Seasonal Microbial Population Shifts in a Bioremediation System Treating Metal and Sulfate-Rich Seepage

Use of propionic acid additions to enhance zinc removal from mine drainage in short residence time, flow-through sulfate-reducing bioreactors

The effectiveness of liquid carbon additions to enhance zinc removal in laboratory-scale short hydraulic residence time (19 h) compost bioreactors receiving synthetic mine water with a high influent zinc concentration (45 mg/L) was investigated. Effective removal of such elevated zinc concentrations could not be sustained by sulfate reduction and/or other attenuation processes without carbon supplementation. Propionic acid addition resulted in improved and sustained performance by promoting the activities of sulfate reducing bacteria, leading to efficient zinc removal (mean 99%) via bacterial sulfate reduction. In contrast, cessation of propionic acid addition led to carbon limitation and the growth of sulfur oxidising bacteria, compromising zinc removal by bacterial sulfate reduction. These research findings demonstrate the potential for modest liquid carbon additions to compost-based passive treatment systems to engineer microbial responses which enhance rates of zinc attenuation in a short hydraulic residence time, enabling remediation of highly polluting mine drainage at sites with limited land availability.

Sulfidic acetate mineralization at 45°C by an aquifer microbial community: key players and effects of heat changes on activity and community structure

High-Temperature Aquifer Thermal Energy Storage (HT-ATES) is a sustainable approach for integrating thermal energy from various sources into complex energy systems. Temperatures ≥45°C, which are relevant in impact zones of HT-ATES systems, may dramatically influence the structure and activities of indigenous aquifer microbial communities. Here, we characterized an acetate-mineralizing, sulfate-reducing microbial community derived from an aquifer and adapted to 45°C. Acetate mineralization was strongly inhibited at temperatures ≤25°C and 60°C. Prolonged incubation at 12°C and 25°C resulted in acetate mineralization recovery after 40-80 days whereas acetate was not mineralized at 60°C within 100 days. Cultures pre-grown at 45°C and inhibited for 28 days by incubation at 12°C, 25°C, or 60°C recovered quickly after changing the temperature back to 45°C. Phylotypes affiliated to the order Spirochaetales and to endospore-forming sulfate reducers of the order Clostridiales were highly abundant in microcosms being active at 45°C highlighting their key role. In summary, prolonged incubation at 45°C resulted in active microbial communities mainly consisting of organisms adapted to temperatures between the typical temperature range of mesophiles and thermophiles and being resilient to temporary heat changes.

First Insight into the Diversity and Antibacterial Potential of Psychrophilic and Psychotrophic Microbial Communities of Abandoned Amber Quarry

Natural habitats, including extreme ones, are potential sources of new antimicrobial compound producers, such as bacteriocins and enzymes, capable of degrading the matrix polysaccharides of bacterial biofilms. This study aimed to investigate biodiversity and evaluate the antibacterial potential of psychrophilic and psychrotrophic microbial communities of the flooded Walter amber quarry (Kaliningrad region, Russia). As a result of 16S rDNA high-throughput profiling, 127 genera of bacteria belonging to 12 phyla of bacteria were found in sediment samples: Acidobacteria sp., Actinobacteria sp., Armatimonadetes sp., Bacteroidetes sp., Chloroflexi sp., Cyanobacteria sp., Firmicutes sp., Gemmatimonadetes sp., Planctomycetes sp., Proteobacteria sp., Tenericutes sp., and Verrucomicrobia sp. The dominant bacteria groups were the families Ruminococcaceae and Lachnospiraceae, belonging to the order Clostridiales phylum Firmicutes. Analysis of enrichment cultures obtained from sediments showed the presence of antibacterial and cellulolytic activity. It seems likely that the bacteria of the studied communities are producers of antimicrobial compounds and have the potential for biotechnological use.

Bacterial communities as indicators of environmental pollution by POPs in marine sediments

Decades of intensive discharge from industrial activities into coastal systems has resulted in the accumulation of a variety of persistent organic pollutants (POPs) in marine waters and sediments, having detrimental impacts on aquatic ecosystems and the resident biota. POPs are among the most hazardous chemicals originating from industrial activities due to their biotoxicity and resistance to environmental degradation. Bacterial communities are known to break down many of these aromatic compounds, and different members of naturally occurring bacterial consortia have been described to work in syntrophic association to thrive in heavily contaminated waters and sediments, making them potential candidates as bioindicators of environmental pollution. In this study environmental, sampling was combined with chemical analysis of pollutants and high-resolution sequencing of bacterial communities using Next Generation Sequencing molecular biology tools. The aim of the present study was to describe the bacterial communities from marine sediments containing high loads of POPs and to identify relevant members of the resident microbial communities that may act as bioindicators of contamination. Marine sediments were collected from a coastal bay area of the Baltic Sea historically influenced by intense industrial activity, including metal smelting, oil processing, and pulp and paper production. Different types of POPs were detected at high concentrations. Fiberbank sediments, resulting from historic paper industry activity, were found to harbour a clearly distinct bacterial community including a number of bacterial taxa capable of cellulolytic and dechlorination activities. Our findings indicate that specific members of the bacterial communities thrive under increasing levels of POPs in marine sediments, and that the abundances of certain taxa correlate with specific POPs (or groups), which could potentially be employed in monitoring, status assessment and environmental management purposes.

Design, application, and microbiome of sulfate-reducing bioreactors for treatment of mining-influenced water

Sulfate-reducing bioreactors, also called biochemical reactors, represent a promising option for passive treatment of mining-influenced water (MIW) based on similar technology to aerobic/anaerobic-constructed wetlands and vertical-flow wetlands. MIW from each mine site has a variety of site-specific properties related to its treatment; therefore, design factors, including the organic substrates and inorganic materials packed into the bioreactor, must be tested and evaluated before installation of full-scale sulfate-reducing bioreactors. Several full-scale sulfate-reducing bioreactors operating at mine sites provide examples, but holistic understanding of the complex treatment processes occurring inside the bioreactors is lacking. With the recent introduction of high-throughput DNA sequencing technologies, microbial processes within bioreactors may be clarified based on the relationships between operational parameters and key microorganisms identified using high-resolution microbiome data. In this review, the test design procedures and precedents of full-scale bioreactor application for MIW treatment are briefly summarized, and recent knowledge on the sulfate-reducing microbial communities of field-based bioreactors from fine-scale monitoring is presented.Key points• Sulfate-reducing bioreactors are promising for treatment of mining-influenced water.• Various design factors should be tested for application of full-scale bioreactors.• Introduction of several full-scale passive bioreactor systems at mine sites.• Desulfosporosinus spp. can be one of the key bacteria within field-based bioreactors.

High-Throughput Recovery and Characterization of Metagenome-Derived Glycoside Hydrolase-Containing Clones as a Resource for Biocatalyst Development

The generation of new biocatalysts for plant biomass degradation and glycan synthesis has typically relied on the characterization and investigation of one or a few enzymes at a time. By coupling functional metagenomic screening and high-throughput functional characterization, we can progress beyond the current scale of catalyst discovery and provide rapid annotation of catalyst function. By functionally screening environmental DNA from many diverse sources, we have generated a suite of active glycoside hydrolase-containing clones and demonstrated their reaction parameters. We then demonstrated the utility of this collection through the generation of a new catalyst for the formation of azido-modified glycans. Further interrogation of this collection of clones will expand our biocatalytic toolbox, with potential application to biomass deconstruction and synthesis of glycans.

Functional metagenomics is a powerful tool for both the discovery and development of biocatalysts. This study presents the high-throughput functional screening of 22 large-insert fosmid libraries containing over 300,000 clones sourced from natural and engineered ecosystems, characterization of active clones, and a demonstration of the utility of recovered genes or gene cassettes in the development of novel biocatalysts. Screening was performed in a 384-well-plate format with the fluorogenic substrate 4-methylumbelliferyl cellobioside, which releases a fluorescent molecule when cleaved by β-glucosidases or cellulases. The resulting set of 164 active clones was subsequently interrogated for substrate preference, reaction mechanism, thermal stability, and optimal pH. The environmental DNA harbored within each active clone was sequenced, and functional annotation revealed a cornucopia of carbohydrate-degrading enzymes. Evaluation of genomic-context information revealed both synteny and polymer-targeting loci within a number of sequenced clones. The utility of these fosmids was then demonstrated by identifying clones encoding activity on an unnatural glycoside (4-methylumbelliferyl 6-azido-6-deoxy-β-d-galactoside) and transforming one of the identified enzymes into a glycosynthase capable of forming taggable disaccharides.

IMPORTANCE The generation of new biocatalysts for plant biomass degradation and glycan synthesis has typically relied on the characterization and investigation of one or a few enzymes at a time. By coupling functional metagenomic screening and high-throughput functional characterization, we can progress beyond the current scale of catalyst discovery and provide rapid annotation of catalyst function. By functionally screening environmental DNA from many diverse sources, we have generated a suite of active glycoside hydrolase-containing clones and demonstrated their reaction parameters. We then demonstrated the utility of this collection through the generation of a new catalyst for the formation of azido-modified glycans. Further interrogation of this collection of clones will expand our biocatalytic toolbox, with potential application to biomass deconstruction and synthesis of glycans.

Simultaneous Biological and Chemical Removal of Sulfate and Fe(II)EDTA-NO in Anaerobic Conditions and Regulation of Sulfate Reduction Products

In the simultaneous flue gas desulfurization and denitrification by biological combined with chelating absorption technology, SO2 and NO are converted into sulfate and Fe(II)EDTA-NO which need to be reduced in biological reactor. Increasing the removal loads of sulfate and Fe(II)EDTA-NO and converting sulfate to elemental sulfur will benefit the application of this process. A moving-bed biofilm reactor was adopted for sulfate and Fe(II)EDTA-NO biological reduction. The removal efficiencies of the sulfate and Fe(II)EDTA-NO were 96% and 92% with the influent loads of 2.88 kg SO42−·m−3·d−1 and 0.48 kg NO·m−3·d−1. The sulfide produced by sulfate reduction could be reduced by increasing the concentrations of Fe(II)EDTA-NO and Fe(III)EDTA. The main reduction products of sulfate and Fe(II)EDTA-NO were elemental sulfur and N2. It was found that the dominant strain of sulfate reducing bacteria in the system was Desulfomicrobium. Pseudomonas, Sulfurovum and Arcobacter were involved in the reduction of Fe(II)EDTA-NO.

How to tackle the stringent sulfate removal requirements in mine water treatment-A review of potential methods

Sulfate (SO₄^2-) is a ubiquitous anion in natural waters. It is not considered toxic, but it may be detrimental to freshwater species at elevated concentrations. Mining activities are one significant source of anthropogenic sulfate into natural waters, mainly due to the exposure of sulfide mineral ores to weathering. There are several strategies for mitigating sulfate release, starting from preventing sulfate formation in the first place and ending at several end-of-pipe treatment options. Currently, the most widely used sulfate-removal process is precipitation as gypsum (CaSO₄·2H₂O). However, the lowest reachable concentration is theoretically 1500 mg L^-1 SO₄^2- due to gypsum's solubility. At the same time, several mines worldwide have significantly more stringent sulfate discharge limits. The purpose of this review is to examine the process options to reach low sulfate levels (< 1500 mg L^-1) in mine effluents. Examples of such processes include alternative chemical precipitation methods, membrane technology, biological treatment, ion exchange, and adsorption. In addition, aqueous chemistry and current effluent standards concerning sulfate together with concentrate treatment and sulfur recovery are discussed.

Semi-passive in-situ pilot scale bioreactor successfully removed sulfate and metals from mine impacted water under subarctic climatic conditions

Mine drainage contaminated with metals is a major environmental threat since it is a source of water pollution with devastating effects on aquatic ecosystems. Conventional active treatment technologies are prohibitively expensive and so there is increasing demand to develop reliable, cost-effective and sustainable passive or semi-passive treatment. These are promising alternatives since they leverage the metabolism of microorganisms native to the disturbed site at in situ or close to in situ conditions. Since this is a biological approach, it is not clear if semi-passive treatment would be effective in remote locations with extremely cold weather such as at mines in the subarctic. In this study we tested the hypothesis that sulfate-reducing bacteria, which are microorganisms that promote metal precipitation, exist in subarctic mine environments and their activity can be stimulated by adding a readily available carbon source. An experiment was setup at a closed mine in the Yukon Territory, Canada, where leaching of Zn and Cd occurs. To test if semi-passive treatment could precipitate these metals and prevent further leaching from waste rock, molasses as a carbon source was added to anaerobic bioreactors mimicking the belowground in-situ conditions. Microbial community analysis confirmed that sulfate-reducing bacteria became enriched in the bioreactors upon addition of molasses. The population composition remained fairly stable over the 14 month operating period despite temperature shifts from 17 to 5 °C. Sulfate reduction functionality was confirmed by quantification of the gene for dissimilatory sulfite reductase. Metals were removed from underground mine drainage fed into the bioreactors with Zn removal efficiency varying between 20.9% in winter and 89.3% in summer, and Cd removal efficiency between 39% in winter and 90.5% in summer. This study demonstrated that stimulation of native SRB in MIW was possible and that in situ semi-passive treatment can be effective in removing metals despite the cold climate.

Effect of hydraulic retention time on microbial community in biochemical passive reactors during treatment of acid mine drainage

The effect of hydraulic retention time (HRT) on the microbial community during acid mine drainage (AMD) treatment was investigated. Physicochemical and molecular (illumina and qPCR) analyses were performed on reactive mixtures collected from seven bioreactors in three-operation period (8, 17 and 36weeks). Long HRT (4day) favored the relative abundance of SRB, causing the increase of residual sulfides and short HRT (1day) affected the anaerobic conditions of the bioreactors and favored the presence the acidophilic chemolithotrophic microorganisms. Besides qPCR indicated that genes related to cellulose degradation were present in low copy numbers and were affected by the HRT. Finally, environmental factors (pH, organic source, metal sulfides, and sulfate concentrations) had significant impact on relative abundance of the phylogenetic lineages, rather than the types of lineages present in the reactive mixture. The findings of this study indicate that HRT affects the stability of passive bioreactors and their microbial communities.

Hydraulic retention time and pH affect the performance and microbial communities of passive bioreactors for treatment of acid mine drainage

For acceleration of removing toxic metals from acid mine drainage (AMD), the effects of hydraulic retention time (HRT) and pH on the reactor performance and microbial community structure in the depth direction of a laboratory-scale packed-bed bioreactor containing rice bran as waste organic material were investigated. The HRT was shortened stepwise from 25 to 12 h, 8 h, and 6 to 5 h under the neutral condition using AMD neutralized with limestone (pH 6.3), and from 25 to 20 h, 12 h, and 8 to 7 h under the acid condition using AMD (pH 3.0). Under the neutral condition, the bioreactor stably operated up to 6 h HRT, which was shorter than under the acid condition (up to 20 h HRT). During stable sulfate reduction, both the organic matter-remaining condition and the low oxidation-reduction potential condition in lower parts of the reactor were observed. Principal coordinate analysis of Illumina sequencing data of 16S rRNA genes revealed a dynamic transition of the microbial communities at the boundary between stable and unstable operation in response to reductions in HRT. During stable operation under both the neutral and acid conditions, several fermentative operational taxonomic units (OTUs) from the phyla Firmicutes and Bacteroidetes dominated in lower parts of the bioreactor, suggesting that co-existence of these OTUs might lead to metabolic activation of sulfate-reducing bacteria. In contrast, during unstable operation at shorter HRTs, an OTU from the candidate phylum OP11 were found under both conditions. This study demonstrated that these microorganisms can be used to monitor the treatment of AMD, which suggests stable or deteriorated performance of the system.