Presence, distribution, and diversity of iron-oxidizing bacteria at a landfill leachate-impacted groundwater surface water interface

Metal-oxide precipitation influences microbiome structure in hyporheic zones receiving acid rock drainage

Streams impacted by historic mining activity are characterized by acidic pH, unique microbial communities, and abundant metal-oxide precipitation, all of which can influence groundwater-surface water exchange. We investigate how metal-oxide precipitates and hyporheic mixing mediate the composition of microbial communities in two streams receiving acid-rock and mine drainage near Silverton, Colorado, USA. A large, neutral pH hyporheic zone facilitated the precipitation of metal particles/colloids in hyporheic porewaters. A small, low pH hyporheic zone, limited by the presence of a low-permeability, iron-oxyhydroxide layer known as ferricrete, led to the formation of steep geochemical gradients and high dissolved-metal concentrations. To determine how these two hyporheic systems influence microbiome composition, we installed well clusters and deployed in situ microcosms in each stream to sample porewaters and sediments for 16S rRNA gene sequencing. Results indicated that distinct hydrogeochemical conditions were present above and below the ferricrete in the low pH system. A positive feedback loop may be present in the low pH stream where microbially mediated precipitation of iron-oxides contributes to additional clogging of hyporheic pore spaces, separating abundant, iron-oxidizing bacteria (Gallionella spp.) above the ferricrete from rare, low-abundance bacteria below the ferricrete. Metal precipitates and colloids that formed in the neutral pH hyporheic zone were associated with a more diverse phylogenetic community of nonmotile, nutrient-cycling bacteria that may be transported through hyporheic pore spaces. In summary, biogeochemical conditions influence, and are influenced by, hyporheic mixing, which mediates the distribution of micro-organisms and, thus, the cycling of metals in streams receiving acid-rock and mine drainage.

IMPORTANCE

In streams receiving acid-rock and mine drainage, the abundant precipitation of iron minerals can alter how groundwater and surface water mix along streams (in what is known as the "hyporheic zone") and may shape the distribution of microbial communities. The findings presented here suggest that neutral pH streams with large, well-mixed hyporheic zones may harbor and transport diverse microorganisms attached to particles/colloids through hyporheic pore spaces. In acidic streams where metal oxides clog pore spaces and limit hyporheic exchange, iron-oxidizing bacteria may dominate and phylogenetic diversity becomes low. The abundance of iron-oxidizing bacteria in acid mine drainage streams has the potential to contribute to additional clogging of hyporheic pore spaces and the accumulation of toxic metals in the hyporheic zone. This research highlights the dynamic interplay between hydrology, geochemistry, and microbiology at the groundwater-surface water interface of acid mine drainage streams.

Exploratory analysis of the microbial community profile of the municipal solid waste leachate treatment system: A case study

Studies on the degradation dynamics of landfill leachate indicate that the microbial community profile is a valuable and sensitive tool for landfill monitoring programs. Although knowledge about the microbial community can improve the efficiency of leachate treatment systems, little is known about the microbial profile changes that occur throughout the leachate attenuation process. In the present work, an exploratory analysis of the microbial community profile of the MSW leachate treatment system in the municipality of Osório (Brazil) was conducted. In this way, a comprehensive analysis of chemical parameters, isotopic signature and microbial profile data were applied to monitor the changes in the structure of the microbial community throughout the leachate attenuation process and to describe the relationship between the microbial community structure and the attenuation of chemical and isotopic parameters. From data analysis, it was possible to assess the microbial community structure and relate it to the attenuation of chemical and isotopic parameters. Based on massive parallel 16S rRNA gene sequencing, it was possible to observe that each leachate treatment unit has a specific microbial consortium, reflecting the adaptation of different microorganisms to changes in leachate characteristics throughout treatment. From our results, we concluded that the structure of the microbial community is sensitive to the leachate composition and can be applied to study the municipal solid waste management system.

Application of humin-immobilized biocathode in a continuous-flow bioelectrochemical system for nitrate removal at low temperature

Solid-phase humic substances (humin) can work as an additional electron donor to support the low temperature denitrification but the reducing capacity of its non-reduced form is limited. In this study, a continuous-flow denitrifying BES with a humin-immobilized biocathode (H-BioC) was established. Humin was expected to function as a redox mediator and be persistently reduced on the cathode to provide reducing power to a denitrifying biofilm. Results showed that the H-BioC maintained a stable denitrification capacity with low nitrite accumulation for more than 100 days at 5 °C, and the specific microbial denitrification rate and electron transfer rate were 3.97-fold and 1.75-fold higher than those of the unaltered cathode. The results of repeated cycles of humin reduction and oxidation experiments further suggested that the redox activity of humin was stable. Acidovorax was the most dominant genus in both H-BioC biofilm and unaltered cathodic biofilm, while Rhodocyclaceae (unclassified_f_) was more enriched in H-BioC biofilm. Further Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analyses indicated that biofilm formation, electron transfer, and nitrate reduction functions were more abundant in H-BioC, suggesting a possible enhancement mechanism by humin. The results of this study raise the possibility that immobilization of solid-phase humin may be a useful strategy for electrostimulated heterotrophic denitrification in groundwater where the indigenous bacteria have poor electroactivity.

Changes in the microbial community during microbial microaerophilic Fe(II) oxidation at circumneutral pH enriched from paddy soil

Fe(II)-oxidizing bacteria (FeOB) are important catalysts for iron cycling in iron-rich marine, groundwater, and freshwater environments. However, few studies have reported the distribution and diversity of these bacteria in flooded paddy soils. This study investigates the microbial structure and diversity of microaerophilic Fe(II)-oxidizing bacteria (mFeOB) and their possible role in Fe(II) oxidation in iron-rich paddy soils. Using enrichment experiments that employed serial transfers, the changes in microaerophilic microbial community were examined via 16S rRNA gene high-throughput sequencing. During enrichments, the Fe(II) oxidation rate decreased as transfers increased, and the maximum rate of Fe(II) oxidation was observed in the first transfer (0.197 mM day^-1). Results from X-ray diffraction of minerals and scanning electron microscopy of the cell-mineral aggregates revealed that cell surfaces in all transfers were partly covered with amorphous iron oxide formed by FeOB. After four transfers, the phyla of Proteobacteria had a dominant presence that reached up to 95%. Compared with the original soil, the relative abundances of Cupriavidus, Massilia, Pseudomonas, Ralstonia, Sphingomonas, and Variovorax increased in FeS gradient tubes and became dominant genera after transfers. Cupriavidus, Pseudomonas, and Ralstonia have been identified as FeOB previously. Furthermore, the structure of the microbial community tended to be stable as transfers increased, indicating that other bacterial species might perform important roles in Fe(II) oxidation. These results suggest the potential involvement of mFeOB and these other microorganisms in the Fe(II)-oxidizing process of soils. It will be helpful for future studies to consider their role in related biogeochemical processes, such as transformation of organic matters and heavy metals.

Diversity of Iron Oxidizers in Groundwater-Fed Rapid Sand Filters: Evidence of Fe(II)-Dependent Growth by Curvibacter and Undibacterium spp

Although earlier circumstantial observations have suggested the presence of iron oxidizing bacteria (IOB) in groundwater-fed rapid sand filters (RSF), ferrous iron (Fe(II)) oxidation in this environment is often considered a chemical process due to the highly oxic and circumneutral pH conditions. The low water temperature (5-10°C), typical of groundwaters, on the other hand, may reduce the rates of chemical Fe(II) oxidation, which may allow IOB to grow and compete with chemical Fe(II) oxidation. Hence, we hypothesized that IOB are active and abundant in groundwater-fed RSFs. Here, we applied a combination of cultivation and molecular approaches to isolate, quantify, and confirm the growth of IOB from groundwater-fed RSFs, operated at different influent Fe(II) concentrations. Isolates related to Undibacterium and Curvibacter were identified as novel IOB lineages. Gallionella spp. were dominant in all waterworks, whereas Ferriphaselus and Undibacterium were dominant at pre-filters of waterworks receiving groundwaters with high (>2 mg/l) Fe(II) concentrations. The high density and diversity of IOB in groundwater-fed RSFs suggest that neutrophilic IOB may not be limited to oxic/anoxic interfaces.

Microbial Diversity in Actively Forming Iron Oxides from Weathered Banded Iron Formation Systems

The surface crust that caps highly weathered banded iron formations (BIFs) supports a unique ecosystem that is a post-mining restoration priority in iron ore areas. Geochemical evidence indicates that biological processes drive the dissolution of iron oxide minerals and contribute to the ongoing evolution of this duricrust. However, limited information is available on present-day biogeochemical processes in these systems, particularly those that contribute to the precipitation of iron oxides and, thus, the cementation and stabilization of duricrusts. Freshly formed iron precipitates in water bodies perched on cangas in Karijini National Park, Western Australia, were sampled for microscopic and molecular analyses to understand currently active microbial contributions to iron precipitation in these areas. Microscopy revealed sheaths and stalks associated with iron-oxidizing bacteria. The iron-oxidizing lineages Sphaerotilus, Sideroxydans, and Pedomicrobium were identified in various samples and Leptothrix was common in four out of five samples. The iron-reducing bacteria Anaeromyxobacter dehalogens and Geobacter lovleyi were identified in the same four samples, with various heterotrophs and diverse cyanobacteria. Given this arid, deeply weathered environment, the driver of contemporary iron cycling in Karijini National Park appears to be iron-reducing bacteria, which may exist in anaerobic niches through associations with aerobic heterotrophs. Overall oxidizing conditions and Leptothrix iron-oxidizers contribute to net iron oxide precipitation in our sampes, rather than a closed biogeochemical cycle, which would result in net iron oxide dissolution as has been suggested for canga caves in Brazil. Enhancements in microbial iron oxide dissolution and subsequent reprecipitation have potential as a surface-crust-ecosystem remediation strategy at mine sites.

Environmental monitoring of a landfill area through the application of carbon stable isotopes, chemical parameters and multivariate analysis

Leachate produced during an organic matter decomposition process has a complex composition and can cause contamination of surface and groundwaters adjacent to a landfill area. The monitoring of these areas is extremely important for the characterization of the leachate produced and to avoid or mitigate environmental damages. Thus, the present study has the objective of monitoring the area of a Brazilian landfill using conventional parameters (dissolved metals and anions in water) and alternative, stable carbon isotopes parameters (δ¹³C of dissolved organic and inorganic carbons in water) in addition to multivariate analysis techniques. The use of conventional and alternative parameters together with multivariate analysis showed that cells of the residues are at different phases of stabilization of the organic matter and probably already at C3 of the methanogenic phase of decomposition. In addition, the data showed that organic matter stabilization ponds present in the landfill are efficient and improve the quality of the leachate. Enrichment of the heavy ¹³C isotope in both surface and groundwater suggested contamination in two sampling sites.

The role of microaerophilic Fe-oxidizing micro-organisms in producing banded iron formations

Despite the historical and economic significance of banded iron formations (BIFs), we have yet to resolve the formation mechanisms. On modern Earth, neutrophilic microaerophilic Fe-oxidizing micro-organisms (FeOM) produce copious amounts of Fe oxyhydroxides, leading us to wonder whether similar organisms played a role in producing BIFs. To evaluate this, we review the current knowledge of modern microaerophilic FeOM in the context of BIF paleoenvironmental studies. In modern environments wherever Fe(II) and O2 co-exist, microaerophilic FeOM proliferate. These organisms grow in a variety of environments, including the marine water column redoxcline, which is where BIF precursor minerals likely formed. FeOM can grow across a range of O2 concentrations, measured as low as 2 μm to date, although lower concentrations have not been tested. While some extant FeOM can tolerate high O2 concentrations, many FeOM appear to prefer and thrive at low O2 concentrations (~3-25 μm). These are similar to the estimated dissolved O2 concentrations in the few hundred million years prior to the 'Great Oxidation Event' (GOE). We compare biotic and abiotic Fe oxidation kinetics in the presence of varying levels of O2 and show that microaerophilic FeOM contribute substantially to Fe oxidation, at rates fast enough to account for BIF deposition. Based on this synthesis, we propose that microaerophilic FeOM were capable of playing a significant role in depositing the largest, most well-known BIFs associated with the GOE, as well as afterward when global O2 levels increased.

Limited reduction of ferrihydrite encrusted by goethite in freshwater sediment

Many physical and chemical processes control the extent of Fe(III) oxyhydroxide reduction by dissimilatory Fe(III)-reducing bacteria. The surface precipitation of secondary Fe minerals on Fe(III) oxyhydroxides limits the extent of microbial Fe(III) reduction, but this phenomenon has not yet been observed in nature. This paper reports the observation of secondary Fe-mineral (goethite) encrustation on ferrihydrite surface within freshwater sediment up to 10 cm deep. The sediment surface was characterized by the predominance of ferrihydrites with biogenic stalks and sheaths. An Fe(II)-oxidizing bacterium (Gallionellaceae) was detected by 16S rRNA gene analysis at sediment depths of 1 and 2 cm. Fe(2+) concentration in the sediment pore water was relatively higher at 2-4 cm depths. The 16S rRNA genes affiliated with dissimilatory Fe(III)-reducing bacteria were detected at 1, 2, and 4 cm depths. The results of the Fe K-edge extended X-ray absorption fine structure (EXAFS) analysis suggested the presence of goethite and siderite at depths below 3 cm. However, the change in the Fe-mineral composition was restricted to sediment depths between 3 and 4 cm, despite the presence of abundant ferrihydrite at depths below 4 cm. An increase in CH4 concentration was observed at deeper than 6 cm. Stable isotopic analysis of CH4 in the pore water indicated that acetoclastic CH4 occurred at depths below 7 cm. Transmission electron microscope observations suggested the presence of goethite and siderite on stalks and sheaths at depths below 3 cm. Results from conversion electron yield EXAFS analysis suggested that goethite dominated at 10 cm depth, thereby indicating that ferrihydrite was encrusted by goethite at this depth. Moreover, the incomplete reduction of ferrihydrite below depths of 4 cm was not due to the lack of organic carbon, but was possibly due to the surface encrustation of goethite on ferrihydrite.

Dominance of 'Gallionella capsiferriformans' and heavy metal association with Gallionella-like stalks in metal-rich pH 6 mine water discharge

Heavy metal-contaminated, pH 6 mine water discharge created new streams and iron-rich terraces at a creek bank in a former uranium-mining area near Ronneburg, Germany. The transition from microoxic groundwater with ~5 mm Fe(II) to oxic surface water may provide a suitable habitat for microaerobic iron-oxidizing bacteria (FeOB). In this study, we investigated the potential contribution of these FeOB to iron oxidation and metal retention in this high-metal environment. We (i) identified and quantified FeOB in water and sediment at the outflow, terraces, and creek, (ii) studied the composition of biogenic iron oxides (Gallionella-like twisted stalks) with scanning and transmission electron microscopy (SEM, TEM) as well as confocal laser scanning microscopy (CLSM), and (iii) examined the metal distribution in sediments. Using quantitative PCR, a very high abundance of FeOB was demonstrated at all sites over a 6-month study period. Gallionella spp. clearly dominated the communities, accounting for up to 88% of Bacteria, with a minor contribution of other FeOB such as Sideroxydans spp. and 'Ferrovum myxofaciens'. Classical 16S rRNA gene cloning showed that 96% of the Gallionella-related sequences had ≥ 97% identity to the putatively metal-tolerant 'Gallionella capsiferriformans ES-2', in addition to known stalk formers such as Gallionella ferruginea and Gallionellaceae strain R-1. Twisted stalks from glass slides incubated in water and sediment were composed of the Fe(III) oxyhydroxide ferrihydrite, as well as polysaccharides. SEM and scanning TEM-energy-dispersive X-ray spectroscopy revealed that stalk material contained Cu and Sn, demonstrating the association of heavy metals with biogenic iron oxides and the potential for metal retention by these stalks. Sequential extraction of sediments suggested that Cu (52-61% of total sediment Cu) and other heavy metals were primarily bound to the iron oxide fractions. These results show the importance of 'G. capsiferriformans' and biogenic iron oxides in slightly acidic but highly metal-contaminated freshwater environments.

Stream microbial diversity in response to environmental changes: review and synthesis of existing research

The importance of microbial activity to ecosystem function in aquatic ecosystems is well established, but microbial diversity has been less frequently addressed. This review and synthesis of 100s of published studies on stream microbial diversity shows that factors known to drive ecosystem processes, such as nutrient availability, hydrology, metal contamination, contrasting land-use and temperature, also cause heterogeneity in bacterial diversity. Temporal heterogeneity in stream bacterial diversity was frequently observed, reflecting the dynamic nature of both stream ecosystems and microbial community composition. However, within-stream spatial differences in stream bacterial diversity were more commonly observed, driven specifically by different organic matter (OM) compartments. Bacterial phyla showed similar patterns in relative abundance with regard to compartment type across different streams. For example, surface water contained the highest relative abundance of Actinobacteria, while epilithon contained the highest relative abundance of Cyanobacteria and Bacteroidetes. This suggests that contrasting physical and/or nutritional habitats characterized by different stream OM compartment types may select for certain bacterial lineages. When comparing the prevalence of physicochemical effects on stream bacterial diversity, effects of changing metal concentrations were most, while effects of differences in nutrient concentrations were least frequently observed. This may indicate that although changing nutrient concentrations do tend to affect microbial diversity, other environmental factors are more likely to alter stream microbial diversity and function. The common observation of connections between ecosystem process drivers and microbial diversity suggests that microbial taxonomic turnover could mediate ecosystem-scale responses to changing environmental conditions, including both microbial habitat distribution and physicochemical factors.

Using in situ voltammetry as a tool to identify and characterize habitats of iron-oxidizing bacteria: from fresh water wetlands to hydrothermal vent sites

Iron-oxidizing bacteria (FeOB) likely play a large role in the biogeochemistry of iron, making the detection and understanding of the biogeochemical processes FeOB are involved in of critical importance. By deploying our in situ voltammetry system, we are able to measure a variety of redox species, specifically Fe(ii) and O2, simultaneously. This technique provides significant advantages in both characterizing the environments in which microaerophilic FeOB are found, and finding diverse conditions in which FeOB could potentially thrive. Described here are four environments with different salinities [one fresh groundwater seep site, one beach-groundwater mixing site, one hydrothermal vent site (Mid-Atlantic Ridge), and one estuary (Chesapeake Bay)] where in situ voltammetry was deployed, and where the presence of FeOB were confirmed by either culturing methods or molecular data. The sites varied in both O2 and Fe(ii) content with O2 ranging from below the 3 μM detection limit of the electrodes at the Chesapeake Bay suboxic zone, to as high 150 μM O2 at the vent site. In addition, a range of Fe(ii) concentrations supported FeOB communities, from 3 μM Fe(ii) in the Chesapeake Bay to 300 μM in the beach aquifer. In situ electrochemistry provides the means to quickly measure these redox gradients at appropriate resolution, making it possible in real time to detect niches likely inhabited by microaerophilic FeOB, then accurately sample for proof of FeOB presence and activity. This study demonstrates the utility of this approach while also greatly expanding our knowledge of FeOB habitats.

Seasonal and spatial variations in microbial activity at various phylogenetic resolutions at a groundwater – surface water interface

We investigated the seasonal and spatial variation in activity and density of the metabolically active in situ microbial community (AIMC) at a landfill leachate-impacted groundwater – surface water interface (GSI). A series of AIMC traps were designed and implemented for AIMC sampling and microbial activity and density examinations. Measurements were made not only at the level of bacterial domain but also at the levels of alphaproteobacterial Rhizobiales order and gammaproteobacterial Pseudomonas genus, both of which included a large number of iron-oxidizing bacteria as revealed from previous analysis. Consistently higher microbial activities with less variation in depth were measured in the AIMC traps than in the ambient sediments. Flood disturbance appeared to control AIMC activity distributions at the gradually elevated GSI. The highest AIMC activities were generally obtained from locations closest to the free surface water boundary except during the dry season when microbial activities were similar across the entire GSI. A clone library of AIMC 16S rRNA genes was constructed, and it confirmed the predominant role of the targeted alphaproteobacterial group in AIMC activity and composition. This taxon constituted 2%–14% of all bacteria with similar activity distribution profiles. The Pseudomonas group occupied only 0.1‰–0.5‰ of the total bacterial density, but its activity was 27 times higher than the bacterial average. Of the 16S rRNA sequences in the AIMC clone library, 7.5% were phylogenetically related to putative IOB, supporting the occurrence and persistence of active microbial iron oxidation across the studied iron-rich GSI ecosystem.

Seasonal arsenic accumulation in stream sediments at a groundwater discharge zone

Seasonal changes in arsenic and iron accumulation rates were examined in the sediments of a brook that receives groundwater discharges of arsenic and reduced iron. Clean glass bead columns were deployed in sediments for known periods over the annual hydrologic cycle to monitor changes in arsenic and iron concentrations in bead coatings. The highest accumulation rates occurred during the dry summer period (July-October) when groundwater discharges were likely greatest at the sample locations. The intermediate flow period (October-March), with higher surface water levels, was associated with losses of arsenic and iron from bead column coatings at depths below 2-6 cm. Batch incubations indicated iron releases from solids to be induced by biological reduction of iron (oxy)hydroxide solids. Congruent arsenic releases during incubation were limited by the high arsenic sorption capacity (0.536 mg(As)/mg(Fe)) of unreacted iron oxide solids. The flooded spring (March-June) with high surface water flows showed the lowest arsenic and iron accumulation rates in the sediments. Comparisons of accumulation rates across a shoreline transect were consistent with greater rates at regions exposed above surface water levels for longer times and greater losses at locations submerged below surface water. Iron (oxy)hydroxide solids in the shallowest sediments likely serve as a passive barrier to sorb arsenic released to pore water at depth by biological iron reduction.

Surprising abundance of Gallionella-related iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations

We identified and quantified abundant iron-oxidizing bacteria (FeOB) at three iron-rich, metal-contaminated creek sites with increasing sediment pH from extremely acidic (R1, pH 2.7), to moderately acidic (R2, pH 4.4), to slightly acidic (R3, pH 6.3) in a former uranium-mining district. The geochemical parameters showed little variations over the 1.5 year study period. The highest metal concentrations found in creek sediments always coincided with the lowest metal concentrations in creek water at the slightly acidic site R3. Sequential extractions of R3 sediment revealed large portions of heavy metals (Ni, Cu, Zn, Pb, U) bound to the iron oxide fraction. Light microscopy of glass slides exposed in creeks detected twisted stalks characteristic of microaerobic FeOB of the family Gallionellaceae at R3 but also at the acidic site R2. Sequences related to FeOB such as Gallionella ferruginea, Sideroxydans sp. CL21, Ferritrophicum radicicola, and Acidovorax sp. BrG1 were identified in the sediments. The highest fraction of clone sequences similar to the acidophilic "Ferrovum myxofaciens" was detected in R1. Quantitative PCR using primer sets specific for Gallionella spp., Sideroxydans spp., and "Ferrovum myxofaciens" revealed that ~72% (R2 sediment) and 37% (R3 sediment) of total bacterial 16S rRNA gene copies could be assigned to groups of FeOB with dominance of microaerobic Gallionella spp. at both sites. Gallionella spp. had similar and very high absolute and relative gene copy numbers in both sediment communities. Thus, Gallionella-like organisms appear to exhibit a greater acid and metal tolerance than shown before. Microaerobic FeOB from R3 creek sediment enriched in newly developed metal gradient tubes tolerated metal concentrations of 35 mM Co, 24 mM Ni, and 1.3 mM Cd, higher than those in sediments. Our results will extend the limited knowledge of FeOB at contaminated, moderately to slightly acidic environments.

Pyrosequencing analysis of the bacterial community in drinking water wells

Wells used for drinking water often have a large biomass and a high bacterial diversity. Current technologies are not always able to reduce the bacterial population, and the threat of pathogen proliferation in drinking water sources is omnipresent. The environmental conditions that shape the microbial communities in drinking water sources have to be elucidated, so that pathogen proliferation can be foreseen. In this work, the bacterial community in nine water wells of a groundwater aquifer in Northern Mexico were characterized and correlated to environmental characteristics that might control them. Although a large variation was observed between the water samples, temperature and iron concentration were the characteristics that affected the bacterial community structure and composition in groundwater wells. Small increases in the concentration of iron in water modified the bacterial communities and promoted the growth of the iron-oxidizing bacteria Acidovorax. The abundance of the genera Flavobacterium and Duganella was correlated positively with temperature and the Acidobacteria Gp4 and Gp1, and the genus Acidovorax with iron concentrations in the well water. Large percentages of Flavobacterium and Pseudomonas bacteria were found, and this is of special concern as bacteria belonging to both genera are often biofilm developers, where pathogens survival increases.

Does soil water saturation mobilize metals from riparian soils to adjacent surface water? A field monitoring study in a metal contaminated region

In the Noorderkempen (NW Belgium), a large area (about 280 km(2)) is contaminated with cadmium (Cd) and zinc (Zn) due to historical pollution by the Zn smelters. Direct aquatic emissions of metals have diminished over time, however the surface water metal concentration largely exceeds quality standards, mainly during winter periods. Monitoring data were analyzed to reveal whether these fluctuations are related to seasonal redox reactions in associated contaminated riparian soils that drain into the rivers. A field survey was set up with soil pore-water and groundwater monitored for three years in transects of soil monitoring points perpendicular to rivers at contaminated and non-contaminated sites. Site averaged surface water concentrations of a 15 year dataset exceeded local quality standards 4 to 200-fold. Winter averaged metal concentrations significantly exceeded the corresponding summer values 1.3-1.8 (Zn) and 1.5-2.4 fold (Cd). Zinc and Cd concentrations in water were positively related to Fe and Mn but not to Ca, K or Na suggesting that redox reactions and not dilution processes are involved. In ground- and pore-water of the associated riparian soils, the concentrations of Zn fluctuate by the same order of magnitude as in surface water but were generally smaller than in the corresponding contaminated rivers. In addition, correlations of dissolved Zn with Fe and Mn were lacking. This analysis suggests that redox reactions in streams, and not in riparian soils, explain the seasonal trends of Zn and Cd in surface water. Hence, river sediments and not riparian soils may be the cause of the winter peaks of Zn and Cd in these rivers.

Freeze-coring method for characterization of microbial community structure and function in wetland soils at high spatial resolution

A simple freeze-coring method was developed to obtain structurally intact cores from wetland soils. A copper tube was inserted into the wetland and filled with ethanol and dry ice to freeze the surrounding soil. Biological structure and function could be analyzed, and labile compounds such as mRNA were recovered.

Changes in bacterial community of anthracene bioremediation in municipal solid waste composting soil

Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in a municipal solid waste (MSW) composting site. Knowledge of changes in microbial structure is useful to identify particular PAH degraders. However, the microbial community in the MSW composting soil and its change associated with prolonged exposure to PAHs and subsequent biodegradation remain largely unknown. In this study, anthracene was selected as a model compound. The bacterial community structure was investigated using terminal restriction fragment length polymorphism (TRFLP) and 16S rRNA gene clone library analysis. The two bimolecular tools revealed a large shift of bacterial community structure after anthracene amendment and subsequent biodegradation. Genera Methylophilus, Mesorhizobium, and Terrimonas had potential links to anthracene biodegradation, suggesting a consortium playing an active role.

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.

Iron-oxidizing bacteria: an environmental and genomic perspective

In the 1830s, iron bacteria were among the first groups of microbes to be recognized for carrying out a fundamental geological process, namely the oxidation of iron. Due to lingering questions about their metabolism, coupled with difficulties in culturing important community members, studies of Fe-oxidizing bacteria (FeOB) have lagged behind those of other important microbial lithotrophic metabolisms. Recently, research on lithotrophic, oxygen-dependent FeOB that grow at circumneutral pH has accelerated. This work is driven by several factors including the recognition by both microbiologists and geoscientists of the role FeOB play in the biogeochemistry of iron and other elements. The isolation of new strains of obligate FeOB allowed a better understanding of their physiology and phylogeny and the realization that FeOB are abundant at certain deep-sea hydrothermal vents. These ancient microorganisms offer new opportunities to learn about fundamental biological processes that can be of practical importance.