Biodegradation of the alkaline cellulose degradation products generated during radioactive waste disposal

The evolution of alkaliphilic biofilm communities in response to extreme alkaline pH values

Extremes of pH present a challenge to microbial life and our understanding of survival strategies for microbial consortia, particularly at high pH, remains limited. The utilization of extracellular polymeric substances within complex biofilms allows micro-organisms to obtain a greater level of control over their immediate environment. This manipulation of the immediate environment may confer a survival advantage in adverse conditions to biofilms. Within the present study alkaliphilic biofilms were created at pH 11.0, 12.0, or 13.0 from an existing alkaliphilic community. In each pH system, the biofilm matrix provided pH buffering, with the internal pH being 1.0-1.5 pH units lower than the aqueous environment. Increasing pH resulted in a reduced removal of substrate and standing biomass associated with the biofilm. At the highest pH investigated (pH 13.0), the biofilms matrix contained a greater degree of eDNA and the microbial community was dominated by Dietzia sp. and Anaerobranca sp.

Methanogenesis from Mineral Carbonates, a Potential Indicator for Life on Mars

Priorities for the exploration of Mars involve the identification and observation of biosignatures that indicate the existence of life on the planet. The atmosphere and composition of the sediments on Mars suggest suitability for anaerobic chemolithotrophic metabolism. Carbonates are often considered as morphological biosignatures, such as stromatolites, but have not been considered as potential electron acceptors. Within the present study, hydrogenotrophic methanogen enrichments were generated from sediments that had received significant quantities of lime from industrial processes (lime kiln/steel production). These enrichments were then supplemented with calcium carbonate powder or marble chips as a sole source of carbon. These microcosms saw a release of inorganic carbon into the liquid phase, which was subsequently removed, resulting in the generation of methane, with 0.37 ± 0.09 mmoles of methane observed in the steel sediment enrichments supplemented with calcium carbonate powder. The steel sediment microcosms and lime sediments with carbonate powder enrichments were dominated by Methanobacterium sp., whilst the lime/marble enrichments were more diverse, containing varying proportions of Methanomassiliicoccus, Methanoculleus and Methanosarcina sp. In all microcosm experiments, acetic acid was detected in the liquid phase. Our results indicate that chemolithotrophic methanogenesis should be considered when determining biosignatures for life on Mars.

Hydrogenotrophic Methanogenesis Under Alkaline Conditions

A cement-based geological disposal facility (GDF) is one potential option for the disposal of intermediate level radioactive wastes. The presence of both organic and metallic materials within a GDF provides the opportunity for both acetoclastic and hydrogenotrophic methanogenesis. However, for these processes to proceed, they need to adapt to the alkaline environment generated by the cementitious materials employed in backfilling and construction. Within the present study, a range of alkaline and neutral pH sediments were investigated to determine the upper pH limit and the preferred route of methane generation. In all cases, the acetoclastic route did not proceed above pH 9.0, and the hydrogenotrophic route dominated methane generation under alkaline conditions. In some alkaline sediments, acetate metabolism was coupled to hydrogenotrophic methanogenesis via syntrophic acetate oxidation, which was confirmed through inhibition studies employing fluoromethane. The absence of acetoclastic methanogenesis at alkaline pH values (>pH 9.0) is attributed to the dominance of the acetate anion over the uncharged, undissociated acid. Under these conditions, acetoclastic methanogens require an active transport system to access their substrate. The data indicate that hydrogenotrophic methanogenesis is the dominant methanogenic pathway under alkaline conditions (>pH 9.0).

Enhanced microbial degradation of irradiated cellulose under hyperalkaline conditions

Intermediate-level radioactive waste includes cellulosic materials, which under the hyperalkaline conditions expected in a cementitious geological disposal facility (GDF) will undergo abiotic hydrolysis forming a variety of soluble organic species. Isosaccharinic acid (ISA) is a notable hydrolysis product, being a strong metal complexant that may enhance the transport of radionuclides to the biosphere. This study showed that irradiation with 1 MGy of γ-radiation under hyperalkaline conditions enhanced the rate of ISA production from the alkali hydrolysis of cellulose, indicating that radionuclide mobilisation to the biosphere may occur faster than previously anticipated. However, irradiation also made the cellulose fibres more available for microbial degradation and fermentation of the degradation products, producing acidity that inhibited ISA production via alkali hydrolysis. The production of hydrogen gas as a fermentation product was noted, and this was associated with a substantial increase in the relative abundance of hydrogen-oxidising bacteria. Taken together, these results expand our conceptual understanding of the mechanisms involved in ISA production, accumulation and biodegradation in a biogeochemically active cementitious GDF.

Microbial Degradation of Cellulosic Material and Gas Generation: Implications for the Management of Low- and Intermediate-Level Radioactive Waste

Deep geologic repositories (DGR) in Canada are designed to contain and isolate low- and intermediate-level radioactive waste. Microbial degradation of the waste potentially produces methane, carbon dioxide and hydrogen gas. The generation of these gases increase rock cavity pressure and limit water ingress which delays the mobility of water soluble radionuclides. The objective of this study was to measure gas pressure and composition over 7 years in experiments containing cellulosic material with various starting conditions relevant to a DGR and to identify micro-organisms generating gas. For this purpose, we conducted experiments in glass bottles containing (1) wet cellulosic material, (2) wet cellulosic material with compost Maker, and (3) wet cellulosic material with compost Accelerator. Results demonstrated that compost accelerated the pressure build-up in the containers and that methane gas was produced in one experiment with compost and one experiment without compost because the pH remained neutral for the duration of the 464 days experiment. Methane was not formed in the other experiment because the pH became acidic. Once the pressure became similar in all containers after 464 days, we then monitored gas pressure and composition in glass bottle containing wet cellulosic material in (1) acidic conditions, (2) neutral conditions, and (3) with an enzyme that accelerated degradation of cellulose over 1965 days. In these experiments, acetogenic bacteria degraded cellulose and produced acetic acid, which acidity suppressed methane production. Microbial community analyses suggested a diverse community of archaea, bacteria and fungi actively degrading cellulose. DNA analyses also confirmed the presence of methanogens and acetogens in our experiments. This study suggests that methane gas will be generated in DGRs if pH remains neutral. However, our results showed that microbial degradation of cellulose not only generated gas, but also generated acidity. This finding is important as acids can limit bentonite swelling and potentially degrade cement and rock barriers, thus this requires consideration in the safety case as appropriate.

Genomic Insights Into A Novel, Alkalitolerant Nitrogen Fixing Bacteria, Azonexus sp. Strain ZS02

Alkaline environments represent a significant challenge to the growth of micro-organisms. Despite this, there are a number of alkaline environments which contain active microbial communities. Here we describe the genome of a diazotrophic, alkalitolerant strain of Azonexus, which was isolated from a microcosm seeded with hyperalkaline soils resulting from lime depositions. The isolate has a genome size 3.60 Mb with 3431 protein coding genes. The proteome indicated the presence of genes associated with the cycling of nitrogen, in particular the fixation of atmospheric nitrogen. Although closely related to Azonexus hydrophilus strain d8-1 by both 16S (97.9%) and in silico gDNA (84.1%) relatedness, the isolate demonstrates a pH tolerance above that reported for this strain. The proteome contained genes for the complete Na⁺/H⁺ antiporter (subunits A to G) for cytoplasmic pH regulation; this may account for the phenotypic characteristics of this strain which exhibited optimal growth conditions of pH 9 and 30°C.

Whole-Genome Sequence of the Anaerobic Isosaccharinic Acid Degrading Isolate, Macellibacteroides fermentans Strain HH-ZS

The ability of micro-organisms to degrade isosaccharinic acids (ISAs) while tolerating hyperalkaline conditions is pivotal to our understanding of the biogeochemistry associated within these environs, but also in scenarios pertaining to the cementitious disposal of radioactive wastes. An alkalitolerant, ISA degrading micro-organism was isolated from the hyperalkaline soils resulting from lime depositions. Here, we report the first whole-genome sequence, ISA degradation profile and carbohydrate preoteome of a Macellibacteroides fermentans strain HH-ZS, 4.08 Mb in size, coding 3,241 proteins, 64 tRNA, and 1 rRNA.

The Impact of Alkaliphilic Biofilm Formation on the Release and Retention of Carbon Isotopes from Nuclear Reactor Graphite

¹⁴C is an important consideration within safety assessments for proposed geological disposal facilities for radioactive wastes, since it is capable of re-entering the biosphere through the generation of ¹⁴C bearing gases. The irradiation of graphite moderators in the UK gas-cooled nuclear power stations has led to the generation of a significant volume of ¹⁴C-containing intermediate level wastes. Some of this ¹⁴C is present as a carbonaceous deposit on channel wall surfaces. Within this study, the potential of biofilm growth upon irradiated and ¹³C doped graphite at alkaline pH was investigated. Complex biofilms were established on both active and simulant samples. High throughput sequencing showed the biofilms to be dominated by Alcaligenes sp at pH 9.5 and Dietzia sp at pH 11.0. Surface characterisation revealed that the biofilms were limited to growth upon the graphite surface with no penetration of the deeper porosity. Biofilm formation resulted in the generation of a low porosity surface layer without the removal or modification of the surface deposits or the release of the associated ¹⁴C/¹³C. Our results indicated that biofilm formation upon irradiated graphite is likely to occur at the pH values studied, without any additional release of the associated ¹⁴C.

Sustained Bauxite Residue Rehabilitation with Gypsum and Organic Matter 16 years after Initial Treatment

Bauxite residue is a high volume byproduct of alumina manufacture which is commonly disposed of in purpose-built bauxite residue disposal areas (BRDAs). Natural waters interacting with bauxite residue are characteristically highly alkaline, and have elevated concentrations of Na, Al, and other trace metals. Rehabilitation of BRDAs is therefore often costly and resource/infrastructure intensive. Data is presented from three neighboring plots of bauxite residue that was deposited 20 years ago. One plot was amended 16 years ago with process sand, organic matter, gypsum, and seeded (fully treated), another plot was amended 16 years ago with process sand, organic matter, and seeded (partially treated), and a third plot was left untreated. These surface treatments lower alkalinity and salinity, and thus produce a substrate more suitable for biological colonisation from seeding. The reduction of pH leads to much lower Al, V, and As mobility in the actively treated residue and the beneficial effects of treatment extend passively 20-30 cm below the depth of the original amendment. These positive rehabilitation effects are maintained after 2 decades due to the presence of an active and resilient biological community. This treatment may provide a lower cost solution to BRDA end of use closure plans and orphaned BRDA rehabilitation.

Floc Formation Reduces the pH Stress Experienced by Microorganisms Living in Alkaline Environments

The survival of microorganisms within a cementitious geological disposal facility for radioactive wastes heavily depends on their ability to survive the calcium-dominated, hyperalkaline conditions resulting from the dissolution of the cementitious materials. The results from this study show that the formation of flocs, composed of a complex mixture of extracellular polymeric substances (EPS), provides protection against alkaline pH values up to 13.0. The flocs were dominated by Alishewanella and Dietzia spp., producing a mannose-rich carbohydrate fraction incorporating extracellular DNA, resulting in Ca²⁺ sequestration. EPS provided a ∼10-μm thick layer around the cells within the center of the flocs, which were capable of growth at pH values of 11.0 and 11.5, maintaining internal pH values of 10.4 and 10.7, respectively. Microorganisms survived at a pH of 12.0, where an internal floc pH of 11.6 was observed, as was a reduced associated biomass. We observed limited floc survival (<2 weeks) at a pH of 13.0. This study demonstrates that flocs maintain lower internal pHs in response to the hyperalkaline conditions expected to occur within a cementitious geological disposal facility for radioactive wastes and indicates that floc communities within such a facility can survive at pHs up to 12.0.IMPORTANCE The role of extracellular polymeric substances (EPS) in the survival of microorganisms in hyperalkaline conditions is poorly understood. Here, we present the taxonomy, morphology, and chemical characteristics of an EPS-based microbial floc, formed by a consortium isolated from an anthropogenic hyperalkaline site. Short-term (<2 weeks) survival of the flocs at a pH of 13 was observed, with indefinite survival observed at a pH of 12.0. Measurements from micro-pH electrodes (10-μm-diameter tip) demonstrated that flocs maintain lower internal pHs in response to hyperalkaline conditions (pH 11.0, 11.5, and 12.0), demonstrating that floc formation and EPS production are survival strategies under hyperalkaline conditions. The results indicate how microbial communities may survive and propagate within the hyperalkaline environment that is expected to prevail in a cementitious geological disposal facility for radioactive wastes; the results are also relevant to the wider extremophile community.

Microbial Community Evolution Is Significantly Impacted by the Use of Calcium Isosaccharinic Acid as an Analogue for the Products of Alkaline Cellulose Degradation

Diasteriomeric isosaccharinic acid (ISA) is an important consideration within safety assessments for the disposal of the United Kingdoms’ nuclear waste legacy, where it may potentially influence radionuclide migration. Since the intrusion of micro-organisms may occur within a disposal concept, the impact of ISA may be impacted by microbial metabolism. Within the present study we have established two polymicrobial consortia derived from a hyperalkaline soil. Here, α-ISA and a diatereomeric mix of ISAs’ were used as a sole carbon source, reflecting two common substrates appearing within the literature. The metabolism of ISA within these two consortia was similar, where ISA degradation resulted in the acetogenesis and hydrogenotrophic methanogenesis. The chemical data obtained confirm that the diastereomeric nature of ISA is likely to have no impact on its metabolism within alkaline environments. High throughput sequencing of the original soil showed a diverse community which, in the presence of ISA allowed for the dominance the Clostridiales associated taxa with Clostridium clariflavum prevalent. Further taxonomic investigation at the genus level showed that there was in fact a significant difference (p = 0.004) between the two community profiles. Our study demonstrates that the selection of carbon substrate is likely to have a significant impact on microbial community composition estimations, which may have implications with respect to a safety assessment of an ILW-GDF.

Role of an organic carbon-rich soil and Fe(III) reduction in reducing the toxicity and environmental mobility of chromium(VI) at a COPR disposal site

Cr(VI) is an important contaminant found at sites where chromium ore processing residue (COPR) is deposited. No low cost treatment exists for Cr(VI) leaching from such sites. This study investigated the mechanism of interaction of alkaline Cr(VI)-containing leachate with an Fe(II)-containing organic matter rich soil beneath the waste. The soil currently contains 0.8% Cr, shown to be present as Cr(III)(OH)3 in EXAFS analysis. Lab tests confirmed that the reaction of Cr(VI) in site leachate with Fe(II) present in the soil was stoichiometrically correct for a reductive mechanism of Cr accumulation. However, the amount of Fe(II) present in the soil was insufficient to maintain long term Cr(VI) reduction at historic infiltration rates. The soil contains a population of bacteria dominated by a Mangroviflexus-like species, that is closely related to known fermentative bacteria, and a community capable of sustaining Fe(III) reduction in alkaline culture. It is therefore likely that in situ fermentative metabolism supported by organic matter in the soil produces more labile organic substrates (lactate was detected) that support microbial Fe(III) reduction. It is therefore suggested that addition of solid phase organic matter to soils adjacent to COPR may reduce the long term spread of Cr(VI) in the environment.

Anoxic Biodegradation of Isosaccharinic Acids at Alkaline pH by Natural Microbial Communities

One design concept for the long-term management of the UK's intermediate level radioactive wastes (ILW) is disposal to a cementitious geological disposal facility (GDF). Under the alkaline (10.0<pH>13.0) anoxic conditions expected within a GDF, cellulosic wastes will undergo chemical hydrolysis. The resulting cellulose degradation products (CDP) are dominated by α- and β-isosaccharinic acids (ISA), which present an organic carbon source that may enable subsequent microbial colonisation of a GDF. Microcosms established from neutral, near-surface sediments demonstrated complete ISA degradation under methanogenic conditions up to pH 10.0. Degradation decreased as pH increased, with β-ISA fermentation more heavily influenced than α-ISA. This reduction in degradation rate was accompanied by a shift in microbial population away from organisms related to Clostridium sporosphaeroides to a more diverse Clostridial community. The increase in pH to 10.0 saw an increase in detection of Alcaligenes aquatilis and a dominance of hydrogenotrophic methanogens within the Archaeal population. Methane was generated up to pH 10.0 with acetate accumulation at higher pH values reflecting a reduced detection of acetoclastic methanogens. An increase in pH to 11.0 resulted in the accumulation of ISA, the absence of methanogenesis and the loss of biomass from the system. This study is the first to demonstrate methanogenesis from ISA by near surface microbial communities not previously exposed to these compounds up to and including pH 10.0.

The enrichment of an alkaliphilic biofilm consortia capable of the anaerobic degradation of isosaccharinic acid from cellulosic materials incubated within an anthropogenic, hyperalkaline environment

Anthropogenic hyperalkaline sites provide an environment that is analogous to proposed cementitious geological disposal facilities (GDF) for radioactive waste. Under anoxic, alkaline conditions cellulosic wastes will hydrolyze to a range of cellulose degradation products (CDP) dominated by isosaccharinic acids (ISA). In order to investigate the potential for microbial activity in a cementitious GDF, cellulose samples were incubated in the alkaline (∼pH 12), anaerobic zone of a lime kiln waste site. Following retrieval, these samples had undergone partial alkaline hydrolysis and were colonized by a Clostridia-dominated biofilm community, where hydrogenotrophic, alkaliphilic methanogens were also present. When these samples were used to establish an alkaline CDP fed microcosm, the community shifted away from Clostridia, methanogens became undetectable and a flocculate community dominated by Alishewanella sp. established. These flocs were composed of bacteria embedded in polysaccharides and proteins stabilized by extracellular DNA. This community was able to degrade all forms of ISA with >60% of the carbon flow being channelled into extracellular polymeric substance (EPS) production. This study demonstrated that alkaliphilic microbial communities can degrade the CDP associated with some radioactive waste disposal concepts at pH 11. These communities divert significant amounts of degradable carbon to EPS formation, suggesting that EPS has a central role in the protection of these communities from hyperalkaline conditions.

Evidence of the generation of isosaccharinic acids and their subsequent degradation by local microbial consortia within hyper-alkaline contaminated soils, with relevance to intermediate level radioactive waste disposal

The contamination of surface environments with hydroxide rich wastes leads to the formation of high pH (>11.0) soil profiles. One such site is a legacy lime works at Harpur Hill, Derbyshire where soil profile indicated in-situ pH values up to pH 12. Soil and porewater profiles around the site indicated clear evidence of the presence of the α and β stereoisomers of isosaccharinic acid (ISA) resulting from the anoxic, alkaline degradation of cellulosic material. ISAs are of particular interest with regards to the disposal of cellulosic materials contained within the intermediate level waste (ILW) inventory of the United Kingdom, where they may influence radionuclide mobility via complexation events occurring within a geological disposal facility (GDF) concept. The mixing of uncontaminated soils with the alkaline leachate of the site resulted in ISA generation, where the rate of generation in-situ is likely to be dependent upon the prevailing temperature of the soil. Microbial consortia present in the uncontaminated soil were capable of surviving conditions imposed by the alkaline leachate and demonstrated the ability to utilise ISAs as a carbon source. Leachate-contaminated soil was sub-cultured in a cellulose degradation product driven microcosm operating at pH 11, the consortia present were capable of the degradation of ISAs and the generation of methane from the resultant H2/CO2 produced from fermentation processes. Following microbial community analysis, fermentation processes appear to be predominated by Clostridia from the genus Alkaliphilus sp, with methanogenesis being attributed to Methanobacterium and Methanomassiliicoccus sp. The study is the first to identify the generation of ISA within an anthropogenic environment and advocates the notion that microbial activity within an ILW-GDF is likely to influence the impact of ISAs upon radionuclide migration.