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Biogeochemical redox cycling of iron (Fe) essentially governs various geochemical processes in nature. However, the mechanistic underpinnings of Fe-redox cycling in deep-sea sediments remain poorly understood, due to the limited access to the deep-sea environment. Here, abyssal sediment collected from a depth of 5800 m in the Pacific Ocean was characterized for its elemental, mineralogical, and biological properties. The sedimentary environment was determined to be oligotrophic with limited nutrition, yet contained a considerable amount of trace elements. Fe-redox reactions in sediment progressed through an initial lag phase, followed by a fast Fe(II) reduction and an extended period of Fe(III) oxidation before achieving equilibrium after 58 days. The presence of an external H2 electron donor significantly increased the extent of Fe(III) bio-reduction by 7.73% relative to an amendment-free control under high pressure of 58 MPa. A similar enhancement of 11.20% was observed following lactate amendment under atmospheric pressure. Fe(II) bio-oxidation occurred after 16 days' anaerobic culturing, coupled with nitrate reduction. During Fe bio-redox reactions, microbial community composition was significantly shaped by the presence/absence of an electron donor, while the hydrostatic pressure levels were the controlling factor. Shewanella spp. emerged as the primary Fe(III)-reducing microorganisms, and were stimulated by supplemented lactate. Marinobacter hydrocarbonoclasticus was the predominant Fe(II)-oxidizing microorganism across all conditions. Our findings illustrate continuous Fe-redox reactions occurring in the deep-sea environment, with coexisting Fe-redox microorganisms determining the oscillation of Fe valence states within the abyssal sediment. [ABSTRACT FROM AUTHOR]

Knowledge of the behavior of microbial communities in ecosystems is limited, yet microbes control partly all element cycles and, in turn, processes influencing pollution and climate change. In particular, heterotrophic denitrification is major process controlling the transformation of nitrogen oxides pollutants, e.g. nitrates (NO4-) and nitrous oxide (N2O), a greenhouse gas. Iron acts as either nutrient or stress in denitrifying microbial communities, yet underlying mechanisms are unclear. We hypothesized that iron plays a vital role in the assembly process of heterotrophic denitrifying microbial communities. To test this hypothesis we cultivated 17 microcosms under carbon- and iron-rich conditions. Geochemical analysis, 16S rRNA gene high-throughput sequencing, and multivariate statistical analysis were implemented to unravel the driving forces that shape the assembly process of microbial communities. Results reveal that iron was the most dominant factor influencing the diversity and composition of heterotrophic denitrifying communities, versus pH, C/N, temperature, nitrate reduction, and iron oxidation rates. Higher Fe concentration induced more clustered microbial interactions. Heterotrophic microbial community assembly is shaped by 90% stochastic processes, whereas deterministic processes rose with Fe(II) concentration. Overall our findings demonstrate that iron controls the balance between the deterministic and stochastic processes of heterotrophic denitrifying microbial communities. These mechanisms may have implications for bioremediation strategies. [ABSTRACT FROM AUTHOR]

The river-lake-floodplain system (RLFS) undergoes intensive surface-groundwater mass and energy exchanges. Some freshwater lakes are groundwater flow-through systems, serving as sinks for nitrogen (N) entering the lake. Despite the threat of cross-nitrogen contamination, the assembly of the microbial communities in the RLFS was poorly understood. Herein, the distribution, co-occurrence, and assembly pattern of microbial community were investigated in a nitrogen-contaminated and hydraulically-connected RLFS. The results showed that nitrate was widely distributed with greater accumulation on the south than on the north side, and ammonia was accumulated in the groundwater discharge area (estuary and lakeshore). The heterotrophic nitrifying bacteria and aerobic denitrifying bacteria were distributed across the entire area. In estuary and lakeshore with low levels of oxidation-reduction potential (ORP) and high levels of total organic carbon (TOC) and ammonia, dissimilatory nitrate reduction to ammonium (DNRA) bacteria were enriched. The bacterial community had close cooperative relationships, and keystone taxa harbored nitrate reduction potentials. Combined with multivariable statistics and self-organizing map (SOM) results, ammonia, TOC, and ORP acted as drivers in the spatial evolution of the bacterial community, coincidence with the predominant deterministic processes and unique niche breadth for microbial assembly. This study provides novel insight into the traits and assembly of bacterial communities and potential nitrogen cycling capacities in RLFS groundwater. [Display omitted] • Estuaries and lakeshore area have high-potentials of nitrogen cycling. • Nitrate reducing bacteria are enriched in lakeshore area. • Microbial ecological network unravels the keystone nitrogen cycling bacteria. • Groundwater microbial community assembly is governed by deterministic process. [ABSTRACT FROM AUTHOR]

Abstract Heterotrophic denitrifiers, capable of simultaneous nitrate reduction and Fe(II) oxidation, can be applied for the remediation of nitrate and Fe(II) combined contamination in groundwater. Under strictly anaerobic condition, denitrifying microbial communities were enriched with the coexistence of soluble nitrate, Fe(II) and associated nutrient elements to monitor the denitrification process. Low abundance of Fe(II) (e.g., 10 mg L−1 in this study) tended to stimulate the activity of denitrifying microbial communities. However, elevated Fe(II) concentration (50 and 100 mg L−1 in this study), acted as a stress, strongly inhibited the activity and reproduction of denitrifiers. Besides, through thermodynamics calculations, methanol rather than Fe(II) was proved to be the preferable electron donors for both energy metabolism and anabolism. Betaproteobacteria was found to be the most predominant (sub)phylum in all enriched microbial assemblages. Methylovesartilis was the most predominant group mainly catalyzed for methanol based denitrification, and others denitrifiers included Methylophilaceae , Dechloromonas and Denitratisoma. Excessive Fe(II) in the solution greatly reduced the proportions of these denitrifying groups, while the influence seemed to be less apparent on functional genes composition. As such, a conceptional metabolism pathway of the most dominant genus (i.e., Methylovesartilis) for nitrate reducing as well as methanol and Fe(II) oxidation confirmed that biotic nitrate reducing and Fe(II) oxidizing were potentially proceeded in cytoplasm by enzymes such as NarGHI. The Fe(II) oxidation rate depended on the rate of Fe(II) entering into the cell. These findings provide a clear mechanistic understanding of heterotrophic denitrification coupling with Fe(II) oxidation, and environmental implication for the bioremediation of nitrate and Fe(II) contaminated groundwater. Highlights • Methanol was preferred for denitrifiers in catabolism and anabolism than Fe(II). • A conceptional model was constructed for denitrification and Fe(II) oxidation. • Fe(II) greatly changed microbial structures but not functional composition. • Fe(II) oxidation rate depended on the rate of Fe(II) entering into the cell. [ABSTRACT FROM AUTHOR]

Abstract: Spatial distribution (horizonal and vertical) of groundwater microbial communities and the hydrogeochemistry in confined aquifers were studied approximately along the groundwater flow path from coteau to plain in the Nomhon area, Qinghai‐Tibet plateau, China. The confined groundwater samples at different depths and locations were collected in three boreholes through a hydrogeological section in this arid and semi‐arid area. The phylogenetic analysis of 16S rRNA genes and multivariate statistical analysis were used to elucidate similarities and differences between groundwater microbial communities and hydrogeochemical properties. The integrated isotopic geochemical measurements were applied to estimate the source and recharge characteristics of groundwater. The results showed that groundwater varied from fresh to saline water, and modern water to ancient water following the flowpath. The recharge characteristics of the saline water was distinct with that of fresh water. Cell abundance did not vary greatly along the hydrogeochemical zonality; however, dissimilarities in habitat‐based microbial community structures were evident, changing from Betaproteobacteria in the apex of alluvial fan to Gammaproteobacteria and then to Epsilonproteobacteria in the core of the basin (alluvial‐lacustrine plain). Rhodoferax, Hydrogenophaga, Pseudomonas, and bacterium isolated from similar habitats unevenly thrived in the spatially distinct fresh water environments, while Sulfurimonas dominanted in the saline water environment. The microbial communities presented likely reflected to the hydrogeochemical similarities and zonalities along groundwater flowpath. [ABSTRACT FROM AUTHOR]

1,2,3-trichloropropane (TCP), a refractory contaminant, can be reductive dehalogenated to allyl chloride (AC) by microorganisms, which has been shown a potential in situ bioremediation (ISB) strategy for TCP remediation in groundwater. In practice, however, it is hard to monitor the bioreduction extent because the TCP concentrations may also be decreased by non-biodegradation processes. Compound specific isotope analysis (CSIA) can be promising in determining the extent of degradation by quantifying the isotope enrichment factors (ε) of relevant degradation mechanisms. To date, no CSIA study has been reported on TCP degradation. In this study, a novel TCP-to-AC transformation enrichment culture (dominated by Azotobacter , Parabacteroides , Fusibacter , Hydrogenophaga , Trichococcus Desulfovibrio, etc) in the absence of the already identified TCP anaerobic reductive dechlorinating microorganisms (e.g., Dehalogenimonas) was derived from a chlorinated hydrocarbon-contaminated aquifer. A TCP degradation experiment was carried out by adding yeast extract to produce hydrogen as an electron donor. The TCP-to-AC transformation was found to conform to zero-order conversion kinetics with the rate constant 11 ± 0.34 μmol L−1 d−1 during the main biodegradation stage. The bulk carbon isotope enrichment factor (ε bulk) of the TCP-to-AC transformation was firstly evaluated as −5.2 ± 0.1‰. This study for the first time characterized the carbon isotope fractionations during TCP biodegradation using a novel enrichment culture, which would provide a promising tool for the incorporation of ISB for TCP removal in the future. [Display omitted] • Demonstrated a novel effective enrichment culture for TCP reductive dehalogenation. • TCP-to-AC was found to be a zero-order reaction with a rapid velocity (11 μM d−1). • The bulk carbon isotope enrichment factor (ε bulk) of TCP-to-AC was firstly evaluated. [ABSTRACT FROM AUTHOR]

Cyanobacterial bloom challenges the aquatic ecosystem and ecological restoration is an effective approach for cyanobacterial bloom control, but the change of aquatic community after ecological restoration is still unclear. Dianchi Lake is an eutrophic lake with frequent cyanobacterial blooms in China, and recent ecological restoration projects in Caohai (north part) have a satisfactory performance. In this study, we collected 249 water samples at 23 sites from Dianchi Lake to explore the relationships between water physicochemical variables and aquatic microbial communities. Water physicochemical variables in Waihai (south part) intensively changed along time, whereas those in Caohai did not. Photoautotrophic communities were significantly divergent between Caohai and Waihai. Waihai had a lower diversity of photoautotrophic community, containing higher abundance of Cyanophyceae (89.9%) than Caohai (42.7%). Nutrient level and Cyanophyceae only exhibited strong correlations in Wahai (p < 0.05). Redundancy analysis and microbial ecological network suggested that microbial communities in Caohai had a higher stability. Deterministic process dominated the microbial assembly (50–80% for bacteria and >90% for photoautotrophs), and particularly in Caohai. Our results unraveled that the structure and assembly of bacterial and photoautotrophic communities significantly changed after ecological restoration, offering valuable suggestions that photosynthetic diversity should be focused for other ecological restoration projects. [Display omitted] • Similar bacterial communities between Waihai and Caohai. • Significant difference in photoautotrophs between Waihai and Caohai. • More stochastic processes for microbial assembly in Waihai than Caohai. • Higher microbial stability in Caohai after ecological restoration. [ABSTRACT FROM AUTHOR]

Degradation of 1,2,3-trichloropropane (TCP) to allyl chloride (AC) by Dehalogenimonas (Dhg), the only reported TCP anaerobic reductive dechlorinating microorganism so far, has been demonstrated to be effective for in-situ bioremediation (ISB) of groundwater. This process is found viable when augmented with the fermentable organic substrate, yet its environmental implication is not yet clear and limited due to the complex environmental conditions and indigenous microbial communities. In this study, using yeast extract as biostimulant, an enrichment culture capable of dechlorinating TCP derived from groundwater well sludge at a chlorinated aliphatic hydrocarbon (CAH)-contaminated site was incubated. Geochemical methods, 16 S rRNA gene and shotgun metagenomic sequencing were used to systematically monitor the TCP biodegradation kinetics and unravel the functional microbial communities that play pivotal roles in this process. The decrease of TCP, along with the increase of AC (the product of TCP degradation) and δ13C-TCP values indicated active biodegradation of TCP. The 16S rRNA phylogenetic tree showed the absence of Dhg , suggesting a putative novel culture for dechlorinating TCP. Several potential anaerobic reductive functional genes and dominant microorganisms were identified and mutualistic interactions were found. Hydrogenase (H 2 ase) genes, responsible for producing the hydrogen, were harbored by Desulfovibrio. Cobalamin synthase (CobS) genes, responsible for synthesizing the cobalamin, an important co-factor for dehalogenation, were harbored by Desulfovibrio , Gracilibacter , Thermococcus. By obtaining the electron donor (hydrogen) and essential cofactors (cobalamin), the reductive dehalogenase (Rdh) gene were harbored by Parabacteroides , Caldisalinibacter , and Desulfovibrio. Based on these findings, Desulfovibrio was deduced to be the most promising genus for TCP degradation. The identified microbial community could collaboratively play critical roles in TCP degradation, and therefore, a new method is expected to be developed. [Display omitted] • A novel enrichment culture of TCP anaerobic reductive dehalogenation was demonstrated. • Parabacteroides , Desulfovibrio were dominant genera in the culture. • Desulfovibrio is the potential TCP-degrading-bacteria for a new promising ISB method. [ABSTRACT FROM AUTHOR]

Excessive loading of nitrogen (N) and phosphorus (P) that leads to eutrophication mutually interacts with sediment microbial community. To unravel the microbial community structures and interaction networks in the urban river sediments with the disturbance of N and P loadings, we used high-throughput sequencing analysis and ecological co-occurrence network methods to investigate the responses of diversity and community composition of bacteria and archaea and identify the keystone species in river sediments. The alpha-diversity of archaea significantly decreased with the increased total nitrogen (TN), whereas the operational taxonomic unit (OTU) number of bacteria increased with the increase of available phosphorus (AP). The beta-diversity of archaea and bacteria was more sensitive to N content than P content. The relative abundance of predominant bacterial and archaeal taxa varied differently in terms of different N and P contents. Complexity and connectivity of bacteria and archaea interaction networks showed significant variations with eutrophication, and competition between bacteria became more significant with the increase of N content. The sensitive and the highest connective species (keystone species) were identified for different N and P loadings. Total carbon (TC), water content (WC), microbial alpha-diversity and interaction networks played pivotal roles in the N and P transformation in urban river sediments. [Display omitted] • The diversity of archaea and bacteria had distinct responses to eutrophication. • Complexity of microbial networks increased with the increase of N in sediment. • We identified keystone microbial species in sediment related to eutrophication. • Microbial community structure and organic matter affected N and P transformation. [ABSTRACT FROM AUTHOR]

Biogeochemical gradient forms in vadose zone, yet little is known about the assembly processes of microbial communities in this zone under petroleum disturbance. This study collected vadose zone soils at three sites with 0, 5, and 30 years of petroleum contamination to unravel the vertical microbial community successions and their assembly mechanisms. The results showed that petroleum hydrocarbons exhibited higher concentrations at the long-term contaminated site, showing negative impacts on some soil properties, retarding in the surface soils and decreasing along soil depth. Cultivable fraction of heterotrophic bacteria and microbial α -diversity decreased along depth in vadose zones with short-term/no contamination history, but exhibited an opposite trend with long-term contamination history. Petroleum contamination intensified the vertical heterogeneity of microbial communities based on the contamination time. Microbial co-occurrence network revealed the lowest species co-occurrence pattern at the long-term contaminated site. The distance-decay patterns and null model analysis together suggested distinct assembly mechanisms at three sites, where dispersal limitation (42–45%) was higher and variable and homogenizing selections were lower (37–38%) in vadose zones under petroleum disturbance than those in the uncontaminated vadose zone. Our findings help to better understand the subsurface biogeochemical cycles and bioremediation of petroleum-contaminated vadose zones. ga1 • Different vertical biogeochemical patterns between contaminated vadose zones. • Petroleum contamination history intensifies microbial vertical heterogeneity. • Long petroleum contamination history drives the lowest species co-occurrence. • Stochastic process explains 60% vertical bacterial assembly at contaminated sites. [ABSTRACT FROM AUTHOR]

Nitrate and ammonia overload in groundwater can lead to eutrophication of surface water in areas where surface water is recharged by groundwater. However, this process remained elusive due to the complicated groundwater N cycling, which is governed by the co-evolution of hydrogeochemical conditions and N-cycling microbial communities. Herein, this process was studied along a generalized groundwater flowpath in Ganjing Delta, Poyang Lake area, China. From groundwater recharge to the discharge area near the lake, oxidation-reduction potential (ORP), NO 3 –N, and NO 2 –N decreased progressively, while NH 3 –N, total organic carbon (TOC), Fe2+, sulfide, and TOC/NO 3 − ratio accumulated in the lakeside samples. The anthropogenic influences such as sewage and agricultural activities drove the nitrate distribution, as observed by Cl− vs. NO 3 −/Cl− ratio and isotopic composition of nitrate. The hydrogeochemical evolution was intimately coupled with the changes in microbial communities. Variations in microbial community structures was significantly explained by Fe2+, NH 3 –N, and sulfide, while TOC/NO 3 − controlled the distribution of predicted N cycling gene. The absence of NH 3 –N in groundwater upstream was accompanied by the enrichment in Acinetobacter capable of nitrification and aerobic denitrification. These two processes were also supported by Ca2+ + Mg2+ vs. HCO 3 − ratio and isotopic composition of NO 3 −. The DNRA process downstream was revealed by both the presence of DNRA-capable microbes such as Arthrobacter and the isotopic composition of NH 4 + in environments with high concentrations of NH 3 –N, TOC/NO 3 −, Fe2+, and sulfide. This coupled evolution of N cycling and microbial community sheds new light on the N biogeochemical cycle in areas where surface water is recharged by groundwater. [Display omitted] • NH 3 –N, TOC, Fe2+, and sulfide accumulated in groundwater-surface water exchange zones. • Microbial communities along groundwater flowpath are shaped by NO 3 –N and Fe2+. • DNRA-capable microbes were enriched downstream near the lake. • Mutual interaction between N cycling and microbial community along flowpath. [ABSTRACT FROM AUTHOR]

The exogenous input of nitrate in groundwater may change microbial community, and in turn, the change of microbial community affects the biogeochemical transformation of nitrate. However, how this mutual interaction varies along the groundwater flowpath remains poorly understood. Herein, we investigated the co-variation of hydrochemical characteristics and microbial community compositions in nitrate-contaminated groundwater along a generalized flowpath in Linzhou-Anyang area, southern North China Plain. The groundwater-rock interactions and human activities collectively controlled the transition patterns of hydrogeochemical conditions. Along the groundwater flowpath, the nitrate, ammonia, major ions, total organic carbon (TOC), C/N, and relative abundance of Proteobacteria and Epsilonbacteraeota subsequently increased, while nitrite, oxidation reduction potential (ORP), and overall microbial diversity decreased. Both microbial community composition and microbial co-occurrence network were primarily governed by the levels of TOC, nitrate, and nitrite, a sum of which explained 48.4% variance of community compositions, greater than the effect of water-rock interaction (basically ion contents, 12.9%) and ORP (4%), suggesting the dominant role of exogenous nitrate and organic carbon inputs in shaping microbial community. Accordingly, the variations of keystone bacterial lineages, e.g., Vogesella sp., Acinetobacter sp., Rhodoferax sp., Pseudomonas sp., and Flavobacterium sp., and archaeal lineage Candidatus Nitrosoarchaeum along the groundwater flowpath were putatively involved in the dissimilatory nitrate reduction, indicating the potential role of heterotrophic nitrate reducers in nitrate transformation. Our findings suggest that microbial community distribution along groundwater flowpath is intimately related to exogenous nitrate and organic carbon inputs, which likely outweigh the effect of groundwater circulation or water-rock interaction. This study could help us to better understand the inter-relationship between hydrochemical environments and microbial communities in nitrate-polluted groundwater. • Increased nitrate, ammonia, and TOC and decreased nitrite and ORP along flowpath. • Proteobacteria and Epsilonbacteraeota increased along flowpath. • Microbial communities in groundwater are shaped by nitrate, TOC, and nitrite. • Nitrogen-related microbes accumulated in the groundwater downstream. [ABSTRACT FROM AUTHOR]