Differential degradation of petroleum hydrocarbons by Shewanella putrefaciens under aerobic and anaerobic conditions.

The complexity of crude oil composition, combined with the fluctuating oxygen level in contaminated environments, poses challenges for the bioremediation of oil pollutants, because of compound-specific microbial degradation of petroleum hydrocarbons under certain conditions. As a result, facultative bacteria capable of breaking down petroleum hydrocarbons under both aerobic and anaerobic conditions are presumably effective, however, this hypothesis has not been directly tested. In the current investigation, Shewanella putrefaciens CN32, a facultative anaerobic bacterium, was used to degrade petroleum hydrocarbons aerobically (using O2 as an electron acceptor) and anaerobically (using Fe(III) as an electron acceptor). Under aerobic conditions, CN32 degraded more saturates (65.65 ± 0.01%) than aromatics (43.86 ± 0.03%), with the following order of degradation: dibenzofurans > n-alkanes > biphenyls > fluorenes > naphthalenes > alkylcyclohexanes > dibenzothiophenes > phenanthrenes. In contrast, under anaerobic conditions, CN32 exhibited a higher degradation of aromatics (53.94 ± 0.02%) than saturates (23.36 ± 0.01%), with the following order of degradation: dibenzofurans > fluorenes > biphenyls > naphthalenes > dibenzothiophenes > phenanthrenes > n-alkanes > alkylcyclohexanes. The upregulation of 4-hydroxy-3-polyprenylbenzoate decarboxylase (ubiD), which plays a crucial role in breaking down resistant aromatic compounds, was correlated with the anaerobic degradation of aromatics. At the molecular level, CN32 exhibited a higher efficiency in degrading n-alkanes with low and high carbon numbers relative to those with medium carbon chain lengths. In addition, the degradation of polycyclic aromatic hydrocarbons (PAHs) under both aerobic and anaerobic conditions became increasingly difficult with increased numbers of benzene rings and methyl groups. This study offers a potential solution for the development of targeted remediation of pollutants under oscillating redox conditions.

Mineral-Bound Trace Metals as Cofactors for Anaerobic Biological Nitrogen Fixation.

Nitrogenase is the only known biological enzyme capable of reducing N2 to bioavailable NH3. Most nitrogenases use Mo as a metallocofactor, while alternative cofactors V and Fe are also viable. Both geological and bioinformatic evidence suggest an ancient origin of Mo-based nitrogenase in the Archean, despite the low concentration of dissolved Mo in the Archean oceans. This apparent paradox would be resolvable if mineral-bound Mo were bioavailable for nitrogen fixation by ancient diazotrophs. In this study, the bioavailability of mineral-bound Mo, V, and Fe was determined by incubating an obligately anaerobic diazotroph Clostridium kluyveri with Mo-, V-, and Fe-bearing minerals (molybdenite, cavansite, and ferrihydrite, respectively) and basalt under diazotrophic conditions. The results showed that C. kluyveri utilized mineral-associated metals to express nitrogenase genes and fix nitrogen, as measured by the reverse transcription quantitative polymerase chain reaction and acetylene reduction assay, respectively. C. kluyveri secreted chelating molecules to extract metals from the minerals. As a result of microbial weathering, mineral surface chemistry significantly changed, likely due to surface coating by microbial exudates for metal extraction. These results provide important support for the ancient origin of Mo-based nitrogenase, with profound implications for coevolution of the biosphere and geosphere.

Inhibition of Extracellular Enzyme Activity by Reactive Oxygen Species upon Oxygenation of Reduced Iron-Bearing Minerals.

The dual roles of minerals in inhibiting and prolonging extracellular enzyme activity in soils and sediments are governed by enzyme adsorption to mineral surfaces. Oxygenation of mineral-bound Fe(II) generates reactive oxygen species (ROS), yet it is unknown whether and how this process alters the activity and functional lifespan of extracellular enzymes. Here, the effect of mineral-bound Fe(II) oxidation on the hydrolytic activity of a cellulose-degrading enzyme ß-glucosidase (BG) was studied using two pre-reduced Fe-bearing clay minerals (nontronite and montmorillonite) and one pre-reduced iron oxide (magnetite) at pH 5 and 7. Under anoxic conditions, BG adsorption to mineral surfaces decreased its activity but prolonged its lifespan. Under oxic conditions, ROS was produced, with the amount of •OH, the most abundant ROS, being positively correlated with the extent of structural Fe(II) oxidation in reduced minerals. •OH decreased BG activity and shortened its lifespan via conformational change and structural decomposition of BG. These results suggest that under oxic conditions, the ROS-induced inhibitory role of Fe(II)-bearing minerals outweighed their adsorption-induced protective role in controlling enzyme activity. These results disclose a previously unknown mechanism of extracellular enzyme inactivation, which have pivotal implications for predicting the active enzyme pool in redox-oscillating environments.

Facile fabrication of flexible AuNPs@CDA SERS substrate for enrichment and detection of thiram pesticide in water.

Pesticide residues in water is one of the most serious problems in developing countries. Surface enhanced Raman spectroscopy (SERS) is widely used in the detection and monitoring of pesticide and other trace compounds because of its low limits of detection (LODs). However, different SERS substrate synthesis methods have different economic benefits and environmental impacts. In this paper, a flexible AuNPs@CDA SERS substrate was fabricated by the gold nanoparticles (AuNPs) and the biomass-based cellulose diacetate (CDA), which had stable test performance and considerable LODs. The substrates were economically viable and environment friendly. The characterization analysis of the substrate allows us to flexibly select different test methods (drop-test or enrichment-test) as coping strategy in different situation. The results showed that the LODs of thiram pesticide in water by enrichment-test could reach 10-7 g/mL, and had a good linear relationship in the concentration range of 10-7-10-6 g/mL. This strategy can realize the rapid and effective detection and monitoring of thiram pesticide in water.

A critical review of mineral-microbe interaction and co-evolution: mechanisms and applications.

Mineral-microbe interactions play important roles in environmental change, biogeochemical cycling of elements and formation of ore deposits. Minerals provide both beneficial (physical and chemical protection, nutrients, and energy) and detrimental (toxic substances and oxidative pressure) effects to microbes, resulting in mineral-specific microbial colonization. Microbes impact dissolution, transformation and precipitation of minerals through their activity, resulting in either genetically controlled or metabolism-induced biomineralization. Through these interactions, minerals and microbes co-evolve through Earth history. Mineral-microbe interactions typically occur at microscopic scale but the effect is often manifested at global scale. Despite advances achieved through decades of research, major questions remain. Four areas are identified for future research: integrating mineral and microbial ecology, establishing mineral biosignatures, linking laboratory mechanistic investigation to field observation, and manipulating mineral-microbe interactions for the benefit of humankind.

Cr(VI) Reduction by Siderophore Alone and in Combination with Reduced Clay Minerals.

Siderophores and iron-containing clays are known to influence the transformation of chromium in the environment. The role of clays in hexavalent chromium [Cr(VI)] reduction has been reported extensively. However, the mechanisms of Cr(VI) reduction by siderophores and their combination with iron-bearing clays are poorly known. Herein, we report the kinetics and products of Cr(VI) reduction by a siderophore alone or in combination with reduced clays. Results showed that Cr(VI) reduction by a tri-hydroxamate siderophore─desferrioxamine B (DFOB)─at a pH of 6 was achieved by one-electron transfer via the formation of Cr(V) intermediate. The formed Cr(V) was further reduced to organically complexed Cr(III). The Cr(VI) reduction rate and extent in the presence of both DFOB and reduced clays unexpectedly decreased relative to that with reduced clays alone, despite both serving as Cr(VI) reductants. The interaction between DFOB and clays (e.g., adsorption/intercalation, dissolution, and/or oxidation) was primarily responsible for Cr(VI) reduction inhibition. The extent of inhibition increased at higher DFOB concentrations in the presence of iron-rich nontronite but decreased in the presence of iron-poor montmorillonite, which may be related to their different Cr(VI) reduction mechanisms. This study highlights the importance of siderophores in chromium transformation and its impact on the reactivity of iron-bearing clays toward heavy metal reduction in the environment.

Synthesis and Characterization of Corn Stover-Based Cellulose Triacetate Catalyzed by Ionic Liquid Phosphotungstate.

Cellulose triacetate (CTA) was successfully synthesized from corn stover cellulose (CSC) in the presence of [PyPS]3PW12O40 (IL-POM). The effects of IL-POM contents, reaction temperature, and reaction time on the yield and degree of substitution of CTA were investigated. The synthesized CTA was characterized by SEM, FTIR, and TGA, and the degree of polymerization and solubility in various organic solvents were evaluated. Results showed that the optimum reaction conditions were as follows: 0.04 g of IL-POM, reaction temperature of 140 °C, and reaction time of 45 min, for 0.4 g of CSC and 9 mL of glacial acetic acid. The yield of CTA under optimum reaction conditions was as high as 79.27%, and the degree of substitution was 2.95. SEM and FTIR results showed that the cellulose acetylation occurred, and CTA was synthesized. The TGA results revealed that the decomposition temperature of CTA increased by about 30 °C when compared with that of CSC. A simple, environment-friendly, and efficient process for the preparation of CTA from CSC was constructed, which provides a new pathway for the high-value utilization of corn stover.

Combined Effects of Fe(III)-Bearing Nontronite and Organic Ligands on Biogenic U(IV) Oxidation.

Bioreduction of soluble U(VI) to sparingly soluble U(IV) solids was proposed as a remediation method for uranium contamination. Therefore, the stability and longevity of biogenic U(IV) are critical to the success of uranium remediation. However, co-occurrence of clay minerals and organic ligands could potentially reoxidize U(IV) to U(VI). Herein, we report a combined effect of Fe(III)-rich nontronite (NAu-2) and environmentally prevalent organic ligands on reoxidation of biogenic U(IV) at circumneutral pH. After 30 days of incubation, structural Fe(III) in NAu-2 oxidized 45.50% U(IV) with an initial rate of 2.7 × 10-3 mol m-2 d-1. Addition of citrate and ethylenediaminetetraacetic acid (EDTA) greatly promoted the oxidative dissolution of U(IV) by structural Fe(III) in NAu-2, primarily through the formation of aqueous ligand-U(IV) complexes. In contrast, a model siderophore, desferrioxamine B (DFOB), partially inhibited U(IV) oxidation due to the formation of stable DFOB-Fe3+ complexes. The resulting U(VI) species intercalated into an NAu-2 interlayer or adsorbed onto an NAu-2 surface. Our results highlight the importance of organic ligands in oxidative dissolution of U(IV) minerals by Fe(III)-bearing clay minerals and have important implications for the design of nuclear waste storage and remediation strategies, especially in clay- and organic-rich environments.

Antibacterial Mechanisms of Reduced Iron-Containing Smectite-Illite Clay Minerals.

Reduced nontronite has been demonstrated to be antibacterial through the production of hydroxyl radical (•OH) from the oxidation of structural Fe(II). Herein, we investigated the antibacterial activity of more common smectite-illite (S-I) clays toward Escherichia coli cells, including montmorillonite SWy-3, illite IMt-2, 50-50 S-I rectorite RAr-1, 30-70 S-I ISCz-1, and nontronite NAu-2. Under an oxic condition, reduced clays (with a prefix r before mineral names) produced reactive oxygen species (ROS), and the antibacterial activity followed the order of rRAr-1 > rSWy-3 ≥ rNAu-2 ≫ rIMt-2 ≥ rISCz-1. The strongest antibacterial activity of rRAr-1 was contributed by a combination of •OH and Fe(IV) generated from structural Fe(II)/adsorbed Fe2+ and soluble Fe2+, respectively. Higher levels of lipid and protein oxidation, intracellular ROS accumulation, and membrane disruption were consistent with this antibacterial mechanism of rRAr-1. The antibacterial activity of other S-I clays depended on layer expandability, which determined the reactivity of structural Fe(II) and the production of •OH, with the expandable smectite being the most antibacterial and nonexpandable illite the least. Our results provide new insights into the antibacterial mechanisms of clay minerals.

Minerals Determined a Special Ecological Niche and Selectively Enriched Microbial Species from Bulk Water Communities in Hot Springs.

Minerals provide physical niches and supply nutrients or serve as electron donors/acceptors for microorganism survival and growth, and thus minerals and microbes co-evolved. Yet, little is known about how sediment minerals impact microbial community assembly in hot springs and to what extent mineralogical composition influences microbial community composition and diversity. Here the influences of minerals on thermophiles in Tengchong hot springs were revealed by network analysis of field samples, as well as in-situ microcosm experiments with minerals. A molecular ecological network was constructed based on high throughput sequencing data of 16S rRNA gene, with a combination of water geochemistry and sedimentary mineralogical compositions. Six modules were identified and this highly modular network structure represents the microbial preference to different abiotic factors, consequently resulting in niche partitioning in sedimentary communities in hot springs. Diverse mineralogical compositions generated special niches for microbial species. Subsequently, the in-situ microcosm experiments with four minerals (aragonite, albite, K-feldspar, and quartz) and spring water were conducted in a silicate-hosted alkaline spring (i.e., Gmq) and a carbonate-hosted neutral hot spring (i.e., Gxs) for 70 days. Different microbial preferences were observed among different mineral types (carbonate versus silicate). Aragonite microcosms in Gmq spring enriched archaeal genera Sulfophobococcus and Aeropyrum within the order Desulfurococcales by comparison with both in-situ water and silicate microcosms. Sulfophobococcus was also accumulated in Gxs aragonite microcosms, but the contribution to overall dissimilarity is much lower than that in Gmq spring. Besides, Caldimicrobium was a bacterial genus enriched in Gxs aragonite microcosms, in contrast to in-situ water and silicate microcosms, whereas Candidatus Kryptobacter and Thermus were more abundant in silicate microcosms. The differences in microbial accumulations among different mineral types in the same spring implied that mineral chemistry may exert extra deterministic selective pressure in drawing certain species from the bulk water communities, in addition to stochastic absorption on mineral surface. Taken together, our results highlight the special niche partitioning determined by mineralogical compositions and further confirm that minerals could be used as "fishing bait" to enrich certain rare microbial species.

Nylon membranes modified by gold nanoparticles as surface-enhanced Raman spectroscopy substrates for several pesticides detection.

Surface enhanced Raman spectroscopy (SERS) is an attractive means for trace compound detection because of its high sensitivity, however, the poor reproducibility is a major challenge. Herein, we propose a facile SERS strategy employing the several developed test processes to improve the repeatability of the SERS analysis based on regular nylon membranes as substrates to detect trace compounds. Various methods, including in situ reduction, immersion adsorption, and filtration, were first compared to prepare composite substrates using nylon membranes and gold nanoparticles. The substrates prepared by filtration showed the best test parallelism (RSD = 7.85%). Its limit of detection (LOD) could reach 10-8 g mL-1 with a good linear relationship in the range 10-8 to 10-7 g mL-1. Finally, three pesticide solutions were tested to verify the substrate applicability. A superior LOD of 10-8 g mL-1 was observed for thiram, whereas the LODs of both phorate and benthiocarb could reach 10-6 g mL-1. Overall, modifying nylon membrane substrates with gold nanoparticles improves the repeatability and economic viability of SERS and favors its wider commercial application for detecting trace compounds.

Contrasting seasonal variations of geochemistry and microbial community in two adjacent acid mine drainage lakes in Anhui Province, China.

Acid mine drainage (AMD) is generated by the bio-oxidation of sulfide minerals. To understand the AMD formation and evolution, it is necessary to determine the composition and variation of acidophilic community, and their role in AMD ecosystem. In this study, we compared seasonal variations of geochemistry and microbial composition of two adjacent AMD lakes with different formation histories in Anhui Province, China. Lake Paitu (PT) formed in 1970s near a mine dump and the pH was in the range of 3.01-3.16, with the lowest in spring and summer while the highest in winter. The main ions in PT were Al and SO42-, whereas Fe concentration was relatively low. The concentrations of these ions were the lowest in summer and the highest in winter. Lake Tafang (TF) formed in around 2013 in a pit was more acidic (pH 2.43-2.75), but the seasonal variation of pH was the same as PT. Compared with Lake PT, TF had higher Fe, lower Al and SO42- concentrations, and showed no significant seasonal changes. Despite salient seasonal variations of prokaryotic composition in Lake PT, Ferrovum was the major iron-oxidizing bacterium in most seasons. Furthermore, Lake PT was also rich in heterotrophic bacteria (48.6 ± 15.9%). Both prokaryotic diversity and evenness of Lake TF were lower than PT, and chemolithotrophic iron-oxidizing bacteria (71.7 ± 25.4%) were dominant in almost all samples. Besides Ferrovum, more acid tolerant iron-oxidizer Leptospirillum and Acidithiobacillus were also abundant in Lake TF. Chlamydomonas was the major eukaryote in Lake PT and it flourished repeatedly at the end of December, causing an extremely high chlorophyll a concentration (587 µg/L) at one sampling site in 2016, which provided rich nutrients for heterotrophic bacteria. The main alga in Lake TF was Chrysonebula, but its concentration was low, apparently because of the strong acidity and dark red color of lake water.

Promotion of Microbial Oxidation of Structural Fe(II) in Nontronite by Oxalate and NTA.

Iron redox cycling occurs extensively in soils and sediments. Previous research has focused on microbially mediated redox cycling of aqueous Fe. At circumneutral pH, most Fe occurs in solid phase, where Fe and organic ligands interact closely. However, the role of organic ligands in microbial oxidation of solid-phase Fe(II) is not well understood. Here, we incubated reduced nontronite NAu-2 (rNAu-2) with an iron-oxidizing bacterium and in the presence of oxalate and nitrilotriacetic acid. These ligands significantly enhanced the rate and extent of microbial oxidation of structural Fe(II) in rNAu-2. Aqueous and solid-phase analyses, coupled with biogeochemical modeling, revealed a pathway for ligand-enhanced bio-oxidation of solid-phase Fe(II): (1) dissolution of rNAu-2 to form aqueous Fe(II)-ligand complex; (2) bio-oxidation to Fe(III)-ligand complex; (3) rapid reduction of Fe(III)-ligand complex to Fe(II)-ligand complex by structural Fe(II) in rNAu-2. In this process, the Fe(II)-ligand and Fe(III)-ligand complexes effectively serve as electron shuttle to expand the bioavailable pool of solid-phase Fe(II). These results have important implications for a better understanding of the bioavailability and reactivity of solid-phase Fe pool in the environment.

Mechanisms of Enhanced Antibacterial Activity by Reduced Chitosan-Intercalated Nontronite.

Previous studies have documented the antibacterial activity of certain iron-containing clays. However, the repulsion between negatively charged bacteria and the clay surface makes this process inefficient. The objective of this study is to improve the bactericidal efficiency of clays by reversing their surface charge from negative to positive. To achieve this objective, positively charged chitosan, a nontoxic and biodegradable polymer, was intercalated into nontronite NAu-2. Chitosan-intercalated NAu-2 (C-NAu-2) was chemically reduced to obtain reduced C-NAu-2 (rC-NAu-2). Relative to reduced nontronite (rNAu-2), the antibacterial activity of rC-NAu-2 is higher and more persistent over a pH range of 6-8. The close spatial association between positively charged rC-NAu-2 and negatively charged bacteria increases the chances of cell membrane attack by extracellular ROS, the influx of soluble Fe2+ into the bacterial cell, and the yield of intracellular ROS. All these factors contribute to the enhanced antibacterial activity of rC-NAu-2. In contrast to rNAu-2 treated E. coli cells, where membrane damage and intracellular ROS/Fe accumulation are restricted to the polar regions, the close bacteria-clay association in rC-NAu-2 results in nonselective membrane damage and more uniform intracellular ROS/Fe distribution across whole bacterial cells. These results advance the antibacterial model by highlighting the importance of bacteria-clay interactions to the antibacterial activity of Fe-bearing clays.