Toxic effects of dissolved heavy metals on Desulfovibrio vulgaris and Desulfovibrio sp. strains

New insights into long-lasting Cr(VI) removal from groundwater using in situ biosulfidated zero-valent iron with sulfate-reducing bacteria

Sulfidation enhances the reactivity of zero-valent iron (ZVI) for Cr(VI) removal from groundwater. Current sulfidation methods mainly focus on chemical and mechanical sulfidation, and there has been little research on biosulfidation using sulfate-reducing bacteria (SRB) and its performance in Cr(VI) removal. Herein, the ability of the SRB-biosulfidated ZVI (SRB-ZVI) system was evaluated and compared with that of the Na2S-sulfidated ZVI system. The SRB-ZVI system forms a thicker and more porous FeSx layer than the Na2S-sulfidated ZVI system, resulting in more sufficient sulfidation of ZVI and a 2.5-times higher Cr(VI) removal rate than that of the Na2S-sulfidated ZVI system. The biosulfidated-ZVI granules and FeSx suspension are the major components of the SRB-ZVI system. The SRB-ZVI system exhibits a long-lasting (11 cycles) Cr(VI) removal performance owing to the regeneration of FeSx. However, the Na2S-sulfidated ZVI system can perform only two Cr(VI) removal cycles. SRB attached to biosulfidated-ZVI can survive in the presence of Cr(VI) because of the protection of the biogenic porous structure, whereas SRB in the suspension is inhibited. After Cr(VI) removal, SRB repopulates in the suspension from biosulfidated-ZVI and produce FeSx, thus providing conditions for subsequent Cr(VI) removal cycles. Overall, the synergistic effect of SRB and ZVI provides a more powerful and environmentally friendly sulfidation method, which has more advantageous for Cr(VI) removal than those of chemical sulfidation. This study provides a visionary in situ remediation strategy for groundwater contamination using ZVI-based technologies.

Enhanced bioremediation of acid mine-influenced groundwater with micro-sized emulsified corn oil droplets (MOD) and sulfate-reducing bacteria (Desulfovibrio vulgaris) in a microcosm assay

High concentrations of metals and sulfates in acid mine drainage (AMD) are the cause of the severe environmental hazard that mining operations pose to the surrounding ecosystem. Little study has been conducted on the cost-effective biological process for treating high AMD. The current research investigated the potential of the proposed carbon source and sulfate reduction bacteria (SRB) culture in achieving the bioremediation of sulfate and heavy metals. This work uses individual and combinatorial bioaugmentation and bio-stimulation methods to bioremediate acid-mine-influenced groundwater in batch microcosm experiments. Bioaugmentation and bio-stimulation methods included pure culture SRB (Desulfovibrio vulgaris) and microsized oil droplet (MOD) by emulsifying corn oil. The research tested natural attenuation (T 1), bioaugmentation (T2), biostimulation (T3), and bioaugmentation plus biostimulation (T4) for AM-contaminated groundwater remediation. Bioaugmentation and bio-stimulation showed the greatest sulfate reduction (75.3%) and metal removal (95-99%). Due to carbon supply scarcity, T1 and T2 demonstrated 15.7% and 27.8% sulfate reduction activities. Acetate concentrations in T3 and T4 increased bacterial activity by providing carbon sources. Metal bio-precipitation was substantially linked with sulfate reduction and cell growth. SEM-EDS study of precipitates in T3 and T4 microcosm spectra indicated peaks for S, Cd, Mn, Cu, Zn, and Fe, indicating metal-sulfide association for metal removal precipitates. The MOD provided a constant carbon source for indigenous bacteria, while Desulfovibrio vulgaris increased biogenic sulfide synthesis for heavy metal removal.

Diversity of Endophytes of Actinidia arguta in Different Seasons

The seasonal changes in environmental conditions can alter the growth states of host plants, thereby affecting the living environment of endophytes and forming different endophytic communities. This study employs Illumina MiSeq next-generation sequencing to analyze the 16SrRNA and ITS rDNA of endophytes in 24 samples of Actinidia arguta stem tissues across different seasons. The results revealed a high richness and diversity of endophytes in Actinidia arguta, with significant seasonal variations in microbial community richness. This study identified 897 genera across 36 phyla for bacteria and 251 genera across 8 phyla for fungi. Notably, 69 bacterial genera and 19 fungal genera significantly contributed to the differences in community structure across seasons. A distinctive feature of coexistence in the endophytic community, both specific and conservative across different seasons, was observed. The bacterial community in winter demonstrated significantly higher richness and diversity compared to the other seasons. Environmental factors likely influence the optimal timing for endophyte colonization. Solar radiation, temperature, precipitation, and relative humidity significantly impact the diversity of endophytic bacteria and fungi. In addition, seasonal variations show significant differences in the nutritional modes of fungal endophytes and the degradation, ligninolysis, and ureolysis functions of bacterial endophytes. This study elucidates the potential role of endophytes in assisting Actinidia arguta in adapting to seasonal changes and provides a theoretical basis for further exploration of functional microbial strains.

Antimicrobial activity of yak beta-defensin 116 against Staphylococcus aureus and its role in gut homeostasis

Staphylococcus aureus (S. aureus) is one of the most common food-borne poisoning microbial agent. However, the antimicrobial activity of β-defensin 116 in yak and its application in S. aureus-induced diarrheal disease have not been reported. In this study, 303 bp cDNA sequence of yak DEFB116 gene was obtained. In addition, the prokaryotic expression vector of DEFB116 protein with a molecular weight of 16 kDa was successfully constructed and expressed. The yak DEFB116 gene can encode 19 amino acids, the percentage of hydrophobic amino acids is 36 % and the total positive charge is 6, which has potential antibacterial potential. Sufficient DEFB116 protein concentration and time can destroy the integrity of the bacterial cell membrane, resulting in leakage of intracellular solutes and thus killing S. aureus. The intestinal histopathological features and the number of inflammatory cells were improved in the diarrhea mouse model under the action of DEFB116 protein. The decrease of goblet cells was reversed, the expression of mucoprotein was increased. DEFB116 protein increased the abundance of Lactobacillus johnsonii, Lactobacillus reuteri and Desulfovibrio, and inhibited the reproduction of pathogenic bacteria. These findings provide new insights into the potential future applications of yak β-defencins in the food industry and medical fields.

Harnessing sulfate-reducing bacteria with plants growing to revitalize metal-tainted coal mine soils in Midwest China: metal sequestration performance, ecological networking interaction, and functional enzymatic prediction

Heavy metal contamination from coal mining calls for advanced bioremediation, i.e., using sulfate-reducing bacteria (SRB) technology. Yet, the interaction of SRB with native soil microbiota during metal sequestration, especially in the presence of plants, remains ambiguous. In this study, we assessed the metal sequestration capabilities, ecological network interactions, and enzymatic functions in soils treated with a predominant SRB consortium, mainly Desulfovibrio (14 OTUs, 42.15%) and Desulfobulbus (7 OTUs, 42.27%), alongside Acacia dealbata (AD) and Pisum sativum (PS) plants. The SRB consortium notably enhanced the immobilization of metals such as Zn, Cu, As, and Pb in soil, with the conversion of metals to residual forms rising from 23.47 to 75.98%. Plant inclusion introduced variability, potentially due to changes in root exudates under metal stress. While AD flourished, PS demonstrated significant enhancement in conjunction with SRB, despite initial challenges. Comprehensive microbial analyses revealed the pivotal role of SRB in influencing microbial networking, underpinning critical ecological links. This interplay between plants and SRB not only enhanced microbial diversity but also enriched soil nutrients. Further, enzymatic assessments, highlighting enzymes like NADH:ubiquinone reductase and non-specific serine/threonine protein kinase, reinforced contribution of SRB to energy metabolism and environmental resilience of the entire soil microbial community. Overall, this research underscores the potential of SRB-driven bioremediation in revitalizing soils affected by coal mining.

The changes in iron ions concentration and organic matter composition during the surface microlayer membrane formation process in freshwater

The surface microlayer membrane (SMM) is a complex and unique water body ecosystem. The SMM has a significant effect on water quality and the water ecological system. However, despite the long-lasting interest in the SMM formation process and its environmental effect mechanism in freshwater, studies on it are still scarce. This paper studied the changes in iron ions concentration and organic matter composition during the SMM formation process. Our results revealed that the iron ions enriched in the SMM, at a concentration of up to 8.02 μg/mL, exist in the form of Fe3+. The main organic matter is polysaccharides and proteins in the SMM. Additionally, the microbial community structure revealed that the changes in iron ion morphology in water and the SMM was a significant association with the presence of Aeromonas and Zoogloea. The rapid enrichment process of iron ions and organic matter in the aquatic surface microlayer is involved in the rapid formation of early SMM. Obviously, these findings provide new insights and a basis for the SMM of freshwater.

The epithelial transcriptome and mucosal microbiota are altered for goats fed with a low-protein diet

Introduction

Feeding low protein (LP) diet to animals impose severe challenge to animals' immune homeostasis. However, limited knowledge about the underlying adaption mechanism of host and ruminal microbiota responding to LP diet were well understood. Herein, this study was performed to examine the changes in relative abundance of ruminal microbiota and host ruminal mucosal transcriptome profiles in response to a LP diet.

Methods

A total of twenty-four female Xiangdong balck goats with similar weight (20.64 ± 2.40 kg) and age (8 ± 0.3 months) were randomly assigned into two groups, LP (5.52% crude protein containing diet) and CON (10.77% crude protein containing diet) groups. Upon completion of the trial, all goats were slaughtered after a 16-hour fasting period in LiuYang city (N 28°15', E 113°63') in China. HE staining, free amino acids measurement, transcriptome analysis and microbiome analysis were applied to detect the morphology alterations, free amino acids profile alterations and the shift in host ruminal mucosal transcriptome and ruminal microbiota communities.

Results

Firstly, the results showed that feeding LP diet to goats decreased the rumen papilla width (P = 0.043), surface area (P = 0.013) and total ruminal free amino acids concentration (P = 0.016). Secondly, microbiome analysis indicated that 9 microbial genera, including Eubacterium and Prevotella, were enriched in LP group while 11 microbial genera, including Butyrivibrio and Ruminococcus, were enriched in CON group. Finally, in terms of immune-related genes, the expression levels of genes involved in tight junction categories (e.g., MYH11, PPP2R2C, and MYL9) and acquired immunity (e.g., PCP4 and CXCL13) were observed to be upregulated in the LP group when compared to the CON group.

Conclusion

Under the LP diet, the rumen exhibited increased relative abundance of pathogenic microbiota and VFA-degrading microbiota, leading to disruptions in immune homeostasis within the host's ruminal mucosa. These findings indicate that the ruminal microbiota interacts with host results in the disruption in animals' immune homeostasis under LP diet challenge.

Acid-tolerant bacteria and prospects in industrial and environmental applications

Acid-tolerant bacteria such as Streptococcus mutans, Acidobacterium capsulatum, Escherichia coli, and Propionibacterium acidipropionici have developed several survival mechanisms to sustain themselves in various acid stress conditions. Some bacteria survive by minor changes in the environmental pH. In contrast, few others adapt different acid tolerance mechanisms, including amino acid decarboxylase acid resistance systems, mainly glutamate-dependent acid resistance (GDAR) and arginine-dependent acid resistance (ADAR) systems. The cellular mechanisms of acid tolerance include cell membrane alteration in Acidithiobacillus thioxidans, proton elimination by F₁-F₀-ATPase in Streptococcus pyogenes, biofilm formation in Pseudomonas aeruginosa, cytoplasmic urease activity in Streptococcus mutans, synthesis of the protective cloud of ammonia, and protection or repair of macromolecules in Bacillus caldontenax. Apart from cellular mechanisms, there are several acid-tolerant genes such as gadA, gadB, adiA, adiC, cadA, cadB, cadC, speF, and potE that help the bacteria to tolerate the acidic environment. This acid tolerance behavior provides new and broad prospects for different industrial applications and the bioremediation of environmental pollutants. The development of engineered strains with acid-tolerant genes may improve the efficiency of the transgenic bacteria in the treatment of acidic industrial effluents. KEY POINTS: • Bacteria tolerate the acidic stress by methylating unsaturated phospholipid tail • The activity of decarboxylase systems for acid tolerance depends on pH • Genetic manipulation of acid-tolerant genes improves acid tolerance by the bacteria.

Acidophilic microorganisms in remediation of contaminants present in extremely acidic conditions

Acidophiles are a group of microorganisms that thrive in acidic environments where pH level is far below the neutral value 7.0. They belong to a larger family called extremophiles, which is a group that thrives in various extreme environmental conditions which are normally inhospitable to other organisms. Several human activities such as mining, construction and other industrial processes release highly acidic effluents and wastes into the environment. Those acidic wastes and wastewaters contain different types of pollutants such as heavy metals, radioactive, and organic, whose have adverse effects on human being as well as on other living organisms. To protect the whole ecosystem, those pollutants containing effluents or wastes must be clean properly before releasing into environment. Physicochemical cleanup processes under extremely acidic conditions are not always successful due to high cost and release of toxic byproducts. While in case of biological methods, except acidophiles, no other microorganisms cannot survive in highly acidic conditions. Therefore, acidophiles can be a good choice for remediation of different types of contaminants present in acidic conditions. In this review article, various roles of acidophilic microorganisms responsible for removing heavy metals and radioactive pollutants from acidic environments were discussed. Bioremediation of various acidic organic pollutants by using acidophiles was also studied. Overall, this review could be helpful to extend our knowledge as well as to do further relevant novel studies in the field of acidic pollutants remediation by applying acidophilic microorganisms.

Treatment and remediation of metal-contaminated water and groundwater in mining areas by biological sulfidogenic processes: A review

Heavy metal pollution in the mining areas leads to serious environmental problems. The biological sulfidogenic process (BSP) mediated by sulfidogenic bacteria has been considered an attractive technology for the treatment and remediation of metal-contaminated water and groundwater. Notwithstanding, BSP driven by different sulfidogenic bacteria could affect the efficiency and cost-effectiveness of the treatment performance in practical applications, such as the microbial intolerance of pH and metal ions, the formation of toxic byproducts, and the consumption of organic electron donors. Sulfur-reducing bacteria (S⁰RB)-driven BSP has been demonstrated to be a promising alternative to the commonly used sulfate-reducing bacteria (SRB)-driven BSP for treating metal-contaminated wastewater and groundwater, due to the cost-saving in chemical addition, the high efficiency in sulfide production and metal removal efficiency. Although the S⁰RB-driven BSP has been developed and applied for decades, the present review works mainly focus on the developments in SRB-driven BSP for the treatment and remediation of metal-contaminated wastewater and groundwater. Accordingly, a comprehensive review for metal-contaminated wastewater treatment and groundwater remediation should be provided with the incorporation of the SRB- and S⁰RB-driven BSP. To identify the bottlenecks and to improve BSP performance, this paper reviews sulfidogenic bacteria presenting in metal-contaminated water and groundwater; highlight the critical factors for the metabolism of sulfidogenic bacteria during BSP; the ecological roles of sulfidogenic bacteria and the mechanisms of metal removal by sulfidogenic bacteria; and the application of the present sulfidogenic systems and their drawbacks. Accordingly, the research knowledge gaps, current process limitations, and future prospects were provided for improving the performance of BSP in the treatment and remediation of metal-contaminated wastewater and groundwater in mining areas.

Treatment of acid rock drainage using a sulphate-reducing bioreactor with a limestone precolumn

Sulphate reducing bacteria (SRB) offer promise for the treatment of mine waste due to their effectiveness removing toxic heavy metals as highly insoluble metal sulphides and their ability to generate alkalinity. The main objective of this study was to develop a treatment composed of a sulphate-reducing bioreactor with a limestone precolumn for the removal of Cu(II) from a synthetic ARD. The purpose of the limestone column was to increase the pH values and decrease the level of Cu in the effluent to prevent SRB inhibition. The system was fed with a pH-2.7 synthetic ARD containing Cu(II) (10-40 mg/L), sulphate (2000 mg/L) and acetate (2.5 g COD/L) for 150 days. Copper removal efficiencies in the two-stage system were very high (95-99%), with a final concentration of 0.53 mg/L Cu, and almost complete removal occurred in the limestone precolumn. In the same manner, the acidity of the synthetic ARD was effectively reduced in the limestone precolumn to 7.3 and the pH was raised in the bioreactor (7.3-8.0). COD consumption by methanogens was predominant from day 0-118, but SRB dominated at the end of the experiment (day 150) when the average COD removal and sulphide production were 74.8% and 61.7%, respectively. Study of the microbial taxonomic composition in the bioreactor revealed that Methanosarcina and Methanosaeta were the most prevalent methanogens while the genera Desulfotomaculum and Syntrophobacter were the dominant SRB. Among the SRB identified Desulfotomaculum intricatum (99% identity) and Desulfotomaculum acetoxidans (96%) were the most abundant sequences of bacteria capable of using acetate.

Molecular regulation of conditioning film formation and quorum quenching in sulfate reducing bacteria

Sensing surface topography, an upsurge of signaling biomolecules, and upholding cellular homeostasis are the rate-limiting spatio-temporal events in microbial attachment and biofilm formation. Initially, a set of highly specialized proteins, viz. conditioning protein, directs the irreversible attachment of the microbes. Later signaling molecules, viz. autoinducer, take over the cellular communication phenomenon, resulting in a mature microbial biofilm. The mandatory release of conditioning proteins and autoinducers corroborated the existence of two independent mechanisms operating sequentially for biofilm development. However, both these mechanisms are significantly affected by the availability of the cofactor, e.g., Copper (Cu). Generally, the Cu concentration beyond threshold levels is detrimental to the anaerobes except for a few species of sulfate-reducing bacteria (SRB). Remarkably SRB has developed intricate ways to resist and thrive in the presence of Cu by activating numerous genes responsible for modifying the presence of more toxic Cu(I) to Cu(II) within the periplasm, followed by their export through the outer membrane. Therefore, the determinants of Cu toxicity, sequestration, and transportation are reconnoitered for their contribution towards microbial adaptations and biofilm formation. The mechanistic details revealing Cu as a quorum quencher (QQ) are provided in addition to the three pathways involved in the dissolution of cellular communications. This review articulates the Machine Learning based data curing and data processing for designing novel anti-biofilm peptides and for an in-depth understanding of QQ mechanisms. A pioneering data set has been mined and presented on the functional properties of the QQ homolog in Oleidesulfovibrio alaskensis G20 and residues regulating the multicopper oxidase properties in SRB.

The Lactobacillus gasseri G098 Strain Mitigates Symptoms of DSS-Induced Inflammatory Bowel Disease in Mice

Inflammatory bowel disease (IBD) is a recurring inflammatory disease of the gastrointestinal tract with unclear etiology, but it is thought to be related to factors like immune abnormalities and gut microbial dysbiosis. Probiotics can regulate host immunity and gut microbiota; thus, we investigated the alleviation effect and mechanism of the strain Lactobacillus gasseri G098 (G098) on dextran sodium sulfate (DSS)-induced colitis in mice. Three groups of mice (n = 8 per group) were included: normal control (NC), DSS-induced colitis mice (DSS), and colitis mice given strain (G098). Our results showed that administering G098 effectively reversed DSS-induced colitis-associated symptoms (mitigating weight loss, reducing disease activity index and pathology scores; p < 0.05 in all cases) and prevented DSS-induced mortality (62.5% in DSS group; 100% in G098 group). The mortality rate and symptom improvement by G098 administration was accompanied by a healthier serum cytokine balance (significant decreases in serum pro-inflammatory factors, interleukin (IL)-6 [p < 0.05], IL-1β [p < 0.01], and tumor necrosis factor (TNF)-α [p < 0.001], and significant increase in the serum anti-inflammatory factor IL-13 [p < 0.01], compared with DSS group) and gut microbiome modulation (characterized by a higher gut microbiota diversity [p < 0.05], significantly more Firmicutes and Lachnoclostridium [p < 0.05], significantly fewer Bacteroidetes [p < 0.05], and significant higher gene abundances of sugar degradation-related pathways [p < 0.05], compared with DSS-treated group). Taken altogether, our results suggested that G098 intake could mitigate DSS-induced colitis through modulating host immunity and gut microbiome, and strain treatment is a promising strategy for managing IBD.

Effects of metals on activity and community of sulfate-reducing bacterial enrichments and the discovery of a new heavy metal-resistant SRB from Santos Port sediment (São Paulo, Brazil)

Sulfate-reducing bacteria (SRB) can be used to remove metals from wastewater, sewage, and contaminated areas. However, metals can be toxic to this group of bacteria. Sediments from port areas present abundance of SRB and also metal contamination. Their microbial community has been exposed to metals and can be a good inoculum for isolation of metal-resistant SRB. The objective of the study was to analyze how metals influence activity and composition of sulfate-reducing bacteria. Enrichment cultures were prepared with a different metal (Zn, Cr, Cu, and Cd) range concentration tracking activity of SRB and 16S rRNA sequencing in order to access the community. The SRB activity decreased when there was an increase in the concentration of the metals tested. The highest concentration of metals precipitated were 0.2 mM of Cd, 5.4 mM of Zn, 4.5 mM of Cu, and 9.6 mM of Cr. The more toxic metals were Cd and Cu and had a greater community similarity with less SRB and more fermenters (e.g., Citrobacter and Clostridium). Meanwhile, the enrichments with less toxic metals (Cr and Zn) had more sequences affiliated to SRB genera (mainly Desulfovibrio). A new Desulfovibrio species was isolated. This type of study can be useful to understand the effects of metals in SRB communities and help to optimize wastewater treatment processes contaminated by metals. The new Desulfovibrio species may be important in future studies on bioremediation of neutral pH effluents contaminated by metals.

Micellar catalysis of the Suzuki Miyaura reaction using biogenic Pd nanoparticles from Desulfovibrio alaskensis

Microorganisms produce metal nanoparticles (MNPs) upon exposure to toxic metal ions. However, the catalytic activity of biosynthesised MNPs remains underexplored, despite the potential of these biological processes to be used for the sustainable recovery of critical metals, including palladium. Herein we report that biogenic palladium nanoparticles generated by the sulfate-reducing bacterium Desulfovibrio alaskensis G20 catalyse the ligand-free Suzuki Miyaura reaction of abiotic substrates. The reaction is highly efficient (>99% yield, 0.5 mol% Pd), occurs under mild conditions (37 °C, aqueous media) and can be accelerated within biocompatible micelles at the cell membrane to yield products containing challenging biaryl bonds. This work highlights how native metabolic processes in anaerobic bacteria can be combined with green chemical technologies to produce highly efficient catalytic reactions for use in sustainable organic synthesis.

Expression, Purification and Characterization of a ZIP Family Transporter from Desulfovibrio vulgaris

The ZIP family transport zinc ions from the extracellular medium across the plasma membrane or from the intracellular compartments across endomembranes, which play fundamental roles in metal homeostasis and are broadly involved in physiological and pathological processes. Desulfovibrio is the predominant sulphate-reducing bacteria in human colonic microbiota, but also a potential choice for metal bioremediation. while, there are no published studies describing the zinc transporters from Desulfovibrio up to now. In this study, we obtained for the first time a heterologously expressed ZIP homolog from Desulfovibrio vulgaris, termed dvZip. The purified dvZip was reconstituted into proteoliposomes, and confirmed its zinc transport ability in vitro. By combining topology prediction, homology modeling and phylogenetic approaches, we also noticed that dvZip belongs to the GufA and probably have 8 transmembrane α-helical segments (TM 1-8) in which both termini are located on the extracellular, with TM2, 4, 5 and 7 create an inner bundle. We believe that purification and characterization of zinc (probably also cadmium) transporters from Desulfovibrio vulgaris such as dvZip could shed light on understanding of metal homeostasis of Desulfovibrio and provided protein products for future detailed function and structural studies.

Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene

This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (dsrB gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of Proteobacteria and Firmicutes across all the samples. However, Actinobacteria, Thermodesulfobacteria, and Chlorobi were also detected. Phylogenetic analysis indicated that unassigned dsrB sequences were related to Deltaproteobacteria and Nitrospirota superclusters, Euryarchaeota, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of dsrAB-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.

Over-sulfated soils and sediments treatment: A brief discussion on performance disparities of biological and non-biological methods throughout the literature

High sulfate concentrations in industrial effluents as well as solid materials (excavated soils, dredged sediments, etc.) are a major hindrance for circular economy outlooks. SO₄^2- acceptability standards are indeed increasingly restrictive, given the potential outcomes for public health and ecosystems. This literature review deals with the treatment pathways relying on precipitation, adsorption and microbial redox principles. Although satisfactory removal performances can be achieved with each of them, significant yield differences are displayed throughout the bibliography. The challenge here was to identify the parameters leading to this variability and to assess their impact. The precipitation pathway is based on the formation of two main minerals (ettringite and barite). It can lead to total sulfate removal but can also be limited by aqueous wastes chemistry. Stabilizer kinetics of formation and equilibrium are highly constrained by background properties such as pH, Eh, SO₄^2- saturation state and inhibiting metal occurrences. Regarding the adsorption route, sorbents' intrinsic features such as the q_max parameter govern removal yields. Concerning the microbial pathway, the chemical oxygen demand/SO₄^2- ratio and the hydraulic retention time, which are classically evoked as yield variation factors, appear here to be weakly influential. The effect of these parameters seems to be overridden by the influence of electron donors, which constitute a first order factor of variability. A second order variability can be read according to the nature of these electron donors. Approaches using simple monomers (ethanol lactates, etc.) perform better than those using predominantly ligneous organic matter.

Pseudodesulfovibrio cashew sp. Nov., a Novel Deep-Sea Sulfate-Reducing Bacterium, Linking Heavy Metal Resistance and Sulfur Cycle

Sulfur cycling is primarily driven by sulfate reduction mediated by sulfate-reducing bacteria (SRB) in marine sediments. The dissimilatory sulfate reduction drives the production of enormous quantities of reduced sulfide and thereby the formation of highly insoluble metal sulfides in marine sediments. Here, a novel sulfate-reducing bacterium designated Pseudodesulfovibrio cashew SRB007 was isolated and purified from the deep-sea cold seep and proposed to represent a novel species in the genus of Pseudodesulfovibrio. A detailed description of the phenotypic traits, phylogenetic status and central metabolisms of strain SRB007 allowed the reconstruction of the metabolic potential and lifestyle of a novel member of deep-sea SRB. Notably, P. cashew SRB007 showed a strong ability to resist and remove different heavy metal ions including Co2+, Ni2+, Cd2+ and Hg2+. The dissimilatory sulfate reduction was demonstrated to contribute to the prominent removal capability of P. cashew SRB007 against different heavy metals via the formation of insoluble metal sulfides.

Nickel complexation as an innovative approach for nickel-cobalt selective recovery using sulfate-reducing bacteria

This study evaluated the differences in nickel (Ni) and cobalt (Co) solubility in the presence of sulfate reducing bacteria (SRB) to evaluate the feasibility of selective recovery of both metals from mine-impacted waters. A series of sulfate reducing activity tests with Ni, Co and both metals showed that up to 99 % Ni remained soluble despite the availability of sulfide for precipitation, while Co sulfide precipitation always occurred (over 84.5 %). The characterization of proteins in the liquid phase of the experiments revealed that some proteins were only produced in the experiments where Ni displayed higher solubility, suggesting their involvement in metal complexation. Some functions of these proteins included maintaining Ni homeostasis, acting as metalloenzymes and containing Ni-binding ligands. Desulfomicrobium baculatum, Stenotrophomonas maltophilia, and Desulfovibrio magneticus, were the main responsible species producing these proteins.

The effect of heavy metals on thiocyanate biodegradation by an autotrophic microbial consortium enriched from mine tailings

Abstract

Bioremediation systems represent an environmentally sustainable approach to degrading industrially generated thiocyanate (SCN⁻), with low energy demand and operational costs and high efficiency and substrate specificity. However, heavy metals present in mine tailings effluent may hamper process efficiency by poisoning thiocyanate-degrading microbial consortia. Here, we experimentally tested the tolerance of an autotrophic SCN⁻-degrading bacterial consortium enriched from gold mine tailings for Zn, Cu, Ni, Cr, and As. All of the selected metals inhibited SCN⁻ biodegradation to different extents, depending on concentration. At pH of 7.8 and 30 °C, complete inhibition of SCN⁻ biodegradation by Zn, Cu, Ni, and Cr occurred at 20, 5, 10, and 6 mg L⁻¹, respectively. Lower concentrations of these metals decreased the rate of SCN⁻ biodegradation, with relatively long lag times. Interestingly, the microbial consortium tolerated As even at 500 mg L⁻¹, although both the rate and extent of SCN⁻ biodegradation were affected. Potentially, the observed As tolerance could be explained by the origin of our microbial consortium in tailings derived from As-enriched gold ore (arsenopyrite). This study highlights the importance of considering metal co-contamination in bioreactor design and operation for SCN⁻ bioremediation at mine sites.

Key points

• Both the efficiency and rate of SCN⁻biodegradation were inhibited by heavy metals, to different degrees depending on type and concentration of metal.

• The autotrophic microbial consortium was capable of tolerating high concentrations of As, potential having adapted to higher As levels derived from the tailings source.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-020-10983-4.

Evaluating the Effect of pH, Temperature, and Hydraulic Retention Time on Biological Sulphate Reduction Using Response Surface Methodology

Biological sulphate reduction (BSR) has been identified as a promising alternative for treating acid mine drainage. In this study, the effect of pH, temperature, and hydraulic retention time (HRT) on BSR was investigated. The Box–Behnken design was used to matrix independent variables, namely pH (4–6), temperature (10–30 °C), and HRT (2–7 days) with the sulphate reduction efficiency and sulphate reduction rate as response variables. Experiments were conducted in packed bed reactors operating in a downflow mode. Response surface methodology was used to statistically analyse the data and to develop statistical models that can be used to fully understand the individual effects and the interactions between the independent variables. The analysis of variance results showed that the data fitted the quadratic models well as confirmed by a non-significant lack of fit. The temperature and HRT effect were significant (p < 0.0001), and these two variables had a strong interaction. However, the influence of pH was insignificant (p > 0.05).

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments

BACKGROUND

Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Bradymonabacteria, representative of the novel order Bradymonadales in δ-Proteobacteria. Compared with those of other bacterial predators (e.g., Myxococcales and Bdellovibrionales), the predatory and living strategies of Bradymonadales are still largely unknown.

RESULTS

Based on individual coculture of Bradymonabacteria with 281 prey bacteria, Bradymonabacteria preyed on diverse bacteria but had a high preference for Bacteroidetes. Genomic analysis of 13 recently sequenced Bradymonabacteria indicated that these bacteria had conspicuous metabolic deficiencies, but they could synthesize many polymers, such as polyphosphate and polyhydroxyalkanoates. Dual transcriptome analysis of cocultures of Bradymonabacteria and prey suggested a potential contact-dependent predation mechanism. Comparative genomic analysis with 24 other bacterial predators indicated that Bradymonabacteria had different predatory and living strategies. Furthermore, we identified Bradymonadales from 1552 publicly available 16S rRNA amplicon sequencing samples, indicating that Bradymonadales was widely distributed and highly abundant in saline environments. Phylogenetic analysis showed that there may be six subgroups in this order; each subgroup occupied a different habitat.

CONCLUSIONS

Bradymonabacteria have unique living strategies that are transitional between the "obligate" and the so-called facultative predators. Thus, we propose a framework to categorize the current bacterial predators into 3 groups: (i) obligate predators (completely prey-dependent), (ii) facultative predators (facultatively prey-dependent), and (iii) opportunistic predators (prey-independent). Our findings provide an ecological and evolutionary framework for Bradymonadales and highlight their potential ecological roles in saline environments. Video abstract.

Sulfate Reduction for Bioremediation of AMD Facilitated by an Indigenous Acidand Metal-Tolerant Sulfate-Reducer

Acid mine drainage (AMD) has been a serious environmental issue that threatens soil and aquatic ecosystems. In this study, an acid-tolerant sulfate-reducing bacterium, strain S4, was isolated from the mud of an AMD storage pond in Vietnam via enrichment in anoxic mineral medium at pH 5. Comparative analyses of sequences of the 16S rRNA gene and dsrB gene involved in sulfate reduction revealed that the isolate belonged to the genus Desulfovibrio, and is most closely related to Desulfovibrio oxamicus (with 99% homology in 16S rDNA sequence and 98% homology in dsrB gene sequence). Denaturing gradient gel electrophoresis (DGGE) analyses of dsrB gene showed that strain S4 represented one of the two most abundant groups developed in the enrichment culture. Notably, strain S4 was capable of reducing sulfate in low pH environments (from 2 and above), and resistance to extremely high concentration of heavy metals (Fe 3,000 mg/l, Zn 100 mg/l, Cu 100 mg/ l). In a batch incubation experiment in synthetic AMD with pH 3.5, strain S4 showed strong effects in facilitating growth of a neutrophilic, metal sensitive Desulfovibrio sp. strain SR4H, which was not capable of growing alone in such an environment. Thus, it is postulated that under extreme conditions such as an AMD environment, acid- and metal-tolerant sulfate-reducing bacteria (SRB)- like strain S4 would facilitate the growth of other widely distributed SRB by starting to reduce sulfate at low pH, thus increasing pH and lowering the metal concentration in the environment. Owing to such unique physiological characteristics, strain S4 shows great potential for application in sustainable remediation of AMD.

Bacterial communities on soil microplastic at Guiyu, an E-Waste dismantling zone of China

Recent studies of microplastic have focused on aquatic environment, but its impacts on soil ecosystems were poorly understood, particularly on bacterial communities. In this study, the bacterial taxon and functional composition of soil microplastic-attached communities at Guiyu, a notorious e-waste dismantling area in Guangdong Province, China, were investigated by means of high-throughput sequencing. The results revealed that fundamental difference in bacterial communities existed among microplastics selected from three plots with different dismantling methods and their surroundings, suggesting that microplastic surface created a new ecological niche in soil environment, and the bacteria adapted well to the surface-related lifestyle. The formation of microplastic-attached bacteria depended not only on various dismantled plastic materials, but also on disassembly methods that caused different soil physicochemical characters which might also influence the bacterial communities. As the hydrocarbon degraders, the family Hyphomonadaceae were also found on soil microplastic, further confirming that microorganisms played a role in biodegrading microplastic in e-waste zone. The analysis of functional profiles speculated that microplastic-attached bacteria had the potential to degrade pollutants. This study provides a new perspective for exploring microplastic-associated bacteria and increasing our understanding of microplastic pollution in terrestrial ecosystems.

Bacterially-assisted recovery of cadmium and nickel as their metal sulfide nanoparticles from spent Ni-Cd battery via hydrometallurgical route

Soaring demand for technology metals (e.g., Cd, Ni) and its ever-depleting primary resources ask for alternative recovery from secondary sources. Ni-Cd battery is one such source that can abridge the gap between demand and supply of such metals. Biogenic recovery, being environmentally benign, is explored for Cd and Ni recovery to manage the menace of spent Ni-Cd battery. Studies with 20, 40 and 60 mg/L Cd²⁺ initial concentrations in batch mode (in triplicates) at pH 7.0 ± 0.2, 30 ± 0.5 °C and 120 rpm were conducted using sulfate-reducing bacteria for 10 days. Analysis of extracellular polymeric substance revealed that protein secretion was enhanced, thereby forming Cd-EPS binding. Biosolids were collected and freeze-dried for morphological analysis viz. FESEM/EDX, PXRD and TEM, which revealed the formation of CdS nanoparticles (JCPDS card #00-042-1411) in range of 2-6 nm. Similarly, combined effect with 5, 10 and 20 mg/L Ni²⁺ at 20 mg/L Cd²⁺ were also investigated. Furthermore, to test the efficacy for real field application, spent Ni-Cd battery was dismantled and its powder was characterized, digested with concentrated HCl at 70 °C and was fed in batch mode after cooling, wherein nanoparticles of Ni and Cd sulfides were formed that has potential as semi-conducting material.

Enhanced reduction of sulfate and chromium under sulfate-reducing condition by synergism between extracellular polymeric substances and graphene oxide

Microbial reduction of sulfate and metal were simultaneously enhanced in the presence of graphene oxide (GO)-like nanomaterials, however, the mechanism remained unclear. In this study, bio-reduction of Cr was compared between free-living bacterium BY7 and immobilized BY7 (BY-rGO) on reduced GO particles. The role of extracellular polymeric substances (EPS) and rGO material on reduction of sulfate and Cr was investigated. Cr(VI) was reduced to Cr(III) and elemental Cr by BY-rGO particles up to 51% and 28%, respectively. EPS produced by the bacterium BY7 mainly consisted of proteins, polysaccharides, nucleic acids and humic substances. Concentration of EPS was sharply increased (about 54%) with the addition of graphene oxide, while the composition of EPS components was strongly affected by the exposure to Cr. By removing surface EPS without breaking the cells, reduction activities of sulfate and chromium by both BY-rGO particles and free-living BY7 cells were decreased. In contrast, reduction of sulfate and Cr by the free-living BY7 cells was enhanced with external addition of extracted EPS. Based on electrochemical analysis, the reduction peak indicating enhanced electron transfer was lost after removing EPS. Moreover, the contribution of each EPS fractions on sulfate and Cr reduction followed an order of polysaccharides > proteins > humic substances. Therefore, microbial sulfate and Cr reduction processes in the presence of BY-rGO particles were enhanced by the increasing amounts of EPS, which likely mediated electron transfer during sulfate and Cr reduction, and relieved bacteria from metal toxicity. Nevertheless, the presence of rGO was crucially important for elemental Cr production under sulfate-reducing condition, which might contribute to lowering electric potential or reducing activation energy for Cr(III) reduction. This work provided direct evidences for enhancing sulfate and Cr reduction activities by supplement of EPS as an additive to increase treatment efficiency in environmental bioremediation.

Biological removal of iron and sulfate from synthetic wastewater of cotton delinting factory by using halophilic sulfate-reducing bacteria

Industrial and agricultural wastewater treatment, which has the potential to cause serious risks to human health and the environment, has special importance at the lowest cost and highest efficiency such as biological processes to treat wastewater. The purpose of the study was removing iron and sulfate from very saline synthetic wastewater by means of halophilic sulfate-reducing bacteria. This process was performed under anaerobic conditions to change wastewater to a chemical fertilizer to use in saline and alkaline soils. Three halophilic SRBs were isolated and purified from wastewater of the cotton delinting factory by Postage C medium which supplemented with sodium chloride and magnesium chloride hexahydrate. The highest NaCl tolerance strain (HSR973) was allocated to Desulfovibrio halophilus sp. This experimental study was conducted in a fluid bed reactor at anaerobic conditions. Diluted concentrations of cotton linters wastewater containing 50–400 ppm iron were added to the reactor. After the bacteria fixation to different iron concentrations, the maximum removal efficiency of iron and sulfate was achieved 85.3 % and 78.4 % at the optimum retention time of 24-hours respectively. Sulfate concentration in samples decreased to about 20 % of initial concentration after 24-h retention time. The highest production of H₂S at optimum operational conditions was about 228 ml l⁻¹. The reduction of sulfate and iron biological precipitation by anaerobic rector presented high performance. This removing accompanied with the alkalinity increase during the process which could be improved condition for acidic wastewater treatment. The produced iron sulfide sludge was not suitable for use as a chemical fertilizer due to its lack of complete separation. However, the total sludge produced was able to be consumed in saline and alkaline soils for various purposes after additional treatment.

Remediation experiment of Ecuadorian acid mine drainage: geochemical models of dissolved species and secondary minerals saturation

Acid mine drainage is one of the main environmental hazards to ecosystems worldwide and it is directly related to mining activities. In Ecuador, such acidic-metallic waters are drained to rivers without treatment. In this research, we tested a laboratory combined (Ca-Mg) Dispersed Alkaline Substrate (DAS) system as an alternative to remediate acid drainage from the Zaruma-Portovelo gold mining site, at El Oro, Ecuador. The system worked at low and high flow hydraulic rates during a period of 8 months, without signs of saturation.. Analysis of physico-chemical parameters and water composition (ICP-OES, ICP-MS) demonstrated that treatment effectively increased water pH and promoted the retention of about 80% of Fe, Al, Mn and Cu. Under acid conditions As, Cr and Pb concentrations decreased with Fe and possible precipitation of jarosite and schwertmannite. However, the homogeneous depletion of Cr at pH above 6 could be related to ferrihydrite or directly with Cr (OH)₃ precipitation. After DAS-Ca, sulphate, phosphate and rare earth elements (REE) concentrations decreased to 1912, 0.85 and 0.07 mg/L respectively, while DAS-Mg contributed to form a complex model of minor carbonate and phosphate phases as main sink of REE. DAS-Mg also promoted the retention of most divalent metals at pH values over seven. Thus, this low cost treatment could avoid environmental pollution and international conflicts. Anyway, further investigations are needed to obtain higher Zn retention values. Graphical abstract.

Evaluation of a zeolite/anaerobic buffled reactor hybrid system for treatment of low bio-degradable effluents

The main objective of this work was to reduce the inhibitory effects of high contents of organics, ammonia, and heavy metals in an anaerobic buffled reactor (ABR), and to prevent the sludge wash-out using zeolites as media. In this work, a pilot scale of ABR with 8 compartments and a working volume of 14.4 L was used, and the last four ABR compartments were filled with a zeolite. The bioreactor was operated at HRTs of 3, 4, and 5 days, zeolite filling ratios of 10, 20, and 30%, and influent chemical oxygen demand (COD) concentrations of 10,000, 20,000, and 30,000 mg/L. The results obtained showed that the maximum removal efficiencies of COD and BOD₅ reached 78 and 68%, respectively. The maximum removal was observed at a HRT of 5 days, a 30% medium filling ratio, and a COD of 10,000 mg/L. Increasing the filling ratio in the reactor increased the removal efficiencies of COD and BOD₅ but increasing the concentration of the influent COD and decreasing HRT reduced the removal efficiency of the reactor. The initial BOD₅/COD ratio was equal to 0.36, which increased by 46% when the medium filling ratio was elevated to 30%. The maximum biogas yield was 0.23 L/g of COD_Removed, and the specific methanogenic activity test verified the toxicity effect of the leachate on the gas-producer organisms. The results of scanning electronic microscopy and EDS showed that the zeolite medium immobilized the microorganisms and a biofilm was formed. Also the zeolite, as a well-known ion exchanger, decreased the concentrations of the major inhibitors (ammonia and heavy metals) and improved the reactor efficiency.

Responses to copper stress in the metal-resistant bacterium Cupriavidus gilardii CR3: a whole-transcriptome analysis

Microbial metal-resistance mechanisms are the basis for the application of microorganisms in metal bioremediation. Despite the available studies of bacterial molecular mechanisms to resistance metals ions (particularly copper), the understanding of bacterial metal resistance is very limited from the transcriptome perspective. Here, responses of the transcriptome (RNA-Seq) was investigated in Cupriavidus gilardii CR3 exposed to 0.5 mM copper, because strain CR3 had a bioremoval capacity of 38.5% for 0.5 mM copper. More than 24 million clean reads were obtained from six libraries and were aligned against the C. gilardii CR3 genome. A total of 310 genes in strain CR3 were significantly differentially expressed under copper stress. Apart from the routine copper resistance operons cus and cop known in previous studies, Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses of differentially expressed genes indicated that the adenosine triphosphate-binding cassette transporter, amino acid metabolism, and negative chemotaxis collectively contribute to the copper-resistant process. More interestingly, we found that the genes associated with the type III secretion system were induced under copper stress. No such results were reordered in bacteria to date. Overall, this comprehensive network of copper responses is useful for further studies of the molecular mechanisms underlying responses to copper stress in bacteria.

Multiple Transcriptional Mechanisms Collectively Mediate Copper Resistance in Cupriavidus gilardii CR3

Bacteria resist copper (Cu) stress by implementing several metabolic mechanisms. However, these mechanisms are not fully understood. We investigated the mechanism of Cu resistance in Cupriavidus gilardii CR3, a Cu-resistant bacterium with a fully sequenced, annotated genome. The growth of CR3 was inhibited by higher Cu concentrations (≥1.0 mM) but not by lower ones (≤0.5 mM). CR3 accumulated Cu intracellularly (ratios of intercellular to extracellular Cu were 11.6, 4.24, and 3.9 in 0.1, 0.5, and 1.5 mM Cu treatments, respectively). A comparative transcriptome analysis of CR3 respectively revealed 310 and 413 differentially expressed genes under 0.5 and 1.5 mM Cu stress, most of which were up-regulated under Cu treatment. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional enrichment analyses uncovered several genotype-specific biological processes related to Cu stress. Besides revealing known Cu resistance-related genes, our global transcriptomics approach indicated that sulfur metabolism, iron-sulfur cluster, and cell secretion systems are involved in mediating Cu resistance in strain CR3. These results suggest that bacteria collectively use multiple systems to cope with Cu stress. Our findings concerning the global transcriptome response to Cu stress in CR3 provide new information for understanding the intricate regulatory network of Cu homeostasis in prokaryotes.

Inhibitory effect of cadmium(II) ion on anodic electrochemically active biofilms performance in bioelectrochemical systems

Cadmium(II) ion can affect the anode performance of bioelectrochemical systems (BES); however, how the presence of Cd²⁺ affect the extracellular electron transfer of anodic electrochemically active biofilms (EABs), the microbial viability and species composition of microorganism on the anode remain poorly understood. Here, we investigated the inhibitory effect of Cd²⁺ at different concentrations on the electrochemical performance and the biofilm community in mixed-culture enriched BES. The electrochemical performance of the BES was not inhibited at 2 mg L^-1 Cd²⁺, while higher concentrations of 5-20 mg L^-1 resulted in the decrease in the maximum power density, with 0.34 ± 0.01 W m^-2 at 5 mg L^-1, 0.28 ± 0.01 W m^-2 at 10 mg L^-1, and 0.17 ± 0 W m^-2 at 20 mg L^-1, respectively. When adding 30 mg/L Cd²⁺, there was almost no power output. The decline of the power output was possibly ascribed to the suppressed viability and the change of species richness as evident from confocal laser scanning microscopy and microbial community analysis. Cyclic voltammogram and electrochemical impedance spectroscopy revealed that high concentration of Cd²⁺ exceeding 5 mg L^-1 can inhibit the secretion of outer membrane cytochromes, thus reducing the electron transfer between the EABs and the anode surface. Analysis of bacterial structures showed a decrease in Geobacter accompanied by an increase in Stenotrophomonas and Azospira in response to Cd²⁺ at 10 and 20 mg L^-1. This study added to the in-depth analysis of the inhibition of Cd²⁺ on EABs, and provided new insights into the removing Cd²⁺ and organics simultaneously in BES.

Enhanced sulfate and metal removal by reduced graphene oxide self-assembled Enterococcus avium sulfate-reducing bacteria particles

Graphene oxide (GO) was introduced to Enterococcus avium strain BY7 sulfate-reducing bacteria culture as a carrier, GO was partially reduced by SRB to reduced graphene oxide (rGO). The rGO could further self-assemble Enterococcus avium strain BY7 sulfate-reducing bacteria to form BY-rGO particles. Growth and sulfate reduction activity of strain BY7 was promoted by rGO, which probably due to the protective effect of rGO, and enhanced electron transfer by rGO as electron shuttle. Effects of pH and temperature variance on strain BY-rGO were remarkably weakened, growth and sulfate reduction were observed from pH 2.0 to 12.0, and from 10 to 45 °C, respectively. Metal toxicity to BY7 strain SRB was sharply decreased in BY-rGO particles and heavy metal removal was remarkably accelerated (up to 50%). The immobilization methods established in this study might open a new way for the application of SRBs, especially under extreme environmental conditions.

The genome of the golden apple snail Pomacea canaliculata provides insight into stress tolerance and invasive adaptation

Background

The golden apple snail (Pomacea canaliculata) is a freshwater snail listed among the top 100 worst invasive species worldwide and a noted agricultural and quarantine pest that causes great economic losses. It is characterized by fast growth, strong stress tolerance, a high reproduction rate, and adaptation to a broad range of environments.

Results

Here, we used long-read sequencing to produce a 440-Mb high-quality, chromosome-level assembly of the P. canaliculata genome. In total, 50 Mb (11.4%) repeat sequences and 21,533 gene models were identified in the genome. The major findings of this study include the recent explosion of DNA/hAT-Charlie transposable elements, the expansion of the P450 gene family, and the constitution of the cellular homeostasis system, which contributes to ecological plasticity in stress adaptation. In addition, the high transcriptional levels of perivitelline genes in the ovary and albumen gland promote the function of nutrient supply and defense ability in eggs. Furthermore, the gut metagenome also contains diverse genes for food digestion and xenobiotic degradation.

Conclusions

These findings collectively provide novel insights into the molecular mechanisms of the ecological plasticity and high invasiveness.

Electrochemical and microbial community responses of electrochemically active biofilms to copper ions in bioelectrochemical systems

Heavy metals play an important role in the conductivity of solution, power generation and activity of microorganisms in bioelectrochemical systems (BESs). However, effect of heavy metal on the process of exoelectrogenesis metabolism and extracellular electron transfer of electrochemically active biofilms (EABs) was poorly understood. Herein, we investigated the impact of Cu²⁺ at gradually increasing concentration on the morphological and electrochemical performance and bacterial communities of anodic biofilms in mixed-culture BESs. The voltage output decreased continuously and dropped to zero at 10 mg L^-1, which was attributed to the toxic inhibition that cased anodic biofilm damage and decreased secretion of outer membrane cytochromes. When stopping the introduction of Cu²⁺ to anodic chamber, the maximum voltage production recovered 75.1% of the voltage produced from BES and coulombic efficiency was higher but acetate removal rate was lower than that before Cu²⁺ addition, demonstrating the recovery capability of EABs was higher compared to nonelectroactive bacteria. Moreover, SEM-EDS and XPS suggested that most of Cu²⁺ was adsorbed by the anode electrode and reduced by EABs on anode. Compared to the open-circuit BES, the flow of electrons through a circuit could improve the reduction of copper. Community analysis showed a decrease in Geobacter accompanied by an increase in Stenotrophomonas in response to Cu²⁺ shock in anodic chamber.

Bioassessment of heavy metal toxicity and enhancement of heavy metal removal by sulfate-reducing bacteria in the presence of zero valent iron

A simple and valid toxicity evaluation of Zn²⁺, Mn²⁺ and Cr⁶⁺ on sulfate-reducing bacteria (SRB) and heavy metal removal were investigated using the SRB system and SRB+Fe⁰ system. The heavy metal toxicity coefficient (β) and the heavy metal concentration resulting in 50% inhibition of sulfate reduction (I) from a modeling process were proposed to evaluate the heavy metal toxicity and nonlinear regression was applied to search for evaluation indices β and I. The heavy metal toxicity order was Cr⁶⁺ > Mn²⁺ > Zn²⁺. Compared with the SRB system, the SRB+Fe⁰ system exhibited a better capability for sulfate reduction and heavy metal removal. The heavy metal removal was above 99% in the SRB+Fe⁰ system, except for Mn²⁺. The energy-dispersive spectroscopy (EDS) analysis showed that the precipitates were removed primarily as sulfide for Zn²⁺ and hydroxide for Mn²⁺ and Cr⁶⁺.The method of evaluating the heavy metal toxicity on SRB was of great significance to understand the fundamentals of the heavy metal toxicity and inhibition effects on the microorganism and regulate the process of microbial sulfate reduction.

A novel bioelectrochemical system for chemical-free permanent treatment of acid mine drainage

The mining sector is currently under unprecedented pressure due to stringent environmental regulations. As a consequence, a permanent acid mine drainage (AMD) treatment is increasingly being regarded as a desirable target with direct benefits for the environment and the operational and economic viability of the resources sector. In this study we demonstrate that a novel bioelectrochemical system (BES) can deliver permanent treatment of acid mine drainage without chemical dosing. The technology consists of a two-cell bioelectrochemical setup to enable the removal of sulfate from the ongoing reduction-oxidation sulfur cycle to less than 550 mg L^-1 (85 ± 2% removal from a real AMD of an abandoned silver mine), thereby also reducing salinity at an electrical energy requirement of 10 ± 0.3 kWh kg^-1 of SO₄^2--S removed. In addition, the BES operation drove the removal and recovery of the main cations Al, Fe, Mg, Zn at rates of 151 ± 0 g Al m^-3 d^-1, 179 ± 1 g Fe m^-3 d^-1, 172 ± 1 g Mg m^-3 d^-1 and 46 ± 0 g Zn m^-3 d^-1 into a concentrate stream containing 263 ± 2 mg Al, 279 ± 2 mg Fe, 152 ± 0 mg Mg and 90 ± 0 mg Zn per gram of solid precipitated after BES fed-rate control treatment. The solid metal-sludge was twice less voluminous and 9 times more readily settleable than metal-sludge precipitated using NaOH. The continuous BES treatment also demonstrated the concomitant precipitation of rare earth elements together with yttrium (REY), with up to 498 ± 70 μg Y, 166 ± 27 μg Nd, 155 ± 14 μg Gd per gram of solid, among other high-value metals. The high-REY precipitates could be used to offset the treatment costs.

Mixed sulfate-reducing bacteria-enriched microbial fuel cells for the treatment of wastewater containing copper

Microbial fuel cells (MFCs) have been widely investigated for organic-based waste/substrate conversion to electricity. However, toxic compounds such as heavy metals are ubiquitous in organic waste and wastewater. In this work, a sulfate reducing bacteria (SRB)-enriched anode is used to study the impact of Cu²⁺ on MFC performance. This study demonstrates that MFC performance is slightly enhanced at concentrations of up to 20 mg/L of Cu²⁺, owing to the stimulating effect of metals on biological reactions. Cu²⁺ removal involves the precipitation of metalloids out of the solution, as metal sulfide, after they react with the sulfide produced by SRB. Simultaneous power generation of 224.1 mW/m² at lactate COD/SO₄^2- mass ratio of 2.0 and Cu²⁺ of 20 mg/L, and high Cu²⁺ removal efficiency, at >98%, are demonstrated in the anodic chamber of a dual-chamber MFC. Consistent MFC performance at 20 mg/L of Cu²⁺ for ten successive cycles shows the excellent reproducibility of this system. In addition, total organic content and sulfate removal efficiencies greater than 85% and 70%, respectively, are achieved up to 20 mg/L of Cu²⁺ in 48 h batches. However, higher metal concentration and very low pH at <4.0 inhibit the SRB MFC system. Microbial community analysis reveals that Desulfovibrio is the most abundant SRB in anode biofilm at the genus level, at 38.1%. The experimental results demonstrate that biological treatment of low-concentration metal-containing wastewater with SRB in MFCs can be an attractive technique for the bioremediation of this type of medium with simultaneous energy generation.

Effect of Nickel and Cobalt on Methanogenic Enrichment Cultures and Role of Biogenic Sulfide in Metal Toxicity Attenuation

Metals play an important role in microbial metabolism by acting as cofactors for many enzymes. Supplementation of biological processes with metals may result in improved performance, but high metal concentrations are often toxic to microorganisms. In this work, methanogenic enrichment cultures growing on H2/CO2 or acetate were supplemented with trace concentrations of nickel (Ni) and cobalt (Co), but no significant increase in methane production was observed in most of the tested conditions. However, high concentrations of these metals were detrimental to methanogenic activity of the cultures. Cumulative methane production (after 6 days of incubation) from H2/CO2 was 40% lower in the presence of 8 mM of Ni or 30 mM of Co, compared to controls without metal supplementation. When acetate was used as substrate, cumulative methane production was also reduced: by 18% with 8 mM of Ni and by 53% with 30 mM of Co (after 6 days of incubation). Metal precipitation with sulfide was further tested as a possible method to alleviate metal toxicity. Anaerobic sludge was incubated with Co (30 mM) and Ni (8 mM) in the presence of sulfate or sulfide. The addition of sulfide helped to mitigate the toxic effect of the metals. Methane production from H2/CO2 was negatively affected in the presence of sulfate, possibly due to competition of hydrogenotrophic methanogens by sulfate-reducing bacteria. However, in the enrichment cultures growing on acetate, biogenically produced sulfide had a positive effect and more methane was produced in these incubations than in similar assays without sulfate addition. The outcome of competition between methanogens and sulfate-reducing bacteria is a determinant factor for the success of using biogenic sulfide as detoxification method.

Heavy metal removal from multicomponent system by sulfate reducing bacteria: Mechanism and cell surface characterization

This study evaluated the combined effect of Cd(II), Cu(II), Ni(II), Fe(III), Pb(II) and Zn(II) on each other removal by anaerobic biomass under sulfate reducing condition. Statistically valid Plackett-Burman design of experiments was employed to carry out this mixture study. The results obtained showed a maximum removal of Cu(II) (98.9%), followed by Ni(II) (97%), Cd(II) (94.8%), Zn(II) (94.6%), Pb(II) (94.4%) and Fe(III) (93.9%). Analysis of variance (ANOVA) of the sulfate and chemical oxygen demand (COD) reduction revealed that the effect due to copper was highly significant (P value<0.05) on sulfate and COD removal. To establish the role of sulfate reducing bacteria (SRB) in the metal removal process, surface morphology and composition of the metal loaded biomass were analyzed by transmission electron microscopy (TEM) equipped with energy dispersive spectroscopy (EDS) and by field emission scanning electron microscopy (FESEM) integrated with energy dispersive X-ray spectroscopy (EDX). The results obtained revealed that the metal precipitates are associated with the outer and inner cell surface of the SRB as a result of the sulfide generated by SRB.

Diverse Profiles of AI-1 Type Quorum Sensing Molecules in Cultivable Bacteria from the Mangrove (Kandelia obovata) Rhizosphere Environment

Mangrove rhizosphere environment harbors diverse populations of microbes, and some evidence showed that rhizobacteria behavior was regulated by quorum sensing (QS). Investigating the diverse profiles of QS molecules in mangrove ecosystems may shed light on the bacterial roles and lead to a better understanding of the symbiotic interactions between plants and microbes. The aims of the current study focus on identifying AI-1 type QS signals, i.e., acyl homoserine lactones (AHLs), in Kandelia obovata rhizosphere environment. Approximately 1200 rhizobacteria were screened and 184 strains (15.3%) tested were positive. Subsequent 16s rRNA gene sequencing and dereplication analyses identified 24 species from the positive isolates, which were affiliated to three different phyla, including Proteobacteria, Firmicutes, and Actinobacteria. Thin-layer chromatography separation of extracts revealed diverse AHL profiles and detected at least one active compound in the supernatant of these 24 cultivable AHL-producers. The active extracts from these bacterial isolates were further evaluated by ultra performance liquid chromatography-mass spectrometry, and the carbon side chain length ranged from C4 to C14. This is the first report on the diversity of AI-1 type auto-inducers in the mangrove plant K. obovata, and it is imperative to expand our knowledge of plant-bacteria interactions with respect to the maintenance of wetland ecosystem health.

Effects of Lead and Mercury on Sulfate-Reducing Bacterial Activity in a Biological Process for Flue Gas Desulfurization Wastewater Treatment

Biological sulfate-reducing bacteria (SRB) may be effective in removing toxic lead and mercury ions (Pb(II) and Hg(II)) from wet flue gas desulfurization (FGD) wastewater through anaerobic sulfite reduction. To confirm this hypothesis, a sulfite-reducing up-flow anaerobic sludge blanket reactor was set up to treat FGD wastewater at metal loading rates of 9.2 g/m³-d Pb(II) and 2.6 g/m³-d Hg(II) for 50 days. The reactor removed 72.5 ± 7% of sulfite and greater than 99.5% of both Hg(II) and Pb(II). Most of the removed lead and mercury were deposited in the sludge as HgS and PbS. The contribution of cell adsorption and organic binding to Pb(II) and Hg(II) removal was 20.0 ± 0.1% and 1.8 ± 1.0%, respectively. The different bioavailable concentration levels of lead and mercury resulted in different levels of lethal toxicity. Cell viability analysis revealed that Hg(II) was less toxic than Pb(II) to the sludge microorganisms. In the batch tests, increasing the Hg(II) feeding concentration increased sulfite reduction rates. In conclusion, a sulfite-reducing reactor can efficiently remove sulfite, Pb(II) and Hg(II) from FGD wastewater.

Preparation of metal-resistant immobilized sulfate reducing bacteria beads for acid mine drainage treatment

Novel immobilized sulfate-reducing bacteria (SRB) beads were prepared for the treatment of synthetic acid mine drainage (AMD) containing high concentrations of Fe, Cu, Cd and Zn using up-flow anaerobic packed-bed bioreactor. The tolerance of immobilized SRB beads to heavy metals was significantly enhanced compared with that of suspended SRB. High removal efficiencies of sulfate (61-88%) and heavy metals (>99.9%) as well as slightly alkaline effluent pH (7.3-7.8) were achieved when the bioreactor was fed with acidic influent (pH 2.7) containing high concentrations of multiple metals (Fe 469 mg/L, Cu 88 mg/L, Cd 92 mg/L and Zn 128 mg/L), which showed that the bioreactor filled with immobilized SRB beads had tolerance to AMD containing high concentrations of heavy metals. Partially decomposed maize straw was a carbon source and stabilizing agent in the initial phase of bioreactor operation but later had to be supplemented by a soluble carbon source such as sodium lactate. The microbial community in the bioreactor was characterized by denaturing gradient gel electrophoresis (DGGE) and sequencing of partial 16S rDNA genes. Synergistic interaction between SRB (Desulfovibrio desulfuricans) and co-existing fermentative bacteria could be the key factor for the utilization of complex organic substrate (maize straw) as carbon and nutrients source for sulfate reduction.

Metals-induced functional stress in sulphate-reducing thermophiles

All toxic metals have been known to inhibit different activities of sulphate-reducing bacteria (SRB) at different concentrations. The present study delineates functional responses of two thermophilic SRB species (Desulfotomaculum reducens-HA1 and Desulfotomaculum hydrothermale-HA2) to toxic metals. Bacterial activity was assessed in terms of sulphate reduction and metal precipitation employing four concentrations (1, 5, 10 and 15 ppm) of three dissolved toxic metals (Cu, Cr and Ni) independently. Both sulphidogenic bacterial species showed results in a very narrow range of fluctuations. In general, bioprecipitation and sulphate reduction were pronounced at lower concentrations (1 and 5 ppm) and got inhibited at higher concentrations (10 and 15 ppm). The order of precipitation and sulphate reduction for the subject metals was Ni > Cr > Cu. The findings of this study will be helpful in developing economical and environmental friendly bioremediation process(es) tending to operate at extreme conditions around the concentrations in indicated suitable metals-loaded effluents.

Recovery of gold(0) nanoparticles from aqueous solutions using effluents from a bioremediation process

Biological processes for the recovery of gold from low-concentration media derived from leaching of secondary sources are of great importance due to the scarcity of the primary resources and the economic and environmental advantages of these methods.

Sulfur Reduction in Acid Rock Drainage Environments

Microbiological suitability of acidophilic sulfur reduction for metal recovery was explored by enriching sulfur reducers from acidic sediments at low pH (from 2 to 5) with hydrogen, glycerol, methanol and acetate as electron donors at 30 °C. The highest levels of sulfide in the enrichments were detected at pH 3 with hydrogen and pH 4 with acetate. Cloning and sequencing of the 16S rRNA gene showed dominance of the deltaproteobacterial sulfur-reducing genus Desulfurella in all the enrichments and subsequently an acidophilic strain (TR1) was isolated. Strain TR1 grew at a broad range of pH (3-7) and temperature (20-50 °C) and showed good metal tolerance (Pb(2+), Zn(2+), Cu(2+), Ni(2+)), especially for Ni(2+) and Pb(2+), with maximal tolerated concentrations of 0.09 and 0.03 mM, respectively. Different sources of sulfur were tested in the enrichments, from which biosulfur showed fastest growth (doubling time of 1.9 days), followed by colloidal, chemical and sublimated sulfur (doubling times of 2.2, 2.5, and 3.6 days, respectively). Strain TR1's physiological traits make it a good candidate to cope with low pH and high metal concentration in biotechnological processes for treatment of metal-laden acidic streams at low and moderately high temperature.