Phylogenetic and physiological diversity of dissimilatory ferric iron reducers in sediments of the polluted Scheldt estuary, Northwest Europe

Enhancement of hydrogenotrophic methanogenesis for methane production by nano zero-valent iron in soils

Nanoscale zero-valent iron (nZVI) is attracting increasing attention as the most commonly used environmental remediation material. However, given the high surface area and strong reducing capabilities of nZVI, there is a lack of understanding regarding its effects on the complex anaerobic methane production process in flooded soils. To elucidate the mechanism of CH4 production in soil exposed to nZVI, paddy soil was collected and subjected to anaerobic culture under continuous flooding conditions, with various dosages of nZVI applied. The results showed that the introduction of nZVI into anaerobic flooded rice paddy systems promoted microbial utilization of acetate and carbon dioxide as carbon sources for methane production, ultimately leading to increased methane production. Following the introduction of nZVI into the soil, there was a rapid increase in hydrogen levels in the headspace, surpassing that of the control group. The hydrogen levels in both the experimental and control groups were depleted by the 29th day of culture. These findings suggest that nZVI exposure facilitates the enrichment of hydrogenotrophic methanogens, providing them with a favorable environment for growth. Additionally, it affected soil physicochemical properties by increasing pH and electrical conductivity. The metagenomic analysis further indicates that under exposure to nZVI, hydrogenotrophic methanogens, particularly Methanobacteriaceae and Methanocellaceae, were enriched. The relative abundance of genes such as mcrA and mcrB associated with methane production was increased. This study provides important theoretical insights into the response of key microbes, functional genes, and methane production pathways to nZVI during anaerobic methane production in rice paddy soils, offering fundamental insights into the long-term fate and risks associated with the introduction of nZVI into soils.

Root exudates increased arsenic mobility and altered microbial community in paddy soils

Root exudates are crucial for plants returning organic matter to soils, which is assumed to be a major source of carbon for the soil microbial community. This study investigated the influence of root exudates on the fate of arsenic (As) with a lab simulation experiment. Our findings suggested that root exudates had a dose effect on the soil physicochemical properties, As speciation transformation and the microbial community structure at different concentrations. The addition of root exudates increased the soil pH while decreased the soil redox potential (Eh). These changes in the soil pH and Eh increased As and ferrous (Fe(II)) concentrations in soil porewater. Results showed that 40 mg/L exudates addition significantly increased arsenite (As(III)) and arsenate (As(V)) by 541 and 10 times respectively within 30 days in soil porewater. The relative abundance of Fe(III)-reducing bacteria Geobacter and Anaeromyxobacter increased with the addition of root exudates, which enhanced microbial Fe reduction. Together these results suggest that investigating how root exudates affect the mobility and transformation of As in paddy soils is helpful to systematically understand the biogeochemical cycle of As in soil-rice system, which is of great significance for reducing the health risk of soil As contamination.

Insight into the structure and metabolic function of iron-rich nanoparticles in anammox bacteria

Anaerobic ammonium-oxidizing (anammox) bacteria are iron abundant and depend heavily on iron-binding proteins. The iron demand of anammox bacteria is relatively large. However, it still remains some doubts where these large quantities of available iron come from and how they are regulated in anammox bacteria. Herein, iron-rich nanoparticles in anammoxosomes were detected by synchrotron soft X-ray tomography coupled with scanning transmission X-ray microscopy (STXM). The iron-rich nanoparticles were identified as ferric oxide (α-Fe₂O₃) mineral cores, and the local atomic structure of iron-rich nanoparticles was obtained by X-ray absorption fine-structure (XAFS) spectra. The bacterioferritin of Q1Q315 and Q1Q5F8 were detected by proteomics analysis. On this basis, the metabolic pathway centered on iron-rich nanoparticles was proposed.

A novel mechanism study of microplastic and As co-contamination on indica rice (Oryza sativa L.)

Although the compound pollution of microplastics and arsenic (As) in paddy soil can affect the growth and quality of rice, relevant research on this phenomenon was limited. Therefore, we combined a pot experiment with computational chemistry to explore the effects and mechanism of polystyrene (PSMP) and polytetrafluoroethylene (PTFE) microplastics on As bioavailability. PSMP and PTFE interacted with rice root exudates through van der Waals forces, approached the rice root system, inhibited root activity, reduced the relative abundance of Geobacteria and Anaeromyxobacter, and consequently reduced the iron plaques on the root surfaces. Consequently, As uptake by the rice was inhibited. PSMP and PTFE reduced the hemoglobin content by directly destroying its tertiary structure, thereby retarding rice growth. In contrast, As increased the hemoglobin content by inducing reactive oxygen species in rice. Under the influence of PSMP, PTFE, and As, the activities of soluble starch synthase and pyrophosphorylase in rice grains were inhibited, and starch accumulation decreased. Thus, PSMP, PTFE, and As reduced rice biomass and yield owing to their physiological toxicity and adverse impacts on root activity. Grain yields in soil with an As content of 86.3 mg·kg^-1, 0.5% small particle-sized PSMP, and 0.5% small particle-sized PTFE decreased by 30.7%, 20.6%, and 19.4%, respectively, compared to the control. This study determined the comprehensive mechanism through which PSMP and PTFE affect As bioavailability, which is critical for managing rice biomass and low yields in As and microplastic co-contaminated soil.

Stabilization of cadmium in contaminated sediment based on a nanoremediation strategy: Environmental impacts and mechanisms

Nanomaterials have great application potential for the remediation of heavy metal contaminated sediments, but their environmental impacts are still limited. Herein, graphene oxide-supported nanoscale zero-valent iron (GNZVI) was synthesized to explore its role in mediating the immobilization of cadmium (Cd) from contaminated river sediments, with the consideration of the potential impacts on sediment enzyme activities and bacterial community. Compared to NZVI and GO, GNZVI could more effectively promote the transformation of mobile Cd into stable speciation with a maximum residual percentage increasing by 64.82% after 56 days of treatment. The activities of urease, catalase and sucrase were gradually increased and stabilized with the prolongation of treatment time, indicating that the metabolic function of sediments was recovered. 16 S rRNA gene sequencing results confirmed that the application of GNZVI increased the abundance of some Fe(III)-reducing bacteria, further stimulating the bioavailability of organic matter. Additionally, the properties of GO were gradually changed via microbial reduction and finally showed similar properties to rGO. The critical role of rGO as an electrical conductor was to promote the electron transfer process of microbial Fe(III) mineral reduction, which redistributes part of the Fe(III) mineral-associated Cd to more stable secondary iron minerals, thereby further improving the stabilization efficiency of r-GNZVI for Cd.

Characterization of tissue-associated bacterial community of two Bathymodiolus species from the adjacent cold seep and hydrothermal vent environments

Deep-sea mussels are widely distributed in marine chemosynthetic ecosystems. Bathymodiolus platifrons and B. japonicus, occurring at both cold seeps and hydrothermal vents, have been reported to house exclusively methanotrophic symbionts in the gill. However, the comparison of microbiota associated with different tissues between these two species from two contrasting habitats is still limited. In this study, using B. platifrons and B. japonicus collected from the adjacent cold seep and hydrothermal vent environments, we sampled different tissues (gill, adductor muscle, mantle, foot, and visceral mass including the gut) to decipher the microbial community structure at the tissue scale by employing 16S rRNA gene sequencing strategy. In the gill of both seep mussels and vent mussels, the symbiont gammaproteobacterial Methylomonaceae was the predominant lineage, and methane oxidation was identified as one of the most abundant putative function. In comparison, abundant families in other tissues were Pseudomonadaceae and Enterobacteriaceae in seep mussels and vent mussels, respectively, which may get involved in element cycling. The results revealed high similarity of community structure between two mussel species from the same habitat. The gill showed distinctive bacterial community structure compared with other tissues within the same environment, while the gill communities from two environments were more similar. Remarkably structural variations of adductor muscle, mantle, foot, and visceral mass were observed between two environments. This study can extend the understanding on the characteristics of tissue-associated microbiota of deep-sea mussels from the adjacent cold seep and hydrothermal vent environments.

Iron and total organic carbon shape the spatial distribution pattern of sediment Fe(III) reducing bacteria in a volcanic lake, NE China

Fe(III) reducing bacteria (FeRB) play a vital role in the biogeochemical cycle of Fe, C and N in nature. The volcanic lake can be considered as an ideal habitat for FeRB. Here, we investigated the diversity and spatial distribution of FeRB in sediments of Wenbo lake in Wudalianchi volcano based on culture-dependent and independent methods. A total of 28 isolates affiliated with the genera of Enterobacter, Bacillus, Pseudomonas and Clostridium were obtained from 18 sediment samples. We detected 783 operational taxonomic units (OTUs) belonged to FeRB using high high-throughput sequencing, and the dominant phyla were Proteobacteria (3.65%), Acidobacteria (0.29%), Firmicutes (10.78%). The representative FeRB genera such as Geobacter, Pseudomonas, Thiobacillus and Acinetobacter distributed widely in Wenbo lake. Results showed that the diversity and abundance of FeRB declined along the water-flow direction from Libo to Jingbo. In contrast, the FeRB diversity decreased and the FeRB abundance increased along with depth transect of sediments. It was found that the dominant phylum changed from Firmicutes to Proteobacteria along the water-flow direction, while changed from Proteobacteria to Firmicutes along with the depth of sediments. RDA indicated that the FeRB distribution were driven by soluble total iron, total organic carbon, Fe(II) and Fe(III). These will provide information for understanding the role of FeRB in the elements geochemical cycles in the volcanic environment.

Inhibition effects of long-term calcium-magnesia phosphate fertilizer application on Cd uptake in rice: Regulation of the iron-nitrogen coupling cycle driven by the soil microbial community

Cadmium (Cd) pollution in paddy soil seriously endangers food safety production. To investigate the effects and microbiological mechanisms of calcium-magnesium-phosphate (CMP) fertilizer application on Cd reduction in rice, field experiments were conducted in Cd-contaminated paddy soil. Compared with conventional compound fertilizer, CMP fertilizer treatments inhibited Cd uptake through plant roots, significantly decreasing Cd content in rice grains from 0.340 to 0.062 mg/kg. Soil pH and total Ca, Mg and P contents increased after CMP fertilizer application, resulting in a further decrease in soil available Cd content from 0.246 to 0.181 mg/kg. Specific extraction analysis recorded a decrease in both available Fe content and the ratio of nitrate to ammonium nitrogen, indicating that the soil Fe-N cycle was affected by the addition of CMP fertilizer. This finding was also recorded using soil bacterial community sequencing, with CMP fertilizer promoting the progress of nitrate-dependent Fe-oxidation driven by Thiobacillus (1.60-2.83%) and subsequent dissimilatory nitrate reduction to ammonium (DNRA) driven by Ignavibacteriae (1.01-1.92%); Fe-reduction driven by Anaeromyxobacter (3.09-2.23%) was also inhibited. Our results indicate that CMP fertilizer application regulates the Fe-N coupling cycle driven by the soil microbial community to benefit remediation of Cd contaminated paddy soil.

Electricity production and microbial community in psychrophilic microbial fuel cells at 10 °C

Psychrophilic microbial fuel cell (PMFC) offers an alternative method for low temperature wastewater treatment, but is seldom reported. In this study, the two-chamber PMFC was constructed at 10 °C using acetate as an electron donor. The maximum voltage under external resistance of 1000 Ω was around 550 mV. The columbic efficiency (CE) was 82.4% under external resistance of 100 Ω and the max power density was 582.4 mW/m². After temperature decreasing to 4 °C, the maximum voltage also reached 530 mV and CE was 38.4%. The direct electron transfer was proposed in PMFC according to cyclic voltammetry curves. The short enriching time (~30 days) of biofilm in the anodic electrode may be due to the high activity of enriched novel exoelectrogens of M. fermentans (46.2%) and E. lemanii (15.4%). The development of PMFC involved biotechnologies in low temperature regions shall benefit for valuable chemicals production and energy generation in the future.

Remediation and its biological responses of Cd contaminated sediments using biochar and minerals with nanoscale zero-valent iron loading

Remediation of Cd pollution in sediments is crucial for the safety of aquatic environments and human health. In this study, four effective, common, and low-cost remediation materials (zeolite, sepiolite, red mud (RM), and biochar (BC)) loaded with nanoscale zero-valent iron (nZVI) and themselves were employed to immobilize Cd in sediments. The effects of different materials on sediment properties, immobilization effectiveness, bacterial communities, enzyme activities, and dissolved organic matter (DOM) were investigated. Results showed that sediment properties were significantly changed by the addition of immobilization materials (P < 0.05). The geochemical fraction analysis showed that the labile Cd was partially transformed to the stable fraction after immobilization, with an 11-47% decrease in the acid-soluble fraction and a 50-1000% increase in the residual fraction. The Cd immobilization effectiveness peaked at the nZVI/RM and nZVI/BC treatments, and the Cd toxicity characteristic leaching procedure (TCLP) leachabilities decreased by 42% and 44%, respectively. The modified materials were more effective for immobilizing Cd than the raw materials owing to the presence of nZVI, and the Cd TCLP leachabilities with the modified materials decreased by 15%-22% compared with the raw material treatments. Immobilization-driven reduction of bioavailable Cd enhanced the richness and diversity of bacterial communities and enzyme activities. Moreover, the immobilization treatment promoted the Fe(III)-reducing process by increasing the Fe(III)-reducing bacteria (e.g. Geobacteraceae, Bacillus, and Clostridium), which are conducive to Cd immobilization. Additionally, the DOM composition presented more autogenetic characteristics in treated groups. BC (nZVI/BC) can be selected as the priority material for Cd immobilization in sediments due to higher immobilization effectiveness and lower adverse effects on sediments.

Effects of disinfection efficiency on microbial communities and corrosion processes in drinking water distribution systems simulated with actual running conditions

The effects of disinfection efficiency on microbial communities and the corrosion of cast iron pipes in drinking water distribution systems (DWDSs) were studied. Two annular reactors (ARs) that simulated actual running conditions with UV/Cl₂ disinfection and chlorination alone were used. High chlorine consumption and corrosion rate were found in the AR with UV/Cl₂. According to functional genes and pyrosequencing tests, a high percentage of iron recycling bacteria was detected within the biofilm of the AR with Cl₂ at early running stage, whereas siderophore-producing bacteria were dominant in the biofilm of the AR with UV/Cl_2. At the early running stage, the sequential use of UV light and an initial high chlorine dosage suppressed the biomass and iron-recycling bacteria in both bulk water and biofilms, thereby forming less protective scales against further corrosion, which enhanced chlorine consumption. Non-metric multidimensional scaling analysis showed that the bacterial communities in the ARs shaped from within rather than being imported by influents. These results indicate that the initial high disinfection efficiency within the distribution system had not contributed to the accumulation of iron-recycling bacteria at the early running stages. This study offer certain implications for controlling corrosion and water quality in DWDSs.

Identification of potential electrotrophic microbial community in paddy soils by enrichment of microbial electrolysis cell biocathodes

Electrotrophs are microbes that can receive electrons directly from cathode in a microbial electrolysis cell (MEC). They not only participate in organic biosynthesis, but also be crucial in cathode-based bioremediation. However, little is known about the electrotrophic community in paddy soils. Here, the putative electrotrophs were enriched by cathodes of MECs constructed from five paddy soils with various properties using bicarbonate as an electron acceptor, and identified by 16S rRNA-gene based Illumina sequencing. The electrons were gradually consumed on the cathodes, and 25%-45% of which were recovered to reduce bicarbonate to acetic acid during MEC operation. Firmicutes was the dominant bacterial phylum on the cathodes, and Bacillus genus within this phylum was greatly enriched and was the most abundant population among the detected putative electrotrophs for almost all soils. Furthermore, several other members of Firmicutes and Proteobacteria may also participate in electrotrophic process in different soils. Soil pH, amorphous iron and electrical conductivity significantly influenced the putative electrotrophic bacterial community, which explained about 33.5% of the community structural variation. This study provides a basis for understanding the microbial diversity of putative electrotrophs in paddy soils, and highlights the importance of soil properties in shaping the community of putative electrotrophs.

Excessive input of phosphorus significantly affects microbial Fe(III) reduction in flooded paddy soils by changing the abundances and community structures of Clostridium and Geobacteraceae

Microbial Fe(III) reduction can make an excellent contribution to the bioremediation of contaminated environments and potentially reduce methanogenesis. Excessive input of phosphorus (P) by P fertilizer application and eutrophied irrigation water might have a substantial influence on the process of microbial Fe(III) reduction in flooded paddy soils. To evaluate the effect of P application on microbial Fe(III) reduction, the responses of Clostridium and Geobacteraceae communities to different concentrations of P addition (CK: 0mmolPkg^-1 soil; P1: 3.3mmolPkg^-1 soil; P2: 20mmolPkg^-1 soil) were investigated in anaerobically incubated paddy slurries. P addition significantly inhibited Fe(III) reduction during the early stage of incubation (from days 0 to 20). Compared with the CK treatment, the maximum Fe(III) reduction rate (V_max) in treatments P1 and P2 remarkably decreased by 0.281 and 0.439mg·g^-1·d^-1, respectively. However, the addition of P had no significant effect on Fe(III) reduction during the later stage of incubation (after 20days). The abundances of Clostridium and Geobacteraceae were suppressed by P addition, and the suppression effect was more obvious with higher P concentration. P addition significantly changed the community structures of Clostridium and Geobacteraceae during the entire incubation. The communities of Clostridium and Geobacteraceae were closely correlated with the process of Fe(III) reduction. In conclusion, P addition could inhibit the microbial reduction of Fe(III) during the early stage of incubation by reducing the abundances and altering the community structures of Clostridium and Geobacteraceae, however, the inhibition could be eliminated with increased incubation time. This study demonstrates that soil microbial communities are sensitive to excessive P application, which can jointly impact relevant biogeochemical processes in flooded paddy soils.

Changes in northern Gulf of Mexico sediment bacterial and archaeal communities exposed to hypoxia

Biogeochemical changes in marine sediments during coastal water hypoxia are well described, but less is known about underlying changes in microbial communities. Bacterial and archaeal communities in Louisiana continental shelf (LCS) hypoxic zone sediments were characterized by pyrosequencing 16S rRNA V4-region gene fragments obtained by PCR amplification of community genomic DNA with bacterial- or archaeal-specific primers. Duplicate LCS sediment cores collected during hypoxia had higher concentrations of Fe(II), and dissolved inorganic carbon, phosphate, and ammonium than cores collected when overlying water oxygen concentrations were normal. Pyrosequencing yielded 158,686 bacterial and 225,591 archaeal sequences from 20 sediment samples, representing five 2-cm depth intervals in the duplicate cores. Bacterial communities grouped by sampling date and sediment depth in a neighbor-joining analysis using Chao-Jaccard shared species values. Redundancy analysis indicated that variance in bacterial communities was mainly associated with differences in sediment chemistry between oxic and hypoxic water column conditions. Gammaproteobacteria (26.5%) were most prominent among bacterial sequences, followed by Firmicutes (9.6%), and Alphaproteobacteria (5.6%). Crenarchaeotal, thaumarchaeotal, and euryarchaeotal lineages accounted for 57%, 27%, and 16% of archaeal sequences, respectively. In Thaumarchaeota Marine Group I, sequences were 96-99% identical to the Nitrosopumilus maritimus SCM1 sequence, were highest in surficial sediments, and accounted for 31% of archaeal sequences when waters were normoxic vs. 13% of archaeal sequences when waters were hypoxic. Redundancy analysis showed Nitrosopumilus-related sequence abundance was correlated with high solid-phase Fe(III) concentrations, whereas most of the remaining archaeal clusters were not. In contrast, crenarchaeotal sequences were from phylogenetically diverse lineages, differed little in relative abundance between sampling times, and increased to high relative abundance with sediment depth. These results provide further evidence that marine sediment microbial community composition can be structured according to sediment chemistry and suggest the expansion of hypoxia in coastal waters may alter sediment microbial communities involved in carbon and nitrogen cycling.

Vertical distribution of Fe and Fe(III)-reducing bacteria in the sediments of Lake Donghu, China

In lake sediments, iron (Fe) is the most versatile element, and the redox cycling of Fe has a wide influence on the biogeochemical cycling of organic and inorganic substances. The aim of the present study was to analyze the vertical distribution of Fe and Fe(III)-reducing bacteria (FeRB) in the surface sediment (30 cm) of Lake Donghu, China. At the 3 sites we surveyed, FeRB and Fe(II)-oxidizing bacteria (FeOB) coexisted in anoxic sediments. Geobacter-related FeRB accounted for 5%-31% of the total Bacteria, while Gallionella-related FeOB accounted for only 0.1%-1.3%. A significant correlation between the relative abundance of poorly crystalline Fe and Geobacter spp. suggested that poorly crystalline Fe favored microbial Fe(III) reduction. Poorly crystalline Fe and Geobacter spp. were significantly associated with solid-phase Fe(II) and total inorganic phosphorus levels. Pore water Fe(II) concentrations negatively correlated with NO3(-) at all sites. We concluded that Geobacter spp. were abundant in the sediments of Lake Donghu, and the redox of Fe might participate in the cycling of nitrogen and phosphorus in sediments. These observations provided insight into the roles of microbial Fe cycling in lake sediments.

Microbially influenced corrosion communities associated with fuel-grade ethanol environments

Microbially influenced corrosion (MIC) is a costly problem that impacts hydrocarbon production and processing equipment, water distribution systems, ships, railcars, and other types of metallic infrastructure. In particular, MIC is known to cause considerable damage to hydrocarbon fuel infrastructure including production, transportation, and storage systems, often times with catastrophic environmental contamination results. As the production and use of alternative fuels such as fuel-grade ethanol (FGE) increase, it is important to consider MIC of engineered materials exposed to these “newer fuels” as they enter existing infrastructure. Reports of suspected MIC in systems handling FGE and water prompted an investigation of the microbial diversity associated with these environments. Small subunit ribosomal RNA gene pyrosequencing surveys indicate that acetic-acid-producing bacteria (Acetobacter spp. and Gluconacetobacter spp.) are prevalent in environments exposed to FGE and water. Other microbes previously implicated in corrosion, such as sulfate-reducing bacteria and methanogens, were also identified. In addition, acetic-acid-producing microbes and sulfate-reducing microbes were cultivated from sampled environments containing FGE and water. Results indicate that complex microbial communities form in these FGE environments and could cause significant MIC-related damage that may be difficult to control. How to better manage these microbial communities will be a defining aspect of improving mitigation of global infrastructure corrosion.

The Significance of Microbe-Mineral-Biomarker Interactions in the Detection of Life on Mars and Beyond

The detection of biomarkers plays a central role in our effort to establish whether there is, or was, life beyond Earth. In this review, we address the importance of considering mineralogy in relation to the selection of locations and biomarker detection methodologies with characteristics most promising for exploration. We review relevant mineral-biomarker and mineral-microbe interactions. The local mineralogy on a particular planet reflects its past and current environmental conditions and allows a habitability assessment by comparison with life under extreme conditions on Earth. The type of mineral significantly influences the potential abundances and types of biomarkers and microorganisms containing these biomarkers. The strong adsorptive power of some minerals aids in the preservation of biomarkers and may have been important in the origin of life. On the other hand, this strong adsorption as well as oxidizing properties of minerals can interfere with efficient extraction and detection of biomarkers. Differences in mechanisms of adsorption and in properties of minerals and biomarkers suggest that it will be difficult to design a single extraction procedure for a wide range of biomarkers. While on Mars samples can be used for direct detection of biomarkers such as nucleic acids, amino acids, and lipids, on other planetary bodies remote spectrometric detection of biosignatures has to be relied upon. The interpretation of spectral signatures of photosynthesis can also be affected by local mineralogy. We identify current gaps in our knowledge and indicate how they may be filled to improve the chances of detecting biomarkers on Mars and beyond.

Long-term nitrogen fertilization of paddy soil shifts iron-reducing microbial community revealed by RNA-(13)C-acetate probing coupled with pyrosequencing

Iron reduction is an important biogeochemical process in paddy soils, yet little is known about the microbial coupling between nitrogen and iron reduction. Here, we investigated the shift of acetate-metabolizing iron-reducers under long-term nitrogen fertilization using (13)C-acetate-based ribosomal RNA (rRNA)-stable isotope probing (SIP) and pyrosequencing in an incubation experiment, and the shift of putative iron-reducers in original field samples were investigated by 16S rRNA gene-based pyrosequencing. During SIP incubations, in the presence of iron(III) oxyhydroxides, more iron(II) formation and less methane production were detected in nitrogen-fertilized (N) compared with non-fertilized (NF) soil. In (13)C-rRNA from microcosms amended with ferrihydrite (FER), Geobacter spp. were the important active iron-reducers in both soils, and labeled to a greater extent in N (31% of the bacterial classified sequences) than NF soils (11%). Pyrosequencing of the total 16S rRNA transcripts from microcosms at the whole community level further revealed hitherto unknown metabolisms of potential FER reduction by microorganisms including Pseudomonas and Solibacillus spp. in N soil, Dechloromonas, Clostridium, Bacillus and Solibacillus spp. in NF soil. Goethite (GOE) amendment stimulated Geobacter spp. to a lesser extent in both soils compared with FER treatment. Pseudomonas spp. in the N soil and Clostridium spp. in the NF soil may also be involved in GOE reduction. Pyrosequencing results from field samples showed that Geobacter spp. were the most abundant putative iron-reducers in both soils, and significantly stimulated by long-term nitrogen fertilization. Overall, for the first time, we demonstrate that long-term nitrogen fertilization promotes iron(III) reduction and modulates iron-reducing bacterial community in paddy soils.

Interaction of microbial sulphate reduction and methanogenesis in oil sands tailings ponds

Anaerobic turnover of organic compounds in oil sands tailings ponds is accomplished by a complex microbial consortium. We examined major electron accepting processes in mature fine tailings (MFT). Beside methanogenesis and sulphate reduction, microbial iron reduction was an important process of anaerobic respiration. Microbial numbers and activity were comparable to those reported for natural lakes. To understand metabolic interactions of indigenous methanogenic and sulphate-reducing communities, we conducted a 6 month microcosm experiment with MFT supplemented with easily available carbon sources and molybdate and/or 2-bromoethane sulphonate (BES) as specific inhibitors for sulphate reduction and methanogenesis. Methanogenesis increased when microcosms were supplemented with extra carbon, but was completely inhibited by the addition of BES. Molybdate not only inhibited sulphate reduction, but also methanogenesis, indicating a positive relation between the two processes. The turnover of extra carbon sources differed between microcosms treated with molybdate and BES. Acetate and propionate were not consumed in microcosms amended with molybdate, indicating that sulphate-reducing bacteria (SRB) were responsible for their metabolisation, and that methane was rather produced by hydrogenotrophic methanogens. In microcosms without molybdate, acetate transiently accumulated, indicating the activity of both incomplete and complete oxidizing SRB. Ethanol and lactate were also consumed in the simultaneous presence of BES and molybdate, demonstrating the occurrence of other anaerobic processes. Biomass increased by the addition of extra carbon, mainly due to a relative increase in the proportion of SRB. The addition of extra carbon lowered the degradation of BTEX compounds.

Identification of key factors in Accelerated Low Water Corrosion through experimental simulation of tidal conditions: influence of stimulated indigenous microbiota

Biotic and abiotic factors favoring Accelerated Low Water Corrosion (ALWC) on harbor steel structures remain unclear warranting their study under controlled experimental tidal conditions. Initial stimulation of marine microbial consortia by a pulse of organic matter resulted in localized corrosion and the highest corrosion rates (up to 12-times higher than non-stimulated conditions) in the low water zone, persisting after nine months exposure to natural seawater. Correlations between corrosion severity and the abundance and composition of metabolically active sulfate-reducing bacteria (SRB) indicated the importance and persistence of specific bacterial populations in accelerated corrosion. One phylotype related to the electrogenic SRB Desulfopila corrodens appeared as the major causative agent of the accelerated corrosion. The similarity of bacterial populations related to sulfur and iron cycles, mineral and tuberculation with those identified in ALWC support the relevance of experimental simulation of tidal conditions in the management of steel corrosion exposed to harbor environments.

Fe(III) reduction during pyruvate fermentation by Desulfotomaculum reducens strain MI-1

Desulfotomaculum reducens MI-1 is a Gram-positive, sulfate-reducing bacterium also capable of reducing several metals, among which is Fe(III). Very limited knowledge is available on the potential mechanism(s) of metal reduction among Gram-positive bacteria, despite their preponderance in the microbial communities that inhabit some inhospitable environments (e.g., thermal or hyperthermal ecosystems, extreme pH or salinity environments, heavy metal or radionuclide contaminated sediments). Here, we show that in the presence of pyruvate, this micro-organism is capable of reducing both soluble Fe(III)-citrate and solid-phase hydrous ferric oxide, although growth is sustained by pyruvate fermentation rather than Fe(III) respiration. Despite the fact that Fe(III) reduction does not support direct energy conservation, D. reducens uses it as a complementary means of discarding excess reducing equivalent after H2 accumulation in the culture headspace renders proton reduction unfavorable. Thus, Fe(III) reduction permits the oxidation of greater amounts of pyruvate than fermentation alone. Fe(III) reduction by D. reducens is mediated by a soluble electron carrier, most likely riboflavin. Additionally, an intracellular electron storage molecule acts as a capacitor and accumulates electrons during pyruvate oxidation for slow release to Fe(III). The reductase responsible for the transfer of electrons from the capacitor to the soluble carrier has not been identified, but data presented here argue against the involvement of c-type cytochromes.

Microbial community dynamics during acetate biostimulation of RDX-contaminated groundwater

Biostimulation of groundwater microbial communities (e.g., with carbon sources) is a common approach to achieving in situ bioremediation of organic pollutants (e.g., explosives). We monitored a field-scale approach to remediate the explosive RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) in an aquifer near the Iowa Army Ammunition Plant in Middletown, IA. The purpose of the study was to gain insight into the effect of biostimulation on the microbial community. Biostimulation with acetate led to the onset of RDX reduction at the site, which was most apparent in monitoring well MW309. Based on previous laboratory experiments, we hypothesized that RDX degradation and metabolite production would correspond to enrichment of one or more Fe(III)-reducing bacterial species. Community DNA from MW309 was analyzed with 454 pyrosequencing and terminal restriction fragment length polymorphism. Production of RDX metabolites corresponded to a microbial community shift from primarily Fe(III)-reducing Betaproteobacteria to a community dominated by Fe(III)-reducing Deltaproteobacteria (Geobacteraceae in particular) and Bacteroidetes taxa. This data provides a firsthand field-scale microbial ecology context to in situ RDX bioremediation using modern sequencing techniques that will inform future biostimulation applications.

Analysis of the attached microbial community on mucilaginous cyanobacterial aggregates in the eutrophic Lake Taihu reveals the importance of Planctomycetes

The phylogenetic diversity of the microbial community assemblage of the carpet-like mucilaginous cyanobacterial blooms in the eutrophic Lake Taihu was investigated. 16S ribosomal DNA clone libraries produced from the DNA of cyanobacterial assemblages that had been washed to remove unattached bacteria contained only cyanobacteria. However, a further treatment which included grinding the freeze-dried material to physically detach cells followed by the removal of larger cells by filtration allowed us to detect a large variety of bacteria within the cyanobacterial bloom community. Interestingly, the dominant members of the microbial community were Planctomycetes followed by Cytophaga-Flavobacterium-Bacteroides (CFB), Betaproteobacteria, and Gammaproteobacteria. The analysis of the 16S ribosomal DNA clone libraries made from enrichment culture revealed much higher phylogenetic diversity of bacteria. Dominant bacterial groups in the enrichment system were identified as members of the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria subdivisions, CFB group, and Planctomycetes. In addition, the clone libraries constructed from Planctomycetes-specific 16S ribosomal RNA primers also verified that the enrichment allowed a diversity of Planctomycetes to proliferate, although the community composition was altered after enrichment.

Enriched Iron(III)-Reducing Bacterial Communities are Shaped by Carbon Substrate and Iron Oxide Mineralogy

Iron (Fe) oxides exist in a spectrum of structures in the environment, with ferrihydrite widely considered the most bioavailable phase. Yet, ferrihydrite is unstable and rapidly transforms to more crystalline Fe(III) oxides (e.g., goethite, hematite), which are poorly reduced by model dissimilatory Fe(III)-reducing microorganisms. This begs the question, what processes and microbial groups are responsible for reduction of crystalline Fe(III) oxides within sedimentary environments? Further, how do changes in Fe mineralogy shape oxide-hosted microbial populations? To address these questions, we conducted a large-scale cultivation effort using various Fe(III) oxides (ferrihydrite, goethite, hematite) and carbon substrates (glucose, lactate, acetate) along a dilution gradient to enrich for microbial populations capable of reducing Fe oxides spanning a wide range of crystallinities and reduction potentials. While carbon source was the most important variable shaping community composition within Fe(III)-reducing enrichments, both Fe oxide type and sediment dilution also had a substantial influence. For instance, with acetate as the carbon source, only ferrihydrite enrichments displayed a significant amount of Fe(III) reduction and the well-known dissimilatory metal reducer Geobacter sp. was the dominant organism enriched. In contrast, when glucose and lactate were provided, all three Fe oxides were reduced and reduction coincided with the presence of fermentative (e.g., Enterobacter spp.) and sulfate-reducing bacteria (e.g., Desulfovibrio spp.). Thus, changes in Fe oxide structure and resource availability may shift Fe(III)-reducing communities between dominantly metal-respiring to fermenting and/or sulfate-reducing organisms which are capable of reducing more recalcitrant Fe phases. These findings highlight the need for further targeted investigations into the composition and activity of speciation-directed metal-reducing populations within natural environments.

Screening of anaerobic activities in sediments of an acidic environment: Tinto River

The Tinto River (Huelva, Spain) is a natural acidic rock drainage environment produced by the bio-oxidation of metallic sulfides from the Iberian Pyritic Belt. A geomicrobiological model of the different microbial cycles operating in the sediments was recently developed through molecular biological methods, suggesting the presence of iron reducers, methanogens, nitrate reducers and hydrogen producers. In this study, we used a combination of molecular biological methods and targeted enrichment incubations to validate this model and prove the existence of those potential anaerobic activities in the acidic sediments of Tinto River. Methanogenic, sulfate-reducing, denitrifying and hydrogen-producing enrichments were all positive at pH between 5 and 7. Methanogenic enrichments revealed the presence of methanogenic archaea belonging to the genera Methanosarcina and Methanobrevibacter. Enrichments for sulfate-reducing microorganisms were dominated by Desulfotomaculum spp. Denitrifying enrichments showed a broad diversity of bacteria belonging to the genera Paenibacillus, Bacillus, Sedimentibacter, Lysinibacillus, Delftia, Alcaligenes, Clostridium and Desulfitobacterium. Hydrogen-producing enrichments were dominated by Clostridium spp. These enrichments confirm the presence of anaerobic activities in the acidic sediments of the Tinto River that are normally assumed to take place exclusively at neutral pH.

First prokaryotic biodiversity assessment using molecular techniques of an acidic river in Neuquén, Argentina

Two acidic hot springs close to the crater of Copahue Volcano (Neuquén, Argentina) are the source of the Río Agrio. The river runs several kilometres before flowing into Caviahue Lake. Along the river, temperature, iron, other metal and proton concentrations decrease gradually with distance downstream. From the source to the lake and depending on the season, pH can rise from 1.0 (or even less) to about 4.0, while temperature values decrease from 70°C to 15°C. Water samples were taken from different stations on the river selected according to their physicochemical parameters. In order to assess prokaryotic biodiversity throughout the water column, different and complementary molecular biology techniques were used, mainly in situ hybridisation and 16S rRNA gene cloning and sequencing. All microorganisms found are typical of acidic environments. Sulphur-oxidizing bacteria like Acidithiobacillus thiooxidans and Acidithiobacillus albertensis were detected in every station. Moderately thermophile iron- and sulphur-oxidizing bacteria like members of Alicyclobacillus and Sulfobacillus genera were also ubiquitous. Strict iron-oxidizing bacteria like Leptospirillum and Ferrimicrobium were present at the source of the river, but disappeared downstream where iron concentrations were much lower. Iron-oxidizing, mesophilic Ferroplasma spp. were the main archaea found. The data presented in this work represent the first molecular assessment of this rare natural acidic environment.

Prokaryotic communities and operating metabolisms in the surface and the permafrost of Deception Island (Antarctica)

In this study we examined the microbial community composition and operating metabolisms on the surface and in the permafrost of Deception Island, (Antarctica) with an on site antibody microarray biosensor. Samples (down to a depth of 4.2 m) were analysed with LDChip300 (Life Detector Chip), an immunosensor containing more than 300 antibodies targeted to bacterial and archaeal antigens. The immunograms showed positive antigen-antibody reactions in all surface samples (lichens, pyroclasts) and the top layer of the permafrost. The results indicated the presence of exopolysaccharides, bacteria belonging to the Alpha-, Delta- and Gammaproteobacteria, Bacteroidetes, Gram-positive Actinobacteria and Firmicutes, as well as archaeal species, most probably Methanobacterium spp. Positive reactions with antibodies to proteins and peptides revealed the presence of nitrogen fixation (NifHD, GlnB, HscA), methanogenic (McrB), iron homeostasis and iron scavenging (ferritins and DPS proteins) proteins, as well as ABC transporters, which indicated that these processes were operating at the time of sampling. These results were validated with other molecular ecology techniques such as oligonucleotide microarrays, 16S bacterial rRNA gene sequence analysis, aerobic viable counts and microscopy. Molecular ecology results showed a differentiated pattern along the depth of the drill, being the top active layer the most diverse, with Acidobacteria, Actinobacteria, Proteobacteria, Bacteroidetes and the phototrophs Cyanobacteria and Chloroflexi as dominant groups. Actinobacteria and Firmicutes were dominant in depths from 0.5 to 2 m, and Betaproteobacteria from 3 to 4.2 m. The geochemical analysis revealed the presence of low molecular weight organic acids (acetate, formate) which could be used by microorganisms as energy sources for sulfate, nitrate and metal reduction under anaerobic conditions.

Characterization of Metabolically Active Bacterial Populations in Subseafloor Nankai Trough Sediments above, within, and below the Sulfate-Methane Transition Zone

A remarkable number of microbial cells have been enumerated within subseafloor sediments, suggesting a biological impact on geochemical processes in the subseafloor habitat. However, the metabolically active fraction of these populations is largely uncharacterized. In this study, an RNA-based molecular approach was used to determine the diversity and community structure of metabolically active bacterial populations in the upper sedimentary formation of the Nankai Trough seismogenic zone. Samples used in this study were collected from the slope apron sediment overlying the accretionary prism at Site C0004 during the Integrated Ocean Drilling Program Expedition 316. The sediments represented microbial habitats above, within, and below the sulfate-methane transition zone (SMTZ), which was observed approximately 20 m below the seafloor (mbsf). Small subunit ribosomal RNA were extracted, quantified, amplified, and sequenced using high-throughput 454 pyrosequencing, indicating the occurrence of metabolically active bacterial populations to a depth of 57 mbsf. Transcript abundance and bacterial diversity decreased with increasing depth. The two communities below the SMTZ were similar at the phylum level, however only a 24% overlap was observed at the genus level. Active bacterial community composition was not confined to geochemically predicted redox stratification despite the deepest sample being more than 50 m below the oxic/anoxic interface. Genus-level classification suggested that the metabolically active subseafloor bacterial populations had similarities to previously cultured organisms. This allowed predictions of physiological potential, expanding understanding of the subseafloor microbial ecosystem. Unique community structures suggest very diverse active populations compared to previous DNA-based diversity estimates, providing more support for enhancing community characterizations using more advanced sequencing techniques.

Low temperature S(0) biomineralization at a supraglacial spring system in the Canadian High Arctic

Elemental sulfur (S(0) ) is deposited each summer onto surface ice at Borup Fiord pass on Ellesmere Island, Canada, when high concentrations of aqueous H(2) S are discharged from a supraglacial spring system. 16S rRNA gene clone libraries generated from sulfur deposits were dominated by β-Proteobacteria, particularly Ralstonia sp. Sulfur-cycling micro-organisms such as Thiomicrospira sp., and ε-Proteobacteria such as Sulfuricurvales and Sulfurovumales spp. were also abundant. Concurrent cultivation experiments isolated psychrophilic, sulfide-oxidizing consortia, which produce S(0) in opposing gradients of Na(2) S and oxygen. 16S rRNA gene analyses of sulfur precipitated in gradient tubes show stable sulfur-biomineralizing consortia dominated by Marinobacter sp. in association with Shewanella, Loktanella, Rubrobacter, Flavobacterium, and Sphingomonas spp. Organisms closely related to cultivars appear in environmental 16S rRNA clone libraries; none currently known to oxidize sulfide. Once consortia were simplified to Marinobacter and Flavobacteria spp. through dilution-to-extinction and agar removal, sulfur biomineralization continued. Shewanella, Loktanella, Sphingomonas, and Devosia spp. were also isolated on heterotrophic media, but none produced S(0) alone when reintroduced to Na(2) S gradient tubes. Tubes inoculated with a Marinobacter and Shewanella spp. co-culture did show sulfur biomineralization, suggesting that Marinobacter may be the key sulfide oxidizer in laboratory experiments. Light, florescence and scanning electron microscopy of mineral aggregates produced in Marinobacter experiments revealed abundant cells, with filaments and sheaths variably mineralized with extracellular submicron sulfur grains; similar biomineralization was not observed in abiotic controls. Detailed characterization of mineral products associated with low temperature microbial sulfur-cycling may provide biosignatures relevant to future exploration of Europa and Mars.

Heavy metal tolerance of Fe(III)-reducing microbial communities in contaminated creek bank soils

Fe(III)-reducing soil enrichment cultures can tolerate 100 μM Cu and Cd, 150 μM Co, 600 μM Ni, and 2,500 μM Zn. Metal-tolerant cultures were dominated by Geobacter-related Deltaproteobacteria and Gram-positive Firmicutes spp. (Clostridia and Sedimentibacter). A Cd- and Cu-tolerant Fe(III)-reducing coculture of Desulfosporosinus and Desulfitobacterium indicated the importance of the Firmicutes for Fe(III) reduction in the presence of metals.

Distribution and diversity of Gallionella-like neutrophilic iron oxidizers in a tidal freshwater marsh

Microbial iron oxidation is an integral part of the iron redox cycle in wetlands. Nonetheless, relatively little is known about the composition and ecology of iron-oxidizing communities in the soils and sediments of wetlands. In this study, sediment cores were collected across a freshwater tidal marsh in order to characterize the iron-oxidizing bacteria (FeOB) and to link their distributions to the geochemical properties of the sediments. We applied recently designed 16S rRNA primers targeting Gallionella-related FeOB by using a nested PCR-denaturing gradient gel electrophoresis (DGGE) approach combined with a novel quantitative PCR (qPCR) assay. Gallionella-related FeOB were detected in most of the samples. The diversity and abundance of the putative FeOB were generally higher in the upper 5 to 12 cm of sediment than in deeper sediment and higher in samples collected in April than in those collected in July and October. Oxygen supply by macrofauna appears to be a major force in controlling the spatial and temporal variations in FeOB communities. The higher abundance of Gallionella-related FeOB in April coincided with elevated concentrations of extractable Fe(III) in the sediments. Despite this coincidence, the distributions of FeOB did not exhibit a simple relationship to the redox zonation inferred from the geochemical depth profiles.

Electricity generation and microbial community response to substrate changes in microbial fuel cell

The effect of substrate changes on the performance and microbial community of two-chamber microbial fuel cells (MFCs) was investigated in this study. The MFCs enriched with a single substrate (e.g., acetate, glucose, or butyrate) had different acclimatization capability to substrate changes. The MFC enriched with glucose showed rapid and higher power generation, when glucose was switched with acetate or butyrate. However, the MFC enriched with acetate needed a longer adaptation time for utilizing glucose. Microbial community was also changed when the substrate was changed. Clostridium and Bacilli of phylum Firmicutes were detected in acetate-enriched MFCs after switching to glucose. By contrast, Firmicutes completely disappeared and Geobacter-like species were specifically enriched in glucose-enriched MFCs after feeding acetate to the reactor. This study further suggests that the type of substrate fed to MFC is a very important parameter for reactor performance and microbial community, and significantly affects power generation in MFCs.

Bio-reduction of Fe(III) ores using three pure strains of Aeromonas hydrophila, Serratia fonticola and Clostridium celerecrescens and a natural consortium

The present work describes a research approach to the anaerobic bioleaching of Fe(III) ores. Three strains (Serratia fonticola, Aeromonas hydrophila and Clostridium celerecrescens) isolated from an acidic abandoned mine were selected to test their ability to reduce dissimilatory Fe(III). Total iron bio-reduction was achieved after 48 h using either the consortium or the Aeromonas cultures. In the latter case, there was no evidence of precipitates and Fe(II) remained in solution at neutral pH through complex formation with citrate. None of the other cultures tested (mixed culture and the two isolates) exhibited this behaviour. Biotechnologically, this is a very promising result since it obviates the problem associated with undesirable precipitation of iron compounds in Fe(III)-reducing bacterial cultures. The performance of the Aeromonas culture was improved progressively by adaptation to moderately acidic pH values (up to 4.5) and to three different Fe(III)-oxyhydroxides as the sole source of iron: ferrihydrite, hematite and jarosite, commonly found as weathering compounds at mine sites. Dissimilatory Fe(III)-reducers for iron extraction from ores is therefore especially attractive in that acidification of the surrounding area can be minimized.

Uranium reduction and resistance to reoxidation under iron-reducing and sulfate-reducing conditions

Oxidation and mobilization of microbially-generated U(IV) is of great concern for in situ uranium bioremediation. This study investigated the reoxidation of uranium by oxygen and nitrate in a sulfate-reducing enrichment and an iron-reducing enrichment derived from sediment and groundwater from the Field Research Center in Oak Ridge, Tennessee. Both enrichments were capable of reducing U(VI) rapidly. 16S rRNA gene clone libraries of the two enrichments revealed that Desulfovibrio spp. are dominant in the sulfate-reducing enrichment, and Clostridium spp. are dominant in the iron-reducing enrichment. In both the sulfate-reducing enrichment and the iron-reducing enrichment, oxygen reoxidized the previously reduced uranium but to a lesser extent in the iron-reducing enrichment. Moreover, in the iron-reducing enrichment, the reoxidized U(VI) was eventually re-reduced to its previous level. In both, the sulfate-reducing enrichment and the iron-reducing enrichment, uranium reoxidation did not occur in the presence of nitrate. The results indicate that the Clostridium-dominated iron-reducing communities created conditions that were more favorable for uranium stability with respect to reoxidation despite the fact that fewer electron equivalents were added to these systems. The likely reason is that more of the added electrons are present in a form that can reduce oxygen to water and U(VI) back to U(IV).

Bioaugmentation for electricity generation from corn stover biomass using microbial fuel cells

Corn stover is usually treated by an energy-intensive or expensive process to extract sugars for bioenergy production. However, it is possible to directly generate electricity from corn stover in microbial fuel cells (MFCs) through the addition of microbial consortia specifically acclimated for biomass breakdown. A mixed culture that was developed to have a high saccharification rate with corn stover was added to single-chamber, air-cathode MFCs acclimated for power production using glucose. The MFC produced a maximum power of 331 mW/m2 with the bioaugmented mixed culture and corn stover, compared to 510 mW/m2 using glucose. Denaturing gradient gel electrophoresis (DGGE) showed the communities continued to evolve on both the anode and corn stover biomass over 60 days, with several bacteria identified including Rhodopseudomonas palustris. The use of residual solids from the steam exploded corn stover produced 8% more power (406 mW/m2) than the raw corn stover. These results show that it is possible to directly generate electricity from waste corn stover in MFCs through bioaugmentation using naturally occurring bacteria.