Physiological and transcriptional studies of Cr(VI) reduction under aerobic and denitrifying conditions by an aquifer-derived pseudomonad

Simultaneous natural attenuation of Cr(VI) and nitrate in the hyporheic zone sediments from an upstream tributary of the Jinsha River in the Sichuan Basin

The coexistence of hexavalent chromium (Cr(VI)) and nitrate (NO3-) in groundwater and surface water presents a considerable challenge for the natural attenuation of these two contaminants because their interactions in nature remain contentious. This study investigated the interplay between Cr(VI) and NO3- in hyporheic zone (HZ) sediments by integrating Cr(VI) reduction kinetics, NO3- transformation, microbial community structure, and a three-rate model. The concurrent natural attenuation of Cr(VI) and NO3- in the sediments was significantly influenced by their initial concentrations and redox conditions. The reduction of low concentrations of Cr(VI) (37.1 and 96.2 μM) was slightly enhanced by NO3-, while inhibitory effects were observed at high concentrations of Cr(VI) (200.0 μM). However, except for an initial low concentration of Cr(VI) (37.1 μM) and NO3- (450 μM), the reduction of NO3- was adversely affected by Cr(VI). The reduction rates and efficiencies of Cr(VI) and NO3- were noticeably lower under aerobic conditions than under anaerobic conditions. This phenomenon can be attributed to the presence of O2, which decreased the selectivity of sediments-associated Fe(II) towards Cr(VI) and NO3- and induced alterations in the microbial community structure, leading to subsequent changes in NO3- transformation. Furthermore, the three-rate model represents a robust approach for elucidating the reduction of Cr(VI) in the presence of co-contaminants, such as NO3- contamination under diverse redox conditions. This study provides further insights into the interaction mechanism between Cr(VI) and NO3- within the HZ, necessitating the consideration of the microbial toxicity of Cr(VI) and electron competition among Cr(VI), NO3-, and O2.

Groundwater Cr(VI) contamination and remediation: A review from 1999 to 2022

Hexavalent chromium (Cr(VI)) contamination of groundwater has traditionally been an environmental issue of great concern due to its bioaccumulative and highly toxic nature. This paper presents a review and bibliometric analysis of the literature on the interest area "Cr(VI) in groundwater" published in the Web of Science Core Collection from 1999 to 2022. First, information on 203 actual Cr(VI)-contaminated groundwater sites around the world was summarized, and the basic characteristics of the sources and concentrations of contamination were derived. 68.95% of the sites were due to human causes and 56.43% of these sites had Cr(VI) concentrations in the range of 0-10 mg/L. At groundwater sites with high Cr(VI) contamination due to natural causes, 75.00% of the sites had Cr(VI) concentrations less than 0.2 mg/L. A total of 936 papers on "Cr(VI) in groundwater" were retrieved for bibliometric analysis: interest in research on Cr(VI) in groundwater has grown rapidly in recent years; 59.4% of the papers were published in the field of environmental sciences. A systematic review of the progress of studies on the Cr(VI) removal/remediation based on reduction, adsorption and biological processes is presented. Out of 666 papers on Cr(VI) removal/remediation, 512, 274, and 75 papers dealt with the topics of reduction, adsorption, and bioremediation, respectively. In addition, several studies have demonstrated the potential applicability of natural attenuation in the remediation of Cr(VI)-contaminated groundwater. This paper will help researchers to understand and investigate methodological strategies to remove Cr(VI) from groundwater in a more targeted and effective manner.

Efficient nitrate and Cr(VI) removal by denitrifier: The mechanism of S. oneidensis MR-1 promoting electron production, transportation and consumption

When Cr(VI) and nitrate coexist, the efficiency of both bio-denitrification and Cr(VI) bio-reduction is poor because chromate hinders bacterial normal functions (i.e., electron production, transportation and consumption). Moreover, under anaerobic condition, the method about efficient nitrate and Cr(VI) removal remained unclear. In this paper, the addition of Shewanella oneidensis MR-1 to promote the electron production, transportation and consumption of denitrifier and cause an increase in the removal of nitrate and Cr(VI). The efficiency of nitrate and Cr(VI) removal accomplished by P. denitrificans as a used model denitrifier increased respectively from 51.3% to 96.1% and 34.3% to 99.8% after S. oneidensis MR-1 addition. The mechanism investigations revealed that P. denitrificans provided S. oneidensis MR-1 with lactate, which was utilized to secreted riboflavin and phenazine by S. oneidensis MR-1. The riboflavin served as coenzymes of cellular reductants (i.e., thioredoxin and glutathione) in P. denitrificans, which created favorable intracellular microenvironment conditions for electron generation. Meanwhile, phenazine promoted biofilm formation, which increased the adsorption of Cr(VI) on the cell surface and accelerated the Cr(VI) reduction by membrane bound chromate reductases thereby reducing damage to other enzymes respectively. Overall, this strategy reduced the negative effect of chromate, thus improved the generation, transportation, and consumption of electrons. SYNOPSIS: The presence of S. oneidensis MR-1 facilitated nitrate and Cr(VI) removal by P. denitrificans through decreasing the negative effect of chromate due to the metabolites' secretion.

Chromate-induced methylglyoxal detoxification system drives cadmium and chromate immobilization by Cupriavidus sp. MP-37

The detoxification of cadmium (Cd) or chromium (Cr) by microorganisms plays a vital role in bacterial survival and restoration of the polluted environment, but how microorganisms detoxify Cd and Cr simultaneously is largely unknown. Here, we isolated a bacterium, Cupriavidus sp. MP-37, which immobilized Cd(II) and reduced Cr(VI) simultaneously. Notably, strain MP-37 exhibited variable Cd(II) immobilization phenotypes, namely, cell adsorption and extracellular immobilization in the co-presence of Cd(II) and Cr(VI), while cell adsorption in the presence of Cd(II) alone. To unravel Cr(VI)-induced extracellular Cd(II) immobilization, proteomic analysis was performed, and methylglyoxal-scavenging protein (glyoxalase I, GlyI) and a regulator (YafY) showed the highest upregulation in the co-presence of Cd(II) and Cr(VI). GlyI overexpression reduced the intracellular methylglyoxal content and increased the immobilized Cd(II) content in extracellular secreta. The addition of lactate produced by GlyI protein with methylglyoxal as substrate increased the Cd(II) content in extracellular secreta. Reporter gene assay, electrophoretic mobility shift assay, and fluorescence quenching assay demonstrated that glyI expression was induced by Cr(VI) but not by Cd(II), and that YafY positively regulated glyI expression by binding Cr(VI). In the pot experiment, inoculation with the MP-37 strain reduced the Cd content of Oryza sativa L., and their secreted lactate reduced the Cr accumulation in Oryza sativa L. This study reveals that Cr(VI)-induced detoxification system drives methylglyoxal scavenging and Cd(II) extracellular detoxification in Cd(II) and Cr(VI) co-existence environment.

Reduction of Chromate via Biotic and Abiotic Pathways in the Presence of Three Co-contaminating Electron Acceptors

Bioreduction of Cr(VI) to Cr(III) is a promising technology for removing Cr(VI), but Cr(VI) reduction alone cannot support microbial growth. This study investigated the reduction of Cr(VI) in the presence of three electron acceptors that typically coexist with Cr(VI): NO3-, SO42-, and Fe(III). All three systems could reduce Cr(VI) to Cr(III), but the fate of Cr, its impacts on reduction of the other acceptors, and its impact on the microbial community differed. Although Cr(VI) was continuously removed in the NO3--reduction systems, batch tests showed that denitrification was inhibited primarily through impeding nitrite reduction. The SO42- and Fe(III) reduction systems reduced Cr(VI) using a combination of biotic and abiotic processes. Across all three systems, the abundance of genera capable of reducing Cr(VI) increased following the introduction of Cr(VI). Conversely, the abundance of genera that cannot reduce or resist Cr(VI) decreased, leading to restructuring of the microbial community. Furthermore, the abundance of sulfide oxidizers and Fe(II) oxidizers substantially increased after the introduction of chromate. This study provides fundamental knowledge about how Cr(VI) bioreduction interacts with bioreductions of three other co-contaminating electron acceptors.

Effects of chromate on nitrogen removal and microbial community in two-stage vertical-flow constructed wetlands

Nitrogen and chromium (Cr(VI)) pollution in waterbodies pose great threats to human health, and a cost-effective alternative with Cr(VI) and nitrogen simultaneous removal is still needed. This study investigated the influence of Cr(VI) on nitrogen removal in the two-stage vertical-flow constructed wetlands (TS-VFCWs) along with iron ore and woodchip, and explored relationship between Cr(VI) and nitrogen removal. The results showed that efficient Cr(VI) and nitrogen removal were simultaneously achieved in TS-VFCWs together with iron-ore and woodchip under 2 mg/L-Cr(VI), whereas 10 mg/L-Cr(VI) gave significant and recoverable inhibition of nitrogen removal. Cr(VI) supplementation promoted the beneficiation of Cr(VI)-reducing/resistant bacteria IMCC26207 and Bryobacter on iron-ore. Woodchip enriched Cr(VI)-reducing bacteria Streptomyces and Thiobacillus. XRD and XPS showed that abundant bound-Cr existed in the surface of iron ore and woodchip, and Cr(III) precipitation/oxide was the major product. High abundances of nitrifying and autotrophic/heterotrophic denitrifying bacteria ensured good nitrogen removal at Cr(VI) stress.

A comprehensive review on chromium (Cr) contamination and Cr(VI)-resistant extremophiles in diverse extreme environments

Chromium (Cr) compounds are usually toxins and exist abundantly in two different forms, Cr(VI) and Cr(III), in nature. Their contamination in any environment is a major problem. Many extreme environments including cold climate, warm climate, acidic environment, basic/alkaline environment, hypersaline environment, radiation, drought, high pressure, and anaerobic conditions have accumulated elevated Cr contamination. These harsh physicochemical conditions associated with Cr(VI) contamination damage biological systems in various ways. However, several unique microorganisms belonging to phylogenetically distant taxa (bacteria, fungi, and microalgae) owing to different and very distinct physiological characteristics can withstand extremities of Cr(VI) in different physicochemical environments. These challenging situations offer great potential and extended proficiencies in extremophiles for environmental and biotechnological applications. On these issues, the present review draws attention to Cr(VI) contamination from diverse extreme environmental regions. The study gives a detailed account on the ecology and biogeography of Cr(VI)-resistant microorganisms in inhospitable environments, and their use for detoxifying Cr(VI) and other applications. The study also focuses on physiological, multi-omics, and genetic engineering approaches of Cr(VI)-resistant extremophiles.

Potential arsenic-chromium-lead Co-contamination in the hilly terrain of Arunachal Pradesh, north-eastern India: Genesis and health perspective

In the recent times, multi-metal co-contamination in the groundwater of various parts of the globe has emerged as a challenging environmental health problems. While arsenic (As) has been reported with high fluoride and at times with uranium; and Cr & Pb are also found in aquifers under high anthropogenic impacts. The present work probably for the first time traces the As-Cr-Pb co-contamination in the pristine aquifers of a hilly terrain that are under relatively less stress from the anthropogenic activities. Based on the analyses of twenty-two (n = 22) groundwater (GW) samples and six (n = 6) sediment samples, it was found that Cr being leached from the natural sources as evident from 100% of samples with dissolve Cr exceeding the prescribed drinking water limit. Generic plots suggests rock-water interaction as the major hydrogeological processes with mixed Ca²⁺-Na⁺-HCO₃^- type water. Wide range of pH suggests localized human interferences, as well as indicative of both calcite and silicate weathering processes. In general water samples were found high only with Cr and Fe, however all sediment samples were found to contain As-Cr-Pb. This implies that the groundwater is under-risk of co-contamination of highly toxic trio of As-Cr-Pb. Multivariate analyses indicate that the changing pH as the causative factor for Cr leaching into the groundwater. This is a new finding for a pristine hilly aquifers, and we suspect such condition may also be present in other parts of globe, and thus precautionary investigations are needed to prevent this catastrophic situation to arise, and to alert the community in advance.

Assessment of natural and anthropogenic contamination sources in a Mediterranean aquifer by combining hydrochemical and stable isotope techniques

The Atalanti basin is an intensively cultivated area in central Greece, facing groundwater quality deterioration threats due to natural and anthropogenic-related contamination sources. A combination of statistical and hydrogeochemical techniques, and stable isotope compositions (δ²H-H₂O and δ¹⁸Ο-Η₂Ο, δ¹⁵Ν-ΝΟ₃^- and δ¹⁸Ο-ΝΟ₃^-, δ³⁴S-SO₄^2- and δ¹⁸O-SO₄^2-) were applied to elucidate the origin of salinity and nitrate contamination, and shed light on the potential associations between geogenic Cr(VI) and NO₃^- sources and transformations. Nitrate and Cr(VI) concentrations reached up to 337 mg L^-1 and 76.1 μg L^-1, respectively, exceeding WHO threshold values in places. The cluster of samples with the high salinity was mostly influenced by irrigation return flow and marine aerosols, and less by seawater intrusion, as evidenced by the ionic ratios (e.g., Na⁺/Cl^-) and the stable isotopes of oxygen and hydrogen in water, and sulphur and oxygen in sulphates. The δ¹⁵Ν-ΝΟ₃^- and δ¹⁸O-NO₃^- values ranged from +2.0 ‰ to +14.5 ‰ and + 0.3 ‰ to +11.0 ‰, respectively. We found that the dominant sources of NO₃^- in groundwater were fertilizers in the central part of the area and sewage waste in the northern part around the residential area of Livanates. The occurrence of denitrification was evident in the northern part of the basin, where the DO levels were lowest (≤ 2.2 mg L^-1), whereas nitrification of NH₄⁺-fertilizers prevailed in the central part. Elevated Cr(VI) values (≥ 20 μg/l) were associated with the lowest deviation of the measured from the theoretical nitrification δ¹⁸Ο-NO₃^- values, whereas the lowest Cr(VI) values were observed in the denitrified water samples. Our isotope findings revealed the strong influence of redox conditions on the biogeochemical transformations of N species and the mobilization of Cr(VI) that will help improve the understanding of the fate of these contaminants from the unsaturated zone to the groundwater in areas of agricultural and urban land use.

Enhanced Natural Attenuation of Groundwater Cr(VI) Pollution Using Electron Donors: Yeast Extract vs. Polyhydroxybutyrate

Remediation interventions based on the native bacteria’s capability to reduce Cr(VI) represent a valid strategy in terms of economic and environmental sustainability. In this study, a bioremediation test was carried out using viable microcosms set with groundwater and deep soil (4:1), collected from the saturated zone of an industrial site in Southern Italy that was polluted by ~130 µg L−1 of Cr(VI). Conditions simulating the potential natural attenuation were compared to the enhanced natural attenuation induced by supplying yeast extract or polyhydroxybutyrate. Sterile controls were set up to study the possible Cr(VI) abiotic reduction. No pollution attenuation was detected in the unamended viable reactors, whereas yeast extract provided the complete Cr(VI) removal in 7 days, and polyhydroxybutyrate allowed ~70% pollutant removal after 21 days. The incomplete abiotic removal of Cr(VI) was observed in sterile reactors amended with yeast extract, thus suggesting the essential role of native bacteria in Cr(VI) remediation. This was in accordance with the results of Pearson’s coefficient test, which revealed that Cr(VI) removal was positively correlated with microbial proliferation (n = 0.724), and also negatively correlated with pH (n = −0.646), dissolved oxygen (n = −0.828) and nitrate (n = −0.940). The relationships between the Cr(VI) removal and other monitored parameters were investigated by principal component analysis, which explained 76.71% of the total variance.

Cloning of Nitrate Reductase and Nitrite Reductase Genes and Their Functional Analysis in Regulating Cr(VI) Reduction in Ectomycorrhizal Fungus Pisolithus sp.1

Assimilatory-type nitrate reductase (NR) and nitrite reductase (NiR) are the key enzymes that involve in nitrate assimilation and nitrogen cycling in microorganisms. NR and NiR with NADH or NADPH and FMN or FAD domains could be coupled to the reduction process of hexavalent chromium [Cr(VI)] in microorganisms. A new assimilatory-type NR gene (named niaD) and a new assimilatory-type NiR gene (named niiA) are cloned, identified, and functionally characterized by 5′ and 3′ RACE, alignment, annotation, phylogenetic tree, and yeast mutant complementation analyses from Pisolithus sp.1, a dominant symbiotic ectomycorrhizal fungi (EMF) that can assist in phytoremediation. Assimilatory-type niaD and niiA were 2,754 bp and 3,468 bp and encode a polypeptide with 917 and 1,155 amino acid residues, respectively. The isoelectric points of NR (Pisolithus sp.1 NR) and NiR (Pisolithus sp.1 NiR) of Pisolithus sp.1 are 6.07 and 6.38, respectively. The calculated molecular mass of Pisolithus sp.1 NR and Pisolithus sp.1 NiR is 102.065 and 126.914 kDa, respectively. Yeast mutant complementation analysis, protein purification, and activities of NR and NiR under Cr treatment suggest that Pisolithus sp.1 NR is a functional NR that mediates Cr(VI) tolerance and reduction. The multiple alignment demonstrates that Pisolithus sp.1 NR is potentially a nicotinamide adenine dinucleotide phosphate-dependent flavin mononucleotide reductase and also Class II chromate reductase. Our results suggest that Pisolithus sp.1 NR plays a key role in Cr(VI) reduction in the EMF Pisolithus sp.1.

Physiological mechanism of the response to Cr(VI) in the aerobic denitrifying ectomycorrhizal fungus Pisolithus sp.1

Pisolithus sp. 1 (P sp. 1) is an ectomycorrhizal fungus (EMF) with a strong Cr(VI) tolerance and reduction ability. The noninvasive microttest technique (NMT), real-time quantitative PCR (qRT-PCR), and the three-dimensional excitation-emission matrix (3D-EEM) were used to deeply explore the physiological mechanism of the P sp. 1 response to Cr(VI) and investigate the relationship between Cr(VI) reduction and denitrification in P sp. Cr(VI) induced the strongest elevations in nitrate reductase (NR) activity and NO production in the mycelia after treatment with Cr(VI) for 48 h under aerobic conditions. The NR inhibitor tungstate significantly inhibited Cr(VI) reduction, proton efflux and the expression of the NR gene (niaD) and NiR gene (niiA). In addition, NO was generated via NR-regulated denitrification. Combined treatments with Cr(VI) and the NO scavenger carboxy-PTIO (cPTIO) significantly increased O₂^-, H₂O₂ and MDA contents and reduced SDH, CAT, GSH, GR and GSNOR activity. Therefore, the NR-driven aerobic denitrifying process requires protons, and the generated NO reduces the oxidative stress effect of Cr(VI) on mycelia by reducing ROS accumulation and lipid peroxidation, enhancing mycelial and CAT activity, and promoting GSH recycling and regeneration. Psp.1 can also secrete humic acid-like and protein-like substances to combine with Cr(III) in a culture system.

Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms

Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing Pseudomonas stutzeri have been used for bioremediation, biocontrol, aquaculture management and wastewater denitrification. Furthermore, the use of P. stutzeri biofilms, in combination with consortia-based approaches, may offer advantages for these processes. Understanding the interspecific interaction within biofilm co-cultures or consortia provides a means for improvement of current technologies. However, the investigation of biofilm-based consortia has been limited. We present an adaptable and scalable method for the analysis of macroscopic interactions (colony morphology, inhibition, and invasion) between colony-forming bacterial strains using an automated printing method followed by analysis of the genes and metabolites involved in the interactions. Using Biofilm Interaction Mapping and Analysis (BIMA), these interactions were investigated between P. stutzeri strain RCH2, a denitrifier isolated from chromium (VI) contaminated soil, and 13 other species of pseudomonas isolated from non-contaminated soil. One interaction partner, Pseudomonas fluorescens N1B4 was selected for mutant fitness profiling of a DNA-barcoded mutant library; with this approach four genes of importance were identified and the effects on interactions were evaluated with deletion mutants and mass spectrometry based metabolomics.

Analysis of microbial community structure and degradation of ammonia nitrogen in groundwater in cold regions

Nitrogen pollution exceeding the standard because of intensive farming and cropping systems has been a widespread problem in Northeast China. This study investigated the characteristics of functional microorganisms in groundwater in the Bang River farming area. Metagenomic sequencing was used to analyze microbial community structures and Canoco was applied to reveal the response relationship between the microbial community and water environmental factors and to identify changes in the microbial population in response to the addition of electronic donors NH₄⁺-N, NO₂^--N, and NO₃^--N. The results showed that the dominant microorganisms in groundwater belong to the genera Exiguobacterium, Citrobacter, Acinetobacter, and Pseudomonas, which accounted for more than 40% of the total microbes in the study area. When combined with the results of a water chemical factor test, the dominant bacteria were found to be correlated with Fe²⁺, Mn²⁺, NH₄⁺, NO₃^-, NO₂^-, HCO₃^-, DOC, and pH in the water. However, the microbial population changed after the addition of the electron donor, with the genera Pseudomonas, Serratia, Enterobacter, Azomonas, and Ewingella accounting for 97.06% of the total sequences. Indigenous nitrogen-degrading bacteria suitable for low temperature, low oxygen, and oligotrophic groundwater were screened out. The total removal efficiency of NH₄⁺-N, NO₂^--N, and NO₃^--N in 120 h was 90.83%, 75.04%, and 73.35%, respectively. According to the experimental results, the degradation reaction kinetics followed a pseudo-second-order equation. The results presented herein provide an important scientific basis for the microbial remediation of groundwater contaminated by ammonia.

Dynamic characteristics of immobilized microorganisms for remediation of nitrogen-contaminated groundwater and high-throughput sequencing analysis of the microbial community

The aim of this study was to investigate the effect of adsorption by a composite active medium (nitrogen-degrading bacteria immobilized on scoria) on the removal of ammonium nitrogen (NH₄⁺-N), nitrite nitrogen (NO₂^-N) and nitrate nitrogen (NO₃^-N). Transport of these three forms of nitrogen was investigated using columns with different flow rates, initial concentrations and depths. Immobilization of the bacteria on the scoria significantly enhanced the ability of the composite active medium to remove nitrogen during the remediation process. As the flow rate increased, the shear force increased and solute diffusion decreased, thereby improving the tolerance of the bacteria for the three forms of nitrogen and reducing the penetration time. Increasing the initial nitrogen concentration resulted in a decrease in the adsorption rate constant (K_Th). The nitrogen-degrading bacteria immobilized on scoria rapidly reached saturation with regards to their nitrogen adsorption capacity. The initial nitrogen concentration of each media layer was different, and the composite active medium had a certain blocking effect, which resulted in a slow increase in the concentration of nitrogen in the deeper media layer. The transport experiments showed that the process accords with the thomas model and the Bohart-Adams model. The contents of the three forms of nitrogen were within acceptable standards for drinking water after 2 months of a column containing the composite active medium. The composite active medium can be used for in situ and ex situ remediation of groundwater containing excessive nitrogen. High-throughput sequencing analysis was used to monitor the composition of the bacterial community present within the composite active medium. During the remediation process, there were only slight changes in the structure and composition of the nitrogen-degrading bacterial community, although there were clear differences in abundance. Pseudomonas, Stenotrophomonas and Serratia were the three bacterial genera that were effective removal of all three forms of nitrogen.

Simultaneous cobalt(III)-histidine reduction and aerobic denitrification by Paracoccus versutus LYM

Cobalt(II)-histidine [Co(II)His] is potentially a better alternative to ferrous complexes in the chemical absorption-biological reduction (CABR) flue gas denitrification process in view of its higher oxygenation reversibility. Though with excellent O₂-resistant ability, Co(II)His was still gradually oxidized into Co(III)His, losing NO binding capacity. Thus, Co(III)His biological reduction is an indispensable step in CABR process. Co(III)His reduction by Paracoccus versutus LYM under aerobic condition in the presence of nitrate or nitrite was investigated. Results indicated that simultaneous Co(III)His reduction and aerobic denitrification were achieved by strain LYM. Co(III)His reduction was significantly promoted by denitrification process, but dramatically inhibited by 5-15 mM sulfite. Co(II)His absorbent regeneration could be facilitated by adjusting O₂ supply properly or adding nitrogen and carbon source regularly. These findings provide a basis for the application of Co(II)His as the absorbent in the CABR process and qualify P. versutus LYM as an applicable and competitive strain for this process.

Application of enhanced bioreduction for hexavalent chromium-polluted groundwater cleanup: Microcosm and microbial diversity studies

Hexavalent chromium (Cr⁶⁺) is a commonly found heavy metal at polluted groundwater sites. In this study, the effectiveness of Cr⁶⁺ bioreduction by the chromium-reducing bacteria was evaluated to remediate Cr⁶⁺-contaminated groundwater. Microcosms were constructed using indigenous microbial consortia from a Cr⁶⁺-contaminated aquifer as the inocula, and slow-releasing emulsified polycolloid-substrate (ES), cane molasses (CM), and nutrient broth (NB) as the primary substrates. The genes responsible for the bioreduction of Cr⁶⁺ and variations in bacterial diversity were evaluated using metagenomics assay. Complete Cr⁶⁺ reduction via the biological mechanism was observed within 80 days using CM as the carbon source under anaerobic processes with the increased trivalent chromium (Cr³⁺) concentrations. Cr⁶⁺ removal efficiencies were 83% and 59% in microcosms using ES and NB as the substrates, respectively. Increased bacterial communities associated with Cr⁶⁺ bioreduction was observed in microcosms treated with CM and ES. Decreased bacterial communities were observed in NB microcosms. Compared to ES, CM was more applicable by indigenous Cr⁶⁺ reduction bacteria and resulted in effective Cr⁶⁺ bioreduction, which was possibly due to the growth of Cr⁶⁺-reduction related bacteria including Sporolactobacillus, Clostridium, and Ensifer. While NB was applied for specific bacterial selection, it might not be appropriate for electron donor application. These results revealed that substrate addition had significant impact on microbial diversities, which affected Cr⁶⁺ bioreduction processes. Results are useful for designing a green and sustainable bioreduction system for Cr⁶⁺-polluted groundwater remediation.

Simultaneous reduction of nitrate and Cr(VI) by Pseudomonas aeruginosa strain G12 in wastewater

The interference of toxic heavy metals in the process of microbial aerobic denitrification is a hot issue in industry wastewater treatment in recent years. In this study, a multifunctional aerobic denitrifying bacterium - Pseudomonas aeruginosa G12 isolated from sewage sludge was used to explore the simultaneous removal ability to NO₃^--N and Cr(VI) in wastewater by a series of batch experiments. The results showed that G12 could effectively remove NO₃^--N (500 mg L^-1) and Cr(VI) (10 mg L^-1) by 98% and 93%, respectively. Meanwhile, the study found that the strain G12 had the potential to adapt to the complex external environment, including different carbon resources, nitrogen sources, and the coexisting heavy metals (Mn²⁺ and Cu²⁺). The strain G12 also had the considerable tolerance to initial NO₃^--N (100-700 mg L^-1) and Cr(VI) (1-20 mg L^-1) concentrations. The instrument analysis methods-Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and X-ray diffraction (XRD), from the molecular level, further confirmed that the strain G12 could remove NO₃^--N by aerobic denitrification, and the reduced functional groups (amino group, amide group, hydroxyl group and carboxyl group) on the surface of bacteria could transform Cr(VI) to Cr(III) (mainly CrCl₃). This study will offer a promising new microbial resource for nitrogen and Cr(VI) removal in industry wastewater treatment.

Coupling enhancement of Chromium(VI) bioreduction in groundwater by phosphorus minerals

Groundwater contaminated by hexavalent chromium (Cr(VI)) has posed severe threat to the environment and public health. Although heterotrophic bioremediation has been known as an efficient approach, little is explored on mineral nutrient source addition such as phosphorus minerals. In this study, the stabilization and sustainability of phosphorus minerals for providing phosphorus has been investigated, and the enhancement of Cr(VI) removal by mixed bacterial consortium coupled with phosphorus minerals was also observed and further verified, with 1.4-3.9 times K values (first-order) increase under different conditions. We demonstrated that the applied of phosphorus minerals facilitated the reduction of Cr(VI) and the removal of Cr(III), promoted the resistance of Cr(VI) and the generation of antioxidase, and engendered the evolution of microbial community structures and functional genes. These findings provide a new insight for enhancement of Cr(VI)-contaminated groundwater in-situ remediation.

Comparative transcriptomic analysis reveals novel insights into the response to Cr(VI) exposure in Cr(VI) tolerant ectomycorrhizal fungi Pisolithus sp. 1 LS-2017

Chromium (Cr) is one of the most toxic heavy metals and a health hazard to millions of people worldwide. Ectomycorrhizal (ECM) fungi can assist plants in phytoremediation of heavy metal contaminated soil. Cr tolerance differs among ECM fungal varieties, but the underlying molecular mechanisms of Cr tolerance in ECM fungi are not clear. This study identified, analysed and compared the Cr(VI)-induced transcriptional changes between Cr(VI)-tolerant strain (Pisolithus sp. 1 LS-2017) and Cr(VI)-sensitive strain (Pisolithus sp. 2 LS-2017) by de novo transcriptomic analysis. The results showed that 93,642 assembled unique transcripts representing the 22,353 (46.76%) unigenes matched the proteins we have known in the Nr database and 47,801 unigenes were got from the Pisolithus spp. For DEGs between the control and 10 mg/L Cr(VI) treatment, cyanoamino acid metabolic, type I diabetes mellitus metabolism, nitrogen metabolism and beta-Alanine metabolism pathways were significantly enriched (p < 0.05) in Pisolithus sp. 1 LS-2017. Two nitrate reductase family genes (nidD, niiA) provide Cr(VI) tolerance for Pisolithus sp. 1 LS-2017 by regulating Cr(VI) reduction. In addition, NO produced by nidD, niiA regulated denitrification can alleviate Cr(VI) induced oxidative stress. In Pisolithus sp. 2 LS-2017, the alcC, aldA and lcf2 gene may alleviate Cr(VI) induced oxidative stress by protecting SH groups and increasing secondary metabolism, reducing detoxify aldehydes to carboxylic acids and producing LCPUFAs respectively; .T gene regulate Cr(VI) induced wound healing by pigmentation and stability of melanin in spore; MKP2 gene accelerate Cr(VI) induced cell death and gpmA gene regulated Cr(VI) induced energy emergency.

Characterisation of the natural attenuation of chromium contamination in the presence of nitrate using isotopic methods. A case study from the Matanza-Riachuelo River basin, Argentina

The groundwater contamination by hexavalent chromium (Cr(VI)) in a site of the Matanza-Riachuelo River basin (MRB), Argentina, has been evaluated by determining the processes that control the natural mobility and attenuation of Cr(VI) in the presence of high nitrate (NO₃^-) contents. The groundwater Cr(VI) concentrations ranged between 1.9E-5 mM and 0.04 mM, while the NO₃^- concentrations ranged between 0.5 mM and 3.9 mM. In order to evaluate the natural attenuation of Cr(VI) and NO₃^- in the MRB groundwater, Cr and N isotopes were measured in these contaminants. In addition, laboratory batch experiments were performed to determine the isotope fractionation (ε) during the reduction of Cr(VI) under denitrifying conditions. While the Cr(VI) reduction rate is not affected by the presence of NO₃^-, the NO₃^- attenuation is slower in the presence of Cr(VI). Nevertheless, no significant differences on ε values were observed when testing the absence or presence of each contaminant. The ε⁵³Cr determined in the batch experiments describe a two- stage trend, in which Stage I is characterized by ε⁵³Cr ~-1.8‰ and Stage II by ε⁵³Cr ~-0.9‰. The respective ε¹⁵N_NO3 obtained is -23.9‰ whereas ε¹⁸O_NO3 amount to -25.7‰. Using these ε values and a Rayleigh fractionation model we estimate that an average of 60% of the original Cr(VI) is removed from the groundwater of the contaminated site. Moreover, the average degree of NO₃^- attenuation by denitrification is found to be about 20%. This study provides valuable information about the dynamics of a complex system that can serve as a basis for efficient management of contaminated groundwater in the most populated and industrialized basin of Argentina.

Removal characteristics of a composite active medium for remediation of nitrogen-contaminated groundwater and metagenomic analysis of degrading bacteria

To investigate the removal characteristics of ammonium-nitrogen (NH₄⁺-N), nitrite-nitrogen (NO₂^--N), nitrate-nitrogen (NO₃^--N), and total nitrogen from groundwater by a degradable composite active medium, kinetics, thermodynamics, and equilibrium adsorption, experiments were performed using scoria and degrading bacteria immobilized on scoria. Removal of NH₄⁺-N, NO₂^--N, and NO₃^--N was conducted in adsorption experiments using different times, initial concentrations, pH values, and groundwater chemical compositions (Ca²⁺, Mg²⁺, HCO₃^-, CO₃^2-, Fe²⁺, Mn²⁺, and SO₄^2-). The results showed that the removal of nitrogen by the composite active medium was obviously better than that of scoria alone. The removal rates of NH₄⁺-N (C₀ = 5 mg/L), NO₂^--N (C₀ = 5 mg/L), and NO₃^--N (C₀ = 100 mg/L) by the composite active medium within 1 h were 96.05%, 82.40%, and 83.16%, respectively. The adsorption kinetics were well fitted to a pseudo-second order model, whereas the equilibrium adsorption agreed with the Freundlich model. With changes in the pH, variation in the removal could be attributed to the combined effect of hydrolysis and competitive ion adsorption, and the optimum pH was 7. Different concentration conditions, hardness, alkalinity, anions, and cations showed different promoting and inhibiting effects on the removal of nitrogen. A careful examination of ionic concentrations in adsorption batch experiments suggested that the sorption behavior of nitrogen onto the immobilized medium was mainly controlled by ion exchange. The degrading bacteria on the scoria surface were eluted and analyzed by metagenomic sequencing. There were significant differences in the number of operational taxons, relative abundances, and community diversity among degrading bacteria after adsorption of the three forms of nitrogen. The relative abundance of degrading bacteria was highest after NO₃^--N removal, and the diversity was highest after NO₂^--N removal. Pseudomonas and Serratia were the dominant genera that could efficiently remove NH₄⁺-N and NO₂^--N.

Use of carbon stable isotopes to monitor biostimulation and electron donor fate in chromium-contaminated groundwater

Hexavalent chromium Cr(VI) is a common inorganic contaminant in industrial areas and represents a serious threat to human health due its toxicity. Here we report experimental results from a field-scale investigation of Cr(VI) bio-immobilization at Hanford 100H reservation, a U.S Department of Energy facility (Washington State, USA). Microbial Cr(VI) reduction was stimulated via injection of a¹³C-labeled sodium lactate solution into the high-permeability aquifer consisting of gravel and coarse sand sediments. Concentrations and carbon isotope ratios of metabolites, including dissolved inorganic carbon and total organic carbon, and compound-specific analysis of acetate and propionate, together with phospholipid fatty acids (biomass) have been analyzed to help provide an understanding of the predominant redox processes accompanying Cr(VI) reduction. Results of our study indicate that the injection of an electron donor caused a sharp decrease of Cr(VI) concentration from ∼32 to ∼10 nM. Cr(VI) reduction was associated with a decrease in the concentration of carboxylic acids, such as lactate (∼6 mM to undetectable), propionate (∼9 mM to undetectable), and acetate (∼6 mM to undetectable), as well as dissolved inorganic carbon (30-10 mM C). Carbon isotope data indicate carbon transfers from the original substrate to organic byproducts and mineralized carbon. Concentrations of metabolites and stable isotope data as well as carbon isotope mass balance calculations were used to monitor biologically mediated reduction of Cr(VI).

Two-stage chromium isotope fractionation during microbial Cr(VI) reduction

Chromium isotope fractionation analysis is a promising approach for the assessment of microbial Cr(VI) reduction in groundwater. Understanding the mechanisms and other parameters that control Cr isotope fractionation factors (between the product Cr(III) and reactant Cr (VI)) in microbial Cr(VI) reduction is critical to this application. To date, such studies are very limited. Here, the influence of critical factors on observed Cr isotope fractionation during Cr(VI) reduction by Shewanella oneidensis MR-1 under various conditions was investigated. The Cr(VI) concentration and Cr isotope ratio measurements were conducted on unreacted Cr(VI) remaining in solution to determine Cr isotope fractionation factors. The changes in ambient environmental conditions (e.g., pH, temperature) have limited influence on Cr isotope fractionation factors. However, as a result of Cr(VI) consumption as the experiments proceed, the change in bioavailability of Cr(VI) has a significant impact on Cr isotope fractionation factors. For example, in temperature-controlled experiments, Cr isotope fractionation showed two-stage behavior: during Stage I, the values of ε were -2.81 ± 0.19‰ and -2.60 ± 0.14‰ at 18 °C and 34 °C, respectively; during Stage II, as Cr(VI) reduction progressed, Cr isotope fractionation was significantly masked, and the ε values decreased to -0.98 ± 0.49‰ and -1.01 ± 0.11‰ at 18 °C and 34 °C, respectively. Similar two-stage isotope fractionation behaviors were observed in pH-controlled experiments (pH = 6.0 and 7.2) and in experiments with and without the addition of a competing electron acceptor (nitrate). Masking of isotope fractionation in Stage II indicated restrictions on the bioavailability of Cr(VI) and mass-transfer limitations. This study provides an explanation for the variation in Cr isotope fractionation factors during microbial Cr(VI) reduction in the environment, furthering the viability of Cr isotope ratio analysis as an approach in understanding Cr biogeochemical cycling.

Hexavalent Chromium Sources and Distribution in California Groundwater

Groundwater resources in California represent a confluence of high-risk factors for hexavalent chromium contamination as a result of industrial activities, natural geology, and, potentially, land use. Here, we examine state-wide links in California between groundwater Cr(VI) concentrations and chemicals that provide signatures for source attribution. In environmental monitoring wells, Cr(VI) had the highest co-occurrence and also clustered with 1,4-dioxane and several chlorinated hydrocarbons indicative of the metal plating industry. Additionally, hotspots of Cr(VI) co-occurring with bromoform result from volatile organic compound remediation using in situ chemical oxidation that inadvertently oxidizes naturally occurring Cr(III). In groundwater supply wells, which are typically free of industrial inputs, Cr(VI) correlates with dichlorodiphenyldichloroethylene (DDE), vanadium, and ammonia and clusters with nitrate and dissolved oxygen, suggesting potential links between agricultural activities and Cr(VI). Specific controls on Cr(VI) vary substantially by region: from the metal plating industry around Los Angeles and the San Francisco Bay areas to natural redox conditions along flow paths in the Mojave Desert and to correlations with agricultural practices in the Central Valley of California. While industrial uses of Cr lead to the most acute cases of groundwater Cr(VI) contamination, oxidation of naturally occurring Cr affects a larger area, more wells, and a greater number of people throughout California.

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

Chromium isotope fractionation during Cr(VI) reduction in a methane-based hollow-fiber membrane biofilm reactor

Chromium (Cr) isotope fractionation analysis is a promising tool for monitoring Cr(VI) reduction in natural aqueous systems. In addition, large amounts of CH₄ in natural aqueous sediments are oxidized to CO₂ through methanotrophs, thereby mitigating emissions to the atmosphere. However, the investigations on the Cr(VI) reduction process with methanotrophs, and the associated Cr isotope fractionation patterns are scarce. In this study, we have shown that Cr(VI) reduction can occur in the presence of CH₄ as the sole electron donor in a hollow-fiber membrane reactor (HfMBR) after direct bacteria enrichment from sediment samples. Products of the methane oxidation by the methanotrophs are used by microbes to reduce Cr(VI) as shown by the progressive increase in δ⁵³Cr with time in the CH₄ feed reactor. The isotope fractionation factor (ε) of -2.62 ± 0.20‰ was obtained from the application of the Rayleigh distillation model. The results of Cr isotope fractionation analysis also explained the decrease of Cr(VI) concentration in the N₂ feed reactor, where the δ⁵³Cr values remained steady in the first two weeks but significantly increased in the last two weeks, indicating that physical adsorption and subsequent Cr(VI) reduction occurred. This study extended the application of Cr isotope fractionation, showing the suitability of this method for clarifying different Cr(VI) removal processes.

Mechanisms of Chromium and Uranium Toxicity in Pseudomonas stutzeri RCH2 Grown under Anaerobic Nitrate-Reducing Conditions

Chromium and uranium are highly toxic metals that contaminate many natural environments. We investigated their mechanisms of toxicity under anaerobic conditions using nitrate-reducing Pseudomonas stutzeri RCH2, which was originally isolated from a chromium-contaminated aquifer. A random barcode transposon site sequencing library of RCH2 was grown in the presence of the chromate oxyanion (Cr[VI]O42−) or uranyl oxycation (U[VI]O22+). Strains lacking genes required for a functional nitrate reductase had decreased fitness as both metals interacted with heme-containing enzymes required for the later steps in the denitrification pathway after nitrate is reduced to nitrite. Cr[VI]-resistance also required genes in the homologous recombination and nucleotide excision DNA repair pathways, showing that DNA is a target of Cr[VI] even under anaerobic conditions. The reduced thiol pool was also identified as a target of Cr[VI] toxicity and psest_2088, a gene of previously unknown function, was shown to have a role in the reduction of sulfite to sulfide. U[VI] resistance mechanisms involved exopolysaccharide synthesis and the universal stress protein UspA. As the first genome-wide fitness analysis of Cr[VI] and U[VI] toxicity under anaerobic conditions, this study provides new insight into the impact of Cr[VI] and U[VI] on an environmental isolate from a chromium contaminated site, as well as into the role of a ubiquitous protein, Psest_2088.

Nitrate effects on chromate reduction in a methane-based biofilm

The effects of nitrate (NO₃^-) on chromate (Cr(VI)) reduction in a membrane biofilm reactor (MBfR) were studied when CH₄ was the sole electron donor supplied with a non-limiting delivery capacity. A high surface loading of NO₃^- gave significant and irreversible inhibition of Cr(VI) reduction. At a surface loading of 500 mg Cr/m²-d, the Cr(VI)-removal percentage was 100% when NO₃^- was absent (Stage 1), but was dramatically lowered to < 25% with introduction of 280 mg N m^-2-d NO₃^- (Stage 2). After ∼50 days operation in Stage 2, the Cr(VI) reduction recovered to only ∼70% in Stage 3, when NO₃^- was removed from the influent; thus, NO₃^- had a significant long-term inhibition effect on Cr(VI) reduction. Weighted PCoA and UniFrac analyses proved that the introduction of NO₃^- had a strong impact on the microbial community in the biofilms, and the changes possibly were linked to the irreversible inhibition of Cr(VI) reduction. For example, Meiothermus, the main genus involved in Cr(VI) reduction at first, declined with introduction of NO₃^-. The denitrifier Chitinophagaceae was enriched after the addition of NO₃^-, while Pelomonas became important when nitrate was removed, suggesting its potential role as a Cr(VI) reducer. Moreover, introducing NO₃^- led to a decrease in the number of genes predicted (by PICRUSt) to be related to chromate reduction, but genes predicted to be related to denitrification, methane oxidation, and fermentation increased.

Reoxidation of Chromium(III) Products Formed under Different Biogeochemical Regimes

Hexavalent chromium, Cr(VI), is a widespread and toxic groundwater contaminant. Reductive immobilization to Cr(III) is a treatment option, but its success depends on the long-term potential for reduced chromium precipitates to remain immobilized under oxidizing conditions. In this unique long-term study, aquifer sediments subjected to reductive Cr(VI) immobilization under different biogeochemical regimes were tested for their susceptibility to reoxidation. After reductive treatment for 1 year, sediments were exposed to oxygenated conditions for another 2 years in flow-through, laboratory columns. Under oxidizing conditions, immobilized chromium reduced under predominantly denitrifying conditions was mobilized at low concentrations (≪1 μM Cr(VI); ∼ 3% of Cr(III) deposited) that declined over time. A conceptual model of a limited pool of more soluble Cr(III), and a larger pool of relatively insoluble Cr(III), is proposed. In contrast, almost no chromium was mobilized from columns reduced under predominantly fermentative conditions, and where reducing conditions persisted for several months after introduction of oxidizing conditions, presumably due to the presence of a reservoir of reduced species generated during reductive treatment. The results from this 3-year study demonstrate that biogeochemical conditions present during reductive treatment, and the potential for buildup of reducing species, will impact the long-term sustainability of the remediation effort.

Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site

Hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground water in several DOE sites, including Hanford 100 H area. In order to stimulate microbially mediated reduction of Cr(VI) at this site, a poly-lactate hydrogen release compound was injected into the chromium contaminated aquifer. Targeted enrichment of dominant nitrate-reducing bacteria post injection resulted in the isolation of Pseudomonas stutzeri strain RCH2. P. stutzeri strain RCH2 was isolated using acetate as the electron donor and is a complete denitrifier. Experiments with anaerobic washed cell suspension of strain RCH2 revealed it could reduce Cr(VI) and Fe(III). The genome of strain RCH2 was sequenced using a combination of Illumina and 454 sequencing technologies and contained a circular chromosome of 4.6 Mb and three plasmids. Global genome comparisons of strain RCH2 with six other fully sequenced P. stutzeri strains revealed most genomic regions are conserved, however strain RCH2 has an additional 244 genes, some of which are involved in chemotaxis, Flp pilus biogenesis and pyruvate/2-oxogluturate complex formation.

Environmental status of groundwater affected by chromite ore processing residue (COPR) dumpsites during pre-monsoon and monsoon seasons

Chromite ore processing residue (COPR) is generated by the roasting of chromite ores for the extraction of chromium. Leaching of carcinogenic hexavalent chromium (Cr(VI)) from COPR dumpsites and contamination of groundwater is a key environmental risk. The objective of the study was to evaluate Cr(VI) contamination in groundwater in the vicinity of three COPR disposal sites in Uttar Pradesh, India, in the pre-monsoon and monsoon seasons. Groundwater samples (n = 57 pre-monsoon, n = 70 monsoon) were taken in 2014 and analyzed for Cr(VI) and relevant hydrochemical parameters. The site-specific ranges of Cr(VI) concentrations in groundwater were <0.005 to 34.8 mg L^-1 (Rania), <0.005 to 115 mg L^-1 (Chhiwali), and <0.005 to 2.0 mg L^-1 (Godhrauli). Maximum levels of Cr(VI) were found close to the COPR dumpsites and significantly exceeded safe drinking water limits (0.05 mg L^-1). No significant dependence of Cr(VI) concentration on monsoons was observed.

Simultaneous aerobic denitrification and Cr(VI) reduction by Pseudomonas brassicacearum LZ-4 in wastewater

Inorganic nitrogen and heavy metals pervasively co-exist in industrial and domestic wastewaters. In this work, Pseudomonas brassicacearum LZ-4 was tested for the simultaneous reduction of Cr(VI) and nitrate. Nitrate was found to be the best inorganic nitrogen source for strain LZ-4, and could promote Cr(VI) reduction. Cr(VI) had a low degree of inhibition on denitrification, and even 50mgL^-1 Cr(VI) did not inhibit reduction of 100mgL^-1 NO₃^--N. The capability of simultaneous reduction of Cr(VI) and nitrate was illustrated by the reductase genes contained in the LZ-4 genome. Application in a batch membrane bioreactor showed that the immobilized strain LZ-4 could remove over 95% of 500mgL^-1 NO₃^--N, 80% of 10mgL^-1 Cr(VI), and 96% of 5000mgL^-1 COD in each batch of 46days. In summary, the strain LZ-4 is an ideal candidate for remediation of co-contaminants.

Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri

Metal ion transport systems have been studied extensively, but the specificity of a given transporter is often unclear from amino acid sequence data alone. In this study, predicted Cu(2+) and Zn(2+) resistance systems in Pseudomonas stutzeri strain RCH2 are compared with those experimentally implicated in Cu(2+) and Zn(2+) resistance, as determined by using a DNA-barcoded transposon mutant library. Mutant fitness data obtained under denitrifying conditions are combined with regulon predictions to yield a much more comprehensive picture of Cu(2+) and Zn(2+) resistance in strain RCH2. The results not only considerably expand what is known about well-established metal ion exporters (CzcCBA, CzcD, and CusCBA) and their accessory proteins (CzcI and CusF), they also reveal that isolates with mutations in some predicted Cu(2+) resistance systems do not show decreased fitness relative to the wild type when exposed to Cu(2+) In addition, new genes are identified that have no known connection to Zn(2+) (corB, corC, Psest_3226, Psest_3322, and Psest_0618) or Cu(2+) resistance (Mrp antiporter subunit gene, Psest_2850, and Psest_0584) but are crucial for resistance to these metal cations. Growth of individual deletion mutants lacking corB, corC, Psest_3226, or Psest_3322 confirmed the observed Zn-dependent phenotypes. Notably, to our knowledge, this is the first time a bacterial homolog of TMEM165, a human gene responsible for a congenital glycosylation disorder, has been deleted and the resulting strain characterized. Finally, the fitness values indicate Cu(2+)- and Zn(2+)-based inhibition of nitrite reductase and interference with molybdenum cofactor biosynthesis for nitrate reductase. These results extend the current understanding of Cu(2+) and Zn(2+) efflux and resistance and their effects on denitrifying metabolism.

IMPORTANCE

In this study, genome-wide mutant fitness data in P. stutzeri RCH2 combined with regulon predictions identify several proteins of unknown function that are involved in resisting zinc and copper toxicity. For zinc, these include a member of the UPF0016 protein family that was previously implicated in Ca(2+)/H(+) antiport and a human congenital glycosylation disorder, CorB and CorC, which were previously linked to Mg(2+) transport, and Psest_3322 and Psest_0618, two proteins with no characterized homologs. Experiments using mutants lacking Psest_3226, Psest_3322, corB, corC, or czcI verified their proposed functions, which will enable future studies of these little-characterized zinc resistance determinants. Likewise, Psest_2850, annotated as an ion antiporter subunit, and the conserved hypothetical protein Psest_0584 are implicated in copper resistance. Physiological connections between previous studies and phenotypes presented here are discussed. Functional and mechanistic understanding of transport proteins improves the understanding of systems in which members of the same protein family, including those in humans, can have different functions.

Enhanced fatty acid production in engineered chemolithoautotrophic bacteria using reduced sulfur compounds as energy sources

Chemolithoautotrophic bacteria that oxidize reduced sulfur compounds, such as H₂S, while fixing CO₂ are an untapped source of renewable bioproducts from sulfide-laden waste, such as municipal wastewater. In this study, we report engineering of the chemolithoautotrophic bacterium Thiobacillus denitrificans to produce up to 52-fold more fatty acids than the wild-type strain when grown with thiosulfate and CO₂. A modified thioesterase gene from E. coli (‘tesA) was integrated into the T. denitrificans chromosome under the control of P_kan or one of two native T. denitrificans promoters. The relative strength of the two native promoters as assessed by fatty acid production in engineered strains was very similar to that assessed by expression of the cognate genes in the wild-type strain. This proof-of-principle study suggests that engineering sulfide-oxidizing chemolithoautotrophic bacteria to overproduce fatty acid-derived products merits consideration as a technology that could simultaneously produce renewable fuels/chemicals as well as cost-effectively remediate sulfide-contaminated wastewater.

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Reduced S compounds and CO₂ can be feedstocks for biobased chemicals and biofuels.

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Fatty acids increased 52-fold in Thiobacillus denitrificans with E. coli ‘tesA.

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Native T. denitrificans promoters driving ‘tesA predictably enhanced fatty acids.

Alleviation of toxic hexavalent chromium using indigenous aerobic bacteria isolated from contaminated tannery industry sites

In the last decade, much attention has been paid to bioremediation of Cr(VI) using various bacterial species. Cr(VI) remediation by indegeneous bacteria isolated from contaminated sites of a tannery industry located in Tamil Nadu, India, was investigated in this study. Three Cr(VI) resistant bacterial strains (TES-1, TEf-1, and TES-2) were isolated and selected based on their Cr(VI) reduction ability in minimal salt medium. Among these three bacterial strains, TES-1 was found to be most efficient in bioreduction, while TES-2 was only found to be Cr(VI) resistant and showed negligible bioreduction, whereas TEf-1 was observed to be most Cr(VI) tolerant. Potential for bioremediation of TES-1 and TEf-1 was further investigated at different concentrations of Cr(VI) in the range of 50 to 350 mg L(-1). TEf-1 showed prominent synchronous growth throughout the experiment, whereas TES-1 took a longer acclimatization time. Minimum inhibitory concentrations (MIC) of Cr(VI) for TES-1 and TEf-1 were approximated as 600 mg L(-1) and 750 mg L(-1), respectively. The kinetic behavior of Cr(VI) reduction by TES-1 and TEf-1 exhibited zero- and first-order removal kinetics for Cr(VI), respectively. The most efficient strain TES-1 was identified as Streptomyces sp. by gene sequencing of 16S rRNA.

Simultaneous removal of chromate and nitrate in a packed-bed bioreactor using biodegradable meal box as carbon source and biofilm carriers

An up-flow packed-bed bioreactor was constructed to investigate the simultaneous removal of chromate and nitrate using biodegradable meal box as carbon source and biofilm carriers. The bioreactor was operated for 164days with varying influent Cr(VI) concentrations (2.0-50.0mg/L) and hydraulic retention times (HRT, 10-24h). It was shown that complete denitrification and Cr(VI) reduction could be achieved when influent Cr(VI) concentrations were lower than 20mg/L with a HRT of 17h. Shortening the HRT could significantly reduce the effluent CODcr. It was also observed that Cr(III) was mainly immobilized on the biofilm. Further investigation on Cr distribution in the biofilm compartments indicated that Cr(VI) reduction occurred in all compartments and the intercellular Cr was dominant. High-throughput sequencing analysis showed that Proteobacteria, Bacteroidetes and Firmicutes were the dominant phyla in the biofilm and Cr(VI) stress had a negative effect on the abundance of most bacteria.

Evaluating simultaneous chromate and nitrate reduction during microbial denitrification processes

Sulfur-based autotrophic denitrification and heterotrophic denitrification have been demonstrated to be promising technological processes for simultaneous removal of nitrate NO3(-) and chromate (Cr (VI)), two common contaminants in surface and ground waters. In this work, a mathematical model was developed to describe and evaluate the microbial and substrate interactions among sulfur oxidizing denitrifying organism, methanol-based heterotrophic denitrifiers and chromate reducing bacteria in the biofilm systems for simultaneous nitrate and chromate removal. The concomitant multiple chromate reduction pathways by these microbes were taken into account in this model. The validity of the model was tested using experimental data from three independent biofilm reactors under autotrophic, heterotrophic and mixotrophic conditions. The model sufficiently described the nitrate, chromate, methanol, and sulfate dynamics under varying conditions. The modeling results demonstrated the coexistence of sulfur-oxidizing denitrifying bacteria and heterotrophic denitrifying bacteria in the biofilm under mixotrophic conditions, with chromate reducing bacteria being outcompeted. The sulfur-oxidizing denitrifying bacteria substantially contributed to both nitrate and chromate reductions although heterotrophic denitrifying bacteria dominated in the biofilm. The mixotrophic denitrification could improve the tolerance of autotrophic denitrifying bacteria to Cr (VI) toxicity. Furthermore, HRT would play an important role in affecting the microbial distribution and system performance, with HRT of higher than 0.15 day being critical for a high level removal of nitrate and chromate (over 90%).

A Slow-Release Substrate Stimulates Groundwater Microbial Communities for Long-Term in Situ Cr(VI) Reduction

Cr(VI) is a widespread environmental contaminant that is highly toxic and soluble. Previous work indicated that a one-time amendment of polylactate hydrogen-release compound (HRC) reduced groundwater Cr(VI) concentrations for >3.5 years at a contaminated aquifer; however, microbial communities responsible for Cr(VI) reduction are poorly understood. In this study, we hypothesized that HRC amendment would significantly change the composition and structure of groundwater microbial communities, and that the abundance of key functional genes involved in HRC degradation and electron acceptor reduction would increase long-term in response to this slowly degrading, complex substrate. To test these hypotheses, groundwater microbial communities were monitored after HRC amendment for >1 year using a comprehensive functional gene microarray. The results showed that the overall functional composition and structure of groundwater microbial communities underwent sequential shifts after HRC amendment. Particularly, the abundance of functional genes involved in acetate oxidation, denitrification, dissimilatory nitrate reduction, metal reduction, and sulfate reduction significantly increased. The overall community dynamics was significantly correlated with changes in groundwater concentrations of microbial biomass, acetate, NO3-, Cr(VI), Fe(II) and SO4(2-). Our results suggest that HRC amendment primarily stimulated key functional processes associated with HRC degradation and reduction of multiple electron acceptors in the aquifer toward long-term Cr(VI) reduction.

Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses

Enzymes of the denitrification pathway play an important role in the global nitrogen cycle, including release of nitrous oxide, an ozone-depleting greenhouse gas. In addition, nitric oxide reductase, maturation factors, and proteins associated with nitric oxide detoxification are used by pathogens to combat nitric oxide release by host immune systems. While the core reductases that catalyze the conversion of nitrate to dinitrogen are well understood at a mechanistic level, there are many peripheral proteins required for denitrification whose basic function is unclear. A bar-coded transposon DNA library from Pseudomonas stutzeri strain RCH2 was grown under denitrifying conditions, using nitrate or nitrite as an electron acceptor, and also under molybdenum limitation conditions, with nitrate as the electron acceptor. Analysis of sequencing results from these growths yielded gene fitness data for 3,307 of the 4,265 protein-encoding genes present in strain RCH2. The insights presented here contribute to our understanding of how peripheral proteins contribute to a fully functioning denitrification pathway. We propose a new low-affinity molybdate transporter, OatABC, and show that differential regulation is observed for two MoaA homologs involved in molybdenum cofactor biosynthesis. We also propose that NnrS may function as a membrane-bound NO sensor. The dominant HemN paralog involved in heme biosynthesis is identified, and a CheR homolog is proposed to function in nitrate chemotaxis. In addition, new insights are provided into nitrite reductase redundancy, nitric oxide reductase maturation, nitrous oxide reductase maturation, and regulation.

Interaction of Cr(VI) reduction and denitrification by strain Pseudomonas aeruginosa PCN-2 under aerobic conditions

Inhibition of efficient denitrification in presence of toxic heavy metals is one of the current problems encountered in municipal wastewater treatment plants. This paper presents how to remove hexavalent chromium (Cr(VI)) and nitrate simultaneously by the novel strain Pseudomonas aeruginosa PCN-2 under aerobic conditions. The capability of strain PCN-2 for Cr(VI) and nitrate reduction was confirmed by PCR analysis of gene ChrR, napA, nirS, cnorB, nosZ, while Cr(VI) reduction was proved via an initial single-electron transfer through Cr(V) detection using electron paramagnetic resonance. Experimental results demonstrated that Cr(VI) and nitrate reduction by strain PCN-2 was much faster at pH 8-9 and higher initial cell concentration. However, increasing Cr(VI) concentration would inhibit aerobic denitrification process and result in an significant delay of nitrate reduction or N2O accumulation, which was attributed to competition between three electron acceptors, i.e., Cr(VI), O2 and nitrate in the electron transport chain.

Molybdenum Availability Is Key to Nitrate Removal in Contaminated Groundwater Environments

The concentrations of molybdenum (Mo) and 25 other metals were measured in groundwater samples from 80 wells on the Oak Ridge Reservation (ORR) (Oak Ridge, TN), many of which are contaminated with nitrate, as well as uranium and various other metals. The concentrations of nitrate and uranium were in the ranges of 0.1 μM to 230 mM and <0.2 nM to 580 μM, respectively. Almost all metals examined had significantly greater median concentrations in a subset of wells that were highly contaminated with uranium (≥126 nM). They included cadmium, manganese, and cobalt, which were 1,300- to 2,700-fold higher. A notable exception, however, was Mo, which had a lower median concentration in the uranium-contaminated wells. This is significant, because Mo is essential in the dissimilatory nitrate reduction branch of the global nitrogen cycle. It is required at the catalytic site of nitrate reductase, the enzyme that reduces nitrate to nitrite. Moreover, more than 85% of the groundwater samples contained less than 10 nM Mo, whereas concentrations of 10 to 100 nM Mo were required for efficient growth by nitrate reduction for two Pseudomonas strains isolated from ORR wells and by a model denitrifier, Pseudomonas stutzeri RCH2. Higher concentrations of Mo tended to inhibit the growth of these strains due to the accumulation of toxic concentrations of nitrite, and this effect was exacerbated at high nitrate concentrations. The relevance of these results to a Mo-based nitrate removal strategy and the potential community-driving role that Mo plays in contaminated environments are discussed.

Characterization of Chromium Bioremediation Products in Flow-Through Column Sediments Using Micro-X-ray Fluorescence and X-ray Absorption Spectroscopy

Microbially mediated reductive immobilization of chromium is a possible remediation technique for sites contaminated with Cr(VI). This study is part of a broader effort investigating the biogeochemical mechanisms for Cr(VI) reduction in Hanford 100H aquifer sediments using flow-through laboratory columns. It had previously been shown that reduced chromium in the solid phase was in the form of freshly precipitated mixed-phase Cr(III)-Fe(III) (hydr)oxides, irrespective of the biogeochemical conditions in the columns. In this study, the reduced Cr phases in the columns were investigated further using spectroscopy to understand the structure and mechanisms involved in the formation of the end products. Several samples representing potential processes that could be occurring in the columns were synthesized in the laboratory and characterized using X-ray absorption near edge structure (XANES) and X-ray scattering. The XANES of Cr(III) particles in the columns most closely resembled those from synthetic samples produced by the abiotic reaction of Cr(VI) with microbially reduced Fe(II). Microbially mediated Cr-Fe reduction products were distinct from abiotic Cr-Fe (hydr)oxides [CrFe(OH)] and organically complexed Cr(III) sorbed onto the surface of a mixed ferrihydrite-goethite mineral phase. Furthermore, analyses of the abiotically synthesized samples revealed that even the end products of purely abiotic, iron-mediated reduction of Cr(VI) are affected by factors such as the presence of excess aqueous Fe(II) and cellular matter. These results suggest that CrFe(OH) phases made under realistic subsurface conditions or in biotic cultures are structurally different from pure Cr(OH) or laboratory-synthesized CrFe(OH). The observed structural differences imply that the reactivity and stability of biogenic CrFe(OH) could potentially be different from that of abiotic CrFe(OH).

Nitrite interference and elimination in diphenylcarbazide (DPCI) spectrophotometric determination of hexavalent chromium

Cr(VI) is highly noted as a carcinogenic, mutagenic, and teratogenic pollutant. However, accurate determination of Cr(VI) in aqueous samples is difficult using the conventional diphenylcarbazide (DPCI) spectrophotometric method upon being interfered by co-existed nitrite. This paper illustrates how to eliminate the nitrite influence in a simple but efficient method based on a detailed analysis of interference mechanism. High-performance liquid chromatography analysis revealed that under acidic condition, DPCI was oxidized by nitrite to other substrates, which could not react with Cr(VI). The final oxidation product of DPCI was further purified by thin-layer chromatography and identified as diaryl carbodiazone by Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry (FTICR-MS) and nuclear magnetic resonance. Consequently, an improved method was proposed by simply adding sulfamic acid for eliminating the nitrite interference in Cr(VI) determination. The proposed method was successfully confirmed by the accurate recovery of Cr(VI) from spiked water samples and further proven with inductively coupled plasma-atomic emission spectroscopy, which demonstrated a great potential for determining Cr(VI) concentration in aqueous samples containing nitrite.

Divergent aquifer biogeochemical systems converge on similar and unexpected Cr(VI) reduction products

In this study of reductive chromium immobilization, we found that flow-through columns constructed with homogenized aquifer sediment and continuously infused with lactate, chromate, and various native electron acceptors diverged to have very different Cr(VI)-reducing biogeochemical regimes characterized by either denitrifying or fermentative conditions (as indicated by effluent chemical data, 16S rRNA pyrotag data, and metatranscriptome data). Despite the two dramatically different biogeochemical environments that evolved in the columns, these regimes created similar Cr(III)-Fe(III) hydroxide precipitates as the predominant Cr(VI) reduction product, as characterized by micro-X-ray fluorescence and micro-X-ray absorption near-edge structure analysis. We discuss two conflicting scenarios of microbially mediated formation of Cr(III)-Fe(III) precipitates, each of which is both supported and contradicted by different lines of evidence: (1) enzymatic reduction of Cr(VI) to Cr(III) followed by coprecipitation of Cr(III) and Fe(III) and (2) both regimes generated at least small amounts of Fe(II), which abiotically reduced Cr(VI) to form a Cr-Fe precipitate. Evidence of zones with different levels of Cr(VI) reduction suggest that local heterogeneity may have confounded interpretation of processes based on bulk measurements. This study indicates that the bulk redox status and biogeochemical regime, as categorized by the dominant electron-accepting process, do not necessarily control the final product of Cr(VI) reduction.

Common occurrence of a positive δ53Cr shift in Central European waters contaminated by geogenic/industrial chromium relative to source values

Carcinogenic effects of hexavalent chromium in waters are of concern in many countries worldwide. We explored Cr isotope systematics at 11 sites in the Czech Republic and Poland. Geogenic Cr pollution was associated with serpentinite bodies at former convergent plate margins, while anthropogenic Cr pollution resulted from electroplating, tanning, and the chemical industry. Cr(VI) concentration in geogenic waters was less than 40 ppb. Anthropogenic waters contained up to 127,000 ppb Cr(VI). At both geogenic and anthropogenic sites, where known, the source of pollution had a low δ53Cr (<1‰). δ53Cr of geogenic and anthropogenic waters was up to 3.9 and 5.8‰, respectively. At both serpentinite-dominated and industrial sites, δ53Cr(VI)aq was shifted toward higher values, compared to the pollution source. At the industrial sites, this positive δ53Cr shift was related to Cr(VI) reduction, a process known to fractionate Cr isotopes. At geogenic sites, the origin of high δ53Cr(VI)aq is tentatively ascribed to preferential release of 53Cr during oxidation of soil Cr(III) and its mobilization to water. δ53Cr(VI) of industrially contaminated waters was significantly higher (p<0.001) compared to δ53Cr of waters carrying geogenic Cr(VI), implying that either the effective fractionation factor or process extent was greater for Cr(VI) reduction than for Cr(III) oxidation.

"Replica-extraction-transfer" nanostructure-initiator mass spectrometry imaging of acoustically printed bacteria

Traditionally, microbes are studied under controlled laboratory conditions as isolates in planktonic culture. However, this is a vast extrapolation from their natural state; development of new techniques is required to decipher the largely unknown world of microbial chemical interactions in more realistic environments. The field of mass spectrometry imaging has made significant progress in localizing metabolites in and around bacterial colonies, primarily by using MALDI and ESI-based techniques that interrogate the top surface of the sample. Unfortunately, surface-based laser-desorption techniques, such as nanostructure-initiator mass spectrometry (NIMS), which has advantages in detection of small metabolite compounds and low background, has not been suitable for direct microbe imaging because desorption/ionization occurs on the bottom of the sample. Here, we describe a "replica-extraction-transfer" (REX) technique that overcomes this barrier by transferring biomolecules from agar cultures of spatially arrayed bacterial colonies onto NIMS surfaces; further, we demonstrate that acoustic printing of bacteria can be used to create complex colony geometries to probe microbial interactions with NIMS imaging. REX uses a solvent-laden semisolid (e.g., gel) to first extract metabolites from a microbial sample, such as a biofilm or agar culture; the metabolites are then replica "stamped" onto the NIMS surface. Using analytical standards we show that REX-NIMS effectively transfers and detects a range of small molecule compounds including amino acids and polyamines. This approach is then used to analyze the metabolite composition of streaked Shewanella oneidensis MR1 and Pseudomonas stutzeri RCH2 colonies and further resolve complex patterns produced by acoustic printing of liquid microbial cultures. Applying multivariate statistical analysis of the NIMS imaging data identified ions that were localized to different regions between and within colonies, as well as to the agar gel. Subsequent high-resolution tandem mass spectrometry was used to characterize two species-specific lipids that correlated with the spatial location of each microbial species and were found to be highly abundant in cell extracts. Overall, the use of acoustic printing of bacteria with REX-NIMS imaging will extend the range of analytical capabilities available for characterization of microbial interactions with mass spectrometry.

Genome-enabled studies of anaerobic, nitrate-dependent iron oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans

Thiobacillus denitrificans is a chemolithoautotrophic bacterium capable of anaerobic, nitrate-dependent U(IV) and Fe(II) oxidation, both of which can strongly influence the long-term efficacy of in situ reductive immobilization of uranium in contaminated aquifers. We previously identified two c-type cytochromes involved in nitrate-dependent U(IV) oxidation in T. denitrificans and hypothesized that c-type cytochromes would also catalyze Fe(II) oxidation, as they have been found to play this role in anaerobic phototrophic Fe(II)-oxidizing bacteria. Here we report on efforts to identify genes associated with nitrate-dependent Fe(II) oxidation, namely (a) whole-genome transcriptional studies [using FeCO3, Fe(2) (+), and U(IV) oxides as electron donors under denitrifying conditions], (b) Fe(II) oxidation assays performed with knockout mutants targeting primarily highly expressed or upregulated c-type cytochromes, and (c) random transposon-mutagenesis studies with screening for Fe(II) oxidation. Assays of mutants for 26 target genes, most of which were c-type cytochromes, indicated that none of the mutants tested were significantly defective in nitrate-dependent Fe(II) oxidation. The non-defective mutants included the c 1-cytochrome subunit of the cytochrome bc 1 complex (complex III), which has relevance to a previously proposed role for this complex in nitrate-dependent Fe(II) oxidation and to current concepts of reverse electron transfer. A transposon mutant with a disrupted gene associated with NADH:ubiquinone oxidoreductase (complex I) was ~35% defective relative to the wild-type strain; this strain was similarly defective in nitrate reduction with thiosulfate as the electron donor. Overall, our results indicate that nitrate-dependent Fe(II) oxidation in T. denitrificans is not catalyzed by the same c-type cytochromes involved in U(IV) oxidation, nor have other c-type cytochromes yet been implicated in the process.

Genomic and physiological characterization of the chromate-reducing, aquifer-derived Firmicute Pelosinus sp. strain HCF1

Pelosinus spp. are fermentative firmicutes that were recently reported to be prominent members of microbial communities at contaminated subsurface sites in multiple locations. Here we report metabolic characteristics and their putative genetic basis in Pelosinus sp. strain HCF1, an isolate that predominated anaerobic, Cr(VI)-reducing columns constructed with aquifer sediment. Strain HCF1 ferments lactate to propionate and acetate (the methylmalonyl-coenzyme A [CoA] pathway was identified in the genome), and its genome encodes two [NiFe]- and four [FeFe]-hydrogenases for H(2) cycling. The reduction of Cr(VI) and Fe(III) may be catalyzed by a flavoprotein with 42 to 51% sequence identity to both ChrR and FerB. This bacterium has unexpected capabilities and gene content associated with reduction of nitrogen oxides, including dissimilatory reduction of nitrate to ammonium (two copies of NrfH and NrfA were identified along with NarGHI) and a nitric oxide reductase (NorCB). In this strain, either H(2) or lactate can act as a sole electron donor for nitrate, Cr(VI), and Fe(III) reduction. Transcriptional studies demonstrated differential expression of hydrogenases and nitrate and nitrite reductases. Overall, the unexpected metabolic capabilities and gene content reported here broaden our perspective on what biogeochemical and ecological roles this species might play as a prominent member of microbial communities in subsurface environments.