Coupling between nitrogen-fixing and iron(III)-reducing bacteria as revealed by the metabolically active bacterial community in flooded paddy soils amended with glucose

High biological N fixation potential dominated by heterotrophic diazotrophs in alpine permafrost rivers on the Qinghai‒Tibet Plateau

Biological nitrogen (N) fixation is a pivotal N source in N-deficient ecosystems. The Qinghai‒Tibet Plateau (QTP) region, which is assumed to be N limited and suboxic, is an ideal habitat for diazotrophs. However, the diazotrophic communities and associated N fixation rates in these high-altitude alpine permafrost QTP rivers remain largely unknown. Herein, we examined diazotrophic communities in the sediment and biofilm of QTP rivers via the nitrogenase (nifH) gene sequencing and assessed their N fixing activities via a 15N isotope incubation assay. Strikingly, anaerobic heterotrophic diazotrophs, such as sulfate- and iron-reducing bacteria, had emerged as dominant N fixers. Remarkably, the nifH gene abundance and N fixation rates increased with altitude, and the average nifH gene abundance (2.57 ± 2.60 × 108 copies g-1) and N fixation rate (2.29 ± 3.36 nmol N g-1d-1) surpassed that documented in most aquatic environments (nifH gene abundance: 1.31 × 105 ∼ 2.57 × 108 copies g-1, nitrogen fixation rates: 2.34 × 10-4 ∼ 4.11 nmol N g-1d-1). Such distinctive heterotrophic diazotrophic communities and high N fixation potential in QTP rivers were associated with low-nitrogen, abundant organic carbon and unique C:N:P stoichiometries. Additionally, the significant presence of psychrophilic bacteria within the diazotrophic communities, along with the enhanced stability and complexity of the diazotrophic networks at higher altitudes, clearly demonstrate the adaptability of diazotrophic communities to extreme cold and high-altitude conditions in QTP rivers. We further determined that altitude, coupled with organic carbon and phosphorus, was the predominant driver shaping diazotrophic communities and their N-fixing activities. Overall, our study reveals high N fixation potential in N-deficient QTP rivers, which provides novel insights into nitrogen dynamics in alpine permafrost rivers.

Immobilization of zinc and cadmium by biochar-based sulfidated nanoscale zero-valent iron in a co-contaminated soil: Performance, mechanism, and microbial response

Mining and smelting of mineral resources causes excessive accumulation of potentially toxic metals (PTMs) in surrounding soils. Here, biochar-based sulfidated nanoscale zero-valent iron (SNZVI/BC) was designed via a one-step liquid phase reduction method to immobilize cadmium (Cd) and zinc (Zn) in a copolluted arable soil. A 60 d soil incubation experiment revealed that Cd and Zn immobilization efficiency by 6 % SNZVI/BC (25.2-26.2 %) was higher than those by individual SNZVI (13.9-18.0 %) or biochar (14.0-19.3 %) based on the changes in diethylene triamine pentaacetic acid (DTPA)-extractable PTM concentrations in soils, exhibiting a synergistic effect. Cd2+ or Zn2+ replaced isomorphously Fe2+ in amorphous ferrous sulfide, as revealed by XRD, XPS, and high-resolution TEM-EDS, forming metal sulfide precipitates and thus immobilizing PTMs. PTM immobilization was further enhanced by adsorption by biochar and oxidation products (Fe2O3 and Fe3O4) of SNZVI via precipitation and surface complexation. SNZVI/BC also increased the concentration of dissolved organic carbon and soil pH, thus stimulating the abundances of beneficial bacteria, i.e., Bacilli, Clostridia, and Desulfuromonadia. These functional bacteria further facilitated microbial Fe(III) reduction, production of ammonium and available potassium, and immobilization of PTMs in soils. The predicted function of the soil microbial community was improved after supplementation with SNZVI/BC. Overall, SNZVI/BC could be a promising functional material that not only immobilized PTMs but also enhanced available nutrients in cocontaminated soils.

Nitrogen fixation and diazotroph diversity in groundwater systems

Biological nitrogen fixation (BNF), the conversion of N2 into bioavailable nitrogen (N), is the main process for replenishing N loss in the biosphere. However, BNF in groundwater systems remains poorly understood. In this study, we examined the activity, abundance, and community composition of diazotrophs in groundwater in the Hetao Plain of Inner Mongolia using 15N tracing methods, reverse transcription qPCR (RT-qPCR), and metagenomic/metatranscriptomic analyses. 15N2 tracing incubation of near in situ groundwater (9.5-585.4 nmol N L-1 h-1) and N2-fixer enrichment and isolates (13.2-1728.4 nmol N g-1 h-1, as directly verified by single-cell resonance Raman spectroscopy), suggested that BNF is a non-negligible source of N in groundwater in this region. The expression of nifH genes ranged from 3.4 × 103 to 1.2 × 106 copies L-1 and was tightly correlated with dissolved oxygen (DO), Fe(II), and NH4+. Diazotrophs in groundwater were chiefly aerobes or facultative anaerobes, dominated by Stutzerimonas, Pseudomonas, Paraburkholderia, Klebsiella, Rhodopseudomonas, Azoarcus, and additional uncultured populations. Active diazotrophs, which prefer reducing conditions, were more metabolically diverse and potentially associated with nitrification, sulfur/arsenic mobilization, Fe(II) transport, and CH4 oxidation. Our results highlight the importance of diazotrophs in subsurface geochemical cycles.

Effects of capping on microbial populations and contaminant immobilization in an old unlined landfill

This research aimed at evaluating the effects of capping on the mitigation of impacts generated by a closed unlined landfill in São Carlos, SP, Brazil. Physicochemical and microbiological analyses (16S rRNA sequencing) of buried solid waste samples were performed, in capped and uncapped areas. Even though leachate pockets could still be encountered in capped areas, the capping construction reduced oxygen availability and created more reducing conditions, propitiating the development of sulfate-reducing bacteria and possibly contributing to the precipitation of the metals Pb, Cd, Ni, Co, As, and Zn as metal sulfides, causing their immobilization. The microbial populations adapted to the anaerobic conditions created under capped zones belonged to the phyla Firmicutes, Chloroflexi, and Euryarchaeota and the genera Methanosaeta, Hydrogenispora, Smithella, and Gelria. Differently, the phyla Acidobacteria, Proteobacteria, Bacteroidetes, and Actinobacteria were more abundant in samples from the uncapped zones, in which the abundance of different genera varied homogeneously. Methanogenic activity was not impaired by the intervention measure, as assessed by the specific methanogenic activity (SMA). Capping of old unlined landfills brings benefits to the immobilization of metals and does not impair microbial degradation, being effective for the mitigation of impacts on soils and water resources.

Changes of bacterial community structure,monosaccharide composition and CO2 exchange along the successional stages of biological soil crusts

Biological soil crusts (BSCs) are a dominant ecological landscape of drylands, which have a significant impact on global biogeochemical flux. However, it is unclear how bacterial community and physiological characteristics vary along the BSCs successional stages. In this study, bacterial community composition, physiological characteristics, and monosaccharide composition of extracellular polysaccharides (EPSs) were compared among different successional stages. Our findings demonstrated that besides the dominant bacterial species, the bacterial communities also showed considerable differences between these two stages. Cyanobacteria were keystone taxa in the early stage, while heterotrophic bacteria (Proteobacteria, Actinobacteria and Acidobacteria) were keystone taxa in the later stages. According to the results of CO₂ exchange, cyanobacterial crusts accumulated net carbon faster than moss crusts, while moss crusts had a significantly higher respiration rate. The monosaccharide analysis indicated that the EPSs components also varied depending on BSCs' successional stages. Specifically, the contents of rhamnose and arabinose were higher in the cyanobacterial crusts than other types of crusts, while the contents of fucose, xylose, mannose and glucose were the highest in cyanobacterial-lichen crusts, and galactose content was highest in the moss crusts. Altogether, our results stress the heterogeneous variation of BSCs along with succession, and this work offered a fresh viewpoint for a deeper comprehension of the interactions between the monosaccharide components of EPS and the networks of bacterial communities in BSCs.

Pollutant impacts on bacteria in surface water and sediment: Conventional versus emerging pollutants in Taihu Lake, China

Bacteria play a critical role in biogeochemical cycling, self-purification, and food web fueling in surface freshwater ecosystems. However, the comparison between the impacts of conventional and emerging pollutants on the bacteria in surface water and sediment remains unclear and requires for an in-depth understanding to assess ecological risk and select associated bioindicators. Taihu Lake, a typical shallow lake in China, was divided into pollutant impacted and less-impacted zones for sampling. Spatial distributions of conventional pollutants, emerging pharmaceuticals, and bacterial communities were investigated in surface water and sediment. The correlations of pollutants with bacterial communities and the variations in bacterial functions were analyzed to help assess the pollutant influences on bacteria. The results showed that the water quality index and trophic level index across the whole lake were at medium to good, and mesotropher to light eutropher grades, respectively, indicating a relatively good control on conventional pollutants in water. Target pharmaceuticals were at much higher concentrations in water of the impacted zone compared to the less-impacted zone, exhibiting close positive relationships with the bacterial phyla in the impacted water. The ratio of Firmicutes to Proteobacteria in surface water is suggested as a plausible bioindicator to evaluate the level of inflow pharmaceutical contamination and the risk of relevant bacterial resistance in the outflow. In sediment, no significant difference was observed for pharmaceuticals between the two zones, whereas total phosphorus and orthophosphate were substantially higher in the impacted zone. Phosphorus pollutants were tightly associated with the bacterial genera in the impacted sediment, likely relating to the increase in iron- or sulfate-reducing bacteria which implies the potential risk of phosphorus releasing from sediment to water.

Seasonal Hypoxia Enhances Benthic Nitrogen Fixation and Shapes Specific Diazotrophic Community in the Eutrophic Marine Ranch

Recently, a growing number of studies have confirmed that biological nitrogen fixation is also an important reactive nitrogen source in coastal regions. However, how benthic nitrogen fixation and diazotrophic community in coastal regions respond to seasonal hypoxia remains largely unknown. In this study, we investigated the spatiotemporal pattern of potential nitrogen fixation rate and diazotrophic abundance and community in sediments of a eutrophic marine ranch experiencing summer hypoxia using 15N tracing and high throughput sequencing techniques. The results showed that potential nitrogen fixation rates ranged from 0.013 to 10.199 μmol kg−1 h−1, and were significantly enhanced by summer hypoxia (ANOVA, p < 0.05). However, nifH gene abundance peaked in June. The diazotrophic community was dominated by Geobacteraceae (>60%), followed by Desulfobulbaceae (13.61%). Bottom water oxygen, pH, Chl-a concentration, and sediment NH4+ significantly regulated benthic nitrogen fixation, while the variation of diazotrophic community was explained by sediment TOC, TN, and Fe content (p < 0.05). This study highlighted that hypoxia stimulated benthic nitrogen fixation, which counteracted the nitrogen removal by denitrification and anammox, and could further aggregate eutrophication of the coastal marine ranch. Moreover, the result emphasized the importance of nitrogen fixation in coastal regions for the global N budget.

Citric acid secretion from rice roots contributes to reduction and immobilization of Cr(VI) by driving microbial sulfur and iron cycle in paddy soil

Root exudates released by plants can promote microbial growth and activity, thereby affecting the transformation and availability of soil pollutants. However, the effects of the root exudates of rice plants on chromium (Cr) transformation in paddy soils and the underlying mechanisms are yet to be elucidated properly. The present study investigated how rice root exudates interact with rhizosphere microorganisms to influence the transformation of Cr and explored the key components in root exudates that affect Cr(VI) reduction. The results showed that the addition of root exudate and citric acid markedly decreased soil pH and increased dissolved organic carbon content that created favorable conditions and provided sufficient electron donors for Cr(VI) reduction, thereby greatly facilitating the reduction of Cr(VI) and the transformation of HOAc-extractable Cr into more stable oxidizable and residual Cr. Additionally, Desulfovibrio-related sulfate-reducing bacteria, Thiobacillus-related sulfide-oxidizing bacteria, and Geobacter-related Fe(III)-reducing bacteria were enriched with the addition of root exudate and citric acid. Among them, sulfate would be reduced by Desulfovibrio to sulfide, which would be further utilized by Thiobacillus to reduce Cr(VI), thereby enabling the continuous reduction of Cr(VI); simultaneously, Geobacter would sustain the reduction of Cr(VI) by reducing Fe(III) to Fe(II). Furthermore, based on the high-level secretion of citric acid in response to Cr(VI) exposure and the similar effects of root exudates and citric acid on Cr(VI) reduction, it is proposed that citric acid is the key component in rice root exudates that affects Cr(VI) reduction. These results suggest that root exudates (citric acid as the key component) contribute to the reduction and immobilization of Cr(VI) by driving microbial S and Fe cycles, with Desulfovibrio, Thiobacillus, and Geobacter being the keystone genera. The study provides a novel insight into the Fe/S/Cr co-transformation processes with microbial involvement, and the artificial root exudate mixtures designed to reduce Cr(VI).

Responses of microbial community composition and function to biochar and irrigation management and the linkage to Cr transformation in paddy soil

Combining biochar with irrigation management to alter the microbial community is a sustainable method for remediating soils contaminated by heavy metals. However, studies on how these treatments promote Cr(VI) reduction are limited, and the corresponding microbial mechanisms are unclear. Therefore, we conducted a pot experiment to explore the responses of soil microbial communities to combined biochar amendment and irrigation management strategies and their involvement in Cr transformation in paddy soils. Six treatments were established using varying concentrations of biochar (0, 1, and 2% [w/w]) combined with two irrigation management strategies (continuous flooding [CF] and dry-wet alternation [DWA]). The results showed that the combined biochar addition and irrigation management strategy significantly altered soil pH, redox potential, organic matter content, and Fe(II) and sulfide concentrations. In addition, the Cr(VI) concentration under CF irrigation management was conspicuously lower (48.2-54.4%) than that under DWA irrigation management. Biochar amendment also resulted in a substantial reduction (8.8-27.4%) in Cr(VI) concentration. Moreover, the changes in soil physicochemical properties remarkably affected the soil microbial community. The microbial diversity and abundance significantly increased with biochar amendment. Furthermore, the combined biochar amendment and CF strategy stimulated the growth of Geobacter- and Anaeromyxobacter-related Fe(III)-reducing bacteria, Gallionella-related Fe(II)-oxidizing bacteria, and Desulfovibro- and Clostridium-related sulfate-reducing bacteria, which simultaneously facilitated the generation of Fe(II) and sulfide, thereby enhancing Cr(VI) reduction. Consequently, our results suggest that the effectively increased abundance of Fe-reducing/oxidizing bacteria and sulfate-reducing bacteria via combined CF irrigation management and biochar addition may be a key factor in reducing Cr(VI) in paddy soil. The keystone genera responsible for Cr(VI) reduction were Geobacter, Anaeromyxobacter, Gallionella, Desulfovibro, and Clostridium. This study provides novel insights into the coupling mechanism of the Fe/S/Cr transformation mediated by Fe-reducing/oxidizing bacteria and sulfate-reducing bacteria.

Simulation of the effects of microplastics on the microbial community structure and nitrogen cycle of paddy soil

Microplastics (MPs) are ubiquitous in farmland soils. However, few studies have evaluated their effects on the microbial community structure and nitrogen cycle of farmland soils. Here, 0.3% and 1% (mass percentage) of polyethylene terephthalate (PET), polyvinyl chloride (PVC), and polylactic acid (PLA) MPs were added to paddy soil to evaluate their impact on the paddy soil microenvironment. The alpha index of the PLA MP treatment was significantly different from that of the control group (p-value < 0.05). In contrast, the indices of the PET and PVC MP treatments were not different from the control (p-value > 0.05). Among the MP treatments, the alpha index of the PLA MP group was significantly different from the PET and PVC MP groups (p-value < 0.05). PCoA analysis also indicated that there were differences between PLA and other MP groups, and different MP concentrations and exposure times had a great impact on microbial composition. The three MPs affected NH₄⁺ metabolism by changing the abundance of a NH₂OH-forming gene (amoA) and an organic nitrogen-forming gene (gdh), as well as the abundances of Thiobacillus, Bradyrhizobium, Anaeromyxobacter, Geobacter, and Desulfobacca. Further, the MPs affected NO₃^- metabolism by regulating the abundance of the nirS and nirK genes and the abundance of Nitrospirae. In contrast, NO₂^- metabolism was not significantly affected by the MPs due to the low concentration of NO₂^-, which was attributed to the high abundance of nirS and nirK in the sample. Taken together, our findings indicated that MP addition may have an inhibitory effect on the nitrogen cycle in paddy soils and that the effect of degradable MPs may be greater than that of their non-degradable counterparts. Given the increasing severity of worldwide MP contamination, additional studies are required to assess their impact on global ecosystems and biogeochemical cycles.

Comparative characterization of microbial communities that inhabit PFAS-rich contaminated sites: A case-control study

The historic usage and discharge of per- and polyfluoroalkyl substances (PFAS) containing chemicals have produced many contaminated sites and PFAS contamination has become a global concern due to their persistence, widespread distribution, and potential adverse impacts for human and environmental health. However, there have been limited investigations on the specific behavior of bacterial communities in PFAS contaminated soils. In this study, a quantitative PCR assay and Illumina MiSeq sequencing were used to investigate the variations of bacterial communities in a regional Australian airport contaminated with PFAS. The dominate PFAS detected in soil samples was Perfluorooctanesulfonic acid (PFOS), which accounted for 82% of total PFAS and the maximum PFOS level was noted (20,947±1824 ng.PFOS/mg.Soil) at the top soil. Irrespective of the degree of PFAS contamination at different depths, the comparable percentile contribution of each PFAS was observed in soil samples. Significantly higher bacteria amplicon sequence variant (ASV) and diversity were noted in uncontaminated soil than PFAS contaminated soil. Bacterial genera Rhodanobacter and Chujaibacter were dominant in the PFAS contaminated soil. Three different bacterial genera of Alphaproteobacteria, Ambiguous taxa of Acidobacteriia, and genus Chujaibacter of Gammaproteobacteria showed a significant positive correlation and RB41, Gaiella showed a significant negative correlation with 11 different PFAS concentrations. Overall, the results presented in this study suggest that the counts and species diversity of soil microorganisms are adversely influenced by PFAS contamination.

Short-Term Legacy Effects of Mercury Contamination on Plant Growth and nifH-Harboring Microbial Community in Rice Paddy Soil

Methylmercury (MeHg), which is formed in rice paddy soil, exhibits strong neurotoxicity through bioaccumulation in the food chain. A few groups of microorganisms drive both mercury methylation and nitrogen fixation in the rhizosphere. Little is known about how the shifted soil microbial community by Hg contamination affects nitrogen fixation rate and plant growth in paddy soil. Here, we examined how stimulated short-term Hg amendment affects the nitrogen fixing microbial community and influences plant-microbe interactions. Soil was treated with low (0.2 mg/kg) and high (1.1 mg/kg) concentrations of Hg for 4 weeks; then, rice (Oryza sativa) was planted and grown for 12 weeks. The nitrogen-fixation rate and rice growth were measured. The diversity and structure of the microbial community were analyzed by sequencing the nifH gene before and after rice cultivation. Hg treatments significantly decreased the nitrogen fixation rate and dry weight of the rice plants. The structure of the nifH-harboring community was remarkably changed after rice cultivation depending on Hg treatments. Iron- or sulfate-reducing bacteria, including Desulfobacca, Desulfoporosimus, and Geobacter, were observed as legacy response groups; their abundances increased in the soil after Hg treatment. The high abundance of those groups were maintained in control, but the abundance drastically decreased after rice cultivation in the soil treated with Hg, indicating that symbiotic behavior of rice plants changes according to the legacy effects on Hg contamination. These results suggested that Hg contamination can persist in soil microbial communities, affecting their nitrogen-fixation ability and symbiosis with rice plants in paddy soil.

Relationships Between the Microbial Composition and the Geochemistry and Mineralogy of the Cobalt-Bearing Legacy Mine Tailings in Northeastern Ontario

Mine tailings host dynamic biogeochemical processes that can mobilize a range of elements from the host material and release them into the environment through acidic, neutral, or alkaline mine drainage. Here we use a combination of mineralogical, geochemical, and microbiological techniques that provide a better understanding of biogeochemical processes within the surficial layers of neutral cobalt and arsenic-rich tailings material at Cobalt, ON, Canada. Tailings material within 30-cm depth profiles from three tailings sites (sites A, B, and C) were characterized for their mineralogical, chemical and microbial community compositions. The tailings material at all sites contains (sulf)arsenides (safflorite, arsenopyrite), and arsenates (erythrite and annabergite). Site A contained a higher and lower amount of (sulf)arsenides and arsenates than site B, respectively. Contrary to site A and B, site C depicted a distinct zoning with (sulf)arsenides found in the deeper reduced zone, and arsenates occurring in the shallow oxidized zone. Variations in the abundance of Co+As+Sb+Zn (Co#), Fe (Fe#), total S (S#), and average valence of As indicated differences in the mineralogical composition of the tailings material. For example, material with a high Co#, lo Fe# and high average valence of As commonly have a higher proportion of secondary arsenate to primary (sulf)arsenide minerals. Microbial community profiling indicated that the Cobalt tailings are primarily composed of Actinobacteria and Proteobacteria, and known N, S, Fe, methane, and possible As-cycling bacteria. The tailings from sites B and C had a larger abundance of Fe and S-cycling bacteria (e.g., Sulfurifustis and Thiobacillus), which are more abundant at greater depths, whereas the tailings of site A had a higher proportion of potential As-cycling and -resistant genera (e.g., Methylocystis and Sphingomonas). A multi-variate statistical analysis showed that (1) distinct site-specific groupings occur for the Co # vs. Fe #, Co# vs. S#'s and for the microbial community structure and (2) microbial communities are statistically highly correlated to depth, S#, Fe#, pH and the average valence of As. The variation in As valence correlated well with the abundance of N, S, Fe, and methane-cycling bacteria. The results of this study provide insights into the complex interplay between minerals containing the critical element cobalt, arsenic, and microbial community structure in the Cobalt Mining Camp tailings.

Functional Interrelationships of Microorganisms in Iron-Based Anaerobic Wastewater Treatment

This study explicated the functional activities of microorganisms and their interrelationships under four previously reported iron reducing conditions to identify critical factors that governed the performance of these novel iron-dosed anaerobic biological wastewater treatment processes. Various iron-reducing bacteria (FeRB) and sulfate reducing bacteria (SRB) were identified as the predominant species that concurrently facilitated organics oxidation and the main contributors to removal of organics. The high organic contents of wastewater provided sufficient electron donors for active growth of both FeRB and SRB. In addition to the organic content, Fe (III) and sulfate concentrations (expressed by Fe/S ratio) were found to play a significant role in regulating the microbial abundance and functional activities. Various fermentative bacteria contributed to this FeRB-SRB synergy by fermenting larger organic compounds to smaller compounds, which were subsequently used by FeRB and SRB. Feammox (ferric reduction coupled to ammonium oxidation) bacterium was identified in the bioreactor fed with wastewater containing ammonium. Organic substrate level was a critical factor that regulated the competitive relationship between heterotrophic FeRB and Feammox bacteria. There were evidences that suggested a synergistic relationship between FeRB and nitrogen-fixing bacteria (NFB), where ferric iron and organics concentrations both promoted microbial activities of FeRB and NFB. A concept model was developed to illustrate the identified functional interrelationships and their governing factors for further development of the iron-based wastewater treatment systems.