Impact of Ammonium on Syntrophic Organohalide-Respiring and Fermenting Microbial Communities

Improve Niche Colonization and Microbial Interactions for Organohalide-Respiring-Bacteria-Mediated Remediation of Chloroethene-Contaminated Sites

Organohalide-respiring bacteria (OHRB)-mediated reductive dehalogenation is promising in in situ bioremediation of chloroethene-contaminated sites. The bioremediation efficiency of this approach is largely determined by the successful colonization of fastidious OHRB, which is highly dependent on the presence of proper growth niches and microbial interactions. In this study, based on two ecological principles (i.e., Priority Effects and Coexistence Theory), three strategies were developed to enhance niche colonization of OHRB, which were tested both in laboratory experiments and field applications: (i) preinoculation of a niche-preparing culture (NPC, being mainly constituted of fermenting bacteria and methanogens); (ii) staggered fermentation; and (iii) increased inoculation of CE40 (a Dehalococcoides-containing tetrachloroethene-to-ethene dechlorinating enrichment culture). Batch experimental results show significantly higher dechlorination efficiencies, as well as lower concentrations of volatile fatty acids (VFAs) and methane, in experimental sets with staggered fermentation and niche-preconditioning with NPC for 4 days (CE40_NPC-4) relative to control sets. Accordingly, a comparatively higher abundance of Dehalococcoides as major OHRB, together with a lower abundance of fermenting bacteria and methanogens, was observed in CE40_NPC-4 with staggered fermentation, which indicated the balanced syntrophic and competitive interactions between OHRB and other populations for the efficient dechlorination. Further experiments with microbial source tracking analyses suggested enhanced colonization of OHRB by increasing the inoculation ratio of CE40. The optimized conditions for enhanced colonization of OHRB were successfully employed for field bioremediation of trichloroethene (TCE, 0.3-1.4 mM)- and vinyl chloride (VC, ∼0.04 mM)-contaminated sites, resulting in 96.6% TCE and 99.7% VC dechlorination to ethene within 5 and 3 months, respectively. This study provides ecological principles-guided strategies for efficient bioremediation of chloroethene-contaminated sites, which may be also employed for removal of other emerging organohalide pollutants.

Decoupling Fe0 Application and Bioaugmentation in Space and Time Enables Microbial Reductive Dechlorination of Trichloroethene to Ethene: Evidence from Soil Columns

Fe⁰ is a powerful chemical reductant with applications for remediation of chlorinated solvents, including tetrachloroethene and trichloroethene. Its utilization efficiency at contaminated sites is limited because most of the electrons from Fe⁰ are channeled to the reduction of water to H₂ rather than to the reduction of the contaminants. Coupling Fe⁰ with H₂-utilizing organohalide-respiring bacteria (i.e., Dehalococcoides mccartyi) could enhance trichloroethene conversion to ethene while maximizing Fe⁰ utilization efficiency. Columns packed with aquifer materials have been used to assess the efficacy of a treatment combining in space and time Fe⁰ and aD. mccartyi-containing culture (bioaugmentation). To date, most column studies documented only partial conversion of the solvents to chlorinated byproducts, calling into question the feasibility of Fe⁰ to promote complete microbial reductive dechlorination. In this study, we decoupled the application of Fe⁰ in space and time from the addition of organic substrates andD. mccartyi-containing cultures. We used a column containing soil and Fe⁰ (at 15 g L^-1 in porewater) and fed it with groundwater as a proxy for an upstream Fe⁰ injection zone dominated by abiotic reactions and biostimulated/bioaugmented soil columns (Bio-columns) as proxies for downstream microbiological zones. Results showed that Bio-columns receiving reduced groundwater from the Fe⁰-column supported microbial reductive dechlorination, yielding up to 98% trichloroethene conversion to ethene. The microbial community in the Bio-columns established with Fe⁰-reduced groundwater also sustained trichloroethene reduction to ethene (up to 100%) when challenged with aerobic groundwater. This study supports a conceptual model where decoupling the application of Fe⁰ and biostimulation/bioaugmentation in space and/or time could augment microbial trichloroethene reductive dechlorination, particularly under oxic conditions.

Continuous-mode acclimation and operation of lignocellulosic sulfate-reducing bioreactors for enhanced metal immobilization from acidic mining-influenced water

Lignocellulosic sulfate-reducing bioreactors are an inexpensive passive approach for treatment of mining-influenced water (MIW). Typically, microbial community acclimation to MIW involves bioreactor batch-mode operation to initiate lignocellulose hydrolysis and fermentation and provide electron donors for sulfate-reducing bacteria. However, batch-mode operation could significantly prolong bioreactor start-up times (up to several months) and select for slow-growing microorganisms. In this study we assessed the feasibility of bioreactor continuous-mode acclimation to MIW (pH 2.5, 6.5 mM SO₄^2-, 18 metal(loid)s) as an alternate start-up method. Results showed that bioreactors with spent brewing grains and sugarcane bagasse achieved acclimation in continuous mode at hydraulic retention times (HRTs) of 7-12-d within 16-22 days. During continuous-mode acclimation, extensive SO₄^2- reduction (80 ± 20% -91 ± 3%) and > 98% metal(loid) removal was observed. Operation at a 3-d HRT further yielded a metal(loid) removal of 97.5 ± 1.3 -98.8 ± 0.9% until the end of operation. Sulfate-reducing microorganisms were detected closer to the influent in the spent brewing grains bioreactors, and closer to the effluent in the sugarcane bagasse bioreactors, giving insight as to where SO₄^2- reduction was occurring. Results strongly support that a careful selection of lignocellulose and bioreactor operating parameters can bypass typical batch-mode acclimation, shortening bioreactor start-up times and promoting effective MIW metal(loid) immobilization and treatment.

Microbial Chain Elongation and Subsequent Fermentation of Elongated Carboxylates as H2-Producing Processes for Sustained Reductive Dechlorination of Chlorinated Ethenes

In situ anaerobic groundwater bioremediation of trichloroethene (TCE) to nontoxic ethene is contingent on organohalide-respiring Dehalococcoidia, the most common strictly hydrogenotrophic Dehalococcoides mccartyi (D. mccartyi). The H₂ requirement for D. mccartyi is fulfilled by adding various organic substrates (e.g., lactate, emulsified vegetable oil, and glucose/molasses), which require fermenting microorganisms to convert them to H₂. The net flux of H₂ is a crucial controlling parameter in the efficacy of bioremediation. H₂ consumption by competing microorganisms (e.g., methanogens and homoacetogens) can diminish the rates of reductive dechlorination or stall the process altogether. Furthermore, some fermentation pathways do not produce H₂ or having H₂ as a product is not always thermodynamically favorable under environmental conditions. Here, we report on a novel application of microbial chain elongation as a H₂-producing process for reductive dechlorination. In soil microcosms bioaugmented with dechlorinating and chain-elongating enrichment cultures, near stoichiometric conversion of TCE (0.07 ± 0.01, 0.60 ± 0.03, and 1.50 ± 0.20 mmol L^-1 added sequentially) to ethene was achieved when initially stimulated by chain elongation of acetate and ethanol. Chain elongation initiated reductive dechlorination by liberating H₂ in the conversion of acetate and ethanol to butyrate and caproate. Syntrophic fermentation of butyrate, a chain-elongation product, to H₂ and acetate further sustained the reductive dechlorination activity. Methanogenesis was limited during TCE dechlorination in soil microcosms and absent in transfer cultures fed with chain-elongation substrates. This study provides critical fundamental knowledge toward the feasibility of chlorinated solvent bioremediation based on microbial chain elongation.

The occurrence and ecology of microbial chain elongation of carboxylates in soils

Chain elongation is a growth-dependent anaerobic metabolism that combines acetate and ethanol into butyrate, hexanoate, and octanoate. While the model microorganism for chain elongation, Clostridium kluyveri, was isolated from a saturated soil sample in the 1940s, chain elongation has remained unexplored in soil environments. During soil fermentative events, simple carboxylates and alcohols can transiently accumulate up to low mM concentrations, suggesting in situ possibility of microbial chain elongation. Here, we examined the occurrence and microbial ecology of chain elongation in four soil types in microcosms and enrichments amended with chain elongation substrates. All soils showed evidence of chain elongation activity with several days of incubation at high (100 mM) and environmentally relevant (2.5 mM) concentrations of acetate and ethanol. Three soils showed substantial activity in soil microcosms with high substrate concentrations, converting 58% or more of the added carbon as acetate and ethanol to butyrate, butanol, and hexanoate. Semi-batch enrichment yielded hexanoate and octanoate as the most elongated products and microbial communities predominated by C. kluyveri and other Firmicutes genera not known to undergo chain elongation. Collectively, these results strongly suggest a niche for chain elongation in anaerobic soils that should not be overlooked in soil microbial ecology studies.

An Ion Chromatography Method for Simultaneous Quantification of Chromate, Arsenate, Selenate, Perchlorate, and Other Inorganic Anions in Environmental Media

Chromium (Cr) (VI) is a toxic, mutagenic, and carcinogenic water pollutant. The standard ion chromatography (IC) method for quantification of Cr (VI) in water samples is Environmental Protection Agency Method 218.7, which requires postcolumn derivatization with 1,5-diphenylcarbazide and UV-Vis spectroscopy detection. Method 218.7 is Cr (VI) specific; thus, it does not allow detection of co-occurring natural and anthropogenic anions in environmental media. In this study, we developed an isocratic IC method with suppressed conductivity detection, a Metrohm Metrosep A Supp 7 column, and sodium carbonate/acetonitrile as mobile phase for simultaneous quantification of Cr (VI),C l O 4 - , As (V) as arsenate, Se (VI) as selenate, and the common anions F-, Cl-,N O 2 - ,N O 3 - , andS O 4 2 - . The determination coefficient for every analyte was >0.99 and the method showed good accuracy in quantification. Cr (VI), As (V), Se (VI), andC l O 4 - limit of detection and limit of quantification were 0.1-0.6 μg/L and 0.5-2.1 μg/L, respectively. Recovery of Cr (VI) in various aqueous samples (tap water, surface water, groundwater, and wastewater) was between 97.2% and 102.8%. Overall, most analytes showed acceptable recovery (80-120%) in the environmental samples tested. The IC method was applied to track Cr (VI) and other anion concentrations in laboratory batch microcosms experiments with soil, surface water, and anaerobic medium. The IC method developed in this study should prove useful to environmental practitioners, academic and research organizations, and industries for monitoring low concentrations of multiple anions in environmental media, helping to decrease the sample requirement, time, and cost of analysis.

Synergistic Zerovalent Iron (Fe0) and Microbiological Trichloroethene and Perchlorate Reductions Are Determined by the Concentration and Speciation of Fe

Trichloroethene (TCE) and perchlorate (ClO₄^-) are cocontaminants at multiple Superfund sites. Fe⁰ is often used during TCE bioremediation with Dehalococcoides mccartyi to establish anoxic conditions in the aquifer. However, the synergy between Fe⁰ abiotic reactions and microbiological TCE and ClO₄^- reductions is poorly understood and seldom addressed in the literature. Here, we investigated the effects of Fe⁰ and its oxidation product, Fe²⁺, at field-relevant concentrations in promoting microbial TCE and ClO₄^- reductions. Using semibatch microcosms with a Superfund site soil and groundwater, we showed that the high Fe⁰ concentration (16.5 g L^-1) expected during Fe⁰in situ injection mostly yielded TCE abiotic reduction to ethene/ethane. However, such concentrations obscured dechlorination by D. mccartyi, impeded ClO₄^- reduction, and enhanced SO₄^2- reduction and methanogenesis. Fe²⁺ at 0.25 g L^-1 substantially delayed conversion of TCE to ethene when compared to no-Fe controls. A low concentration of aged-Fe⁰ synergistically promoted microbiological TCE dechlorination to ethene while achieving complete ClO₄^- reduction. Collectively, these results illustrate scenarios relevant at or downstream of Fe⁰ injection zones when Fe⁰ is used to facilitate microbial dechlorination. Results also underscore the potential detrimental effects of Fe⁰ and bioaugmentation cultures coinjection for in situ treatment of chlorinated ethenes and ClO₄^-.

Urine dilution with a synthetic wastewater (Syntho) boosts the electricity production in a bio-electrochemical system powered by un-pretreated human urine

Human urine can be turned into electricity in bio-electrochemical systems. The acclimation of electro-active bacteria to culture media with increasing urine concentrations has led to raising the obtained current densities, which typically followed a Monod-like evolution profile as a function of urine concentration. However, the acclimation protocol has been so far evaluated using pretreated urine samples (fermented or precipitated), not raw (un-pretreated) urine. We demonstrate that, when un-pretreated urine is used, the microbial adaptation to increasingly concentrated urine leads to a current density profile that does not reach a saturation-like phase, but follows a Han/Levenspiel-type trend (bell-shaped). By diluting un-pretreated urine with a synthetic domestic wastewater (Syntho) up to concentrations matching those of the maximum in the Han/Levenspiel-like current profile (15-20% v/v) it is possible to avoid the drop in the electro-active response, generating anodic current densities as high as 3.6 ± 0.2 A.m^-2 (per actual surface area), 35-fold higher than those reached in pure un-pretreated urine.

Impact of Fixed Nitrogen Availability on Dehalococcoides mccartyi Reductive Dechlorination Activity

Biostimulation to promote reductive dechlorination is widely practiced, but the value of adding an exogenous nitrogen (N) source (e.g., NH₄⁺) during treatment is unclear. This study investigates the effect of NH₄⁺ availability on organohalide-respiring Dehalococcoides mccartyi (Dhc) growth and reductive dechlorination in enrichment cultures derived from groundwater (PW4) and river sediment (TC) impacted with chlorinated ethenes. In PW4 cultures, the addition of NH₄⁺ increased cis-1,2-dichloroethene (cDCE)-to-ethene dechlorination rates about 5-fold (20.6 ± 1.6 versus 3.8 ± 0.5 μM Cl^- d^-1), and the total number of Dhc 16S rRNA gene copies were about 43-fold higher in incubations with NH₄⁺ ((1.8 ± 0.9) × 10⁸ mL^-1) compared to incubations without NH₄⁺ ((4.1 ± 0.8) × 10⁷ mL^-1). In TC cultures, NH₄⁺ also stimulated cDCE-to-ethene dechlorination and Dhc growth. Quantitative polymerase chain reaction (qPCR) revealed that Cornell-type Dhc capable of N₂ fixation dominated PW4 cultures without NH₄⁺, but their relative abundance decreased in cultures with NH₄⁺ amendment (i.e., 99 versus 54% of total Dhc). Pinellas-type Dhc incapable of N₂ fixation were responsible for cDCE dechlorination in TC cultures, and diazotrophic community members met their fixed N requirement in the medium without NH₄⁺. Responses to NH₄⁺ were apparent at the community level, and N₂-fixing bacterial populations increased in incubations without NH₄⁺. Quantitative assessment of Dhc nitrogenase genes, transcripts, and proteomics data linked Cornell-type Dhc nifD and nifK expression with fixed N limitation. NH₄⁺ additions also demonstrated positive effects on Dhc in situ dechlorination activity in the vicinity of well PW4. These findings demonstrate that biostimulation with NH₄⁺ can enhance Dhc reductive dechlorination rates; however, a "do nothing" approach that relies on indigenous diazotrophs can achieve similar dechlorination end points and avoids the potential for stalled dechlorination due to inhibitory levels of NH₄⁺ or transformation products (i.e., nitrous oxide).

Coupling Bioflocculation of Dehalococcoides mccartyi to High-Rate Reductive Dehalogenation of Chlorinated Ethenes

Continuous bioreactors operated at low hydraulic retention times have rarely been explored for reductive dehalogenation of chlorinated ethenes. The inability to consistently develop such bioreactors affects the way growth approaches for Dehalococcoides mccartyi bioaugmentation cultures are envisioned. It also affects interpretation of results from in situ continuous treatment processes. We report bioreactor performance and dehalogenation kinetics of a D. mccartyi-containing consortium in an upflow bioreactor. When fed synthetic groundwater at 11-3.6 h HRT, the upflow bioreactor removed >99.7% of the influent trichloroethene (1.5-2.8 mM) and produced ethene as the main product. A trichloroethene removal rate of 98.51 ± 0.05 me^- equiv L^-1 d^-1 was achieved at 3.6 h HRT. D. mccartyi cell densities were 10¹³ and 10¹² 16S rRNA gene copies L^-1 in the bioflocs and planktonic culture, respectively. When challenged with a feed of natural groundwater containing various competing electron acceptors and 0.3-0.4 mM trichloroethene, trichloroethene removal was sustained at >99.6%. Electron micrographs revealed that D. mccartyi were abundant within the bioflocs, not only in multispecies structures, but also as self-aggregated microcolonies. This study provides fundamental evidence toward the feasibility of upflow bioreactors containing D. mccartyi as high-density culture production tools or as a high-rate, real-time remediation biotechnology.

Archaea and Bacteria Acclimate to High Total Ammonia in a Methanogenic Reactor Treating Swine Waste

Inhibition by ammonium at concentrations above 1000 mgN/L is known to harm the methanogenesis phase of anaerobic digestion. We anaerobically digested swine waste and achieved steady state COD-removal efficiency of around 52% with no fatty-acid or H₂ accumulation. As the anaerobic microbial community adapted to the gradual increase of total ammonia-N (NH₃-N) from 890 ± 295 to 2040 ± 30 mg/L, the Bacterial and Archaeal communities became less diverse. Phylotypes most closely related to hydrogenotrophic Methanoculleus (36.4%) and Methanobrevibacter (11.6%), along with acetoclastic Methanosaeta (29.3%), became the most abundant Archaeal sequences during acclimation. This was accompanied by a sharp increase in the relative abundances of phylotypes most closely related to acetogens and fatty-acid producers (Clostridium, Coprococcus, and Sphaerochaeta) and syntrophic fatty-acid Bacteria (Syntrophomonas, Clostridium, Clostridiaceae species, and Cloacamonaceae species) that have metabolic capabilities for butyrate and propionate fermentation, as well as for reverse acetogenesis. Our results provide evidence countering a prevailing theory that acetoclastic methanogens are selectively inhibited when the total ammonia-N concentration is greater than ~1000 mgN/L. Instead, acetoclastic and hydrogenotrophic methanogens coexisted in the presence of total ammonia-N of ~2000 mgN/L by establishing syntrophic relationships with fatty-acid fermenters, as well as homoacetogens able to carry out forward and reverse acetogenesis.