Determinants of the microbial community structure of eutrophic, hyporheic river sediments polluted with chlorinated aliphatic hydrocarbons

Enhancement effects of decabromodiphenyl ether on microbial sulfate reduction in eutrophic lake sediments: A study on sulfate-reducing bacteria using dsrA and dsrB amplicon sequencing

Although sulfate (SO₄^2-) reduction by sulfate-reducing bacteria (SRB) is an important sulfur cycling processes, little is known about how the persistent organic pollutants affect the SO₄^2- reduction process in the eutrophic lake sediments. Here, we carried out a 120-day microcosm experiment to explore the effects of decabromodiphenyl ether (BDE-209) on SO₄^2- reduction mediated by SRB in sediment collected from Taihu Lake, a typical eutrophic lake in China. The results showed that BDE-209 contamination significantly enhanced the activity of dissimilatory sulfite reductase (DSR) (r = 0.83), which led to an increased concentration of sulfide produced by SO₄^2- reduction. This stimulatory effect of BDE-209 on DSR activity was closely related to variations in the dsrA- and dsrB-type SRB communities. The abundances and diversities of the dsrA- and dsrB-containing SRB increased and their community composition varied in response to BDE-209 contamination. The gene copies (r = 0.72), Chao 1 (r = 0.50), Shannon (r = 0.55), and Simpson (r = 0.70) indices of dsrB-containing SRB was positively correlated with BDE-209 contamination. Co-occurrence network analysis revealed that network complexity, connectivity, and the interspecific cooperative relationship in SRB were strengthened by BDE-209 contamination. The keystone species identified in the SRB community mainly belonged to the genera Candidatus Sulfopaludibacter for the dsrA-containing SRB and Desulfatiglans for the dsrB-containing SRB, and their relative abundances were positively correlated with DSR activity in the sediment. The relative abundance of the keystone species and SRB diversity were important microbial factors directly contributing to the variations in DSR activity based on structural equation modeling analysis. Notably, the results of abundance, community structure, and interspecific relationships showed that the dsrB-containing SRB may be more sensitive to the BDE-209 contamination than the dsrA-containing SRB. These results will help us understand the effects of BDE-209 on microbial sulfate reduction in eutrophic lakes.

Urease and nitrification inhibitors with pig slurry effects on ammonia and nitrous oxide emissions, nitrate leaching, and nitrogen use efficiency in perennial ryegrass sward

OBJECTIVE

The present study was conducted to assess the effect of urease inhibitor (hydroquinone [HQ]) and nitrification inhibitor (dicyandiamide [DCD]) on nitrogen (N) use efficiency of pig slurry for perennial ryegrass regrowth yield and its environmental impacts.

METHODS

A micro-plot experiment was conducted using pig slurry-urea 15N treated with HQ and/or DCD and applied at a rate of 200 kg N/ha. The flows of N derived from the pig slurry urea to herbage regrowth and soils as well as soil N mineralization were estimated by tracing pig slurry-urea 15N, and the N losses via ammonia (NH3), nitrous oxide (N2O) emission, and nitrate (NO3-) leaching were quantified for a 56 d regrowth of perennial ryegrass (Lolium perenne) sward.

RESULTS

Herbage dry matter at the final regrowth at 56 d was significantly higher in the HQ and/or DCD applied plots, with a 24.5% to 42.2% increase in 15N recovery by herbage compared with the control. Significant increases in soil 15N recovery were also observed in the plots applied with the inhibitors, accompanied by the increased N content converted to soil inorganic N (NH4+ +NO3-) (17.3% to 28.8% higher than that of the control). The estimated loss, which was not accounted for in the herbage-soil system, was lower in the plots applied with the inhibitors (25.6% on average) than that of control (38.0%). Positive effects of urease and/or nitrification inhibitors on reducing N losses to the environment were observed at the final regrowth (56 d), at which cumulative NH3 emission was reduced by 26.8% (on average 3 inhibitor treatments), N2O emission by 50.2% and NO3- leaching by 10.6% compared to those of the control.

CONCLUSION

The proper application of urease and nitrification inhibitors would be an efficient strategy to improve the N use efficiency of pig slurry while mitigating hazardous environmental impacts.

Natural attenuation of a chlorinated ethene plume discharging to a stream: Integrated assessment of hydrogeological, chemical and microbial interactions

Attenuation processes of chlorinated ethenes in complex near-stream systems result in site-specific outcomes of great importance for risk assessment of contaminated sites. Additional interdisciplinary and comprehensive field research is required to enhance process understanding in these systems. In this study, several methods were combined in a multi-scale interdisciplinary in-situ approach to assess and quantify the near-stream attenuation of a chlorinated ethene plume, mainly consisting of cis-dichloroethene (cis-DCE) and vinyl chloride (VC), discharging to a lowland stream (Grindsted stream, Denmark) over a monitoring period of seven years. The approach included: hydrogeological characterisation, reach scale contaminant mass balance analysis, quantification of contaminant mass discharge, streambed fluxes of chlorinated ethenes quantified using Sediment Bed Passive Flux Meters (SBPFMs), assessment of redox conditions, temporal assessment of contaminant concentrations, microbial analysis, and compound-specific isotope analysis (CSIA). This study site exhibits a special attenuation behaviour not commonly encountered in field studies: the conversion from an initially limited degradation case (2012-16), despite seemingly optimal conditions, to one presenting notable levels of degradation (2019). Hence, this study site provides a new piece to the puzzle, as sites with different attenuation behaviours are required in order to acquire the full picture of the role groundwater-surface water interfaces have in risk mitigation. In spite of the increased degradation in the near-stream plume core, the contaminant attenuation was still incomplete in the discharging plume. A conceptualization of flow, transport and processes clarified that hydrogeology was the main control on the natural attenuation, as short residence times of 0.5-37 days restricted the time in which dechlorination could occur. This study reveals the importance of: taking an integrated approach to understand the influence of all attenuation processes in groundwater - surface water interactions; considering the scale and domain of interest when determining the main processes; and monitoring sufficiently both spatially and temporally to cover the transient conditions.

Profiling microbial communities in a watershed undergoing intensive anthropogenic activities

In lotic ecosystems highly susceptible to anthropogenic activities, the influences of environmental variables on microbial communities and their functions remain poorly understood, despite our rapidly increasing sequencing ability. In this study, we profiled the microbial communities in the hyporheic sediments of a watershed undergoing intensive anthropogenic activities via next-generation sequencing of 16S rRNA V4-V5 hypervariable regions on Illumina MiSeq platform. Tidal impacts on microbial communities were investigated via co-occurrence networks. In addition, the influences of physicochemical variables including salinity, and the concentrations of nutrients, organic matter and heavy metals on the microbial communities were explored via canonical correspondence analyses. The sediment samples were collected from 19 sites covering the whole main river stem of the target watershed (n = 19; Maozhou river watershed, Shenzhen, China). The samples were sub-divided in the field for microbiological analyses and measurements of physicochemical variables. The results indicated that core microbiome was associated with archaea methanogens and bacteria members from Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, Synergistetes and Firmicutes, among which, gram-negative and anaerobic bacteria genera contributing to the cycling of carbon, nitrogen and sulfur were predominant. Site-specific microbiomes were revealed that may serve as indicators of local environmental conditions (e.g., members affiliated to Oceanospirillales were abundant at sites with salt intrusion). Distinct microbial co-occurrence networks were identified for non-tidal, inter-tidal and tidal sites. Major environmental factors influencing microbial community composition included the concentrations of nitrate and bicarbonate in river water, pore water concentrations of sulfate, dissolved organic carbon and electrical conductivity, as well as manganese concentrations associated with the solid sediment. Collectively, the results of this study provide fundamental insights into the influence of environmental perturbations on microbial community composition in a lotic system, which may aid in the design of effective remediation and/or restoration strategies in the target watershed and beyond.

Application of the microbial community coalescence concept to riverine networks

Flows of water, soil, litter, and anthropogenic materials in and around rivers lead to the mixing of their resident microbial communities and subsequently to a resultant community distinct from its precursors. Consideration of these events through a new conceptual lens, namely, community coalescence, could provide a means of integrating physical, environmental, and ecological mechanisms to predict microbial community assembly patterns better in these habitats. Here, we review field studies of microbial communities in riverine habitats where environmental mixing regularly occurs, interpret some of these studies within the community coalescence framework and posit novel hypotheses and insights that may be gained in riverine microbial ecology through the application of this concept. Particularly in the face of a changing climate and rivers under increasing anthropogenic pressures, knowledge about the factors governing microbial community assembly is essential to forecast and/or respond to changes in ecosystem function. Additionally, there is the potential for microbial ecology studies in rivers to become a driver of theory development: riverine systems are ideal for coalescence studies because regular and predictable environmental mixing occurs. Data appropriate for testing community coalescence theory could be collected with minimal alteration to existing study designs.

Acidification of pig slurry effects on ammonia and nitrous oxide emissions, nitrate leaching, and perennial ryegrass regrowth as estimated by 15N-urea flux

OBJECTIVE

The present study aimed to assess the nitrogen (N) use efficiency of acidified pig slurry for regrowth yield and its environmental impacts on perennial ryegrass swards.

METHODS

The pH of digested pig slurry was adjusted to 5.0 or 7.0 by the addition of sulfuric acid and untreated as a control. The pig slurry urea of each treatment was labeled with 15N urea and applied at a rate of 200 kg N/ha immediately after cutting. Soil and herbage samples were collected at 7, 14, and 56 d of regrowth. The flux of pig slurry-N to regrowth yield and soil N mineralization were analyzed, and N losses via NH3, N2O emission and NO3- leaching were also estimated.

RESULTS

The pH level of the applied slurry did not have a significant effect on herbage yield or N content of herbage at the end of regrowth, whereas the amount of N derived from pig slurry urea (NdfSU) was higher in both herbage and soils in pH-controlled plots. The NH4+-N content and the amount of N derived from slurry urea into soil NH4+ fraction (NdfSU-NH4+) was significantly higher in in the pH 5 plot, whereas NO3- and NdfSU-NO3- were lower than in control plots over the entire regrowth period. Nitrification of NH4+-N was delayed in soil amended with acidified slurry. Compared to non-pH-controlled pig slurry (i.e. control plots), application of acidified slurry reduced NH3 emissions by 78.1%, N2O emissions by 78.9% and NO3- leaching by 17.81% over the course of the experiment.

CONCLUSION

Our results suggest that pig slurry acidification may represent an effective means of minimizing hazardous environmental impacts without depressing regrowth yield.

Natural attenuation of chlorinated ethenes in hyporheic zones: A review of key biogeochemical processes and in-situ transformation potential

Chlorinated ethenes (CEs) are legacy contaminants whose chemical footprint is expected to persist in aquifers around the world for many decades to come. These organohalides have been reported in river systems with concerning prevalence and are thought to be significant chemical stressors in urban water ecosystems. The aquifer-river interface (known as the hyporheic zone) is a critical pathway for CE discharge to surface water bodies in groundwater baseflow. This pore water system may represent a natural bioreactor where anoxic and oxic biotransformation process act in synergy to reduce or even eliminate contaminant fluxes to surface water. Here, we critically review current process understanding of anaerobic CE respiration in the competitive framework of hyporheic zone biogeochemical cycling fuelled by in-situ fermentation of natural organic matter. We conceptualise anoxic-oxic interface development for metabolic and co-metabolic mineralisation by a range of aerobic bacteria with a focus on vinyl chloride degradation pathways. The superimposition of microbial metabolic processes occurring in sediment biofilms and bulk solute transport delivering reactants produces a scale dependence in contaminant transformation rates. Process interpretation is often confounded by the natural geological heterogeneity typical of most riverbed environments. We discuss insights from recent field experience of CE plumes discharging to surface water and present a range of practical monitoring technologies which address this inherent complexity at different spatial scales. Future research must address key dynamics which link supply of limiting reactants, residence times and microbial ecophysiology to better understand the natural attenuation capacity of hyporheic systems.

Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. This study investigates the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26) with DCM contamination ranging from 0.89 to 9,800,000 μg/L. Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. Across all samples, a total of 6,134 unique operational taxonomic units (OTUs) were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration ranges, indicating niche-specific responses of these autochthonous populations. Altogether, our findings suggest that monitored natural attenuation is an appropriate remediation strategy for DCM contamination, and that high-throughput sequencing technologies are a robust method for assessing the potential role of biodegrading bacterial assemblages in the apparent reduction of DCM concentrations in environmental scenarios.

Natural Attenuation in Streambed Sediment Receiving Chlorinated Solvents from Underlying Fracture Networks

Contaminant discharge from fractured bedrock formations remains a remediation challenge. We applied an integrated approach to assess the natural attenuation potential of sediment that forms the transition zone between upwelling groundwater from a chlorinated solvent-contaminated fractured bedrock aquifer and the receiving surface water. In situ measurements demonstrated that reductive dechlorination in the sediment attenuated chlorinated compounds before reaching the water column. Microcosms established with creek sediment or in situ incubated Bio-Sep beads degraded C1-C3 chlorinated solvents to less-chlorinated or innocuous products. Quantitative PCR and 16S rRNA gene amplicon sequencing revealed the abundance and spatial distribution of known dechlorinator biomarker genes within the creek sediment and demonstrated that multiple dechlorinator populations degrading chlorinated C1-C3 alkanes and alkenes co-inhabit the sediment. Phylogenetic classification of bacterial and archaeal sequences indicated a relatively uniform distribution over spatial (300 m horizontally) scale, but Dehalococcoides and Dehalobacter were more abundant in deeper sediment, where 5.7 ± 0.4 × 105 and 5.4 ± 0.9 × 106 16S rRNA gene copies per g of sediment, respectively, were measured. The microbiological and hydrogeological characterization demonstrated that microbial processes at the fractured bedrock-sediment interface were crucial for preventing contaminants reaching the water column, emphasizing the relevance of this critical zone environment for contaminant attenuation.

Geochemical Parameters and Reductive Dechlorination Determine Aerobic Cometabolic vs Aerobic Metabolic Vinyl Chloride Biodegradation at Oxic/Anoxic Interface of Hyporheic Zones

Hyporheic zones mediate vinyl chloride (VC) biodegradation in groundwater discharging into surface waters. At the oxic/anoxic interface (OAI) of hyporheic zones subjected to redox oscillations, VC is degraded via coexisting aerobic ethenotrophic and anaerobic reductive dechlorination pathways. However, the identity of aerobic VC degradation pathways (cometabolic vs metabolic) and their interactions with reductive dechlorination in relation to riverbed sediment geochemistry remain ill-defined. We addressed this using microcosms containing OAI sediments incubated under fluctuating oxic/anoxic atmosphere. Under oxic atmosphere, aerobic metabolic VC oxidation was absent in sediments with high total organic carbon (TOC) and VC was reductively dechlorinated to ethene. Ethene was oxidized by ethenotrophs that can degrade VC cometabolically. Contrastingly, VC was metabolically oxidized by ethenotrophs in low-TOC sediments with low reductive dechlorination potential. Accordingly, enrichment and isolation of metabolic VC-oxidizing ethenotrophs was successful only from the low-TOC sediment. Sequence analysis of etnE genes from the microcosms as well phylogenetic typing of the isolates showed that ethenotrophs in the sediments were facultative anaerobic Proteobacteria capable of coping with OAI-associated redox fluctuations. Our results suggest that local sediment heterogeneity supports/selects divergent VC degradation processes at the OAI and that high reductive dechlorination potential suppresses development of aerobic metabolic VC oxidation potential.

Comparative nitrogen use efficiency of urea and pig slurry for regrowth yield and nutritive value in perennial ryegrass sward

Objective

The study aimed to assess the N use efficiency (NUE) of pig slurry (in comparison with chemical fertilizer) for each regrowth yield and annual herbage production and their nutritive value.

Methods

Consecutive field experiments were separately performed using a single application with a full dose of N (200 kg N/ha) in 2014 and by four split applications in 2015 in different sites. The experiment consisted of three treatments: i) control plots that received no additional N, ii) chemical fertilizer-N as urea, and iii) pig-slurry-N with five replicates.

Results

The effect of N fertilization on herbage yield, N recovery in herbage, residual inorganic N in soil, and crude protein were significantly positive. When comparing the NUE between the two N sources (urea and pig slurry), pig slurry was significantly less effective for the earlier two regrowth periods, as shown by lower regrowth dry matter (DM) yield, N amount recovered in herbage, and inorganic N availability in soil at the 1st and 2nd cut compared to those of urea-applied plots. However, the effect of split application of the two N sources was significantly positive at the last two regrowth periods (at the 3rd and 4th cut). The two N sources and/or split application had little or no influence on neutral detergent fiber (NDF) content, acid detergent fiber (ADF) content, and in vitro DM digestibility, whereas cutting date was a large source of variation for these variables, resulting in a significant increase in in vitro DM digestibility for the last two regrowth periods when an increase in NDF and ADF content occurred. Split application of N reduced the N loss via nitrate leaching by 36% on average for the two N sources compared to a single application.

Conclusion

The pig slurry-N was utilized as efficiently as urea-N for annual herbage yield, with a significant increase in NUE especially for the latter regrowth periods.