contaminant removal.

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.

Impacts of Human Activities on the Composition and Abundance of Sulfate-Reducing and Sulfur-Oxidizing Microorganisms in Polluted River Sediments

Water system degradation has a severe impact on daily life, especially in developing countries. However, microbial changes associated with this degradation, especially changes in microbes related to sulfur (S) cycling, are poorly understood. In this study, the abundance, structure, and diversity of sulfate-reducing microorganisms (SRM) and sulfur-oxidizing microorganisms (SOM) in the sediments from the Ziya River Basin, which is polluted by various human interventions (urban and agricultural activities), were investigated. Quantitative real-time PCR showed that the S cycling-related (SCR) genes (dsrB and soxB) were significantly elevated, reaching 2.60 × 10⁷ and 1.81 × 10⁸ copies per gram of dry sediment, respectively, in the region polluted by human urban activities (RU), and the ratio of dsrB to soxB abundance was significantly elevated in the region polluted by human agricultural activities (RA) compared with those in the protected wildlife reserve (RP), indicating that the mechanisms underlying water system degradation differ between RU and RA. Based on a 16S rRNA gene analysis, human interventions had substantial effects on microbial communities, particularly for microbes involved in S cycling. Some SCR genera (i.e., Desulfatiglans and Geothermobacter) were enriched in the sediments from both RA and RU, while others (i.e., Desulfofustis and Desulfonatronobacter) were only enriched in the sediments from RA. A redundancy analysis indicated that NH₄⁺-N and total organic carbon significantly influenced the abundance of SRM and SOM, and sulfate significantly influenced only the abundance of SRM. A network analysis showed high correlation between SCR microorganisms and other microbial groups for both RU and RA, including those involved in carbon and metal cycling. These findings indicated the different effects of different human interventions on the microbial community composition and water quality degradation.

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

In this study, we sampled rhizosphere soils from seven different agricultural fields adjacent to mining areas and cultivated with different crops (corn, rice, or soybean), to study the interactions among the innate microbiota, soil chemical properties, plants, and metal contamination. The rhizosphere bacterial communities were characterized by Illumina sequencing of the 16S rRNA genes, and their interactions with the local environments, including biotic and abiotic factors, were analyzed. Overall, these soils were heavily contaminated with multiple metal(loid)s, including V, Cr, Cu, Sb, Pb, Cd, and As. The interactions between environmental parameters and microbial communities were identified using multivariate regression tree analysis, canonical correspondence analysis, and network analysis. Notably, metal-microbe interactions were observed to be crop specific. The rhizosphere communities were strongly correlated with V and Cr levels, although these sites were contaminated from Sb and Zn/Pb mining, suggesting that these two less-addressed metals may play important roles in shaping the rhizosphere microbiota. Members of Gaiellaceae cooccurred with other bacterial taxa (biotic interactions) and several metal(loid)s, suggesting potential metal(loid) resistance or cycling involving this less-well-known taxon.IMPORTANCE The rhizosphere is the "hub" for plant-microbe interactions and an active region for exchange of nutrients and energy between soil and plants. In arable soils contaminated by mining activities, the rhizosphere may be an important barrier resisting metal uptake. Therefore, the responses of the rhizosphere microbiota to metal contamination involve important biogeochemical processes, which can affect metal bioavailability and thus impact food safety. However, understanding these processes remains a challenge. The current study illustrates that metal-microbe interactions may be crop specific and some less-addressed metals, such as V and Cr, may play important roles in shaping bacterial communities. The current study provides new insights into metal-microbe interactions and contributes to future implementation and monitoring efforts in contaminated arable soils.

The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

BACKGROUND

Paddy soil dissolved organic matter (DOM) represents a major hotspot for soil biogeochemistry, yet we know little about its chemodiversity let alone the microbial community that shapes it. Here, we leveraged ultrahigh-resolution mass spectrometry, amplicon, and metagenomic sequencing to characterize the molecular distribution of DOM and the taxonomic and functional microbial diversity in paddy soils across China. We hypothesized that variances in microbial community significantly associate with changes in soil DOM molecular composition.

RESULTS

We report that both microbial and DOM profiles revealed geographic patterns that were associated with variation in mean monthly precipitation, mean annual temperature, and pH. DOM molecular diversity was significantly correlated with microbial taxonomic diversity. An increase in DOM molecules categorized as peptides, carbohydrates, and unsaturated aliphatics, and a decrease in those belonging to polyphenolics and polycyclic aromatics, significantly correlated with proportional changes in some of the microbial taxa, such as Syntrophobacterales, Thermoleophilia, Geobacter, Spirochaeta, Gaiella, and Defluviicoccus. DOM composition was also associated with the relative abundances of the microbial metabolic pathways, such as anaerobic carbon fixation, glycolysis, lignolysis, fermentation, and methanogenesis.

CONCLUSIONS

Our study demonstrates the continental-scale distribution of DOM is significantly correlated with the taxonomic profile and metabolic potential of the rice paddy microbiome. Abiotic factors that have a distinct effect on community structure can also influence the chemodiversity of DOM and vice versa. Deciphering these associations and the underlying mechanisms can precipitate understanding of the complex ecology of paddy soils, as well as help assess the effects of human activities on biogeochemistry and greenhouse gas emissions in paddy soils.