Biotic Experiments Research Articles

Copper and zinc sulfides bioleaching by an extremely thermophilic archaeon in high NaCl concentration

Chloride bioleaching has received attention of several mineral processing industries, particularly in countries where there is scarcity of freshwater and only chloride-containing waters can be used. Therefore, the present work investigated the effect of NaCl (1.0 mol L−1) on the bioleaching of three sulfide minerals: chalcopyrite, bornite, and sphalerite by the thermophilic archaea Sulfolobus acidocaldarius. Chalcopyrite dissolution was only 25 % in the biotic experiment in the absence of chloride, but reached 90 % in the presence of both microorganisms and chloride, while less than 60 % extraction was observed in the abiotic experiment with chloride. In the experiments of bornite bioleaching, 86 % and 77 % of copper were extracted in the biotic and abiotic tests with chloride, respectively. In the absence of NaCl, the biotic and abiotic experiments presented similar copper dissolution (∼35 %). Finally, bioleaching experiments carried out with sphalerite showed zinc extractions below 35 % in all conditions tested. The main contribution from the archaea was its ability to produce low concentrations of ferric ion, which was partially precipitated as jarosite, resulting in low redox potential values (< 450 mV vs. Ag/AgCl), and efficiently bioleached bornite and chalcopyrite. Furthermore, XRD and SEM-EDS analyses demonstrated that sphalerite was practically not leached while bornite was transformed into new copper sulfide phases (CuS and Cu3FeS4). Jarosite and elemental sulfur were products of chalcopyrite and bornite bioleaching in the presence of chloride.

Antimony isotopic fractionation during Sb(III) oxidation to Sb(V): Biotic and abiotic processes

Oxidation of antimonite (Sb(III)) to antimonate (Sb(V)) plays an important role in the control of Sb mobility in aquatic systems. Fractionation of Sb isotopes (123Sb/121Sb) during Sb(III) oxidation has been investigated in the present study at concentrations relevant to mining environments. The isotopic composition (δ123Sb) of dissolved Sb(III) and Sb(V) species was analysed during biotic oxidation of Sb(III) at pH 6 and ∼ 0.1 mM Sb. Biotic experiments used a aioA gene carrier bacterial strain of the genus Ensifer isolated from Sb-rich river sediments. Chemical oxidation experiments with H2O2 were also conducted either in NaNO3 or HCl medium. During biotic oxidation, the Sb(V) produced was enriched in the light isotope compared to Sb(III), with an apparent fractionation factor Δ123SbSb(V)-Sb(III) of −0.20 ± 0.07 ‰. The Δ123Sb value was independent of the oxidation kinetics within the range 0.03 to 0.05 μmol.L−1.min−1; the fractionation observed was rather attributed to kinetic effect that weakens over time in the experiments, although this hypothesis would require further investigation. During abiotic experiments in NaNO3 medium, the Sb(V) produced was not isotopically fractionated relatively to Sb(III), while in HCl medium, the Sb(V) produced was enriched with the heavier isotope relatively to Sb(III), with a Rayleigh fractionation factor ε123Sb of +0.30 ± 0.05 ‰. These differences were attributed to different reaction pathways involving multi-step reactions and either hydroxy- or chloride-Sb species. Altogether, these results showed a low fractionation of Sb isotopes during Sb(III) oxidation, although significant variability occurred according to experimental conditions. Further experimental research and confrontation with natural systems is necessary before applying Sb isotopes as process tracer in water.

Contrasting effects of dissimilatory Fe(III)/As(V) reduction on arsenic mobilization of Al coprecipitated ferrihydrite in simulated groundwater

Arsenic pollution caused by dissimilatory As(V)/Fe(III)-reducing microorganisms in oxygen-starved sediments has aroused widespread concern. During the alternate redox cycles, precipitation and dissolution of iron (oxyhydr)-oxides often introduce various impurities, among which aluminum (Al) is the most prevalent one. Therefore, it is of great significance to devote some of our attention to the arsenic contamination induced by the bio-reduction of aluminum‑iron (oxyhydr)-oxides. In this study, we synthesized aluminum-ferrihydrite (AlFh) with Al/(Al + Fe) mol% of 0, 10, 20 and 30 successfully. After discussing the adsorption mechanism of arsenate by these materials, the biotic experiment with the presence of Shewanella oneidensis MR–1 (MR-1) or As(V) reducing bacteria Citrobacter sp. JH012–1 (JH012–1) were conducted. Our results suggested that the coprecipitated of Al inhibited the bio-reduction of Fe(III). In MR–1 incubation systems, due to the impaired Fe(III) reduction, As(V) release in the initial stage of Al coprecipitate Fh was inhibited. The released As(V) was then immobilized into the secondary mineral phases. In JH012–1 incubation systems the incorporated aluminum result in a higher degree of As dissolution and As(III) accounts for a relatively high proportion in the liquid phase. Spectroscopic analysis demonstrated that with the increase of Al content in AlFh, the relative proportions of surface As(III) were 63.53%, 58.60%, 54.91% and 50.35% respectively. The enhanced release of As in JH012–1 experiment was mainly ascribed to the poor adsorption capacity of As(III) on AlFh. These findings will help to complement the bio-migration behavior of As in natural aluminum‑iron (oxyhydr)-oxides.

Dynamics of gas distribution in batch-scale fermentation experiments: The unpredictive distribution of biogas between headspace and gas collection device

Biohydrogen potential of biodegradable samples is often evaluated with batch experiments, where gas collection devices (gasbags, syringes, water displacement units) are used for gas quantification and analysis. When calculating biohydrogen production rate and yield, the biogas distribution in headspace and gas collection devices is often assumed to be identical. For the first time, the effect of gas generation rate and headspace volume on gas distribution in these two locations was examined. Based on abiotic studies, a model for the biogas distribution was developed and experimentally validated. The results suggested a minimum 5% and a maximum 30% difference in biogas concentration between headspace and gas collection unit when the volume of biogas produced was between 0.1 and 20 times the headspace volume. The maximum difference (ca. 30%) was detected when volume of biogas production reached 1.6 times the volume of headspace. While a precise difference was evident with abiotic experiments, such a predictable difference was not observed with biotic experiments due to the dynamic nature of biological systems. Given this difference of biogas measurements between headspace and gas collection device was largely ignored in past research, the purity of produced biohydrogen reported in some literature remains notably inaccurate, specifically when concentrations reported were derived only with a measurement of biogas in either headspace or gas collection device. Further, this error in measurement in batch experiments carried out by industry to examine biogas potential, gas quality assurance and quality control has also likely negatively impacted industry operations, industry insights, strategic decision making, and regulatory compliance. This error in biogas measurement in batch experiments can be rectified by considering the biogas composition in both headspace and gas collection device.

Impact of a Mn-oxidizing bacterial strain on the dissolution and browning of a Mn-bearing potash-lime silicate glass

This work aims to investigate the role played by a model Mn-oxidizing bacterial strain and its exudates on the alteration of Mn-bearing potash-lime silicate glasses representative of medieval stained glass windows. Two model glasses, with or without manganese, were prepared and used for abiotic and Pseudomonas putida inoculated dissolution experiments. Results show that the presence of P. putida slows down the dissolution kinetics while changing the dissolution stoichiometry. In biotic experiments, the acidification of the solution at the beginning of the experiment favors the release of K. After a few days, a drop in Mn and P in solution is observed, retained by bacterial cells. Reciprocally, the amount of glass influences bacterial behavior. The more glass, the faster the bacterial population increases in size and produces siderophore. In the presence of the Mn-bearing glass, siderophore production is followed by the formation of brown phases, identified as Mn oxides.

Alternating direction of catholyte forced flow-through 3D-electrodes improves start-up time in microbial electrosynthesis at applied high current density

Microbial electrosynthesis is an uprising concept for the combined carbon dioxide reduction and electricity storage in the form of green chemical compounds. Although several proof of principle studies show great promise, mass-transfer limitations of substrates, protons and products remains one of the issues that needs to be addressed to bring the systems towards greater scale applications. A previously tested solution formed force flow-through catholyte recirculation, but this set-up encountered difficulties with gas accumulation during start-up at higher current densities (∼ −10 kA/m3), creating the need for a bypass to release gas. In this study, start-up at high current density was achieved without a bypass by using an alternating flow-through regime. This regime decreased the operating energy input from 221 to 136 kWh per kg of produced hydrogen and reached acetate production within 10 days after start-up at high current density and elongation to n-caproate after 45 days. Mass-transfer studies were included by microsensor measurements of local conditions (hydrogen concentration, pH) combined with thermodynamic calculations at the start and end of 60-days biotic experiments. The microorganisms on the cathode decreased pH gradients and consumed the formed hydrogen. The presence of Clostridium sensu stricto 12 and Peptococcaceae species were related to chain elongation activity, and the presence of Methanobrevibacter was linked to methanogenesis activity. By identifying the effects of different flow-through strategies on local concentrations and functional microbial groups, this work provides insights on the optimal conditions for microbial CO2 conversion and highlight the application potential of microbial electrosynthesis.

Hydrobiological Mechanism Controlling the Synergistic Effects of Unsaturated Flow and Soil Organic Matter on the Degradation of Emerging Organic Contaminants in Soils.

Hydrology is a key factor influencing microbial degradation of emerging organic contaminants (EOCs) in soils, but the underlying mechanisms are not clear. In this study, biotic and abiotic column experiments were performed to investigate the removal and degradation of five EOCs in soils with different soil organic matter (SOM) contents under saturated and unsaturated flow conditions. In biotic experiments, 54-90% of bisphenol A (BPA) and 9-22% of ibuprofen (IBU) were removed from the aqueous phase of saturated columns due to adsorption and biodegradation. The biodegradation removed 26-65% of BPA and 1-22% of IBU. Decreasing soil pore water saturation from 100 to 80% increased BPA removal to 97-100% and IBU removal to 42-43% due to increased biodegradation (67-81% for BPA and 36-39% for IBU). No significant removal of BPA and IBU was observed in SOM-removed soils under saturated and unsaturated flow conditions. The desaturation did not influence sorptive losses of BPA (<27%) and IBU (<7%), suggesting their negligible adsorption at air-water interfaces but increased biodegradation of BPA and IBU sorbed at SOM-water interfaces. The study shows that soil drying and SOM can synergistically degrade BPA and IBU but have no effect on recalcitrant carbamazepine, tetracycline, and ciprofloxacin.

Magnesium isotope fractionation during carbonate precipitation associated with bacteria and extracellular polymeric substances

Magnesium (Mg) is abundant on Earth's surface aquatic environments and plays an important role during the precipitation of biogenic CaCO3 minerals. Moreover, Mg isotopes are increasingly used to study a number of bio-induced mineralization processes of calcite. In this study, Mg isotope signatures during calcite and aragonite precipitation in the presence of Curvibacter sp. HJ-1 and of their extracellular polymeric substances (EPS) were investigated and the evolution of mineralogical and liquid composition were tracked over time. The results showed that light Mg isotopes were preferentially incorporated into the precipitated solids in all the experiments with and without bacteria. Significant Mg isotope fractionation was associated with the transformation of amorphous calcium carbonate (ACC) to crystal carbonate (Δ26Mgcrystals-ACC = −0.9‰ and −0.7‰ in biotic and EPS experiments, respectively), and obvious Mg isotope fractionation was noted between solids and liquid (Δ26Mgsolid-liquid achieved −2.2‰ and −2.0‰ in biotic and EPS experiments, respectively). Besides, δ26Mg values were significantly correlated with pH, Mg content in liquid and solid, bacterial density and presence of EPS in biotic experiments. These findings indicated that strain HJ-1 had an effect on Mg isotope fractionation during calcite and aragonite precipitation. The difference in Mg isotope fractionation may be a new tool for understanding the biologically mediated effects on Mg-bearing carbonate precipitation, and serves as a useful alternative for aqueous Mg isotope, which is vital for reconstructing past environmental changes.

The Catalytic Effect of the Heterotrophic Bacterium Virgibacillus marismortui on Basaltic Rock Dissolution Under Excess Nutrient Conditions

Biotic and abiotic batch experiments were performed in the presence of excess nutrients (N and P) and basaltic rocks in the medium under various conditions (NA, non-agitated; A, agitated). Changes in solution chemistry were monitored to characterize the influence of aerobic heterotrophic bacteria (Virgibacillus marismortui) on the dissolution rates and mechanisms of two basaltic rocks collected from King George (BAn; basaltic andesine) and Deception Island (BD, basalt), Antarctica. The presence of bacteria in the medium accelerated dissolution of basaltic rocks by a factor of 1.5 to 3 depending on both the rock composition and experimental conditions. The calculated linear element release rates in the biotic experiments (B, biotic) are enhanced in comparison with abiotic systems (A, abiotic) in the order: BD-B-NA > BD-B-A > BAn-B-NA. Unlike the abiotic reference experiments (BD-A-NA; BD-A-A, BAn-A-NA) with pH shifts of less than 0.5 units an accelerated release of Si, Ca, Mg, Fe and Al coincided with an increase in protein concentrations and a marked decrease in pH in the biotic experiments. As indicated by solution acidity, element release, trends of the reactive fluids and surface chemistry of the reacted rock samples, the catalytic effect of bacteria on mineral dissolution reactions was predominantly acidification due to bacterial metabolism. The major catalytic effect of acidification on mineral dissolution was likely suppressed by ammonification, resulting in a pH increase in the reactive fluid. The absence of secondary phases (e.g. Fe and Al oxyhydroxides) on the surface of biotically reacted rock particles and the presence of divalent cations (i.e. Ca and Mg) on the cell surfaces further show the role of the bacteria and associated organic ligands for metal-complexation reactions during basalt dissolution. This study shows that aerobic heterotrophic bacteria may play a critical role for acidity driven silicate dissolution in environments rich in nitrogenated organic compounds and may even influence the amount of Ca and Mg being released from Ca and Mg rich silicates to environments.

Stable Fe isotope fractionation during dissimilatory Fe(III) reduction by a thermoacidophile in acidic hydrothermal environments

Dissimilatory iron reduction (DIR) plays an essential role in biogeochemical Fe cycling in anoxic environments. At near-neutral pH, in both biotic and abiotic systems, aqueous Fe(II) (Fe(II)aq) interacts with reactive ferric (hydr)oxides via electron transfer and atom exchange that is catalyzed by large amounts of sorbed Fe(II). This may result in substantial Fe isotope exchange, which, at equilibrium, produces up to a ∼4‰ 56Fe/54Fe fractionation between coexisting oxide/hydroxide and Fe(II)aq, depending on mineralogy. The role of biology in such systems has been interpreted to lie in the production of Fe(II) rather than a specific “vital” effect, such as enzymatic and kinetic processes. Under acidic abiotic conditions, however, the lack of sorbed Fe(II) generates little Fe isotope exchange, and, by extension, it has been expected that little exchange would occur during DIR at low pH if sorbed Fe(II) is the key component for catalyzing isotopic exchange.In this study, we explored the extent and mechanism of Fe isotope exchange between Fe(II)aq and ferric hydroxides (ferrihydrite and goethite), including determination of the 56Fe/54Fe fractionations during DIR by Acidianus strain DS80 at pH ∼ 3.0 and 80 °C, over 19 days of incubation. Significant Fe(III) reduction occurred for both minerals along with large changes in Fe isotope compositions for Fe(II)aq, indicating Fe isotope exchange. Solid-phase extractions using HCl confirmed a lack of sorbed Fe(II), which suggests that a mechanism other than sorption is required to catalyze Fe isotope exchange during DIR at low pH. Reactive Fe(III) (Fe(III)reac) extracted from the mineral surface allowed for the calculation of the Fe pools that underwent isotopic exchange. A total of ∼20% of goethite and ∼60% of ferrihydrite underwent isotopic exchange over 19 days. For goethite from biotic experiments, we calculate a Fe(III)reac-Fe(II)aq fractionation factor of 1.57 ± 0.52‰, which is larger than the abiotic equilibrium fractionation factor (∼0.73‰ at 80 °C). This result is consistent with previous work on DIR of goethite at neutral pH, where a fractionation factor larger than equilibrium was interpreted to reflect an isotopically distinct “distorted surface layer” of goethite produced during exchange with Fe(II)aq. In contrast to goethite, the difference between the Fe(III)reac-Fe(II)aq fractionation factor for ferrihydrite from our biotic reactors (2.91 ± 0.40‰) and the abiotic equilibrium fractionation factor (∼2.28‰ at 80 °C, under silica-free conditions) is smaller.Ultimately, the contrast in the extent of Fe isotope exchange between biotic and abiotic experiments emphasizes the importance of biology in promoting Fe isotope exchange in acidic systems. We speculate that the unique role of biology at low pH in catalyzing Fe isotope exchange, not seen in equivalent abiotic systems, must lie in the transport of electrons to the ferric hydroxide surface that produces Fe(II) atoms in situ. This suggests that isotopic exchange occurs on an atom-by-atom basis as Fe(III) is reduced to Fe(II), followed by the release of Fe(II) into solution. This study demonstrates that significant variations in Fe isotope compositions may be uniquely produced in acidic environments where microbial Fe cycling occurs via DIR, compared to minor isotopic variations observed previously in acidic abiotic systems.

Effect of common bean (Phaseolus vulgaris) on apatite weathering under elevated CO2

Plants accelerate chemical weathering of minerals through the production of carbonic acid during root respiration, root exudation, and uptake of ions. These plant processes are increased by elevated concentrations of atmospheric CO2 and may in turn affect mineral weathering. We seek to understand the effect of predicted atmospheric CO2 concentrations on plant-mediated soil mineral weathering. Phaseolus vulgaris (common bean) was grown in flow-through microcosms consisting of a mixture of 85% quartz and 15% apatite sands (by weight). Nutrient release from apatite was measured using plants grown under two atmospheric conditions: ambient CO2 (~400 ppm) and elevated CO2 (~1000 ppm). To sustain plant growth, a nutrient solution without calcium (Ca) or phosphorous (P) was supplied to the plants using peristaltic pumps. Unplanted microcosms receiving the same nutrient solution served as abiotic controls in both CO2 treatments. Using atomic absorption spectroscopy and colorimetry, Ca and P concentrations of the leachate and plant tissue were measured as proxies for apatite dissolution. Plants were harvested every 2 weeks during the 8-week experiment to understand how Ca and P release in the two CO2 treatments changed over time. After 8 weeks, P. vulgaris grown in elevated CO2 had a greater root to shoot ratio than plants grown in ambient CO2. Plants grown in elevated CO2 released more P than plants grown in ambient conditions, possibly due to greater demands for mineral nutrients. P was preferentially released by the plants and there were no significant differences in Ca released by plants. Both elevated and ambient planted microcosms had a lower pH than abiotic controls, likely due to root respiration, nutrient uptake and exudation of organic acids. Organic acids were not identified in the leachate likely due to their low concentrations and rapid breakdown. Plants released as much as 7 times more Ca than abiotic controls, regardless of CO2 concentrations. Biotic experiments released over 200 times more P than abiotic experiments. Our results show increased atmospheric CO2 can determine rhizosphere processes, which in turn affect weathering products. Thus, mineral nutrient fluxes and C sequestration in inorganic pools are likely to increase as CO2 concentrations rise.

The influence of metal mobility on resource potential in circumneutral pH iron-rich copper mine waste rocks

Waste rocks from iron-oxide copper-gold (IOCG) deposits are dominated by Fe-bearing silicates and oxides, with only minor sulphides and potentially no pyrite. Hence, waste rock piles typically have circumneutral pH. However, oxidation of minor sulphides and Fe-bearing minerals can cause localised acidification at the mineral grain scale, especially where Fe oxidation and ferrihydrite precipitation is facilitated by bacteria. This study characterises the general biogeochemical system of waste rock piles at the Salobo IOCG mine, Brazil using a combination of biotic and abiotic leaching experiments on typical, weakly mineralised rocks, and observations of mineralogical changes and associated metal mobility in incipiently weathered, Cu-bearing overburden. Biotic experiments used a strain of the Fe- and S-oxidising Acidithiobacillus ferrooxidans subsp. cultured from the Salobo mine site. Most of the acid generated during oxidation of Salobo rocks is neutralised by alteration of labile Fe-silicates, particularly biotite, chlorite, olivine and amphiboles. Copper in our laboratory experiments was mobilised into solution (up to 1000 mg/l) from disseminated Cu-sulphide minerals during this acidification, and re-precipitated nearby (on the m-scale) within the rock mass during neutralisation. Much of this Cu precipitated with the abundant ferrihydrite, with some Cu precipitating locally with Mn-oxides, suggesting that secondary ferrihydrite and Mn-oxides represent possible exploration targets associated with comparable near-surface, weathered targets. Primary microparticulate gold was found encapsulated in magnetite and Cu-sulphides, with the sulphide-bearing portion of gold liberated during oxidation. Magnetite only demonstrated minor alteration (μm-scale) during short-term acidic oxidation (months). All these alteration processes are expected to occur within the waste piles during storage at the site, and could enhance the metallurgical leachability of these low-grade rocks for future re-processing. In the meantime, the lack of large-scale acidification, and adsorption of mobilised trace metals to the abundant ferrihydrite will ensure that the waste rocks remain environmentally benign.

How the rock-inhabiting fungus K. petricola A95 enhances olivine dissolution through attachment

Free-living and mycorrhizal fungi are able to enhance the weathering of rock and other solid substrates. Deciphering the exact mechanisms of these natural processes requires their experimental simulation. Moreover, by performing these simulations with genetically amenable rock-weathering fungi, one can knock-out certain fungal traits and consequently identify their weathering-relevant function. Here, the effect of the rock-inhabiting fungus, Knufia petricola A95, on the dissolution kinetics of an Fe-bearing olivine (Mg1.86Fe0.19SiO4) is investigated at 25 °C and pH 6 using reproducible batch and mixed flow experiments. The availability of a melanin-deficient mutant (ΔKppks) of K. petricola A95, which produces more extracellular polymeric substances (EPS) than the wild type (WT), enables the comparative study of the role of melanin and EPS in olivine dissolution. In abiotic dissolution experiments, the olivine dissolution rate decreased considerably over time at pH 6 but not at pH 3.5. This inhibition of abiotic olivine dissolution at pH 6 was most likely caused by the in-situ oxidation of ferrous Fe and/or the precipitation of ferric hydroxides at the olivine surface. In corresponding biotic experiments at pH 6, both the wild type K. petricola and its melanin-deficient mutant ΔKppks solubilised and bound significant amounts of Fe released by olivine dissolution. Fe oxidation and precipitation were thus prevented and olivine dissolution proceeded faster than in the abiotic experiments. By sequestering Fe directly at the olivine surface, the attached wild type K. petricola cells were particularly efficient at preventing the oxidation of Fe at the mineral surface: the slowdown of olivine dissolution almost completely disappeared. The attachment capacity of these wild type cells is most likely mediated by wild type-specific EPS. Our presented experimental systems allow the oxidation of mineral-released Fe and include a rock-inhabiting fungus, thus simulating chemical, physical and biological conditions that set dissolution rates in a way that is relevant to natural ecosystems.

Mechanism of microbial dissolution and oxidation of antimony in stibnite under ambient conditions

In this study, we demonstrate that a bacterial isolate Paraccocus versutus XT0.6 from the Xikuangshan antimony mine, the world largest antimony deposit, is capable of stibnite dissolution, oxidation of Sb(III), and formation of secondary Sb(V) bearing mineral. The isolate could oxidize dissolved Sb(III) aerobically and anaerobically. It was able to dissolve Sb(III) in solid minerals, which was subsequently oxidized to Sb(V) completely. Part of Sb(V) was scavenged by the formation of secondary Sb(V)-bearing mineral mopungite [NaSb(OH)6] in the biotic experiments. In contrast, Sb(III) released from mineral/rocks was only partially oxidized to Sb(V) and no secondary Sb-bearing mineral was formed in abiotic controls. These results demonstrated that microbial processes involved in the mobilization, oxidation, and transformation of antimony in minerals/rocks under ambient environmental conditions and offer new insights in biogeochemistry of Sb at mining areas.

Amount of Escape Estimation Based on Bayesian and MCMC Approaches for RNA Interference

The amount of short interfering RNA (siRNA) escaping from the endosome has a significant impact on the efficiency of RNAi. In general, the initial injected amount of siRNAs during the experiment is known, and also the amount of siRNAs after the experiment can be revealed by the level of mRNA measured. However, it is impossible to measure the amount of siRNAs that escape from the endosome and really take part in the chemical reaction of RNAi by detecting the biological organism and its tissues. Inspired by the bottleneck effect in the virus, we introduce the Bayesian approach to infer the amount of escape based on a single type and multiple types of siRNA, respectively. With the consideration of the large calculation quantity of the accurate posterior distribution and the unavailable analytic expression of the likelihood function, our article proposes to take samples by the improved Markov chain Monte Carlo (MCMC) method. The article takes the silencing gene of the synthesis of chitin and the interfering multiple target oncogene as numerical examples to show that our improved MCMC method has higher operation efficiency compared to the Bayesian approach. Our research models siRNA endosome escape using statistical methods for the first time. It perhaps provides a theoretical basis to decrease the cost of a biotic experiment for the future and the standardized statistical approaches for the amount of escape estimation.

Biosafety of cadmium contaminated sediments after treated by indigenous sulfate reducing bacteria: Based on biotic experiments and DGT technique

Sulfate reducing bacteria (SRB) biostabilization has attracted particular attention due to its ability to prevent and control heavy metal pollution. In this study, biotic experiments (immobilisation test of Daphnia (D.) magna, germination experiment of cucumber seeds, and in vitro experiment using gut juices of Sipunculus (S.) nudus) and diffusive gradients in thin films (DGT) technique were performed to investigate the biosafety of cadmium (Cd) contaminated sediments after being treated by indigenous SRB. Results showed that SRB treatment reduced Cd bioaccessibility of sediment to S. nudus, Cd levels in the overlying water and Cd bioavailability to D. magna. However, the treatment increased the biotoxicity of overlying water due to significant reduction in the root length and germination index of cucumber seeds. DGT results confirmed that SRB treatment increased Cd stability in sediment, and reduced its release from the sediment into the overlying water. The biotoxicity of overlying water was not caused by Cd, but possibly by the added culture medium, SRB itself, or its metabolites. More attention is required to assess the safety of SRB treatment when it is used to remediate environmental matrix contaminated by heavy metals.

Mechanisms of olivine dissolution by rock-inhabiting fungi explored using magnesium stable isotopes

To unravel the dissolution mechanisms of olivine by a rock-inhabiting fungus we determined the stable isotope ratios of Mg on solutions released in a laboratory experiment. We found that in the presence of the fungus Knufia petricola the olivine dissolution rates were about seven-fold higher (1.04 × 10−15 mol cm−2 s−1) than those in the abiotic experiments (1.43 × 10−16 mol cm−2 s−1) conducted under the same experimental condition (pH 6, 25 °C, 94 days). Measured element concentrations and Mg isotope ratios in the supernatant solutions in both the biotic and the abiotic experiment followed a dissolution trend in the initial phase of the experiment, characterized by non-stoichiometric release of Mg and Si and preferential release of 24Mg over 26Mg. In a later phase, the data indicates stoichiometric release of Mg and Si, as well as isotopically congruent Mg release. We attribute the initial non-stoichiometric phase to the rapid replacement of Mg2+ in the olivine with H+ along with simultaneous polymerization of Si tetrahedra, resulting in high dissolution rates, and the stoichiometric phase to be influenced by the accumulation of a Si-rich amorphous layer that slowed olivine dissolution. We attribute the accelerated dissolution of olivine during the biotic experiment to physical attachment of K. petricola to the Si-rich amorphous layer of olivine which potentially results in its direct exposure to protons released by the fungal cells. These additional protons can diffuse through the Si-rich amorphous layer into the crystalline olivine. Our results also indicate the ability of K. petricola to dissolve Fe precipitates in the Si-rich amorphous layer either by protonation, or by Fe(III) chelation with siderophores. Such dissolution of Fe precipitates increases the porosity of the Si-rich amorphous layer and hence enhances olivine dissolution. The acceleration of mineral dissolution in the presence of a rock-dissolving fungus further suggests that its presence in surficial CO2 sequestration plants may aid to accelerate CO2 binding.

Mass Transfer Limitation during Slow Anaerobic Biodegradation of 2-Methylnaphthalene.

While they are theoretically conceptualized to restrict biodegradation of organic contaminants, bioavailability limitations are challenging to observe directly. Here we explore the onset of mass transfer limitations during slow biodegradation of the polycyclic aromatic hydrocarbon 2-methylnaphthalene (2-MN) by the anaerobic, sulfate-reducing strain NaphS2. Carbon and hydrogen compound specific isotope fractionation was pronounced at high aqueous 2-MN concentrations (60 μM) (εcarbon = -2.1 ± 0.1‰/εhydrogen = -40 ± 7‰) in the absence of an oil phase but became significantly smaller (εcarbon = -0.9 ± 0.3‰/εhydrogen = -6 ± 3‰) or nondetectable when low aqueous concentrations (4 μM versus 0.5 μM) were in equilibrium with 80 or 10 mM 2-MN in hexadecane, respectively. This masking of isotope fractionation directly evidenced mass transfer limitations at (sub)micromolar substrate concentrations. Remarkably, oil-water mass transfer coefficients were 60-90 times greater in biotic experiments than in the absence of bacteria (korg-aq2-MN = 0.01 ± 0.003 cm h-1). The ability of isotope fractionation to identify mass transfer limitations may help study how microorganisms adapt and navigate at the brink of bioavailability at low concentrations. For field surveys our results imply that, at trace concentrations, the absence of isotope fractionation does not necessarily indicate the absence of biodegradation.

Increased Mg release rates and related Mg isotopic signatures during bacteria-phlogopite interactions

Phlogopite weathering experiments were carried out under aerobic conditions in a closed system to study Mg isotopic fractionation during the dissolution and processes involved in the presence of bacterial strains. Four different bacterial strains with different metabolisms were chosen. Biotic experiments were performed in batch reactors at 24 °C for 12 days. In parallel, abiotic phlogopite weathering experiments were also performed using organic and nitric acids. Citric and gluconic acids were used to model the effects of chelating agents produced by bacteria, and nitric acid was used to model the effects of acidifying agents. The results indicate that both decreases in pH and the production of metabolites during heterotrophic bacterial activities significantly accelerate the release of Mg and Si in solution. Also, at a given pH, the fraction of elements released in solution is greater in the presence of bacteria or citric acid compared to that released in the presence of nitric and gluconic acids. Magnesium isotopic analyses indicate that the solutions obtained using nitric acid and acidifying bacterial strains display, on average, δ26Mg values that are close to or slightly heavier (by 0.4‰) than those of fresh phlogopite (−1.2‰ ± 0.08). In contrast, in experiments performed with citric acid, the Mg leached into solution is slightly enriched in light isotopes by −0.3‰ relative to the initial phlogopite, while its binding to organics is expected to be related to its preferential enrichment in heavy isotopes. Despite its small range of variations, the δ26Mg values of solutions vary inversely with pH, thus suggesting that secondary phases preferentially enriched in 26Mg at the highest pH values may play a key role.

Isotopic fractionation associated to nitrate attenuation by ferrous iron containing minerals

Biotic and abiotic laboratory experiments of nitrate and nitrite reduction by Fe-containing minerals were performed and the isotopic fractionation of the different reactions was calculated in order to determine whether it is possible to distinguish biotic and abiotic reactions involving N compounds. Results of biotic experiments showed nitrate reduction up to 96 % with transient NO2- accumulation and no significant N2O production. No significant nitrate attenuation was observed in abiotic nitrate reduction experiments. Abiotic experiments of nitrite reduction showed a rapid decrease in nitrite concentrations in those experiments with added Fe2+ coupled with a significant N2O production. Preliminary results of the N and O isotopic fractionation of the biotic experiments of nitrate reduction show differences in the ε15NNO3 and ε18ONO3 when different minerals were added. The abiotic experiments of nitrite reduction contrarily, showed similar ε15NNO2 in all the experiments.