Soil microbial community responses to additions of organic carbon substrates and heavy metals (Pb and Cr)

Deciphering Vanadium Speciation in Smelting Ash and Adaptive Responses of Soil Microorganisms

Abundant smelting ash is discharged during pyrometallurgical vanadium (V) production. However, its associated V speciation and resultant ecological impact have remained elusive. In this study, V speciation in smelting ash and its influence on the metabolism of soil microorganisms were investigated. Smelting ashes from V smelters contained abundant V (19.6-115.9 mg/g). V(V) was the dominant species for soluble V, while solid V primarily existed in bioavailable forms. Previously unrevealed V nanoparticles (V-NPs) were prevalently detected, with a peak concentration of 1.3 × 1013 particles/g, a minimal size of 136.0 ± 0.6 nm, and primary constituents comprising FeVO4, VO2, and V2O5. Incubation experiments implied that smelting ash reshaped the soil microbial community. Metagenomic binning, gene transcription, and component quantification revealed that Microbacterium sp. and Tabrizicola sp. secreted extracellular polymeric substances through epsB and yhxB gene regulation for V-NPs aggregation to alleviate toxicity under aerobic operations. The V K-edge X-ray absorption near-edge structure (XANES) spectra suggested that VO2 NPs were oxidized to V2O5 NPs. In the anaerobic case, Comamonas sp. and Achromobacter sp. reduced V(V) to V(IV) for detoxification regulated by the napA gene. This study provides a deep understanding of the V speciation in smelting ash and microbial responses, inspiring promising bioremediation strategies to reduce its negative environmental impacts.

Exploring the relationship between metal(loid) contamination rate, physicochemical conditions, and microbial community dynamics in industrially contaminated urban soils

Increasing metal(loid) contamination in urban soils and its impact on soil microbial community have attracted considerable attention. In the present study, the physicochemical parameters and the effects of twelve metal(loid) pollution on soil microbial diversity, their ecotoxic effects, and human health risk assessment in urban soils with different industrial background were studied in comparison with an unpolluted forest soil sample. Results showed that urban soils were highly contaminated, and metal(loid) contamination significantly influenced structure of the soil microbial communities. In all samples the bacterial community was dominated by Proteobacteria, and on the level of phyla characteristic differences were not possible to observe between polluted and control sampling sites. However, clear differences emerged at class and genus level, where several rare taxa disappeared from contaminated urban soils. Simper test results showed that there is 71.6 % bacterial OTU and 9.5 % bacterial diversity dissimilarity between polluted and control samples. Ratio of Patescibacteria, Armatimonadetes, Chlamydiae, Fibrobacteres, and Gemmatimonadetes indicated a significant (p < 0.05) positive correlation with soil Zn, Cr, Pb, Sn, Cu, Mn content, suggest that metal(loid)s strongly influence the structure of microbial community. In contrast, the presence of metal(loid) contamination in urban soils has been found to significantly reduce the population of Archaeal communities. This can be attributed to the depletion of organic matter caused by contamination that reached a minimum of 0.5 m/m% for nitrate and 0.9 m/m% for total organic carbon. The values of urban soil pH were close to neutral, ranging from 5.9 to 8.3. The findings of ecotoxicology test are alarming, as all the studied urban soil sites were cytotoxic to soil microorganisms, and in one site metal(loid) contamination reached genotoxic level. Moreover, all the metal(loid) contaminated sites pose severe and persistent health risk to children, highlighting the urgent need for effective measures to mitigate metal(loid) pollution in urban areas.

Vertical and seasonal dynamics of bacterial pathogenic communities at an aged organic contaminated site: Insights into microbial diversity, composition, interactions, and assembly processes

Under the background of the Coronavirus Disease 2019 (COVID-19) pandemic, research on pathogens deserves greater attention in the natural environment, especially in the widely distributed contaminated sites with complicated and severe organic pollution. In this study, the community composition and assembly of soil pathogens identified by the newly-developed 16S-based pipeline of multiple bacterial pathogen detection (MBPD) have been investigated on spatiotemporal scales in the selected organic polluted site. We demonstrated that the richness and diversity of the pathogenic communities were primarily controlled by soil depth, while the structure and composition of pathogenic communities varied pronouncedly with seasonal changes, which were driven by the alterations in both physiochemical parameters and organic contaminants over time. Network analysis revealed that the overwhelmingly positive interactions, identified multiple keystone species, and a well-organized modular structure maintained the stability and functionality of the pathogenic communities under environmental pressures. Additionally, the null-model analysis showed that deterministic processes dominated the pathogenic community assembly across soil profiles. In three seasons, stochasticity-dominated processes in spring and summer changed into determinism-dominated processes in winter. These findings extend our knowledge of the response of the bacterial pathogenic community to environmental disruptions brought on by organic contaminated sites.

Heavy metal contamination affects the core microbiome and assembly processes in metal mine soils across Eastern China

Mining activities in metal mine areas cause serious environmental pollution, thereby imposing stresses to soil ecosystems. Investigating the ecological pattern underlying contaminated soil microbial diversity is essential to understand ecosystem responses to environment changes. Here we collected 624 soil samples from 49 representative metal mines across eastern China and analyzed their soil microbial diversity and biogeographic patterns by using 16 S rRNA gene amplicons. The results showed that deterministic factors dominated in regulating the microbial community in non-contaminated and contaminated soils. Soil pH played a key role in climatic influences on the heavy metal-contaminated soil microbial community. A core microbiome consisting of 25 taxa, which could be employed for the restoration of contaminated soils, was identified. Unlike the non-contaminated soil, stochastic processes were important in shaping the heavy metal-contaminated soil microbial community. The largest source of variations in the soil microbial community was land use type. This result suggests that varied specific ecological remediation strategy ought to be developed for differed land use types. These findings will enhance our understanding of the microbial responses to anthropogenically induced environmental changes and will further help to improve the practices of soil heavy metal contamination remediation.

Effect of metal pollution on the distribution and co-occurrence pattern of bacterial, archaeal and fungal communities throughout the soil profiles

Metal pollution has raised negative impact on microbes, but little is known about the distribution and co-occurrence pattern of bacterial, fungal and archaeal communities along the soil profiles at multiple metal contamination sites. Here, we characterized the variations of metal concentrations and microbial communities with soil depth along five deep bores at the Tanghe Sewage Reservoir, a typical metal contamination area on the North China Plain. Co, Cd, Mg, Se, and Li were identified as the major contaminants in this area, and the pollution load index was 1.88, 1.54 and 1.62 in the shallow layer (0-0.6 m), deep layer (>2.0 m) and middle layer (0.6-2.0 m), respectively. The diversities and compositions of bacterial, archaeal and fungal communities varied significantly along the soil profiles. Deterministic process played a crucial role in shaping the difference of microbial community compositions among different soil layers, in which metal levels contributed more than soil physiochemical parameters. Furthermore, the interspecific co-occurrence network was most complex in the middle layer, indicating that metal pollution could decrease microbial network complexity. Bacterial keystone species in the co-occurrence networks showed both positive and negative correlations with polluted metals, whereas most archaeal and fungal keystone species were negatively related to multiple metals. These findings increased our understanding of distribution patterns, co-occurrence networks and environmental drivers of microbial communities in metal pollution soils.

Chemical Structure of Stabilizing Layers of Negatively Charged Silver Nanoparticles as an Effector of Shifts in Soil Bacterial Microbiome under Short-Term Exposure

In this work, we have assessed the exposure of soil bacteria from potato monoculture to three types of silver nanoparticles (AgNPs) as well as silver ions (Ag⁺ ions) delivered in the form of silver nitrate and a commercially available fungicide. The diversity of the soil microbial community, enzymatic activity, and carbon source utilization were evaluated. It was found that only the fungicide significantly limited the abundance and activity of soil bacteria. Silver ions significantly reduced bacterial metabolic activity. In turn, one type of AgNPs prepared with the use of tannic acid (TA) increased bacterial load and activity. There was found in all AgNPs treated soils (1) a greater proportion of all types of persistent bacteria, i.e., Bacillus, Paenibacillus, and Clostridium; (2) a visible decrease in the proportion of Nocardioides, Arthrobacter, and Candidatus Solibacter; (3) almost complete depletion of Pseudomonas; (4) increase in the number of low-frequency taxa and decrease in dominant taxa compared to the control soil. Despite the general trend of qualitative changes in the bacterial community, it was found that the differences in the chemical structure of the AgNP stabilizing layers had a significant impact on the specific metabolic activity resulting from qualitative changes in the microbiome.

Shifts in a Phenanthrene-Degrading Microbial Community are Driven by Carbohydrate Metabolism Selection in a Ryegrass Rhizosphere

Plants usually promote pollutant bioremediation by several mechanisms including modifying the diversity of functional microbial species. However, conflicting results are reported that root exudates have no effects or negative effects on organic pollutant degradation. In this study, we investigated the roles of ryegrass in phenanthrene degradation in soils using DNA stable isotope probing (SIP) and metagenomics to reveal a potential explanation for conflicting results among phytoremediation studies. Phenanthrene biodegradation efficiency was improved by 8% after 14 days of cultivation. Twelve and ten operational taxonomic units (OTUs) were identified as active phenanthrene degraders in non-rhizosphere and rhizosphere soils, respectively. The active phenanthrene degraders exhibited higher average phylogenetic distances in rhizosphere soils (0.33) than non-rhizosphere soils (0.26). The K_a/K_s values (the ratio of nonsynonymous to synonymous substitutions) were about 10.37% higher in the rhizosphere treatment among >90% of all key carbohydrate metabolism-related genes, implying that ryegrass may be an important driver of microbial community variation in the rhizosphere by relieving the carbohydrate metabolism pressure and improving the survival ability of r-strategy microbes. Most K_a/K_s values of root-exudate-related metabolism genes exhibited little change, except for fumarate hydratase that increased 13-fold in the rhizosphere compared to that in the non-rhizosphere treatment. The K_a/K_s values of less than 50% phenanthrene-degradation-related genes were affected, 30% of which increased and 70% behaved oppositely. Genes with altered K_a/K_s values had a low percentage and followed an inconsistent changing tendency, indicating that phenanthrene and its metabolites are not major factors influencing the active degraders. These results suggested the importance of carbohydrate metabolism, especially fumaric acid, in rhizosphere community shift, and hinted at a new hypothesis that the rhizosphere effect on phenanthrene degradation efficiency depends on the existence of active degraders that have competitive advantages in carbohydrate and fumaric acid metabolism.

A comprehensive review of biogeochemical distribution and fractionation of lead isotopes for source tracing in distinct interactive environmental compartments

Lead (Pb) is a non-essential and extremely noxious metallic-element whose biogeochemical cycle has been influenced predominantly by increasing human activities to a great extent. The introduction and enrichment of this ubiquitous contaminant in the terrestrial-environment has a long history and getting more attention due to its adverse health effects to living organisms even at very low exposure levels. Its lethal-effects can vary widely depending on the atmospheric-depositions, fates and distribution of Pb isotopes (i.e., ²⁰⁴Pb, ²⁰⁶Pb, ²⁰⁷Pb &²⁰⁸Pb) in the terrestrial-environment. Thus, it is essential to understand the depositional behavior and transformation mechanism of Pb and the factors affecting Pb isotopes composition in the terrestrial-compartments. Owing to the persistence nature of Pb-isotopic fractions, regardless of ongoing biogeochemical-processes taking place in soils and in other interlinked terrestrial-compartments of the biosphere makes Pb isotope ratios (Pb-IRs) more recognizable as a powerful and an efficient-tool for tracing the source(s) and helped uncover pertinent migration and transformation processes. This review discusses the ongoing developments in tracing migration pathway and distribution of lead in various terrestrial-compartments and investigates the processes regulating the Pb isotope geochemistry taking into account the source identification of lead, its transformation among miscellaneous terrestrial-compartments and detoxification mechanism in soil-plant system. Additionally, this compendium reveals that Pb-pools in various terrestrial-compartments differ in Pb isotopic fractionations. In order to improve understanding of partition behaviors and biogeochemical pathways of Pb isotope in the terrestrial environment, future works should involve investigation of changes in Pb isotopic compositions during weathering processes and atmospheric-biological sub-cycles.

Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics

A total of 16 different strains of Microbacterium spp. were isolated from contaminated soil and enriched on the carcinogen, hexavalent chromium [Cr(VI)]. The majority of the isolates (11 of the 16) were able to tolerate concentrations (0.1 mM) of cobalt, cadmium, and nickel, in addition to Cr(VI) (0.5–20 mM). Interestingly, these bacteria were also able to tolerate three different antibiotics (ranges: ampicillin 0–16 μg ml⁻¹, chloramphenicol 0–24 μg ml⁻¹, and vancomycin 0–24 μg ml⁻¹). To gain genetic insight into these tolerance pathways, the genomes of these isolates were assembled and annotated. The genomes of these isolates not only have some shared genes (core genome) but also have a large amount of variability. The genomes also contained an annotated Cr(VI) reductase (chrR) that could be related to Cr(VI) reduction. Further, various heavy metal tolerance (e.g., Co/Zn/Cd efflux system) and antibiotic resistance genes were identified, which provide insight into the isolates’ ability to tolerate metals and antibiotics. Overall, these isolates showed a wide range of tolerances to heavy metals and antibiotics and genetic diversity, which was likely required of this population to thrive in a contaminated environment.

Impact of heavy metals on inhibitory concentration of Escherichia coli-a case study of river Yamuna system, Delhi, India

The occurrence of resistant bacteria to specific heavy metals can be associated with increasing load of the metals in the environment. River Yamuna is polluted by various toxic heavy metals discharged by several industrial and agricultural sources. Therefore, the use of heavy metal-resistant bacteria as an indicator of metal pollution was tested in the present study. For the purpose of the study, the heavy metal resistance status of 42 Escherichia coli strains isolated from River Yamuna water from 7 sampling sites within a span of 2 years was determined using growth curves and plate dilution method in terms of minimum inhibitory concentration (MIC) values by comparing with MIC value of control strain. Seasonally, the lowest mean MIC value was observed for bacterial strains isolated in post-monsoon (December) 2013 and highest mean MIC value was observed for bacterial strains isolated in monsoon (August) 2015. Site-wise analysis of the maximum mean MIC values for all the isolated strains showed the highest mean Ni MIC value for the bacterial strains isolated from site S4 (ITO), highest mean Cu MIC, Cr MIC, and Fe MIC values for the bacterial strains isolated from site S2 (Najafgarh drain intermixing zone) and highest mean Cd MIC, Pb MIC, and Zn MIC values for the bacterial strains isolated from site S7 (Shahdara drain intermixing zone). Correlation analysis between mean MIC site-wise results with mean heavy metal site-wise concentrations showed significant positive correlation indicating that the higher the mean concentration of a given heavy metal at a given site, the higher the mean MIC value for the strains isolated from the same site indicating higher level of resistance. Overall, the present study has shown that the presence of heavy metals in River Yamuna caused due to indiscriminate discharge of various effluents from different kind of sources as well as due to insufficient treatment capacity of sewage treatment plants as well as common effluent treatment plants, has serious impacts on its bacterial microflora as it leads to the development of resistant strains.

Carbon-dependent chromate toxicity mechanism in an environmental Arthrobacter isolate

Arthrobacter spp. are widespread in soil systems and well-known for their Cr(VI) reduction capabilities making them attractive candidates for in situ bioremediation efforts. Cellulose drives carbon flow in soil systems; yet, most laboratory studies evaluate Arthrobacter-Cr(VI) interactions solely with nutrient-rich media or glucose. This study aims to determine how various cellulose degradation products and biostimulation substrates influence Cr(VI) toxicity, reduction, and microbial growth of an environmental Arthrobacter sp. isolate. Laboratory culture-based studies suggest there is a carbon-dependent Cr(VI) toxicity mechanism that affects subsequent Cr(VI) reduction by strain LLW01. Strain LLW01 could only grow in the presence of, and reduce, 50 μM Cr(VI) when glucose or lactate were provided. Compared to lactate, Cr(VI) was at least 30-fold and 10-fold more toxic when ethanol or butyrate was the sole carbon source, respectively. The addition of sulfate mitigated toxicity somewhat, but had no effect on the extent of Cr(VI) reduction. Cell viability studies indicated that a small fraction of cells were viable after 8 days suggesting cell growth and subsequent Cr(VI) reduction may resume. These results suggest when designing bioremediation strategies with Arthrobacter spp. such as strain LLW01, carbon sources such as glucose and lactate should be considered over ethanol and butyrate.

Microbial Reduction of Fe(III) and SO42- and Associated Microbial Communities in the Alluvial Aquifer Groundwater and Sediments

Agricultural demands continuously increased use of groundwater, causing drawdown of water table and need of artificial recharge using adjacent stream waters. River water intrusion into groundwater can alter the geochemical and microbiological characteristics in the aquifer and subsurface. In an effort to investigate the subsurface biogeochemical activities before operation of artificial recharge at the test site, established at the bank of Nakdong River, Changwon, South Korea, organic carbon transported from river water to groundwater was mimicked and the effect on the indigenous microbial communities was investigated with the microcosm incubations of the groundwater and subsurface sediments. Laboratory incubations indicated microbial reduction of Fe(III) and sulfate. Next-generation Illumina MiSeq sequences of V4 region of 16S rRNA gene provided that the shifts of microbial taxa to Fe(III)-reducing and/or sulfate-reducing microorganisms such as Geobacter, Albidiferax, Desulfocapsa, Desulfuromonas, and Desulfovibrio were in good correlation with the sequential flourishment of microbial reduction of Fe(III) and sulfate as the incubations progressed. This suggests the potential role of dissolved organic carbons migrated with the river water into groundwater in the managed aquifer recharge system on the indigenous microbial community composition and following alterations of subsurface biogeochemistry and microbial metabolic activities.

Assessment on cadmium and lead in soil based on a rhizosphere microbial community

The soil ecosystem is easily polluted by heavy metals. Cadmium (Cd) and lead (Pb), as the main pollutants of heavy metals, cause much harm to the soil ecosystem. However, the impact of the two chemicals on rhizosphere microorganisms remains almost unknown. The change of catalase (CAT) activity was consistent with the microbial biomass. 16S rRNA gene sequencing was performed on soil samples to study the toxic effect of heavy metals. On performing sequence analysis at the phylum and family taxonomic levels, 32 identified phyla and 303 families were observed. The dominant phylum was Proteobacteria followed by Bacteroidetes, Acidobacteria, and Actinobacteria. The relative abundance of the dominant phyla was obviously changed under the stress of Cd and Pb, suggesting that the heavy metal input had affected the microbial community structure. At the Order and Family levels, there was different variation of richness and diversity in Cd and Pb group as compared to those in the control group. Furthermore, abundance and similarity analysis showed the differences between Cd and Pb, indicating different toxicology effect on rhizosphere microbial communities because of the unique properties. This study provided a novel insight into the composition of microbial communities of rhizosphere, which could be used to evaluate the soil environment.

Fine Spatial Scale Variation of Soil Microbial Communities under European Beech and Norway Spruce

The complex interactions between trees and soil microbes in forests as well as their inherent seasonal and spatial variations are poorly understood. In this study, we analyzed the effects of major European tree species (Fagus sylvatica L. and Picea abies (L.) Karst) on soil bacterial and fungal communities. Mineral soil samples were collected from different depths (0-10, 10-20 cm) and at different horizontal distances from beech or spruce trunks (0.5, 1.5, 2.5, 3.5 m) in early summer and autumn. We assessed the composition of soil bacterial and fungal communities based on 16S rRNA gene and ITS DNA sequences. Community composition of bacteria and fungi was most strongly affected by soil pH and tree species. Different ectomycorrhizal fungi (e.g., Tylospora) known to establish mutualistic associations with plant roots showed a tree species preference. Moreover, bacterial and fungal community composition showed spatial and seasonal shifts in soil surrounding beech and spruce. The relative abundance of saprotrophic fungi was higher at a depth of 0-10 vs. 10-20 cm depth. This was presumably a result of changes in nutrient availability, as litter input and organic carbon content decreased with soil depth. Overall bacterial community composition showed strong variations under spruce with increasing distance from the tree trunks, which might be attributed in part to higher fine root biomass near spruce trunks. Furthermore, overall bacterial community composition was strongly affected by season under deciduous trees.

Response of enzyme activities and microbial communities to soil amendment with sugar alcohols

Changes in microbial community structure are widely known to occur after soil amendment with low-molecular-weight organic compounds; however, there is little information on concurrent changes in soil microbial functional diversity and enzyme activities, especially following sorbitol and mannitol amendment. Soil microbial functional diversity and enzyme activities can be impacted by sorbitol and mannitol, which in turn can alter soil fertility and quality. The objective of this study was to investigate the effects of sorbitol and mannitol addition on microbial functional diversity and enzyme activities. The results demonstrated that sorbitol and mannitol addition altered the soil microbial community structure and improved enzyme activities. Specifically, the addition of sorbitol enhanced the community-level physiological profile (CLPP) compared with the control, whereas the CLPP was significantly inhibited by the addition of mannitol. The results of a varimax rotated component matrix demonstrated that carbohydrates, polymers, and carboxylic acids affected the soil microbial functional structure. Additionally, we found that enzyme activities were affected by both the concentration and type of inputs. In the presence of high concentrations of sorbitol, the urease, catalase, alkaline phosphatase, β-glucosidase, and N-acetyl-β-d-glucosaminidase activities were significantly increased, while invertase activity was decreased. Similarly, this increase in invertase, catalase, and alkaline phosphatase and N-acetyl-β-d-glucosaminidase activities was especially evident after mannitol addition, and urease activity was only slightly affected. In contrast, β-glucosidase activity was suppressed at the highest concentration. These results indicate that microbial community diversity and enzyme activities are significantly affected by soil amendment with sorbitol and mannitol.

Microbial communities in riparian soils of a settling pond for mine drainage treatment

Mine drainage leads to serious contamination of soil. To assess the effects of mine drainage on microbial communities in riparian soils, we used an Illumina MiSeq platform to explore the soil microbial composition and diversity along a settling pond used for mine drainage treatment. Non-metric multidimensional scaling analysis showed that the microbial communities differed significantly among the four sampling zones (influent, upstream, downstream and effluent), but not seasonally. Constrained analysis of principal coordinates indicated heavy metals (zinc, lead and copper), total sulphur, pH and available potassium significantly influenced the microbial community compositions. Heavy metals were the key determinants separating the influent zone from the other three zones. Lower diversity indices were observed in the influent zone. However, more potential indicator species, related to sulphur and organic matter metabolism were found there, such as the sulphur-oxidizing genera Acidiferrobacter, Thermithiobacillus, Limnobacter, Thioprofundum and Thiovirga, and the sulphur-reducing genera Desulfotomaculum and Desulfobulbus; the organic matter degrading genera, Porphyrobacter and Paucimonas, were also identified. The results indicated that more microorganisms related to sulphur- and carbon-cycles may exist in soils heavily contaminated by mine drainage.

Effect of long-term industrial waste effluent pollution on soil enzyme activities and bacterial community composition

Although numerous studies have addressed the influence of exogenous pollutants on microorganisms, the effect of long-term industrial waste effluent (IWE) pollution on the activity and diversity of soil bacteria was still unclear. Three soil samples characterized as uncontaminated (R1), moderately contaminated (R2), and highly contaminated (R3) receiving mixed organic and heavy metal pollutants for more than 20 years through IWE were collected along the Mahi River basin, Gujarat, western India. Basal soil respiration and in situ enzyme activities indicated an apparent deleterious effect of IWE on microbial activity and soil function. Community composition profiling of soil bacteria using 16S rRNA gene amplification and denaturing gradient gel electrophoresis (DGGE) method indicated an apparent bacterial community shift in the IWE-affected soils. Cloning and sequencing of DGGE bands revealed that the dominated bacterial phyla in polluted soil were affiliated with Firmicutes, Acidobacteria, and Actinobacteria, indicating that these bacterial phyla may have a high tolerance to pollutants. We suggested that specific bacterial phyla along with soil enzyme activities could be used as relevant biological indicators for long-term pollution assessment on soil quality. Graphical Abstract Bacterial community profiling and soil enzyme activities in long-term industrial waste effluent polluted soils.

High throughput sequencing analysis of the joint effects of BDE209-Pb on soil bacterial community structure

Decabromodiphenyl ether (BDE209) and Lead (Pb) are the main pollutants at e-waste recycling sites (EWRSs). However, the impact on soil microorganism of joint exposure to the two chemicals remains almost unknown. Therefore, the indoor incubation tests were performed to determine the response of soil microbial biomass and activity as well as bacterial community structure in the presence of the two chemicals during 60 d incubation period. The results indicated that after Pb alone or BDE209-Pb exposure, soil microbial biomass C (Cmic) was significantly lower (p<0.01), and soil basal respiration (SBR) and metabolic quotient (qCO2) were enhanced, while BDE209 barely resulted in significant influence (p>0.05). 16S rRNA gene sequencing on the Illumina MiSeq platform demonstrated that a total 49,405 valid sequences widely represented the diversity of microbial community. Sequence analyses at phylum and genus taxonomic levels illustrated that 11 identified phyla and 297 genera were observed among all the soil samples, and the contaminants input had affected bacterial community structure, suggesting that Proteobacteria, Actinobacteria and Acidobacteria were the dominant phyla, and the genera Massilia and Bacillus were enriched in contaminated soil. BDE209 exposure alone in all the samples indicated a more similar community structure compared to the control. The results of these observations have provided a better understanding of ecotoxicological effects of BDE209 and Pb joint exposure on indigenous microorganisms in soil at EWRSs.

Heavy metal-immobilizing organoclay facilitates polycyclic aromatic hydrocarbon biodegradation in mixed-contaminated soil

Soils contaminated with a mixture of heavy metals and polycyclic aromatic hydrocarbons (PAHs) pose toxic metal stress to native PAH-degrading microorganisms. Adsorbents such as clay and modified clay minerals can bind the metal and reduce its toxicity to microorganisms. However, in a mixed-contaminated soil, an adsorption process more specific to the metals without affecting the bioavailability of PAHs is desired for effective degradation. Furthermore, the adsorbent should enhance the viability of PAH-degrading microorganisms. A metal-immobilizing organoclay (Arquad(®) 2HT-75-bentonite treated with palmitic acid) (MIOC) able to reduce metal (cadmium (Cd)) toxicity and enhance PAH (phenanthrene) biodegradation was developed and characterized in this study. The MIOC differed considerably from the parent clay in terms of its ability to reduce metal toxicity (MIOC>unmodified bentonite>Arquad-bentonite). The MIOC variably increased the microbial count (10-43%) as well as activities (respiration 3-44%; enzymatic activities up to 68%), and simultaneously maintained phenanthrene in bioavailable form in a Cd-phenanthrene mixed-contaminated soil over a 21-day incubation period. This study may lead to a new MIOC-assisted bioremediation technique for PAHs in mixed-contaminated soils.

Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment

Hexavalent chromium [Cr(VI)] is a soluble carcinogen that has caused widespread contamination of soil and water in many industrial nations. Bacteria have the potential to aid remediation as certain strains can catalyze the reduction of Cr(VI) to insoluble and less toxic Cr(III). Here, we examine Cr(VI) reducing Microbacterium spp. (Cr-K1W, Cr-K20, Cr-K29, and Cr-K32) isolated from contaminated sediment (Seymore, Indiana) and show varying chromate responses despite the isolates' phylogenetic similarity (i.e., identical 16S rRNA gene sequences). Detailed analysis identified differences based on genomic metabolic potential, growth and general metabolic capabilities, and capacity to resist and reduce Cr(VI). Taken together, the discrepancies between the isolates demonstrate the complexity inter-strain variation can have on microbial physiology and related biogeochemical processes.

Arsenic(V) reduction in relation to Iron(III) transformation and molecular characterization of the structural and functional microbial community in sediments of a basin-fill aquifer in Northern Utah

Basin-fill aquifers of the Southwestern United States are associated with elevated concentrations of arsenic (As) in groundwater. Many private domestic wells in the Cache Valley Basin, UT, have As concentrations in excess of the U.S. EPA drinking water limit. Thirteen sediment cores were collected from the center of the valley at the depth of the shallow groundwater and were sectioned into layers based on redoxmorphic features. Three of the layers, two from redox transition zones and one from a depletion zone, were used to establish microcosms. Microcosms were treated with groundwater (GW) or groundwater plus glucose (GW+G) to investigate the extent of As reduction in relation to iron (Fe) transformation and characterize the microbial community structure and function by sequencing 16S rRNA and arsenate dissimilatory reductase (arrA) genes. Under the carbon-limited conditions of the GW treatment, As reduction was independent of Fe reduction, despite the abundance of sequences related to Geobacter and Shewanella, genera that include a variety of dissimilatory iron-reducing bacteria. The addition of glucose, an electron donor and carbon source, caused substantial shifts toward domination of the bacterial community by Clostridium-related organisms, and As reduction was correlated with Fe reduction for the sediments from the redox transition zone. The arrA gene sequencing from microcosms at day 54 of incubation showed the presence of 14 unique phylotypes, none of which were related to any previously described arrA gene sequence, suggesting a unique community of dissimilatory arsenate-respiring bacteria in the Cache Valley Basin.

Chromium-resistant bacteria promote the reduction of hexavalent chromium in soils

Knowledge of the chromium (Cr) redox process in soil is important in addressing Cr bioavailability and risk assessment of contaminated soils. In this study, seven representative agricultural soils with different physicochemical properties were used to investigate the importance of microbially mediated Cr(VI) reduction and the response of soil bacterial community to Cr contamination. Chromium application increased soil bacterial diversity in Periudic Argosols, Calcaric Regosols, Stagnic Anthrosols, Mollisols, Typic Haplustalfs, and Ustic Cambosols, with an exception of Udic Ferrisols. The soil bacterial community responded to Cr contamination through changes in bacterial community structure, with Cr-resistant bacteria becoming the dominant species, and the percentage of Cr-resistant bacteria of total cultivable bacteria was 89.9, 75.2, 92.8, 65.3, 72.8, 77.3, and 65.4%, respectively, for Periudic Argosols, Udic Ferrisols, Calcaric Regosols, Stagnic Anthrosols, Mollisols, Typic Haplustalfs, and Ustic Cambosols. , , , , , , , , , and were identified as the Cr-resistant bacteria. Moreover, our results demonstrated that microbial reduction was an important Cr(VI) reduction pathway, and the relative contribution of microorganisms to Cr(VI) reduction was 14.4, 44.0, 20.6, 34.9, 21.9, 21.7, and 22.0%, respectively for Periudic Argosols, Udic Ferrisols, Calcaric Regosols, Stagnic Anthrosols, Mollisols, Typic Haplustalfs, and Ustic Cambosols. Soil properties, especially Fe(II) and soil particle distribution, affected the microbially mediated Cr(VI) reduction. These results provide useful information for the bioremediation of Cr-contaminated soils under a wide range of environmental conditions.

Fine-scale spatial patterns in bacterial community composition and function within freshwater ponds

The extent to which non-host-associated bacterial communities exhibit small-scale biogeographic patterns in their distribution remains unclear. Our investigation of biogeography in bacterial community composition and function compared samples collected across a smaller spatial scale than most previous studies conducted in freshwater. Using a grid-based sampling design, we abstracted 100+ samples located between 3.5 and 60 m apart within each of three alpine ponds. For every sample, variability in bacterial community composition was monitored using a DNA-fingerprinting methodology (automated ribosomal intergenic spacer analysis) whereas differences in bacterial community function (that is, carbon substrate utilisation patterns) were recorded from Biolog Ecoplates. The exact spatial position and dominant physicochemical conditions (for example, pH and temperature) were simultaneously recorded for each sample location. We assessed spatial differences in bacterial community composition and function within each pond and found that, on average, community composition or function differed significantly when comparing samples located >20 m apart within any pond. Variance partitioning revealed that purely spatial variation accounted for more of the observed variability in both bacterial community composition and function (range: 24-38% and 17-39%) than the combination of purely environmental variation and spatially structured environmental variation (range: 17-32% and 15-20%). Clear spatial patterns in bacterial community composition, but not function were observed within ponds. We therefore suggest that some of the observed variation in bacterial community composition is functionally 'redundant'. We confirm that distinct bacterial communities are present across unexpectedly small spatial scales suggesting that populations separated by distances of >20 m may be dispersal limited, even within the highly continuous environment of lentic water.

Analysis of the diversity of substrate utilisation of soil bacteria exposed to Cd and earthworm activity using generalised additive models

Biolog EcoPlates™ can be used to measure the carbon substrate utilisation patterns of microbial communities. This method results in a community-level physiological profile (CLPP), which yields a very large amount of data that may be difficult to interpret. In this work, we explore a combination of statistical techniques (particularly the use of generalised additive models [GAMs]) to improve the exploitation of CLPP data. The strength of GAMs lies in their ability to address highly non-linear relationships between the response and the set of explanatory variables. We studied the impact of earthworms (Aporrectodea caliginosa Savigny 1826) and cadmium (Cd) on the CLPP of soil bacteria. The results indicated that both Cd and earthworms modified the CLPP. GAMs were used to assess time-course changes in the diversity of substrate utilisation (DSU) using the Shannon-Wiener index. GAMs revealed significant differences for all treatments (compared to control -S-). The Cd exposed microbial community presented very high metabolic capacities on a few substrata, resulting in an initial acute decrease of DSU (i.e. intense utilization of a few carbon substrata). After 54 h, and over the next 43 h the increase of the DSU suggest that other taxa, less dominant, reached high numbers in the wells containing sources that are less suitable for the Cd-tolerant taxa. Earthworms were a much more determining factor in explaining time course changes in DSU than Cd. Accordingly, Ew and EwCd soils presented similar trends, regardless the presence of Cd. Moreover, both treatments presented similar number of bacteria and higher than Cd-treated soils. This experimental approach, based on the use of DSU and GAMs allowed for a global and statistically relevant interpretation of the changes in carbon source utilisation, highlighting the key role of earthworms on the protection of microbial communities against the Cd.

Impact of Zn and Cu on the development of phenanthrene catabolism in soil

Mixtures of polycyclic aromatic hydrocarbons (PAHs) and heavy metals are of major concern in contaminated soil. Biodegradation of PAHs in metal-contaminated soils is complicated because metals are toxic and cannot be degraded by biological processes. This investigation considered the effects of Zn and Cu (50, 100, 500 and 1,000 mg/kg) on (14)C-phenanthrene biodegradation in soil over 60-day contact time. The presence of Zn at all concentrations and low concentrations of Cu (50 and 100 mg/kg) had no significant effect (p > 0.05) on the development of phenanthrene catabolism; however, at higher Cu concentrations, the development of phenanthrene catabolism and bacterial cell numbers were significantly reduced (p < 0.05). This suggests that Cu is more toxic than Zn to soil microbial PAH catabolic activity. Metal/PAH-contaminated soils represent one of the most difficult remedial challenges and insights into PAH biodegradation in the presence of metals is necessary in order to assess the potential for bioremediation.

Environmental controls on the activity of aquifer microbial communities in the 300 area of the Hanford site

Aquifer microbes in the 300 Area of the Hanford Site in southeastern Washington State, USA, are located in an oligotrophic environment and are periodically exposed to U(VI) concentrations that can range up to 10 μM in small sediment fractures. Assays of (3)H-leucine incorporation indicated that both sediment-associated and planktonic microbes were metabolically active, and that organic C was growth-limiting in the sediments. Although bacteria suspended in native groundwater retained high activity when exposed to 100 μM U(VI), they were inhibited by U(VI) <1 μM in synthetic groundwater that lacked added bicarbonate. Chemical speciation modeling suggested that positively charged species and particularly (UO2)3(OH)5 (+) rose in concentration as more U(VI) was added to synthetic groundwater, but that carbonate complexes dominated U(VI) speciation in natural groundwater. U toxicity was relieved when increasing amounts of bicarbonate were added to synthetic groundwater containing 4.5 μM U(VI). Pertechnetate, an oxyanion that is another contaminant of concern at the Hanford Site, was not toxic to groundwater microbes at concentrations up to 125 μM.

Complete genome sequence of Arthrobacter sp. strain FB24

Arthrobacter sp. strain FB24 is a species in the genus Arthrobacter Conn and Dimmick 1947, in the family Micrococcaceae and class Actinobacteria. A number of Arthrobacter genome sequences have been completed because of their important role in soil, especially bioremediation. This isolate is of special interest because it is tolerant to multiple metals and it is extremely resistant to elevated concentrations of chromate. The genome consists of a 4,698,945 bp circular chromosome and three plasmids (96,488, 115,507, and 159,536 bp, a total of 5,070,478 bp), coding 4,536 proteins of which 1,257 are without known function. This genome was sequenced as part of the DOE Joint Genome Institute Program.

Are uncultivated bacteria really uncultivable?

Many strategies have been used to increase the number of bacterial cells that can be grown from environmental samples but cultivation efficiency remains a challenge for microbial ecologists. The difficulty of cultivating a fraction of bacteria in environmental samples can be classified into two non-exclusive categories. Bacterial taxa with no cultivated representatives for which appropriate laboratory conditions necessary for growth are yet to be identified. The other class is cells in a non-dividing state (also known as dormant or viable but not culturable cells) that require the removal or addition of certain factors to re-initiate growth. A number of strategies, from simple to high throughput techniques, are reviewed that have been used to increase the cultivation efficiency of environmental samples. Some of the underlying mechanisms that contribute to the success of these cultivation strategies are described. Overall this review emphasizes the need of researchers to first understand the factors that are hindering cultivation to identify the best strategies to improve cultivation efficiency.

The exposition of a calcareous Mediterranean soil to toxic concentrations of Cr, Cd and Pb produces changes in the microbiota mainly related to differential metal bioavailability

The involvement of the bacterial community of an agricultural Mediterranean calcareous soil in relation to several heavy metals has been studied in microcosms under controlled laboratory conditions. Soil samples were artificially polluted with Cr(VI), Cd(II) and Pb(II) at concentrations ranging from 0.1 to 5000 mg kg(-1) and incubated along 28 d. The lowest concentrations with significant effects in soil respirometry were 10 mg kg(-1) Cr and 1000 mg kg(-1) Cd and Pb. However, only treatments showing more than 40% inhibition of respirometric activity led to significant changes in bacterial composition, as indicated by PCR-DGGE analyses. Presumable Cr- and Cd-resistant bacteria were detected in polluted microcosms, but development of the microbiota was severely impaired at the highest amendments of both metals. Results also showed that bioavailability is an important factor determining the impact of the heavy metals assayed, and even an inverted potential toxicity ranking could be achieved if their soluble fraction is considered instead of the total concentration. Moreover, multiresistant bacteria were isolated from Cr-polluted soil microcosms, some of them showing the capacity to reduce Cr(VI) concentrations between 26% and 84% of the initial value. Potentially useful strains for bioremediation were related to Arthrobacter crystallopoietes, Stenotrophomonas maltophilia and several species of Bacillus.

Reduction kinetics of hexavalent chromium in soils and its correlation with soil properties

The toxicity of chromium (Cr) to biota is related to its chemical forms and consequently to the redox conditions of soils. Hexavalent Cr[Cr(VI)] may undergo natural attenuation through reduction processes. In this study, the reduction kinetics of Cr(VI) in seven soils and its relationships with soil properties were investigated with laboratory incubation experiments. The results indicate that the reduction of Cr(VI) can be described by a first-order reaction. The reduction rates of Cr(VI) in the seven soils decreased in the order: Udic Ferrisols > Stagnic Anthrosols > Calcaric Regosols > Mollisol > Typic Haplustalf > Periudic Argosols > Ustic Cambosols. Simple correlation analysis revealed that the reduction of Cr(VI) in soils was positively related to organic matter content, dissolved organic matter content, Fe(II) content, clay fraction, and to the diversity index of the bacterial community but negatively correlated with easily reducible Mn content. Using stepwise regression, the reduction of Cr(VI) in soil could be quantitatively predicted by the measurement of dissolved organic matter content, Fe(II) content, pH, and soil particle size distribution, with a fitting level of 95.5%. The results indicated that the reduction of Cr(VI) in natural soils is not controlled by a single soil property but is the result of the combined effects of dissolved organic matter, Fe(II), pH, and soil particle size distribution.

Surface enhanced Raman spectroscopy (SERS) for the discrimination of Arthrobacter strains based on variations in cell surface composition

Surface enhanced Raman spectroscopy (SERS) is a rapid and highly sensitive spectroscopic technique that has the potential to measure chemical changes in bacterial cell surface in response to environmental changes. The objective of this study was to determine whether SERS had sufficient resolution to differentiate closely related bacteria within a genus grown on solid and liquid medium, and a single Arthrobacter strain grown in multiple chromate concentrations. Fourteen closely related Arthrobacter strains, based on their 16S rRNA gene sequences, were used in this study. After performing principal component analysis in conjunction with Linear Discriminant Analysis, we used a novel, adapted cross-validation method, which more faithfully models the classification of spectra. All fourteen strains could be classified with up to 97% accuracy. The hierarchical trees comparing SERS spectra from the liquid and solid media datasets were different. Additionally, hierarchical trees created from the Raman data were different from those obtained using 16S rRNA gene sequences (a phylogenetic measure). A single bacterial strain grown on solid media culture with three different chromate levels also showed significant spectral distinction at discrete points identified by the new Elastic Net regularized regression method demonstrating the ability of SERS to detect environmentally induced changes in cell surface composition. This study demonstrates that SERS is effective in distinguishing between a large number of very closely related Arthrobacter strains and could be a valuable tool for rapid monitoring and characterization of phenotypic variations in a single population in response to environmental conditions.

Firing range soils yield a diverse array of fungal isolates capable of organic acid production and Pb mineral solubilization

Anthropogenic sources of lead contamination in soils include mining and smelting activities, effluents and wastes, agricultural pesticides, domestic garbage dumps, and shooting ranges. While Pb is typically considered relatively insoluble in the soil environment, some fungi may potentially contribute to mobilization of heavy metal cations by means of secretion of low-molecular-weight organic acids (LMWOAs). We sought to better understand the potential for metal mobilization within an indigenous fungal community at an abandoned shooting range in Oak Ridge, TN, where soil Pb contamination levels ranged from 24 to >2,700 mg Pb kg dry soil(-1). We utilized culture-based assays to determine organic acid secretion and Pb-carbonate dissolution of a diverse collection of soil fungal isolates derived from the site and verified isolate distribution patterns within the community by 28S rRNA gene analysis of whole soils. The fungal isolates examined included both ascomycetes and basidiomycetes that excreted high levels (up to 27 mM) of a mixture of LMWOAs, including oxalic and citric acids, and several isolates demonstrated a marked ability to dissolve Pb-carbonate at high concentrations up to 10.5 g liter(-1) (18.5 mM) in laboratory assays. Fungi within the indigenous community of these highly Pb-contaminated soils are capable of LMWOA secretion at levels greater than those of well-studied model organisms, such as Aspergillus niger. Additionally, these organisms were found in high relative abundance (>1%) in some of the most heavily contaminated soils. Our data highlight the need to understand more about autochthonous fungal communities at Pb-contaminated sites and how they may impact Pb biogeochemistry, solubility, and bioavailability, thus consequently potentially impacting human and ecosystem health.

Groundwater remediation using an enricher reactor-permeable reactive biobarrier for periodically absent contaminants

A combined enricher reactor (ER)-permeable reactive biobarrier (PRBB) system was developed to treat groundwater with contaminants that appear in batches. An enricher reactor is an offline reactor used to enrich contaminant degraders by supplying necessary growth materials, and the enriched degraders are used to augment PRBB to increase its performance after a period of contaminant absence. Bench-scale experiments on PRBBs with and without bacterial supply from the enricher reactor were conducted to evaluate PRBB removal performances for benzene, which was used as a model contaminant. Benzene absence periods of 10 and 25 days were tested in the presence and absence of ethanol. The PRBBs without the bioaugmentation from the enricher reactor experienced a decrease in performance from approximately 65% to 30% after benzene reappeared. The presence of ethanol accelerated the benzene removal performance recovery of PRBBs. The 25-day benzene absence period caused greater changes in the bacterial community structure, regardless of the ethanol availability.

Surface-enhanced Raman imaging of intracellular bioreduction of chromate in Shewanella oneidensis

This proposed research aims to use novel nanoparticle sensors and spectroscopic tools constituting surface-enhanced Raman spectroscopy (SERS) and Fluorescence Lifetime imaging (FLIM) to study intracellular chemical activities within single bioremediating microorganism. The grand challenge is to develop a mechanistic understanding of chromate reduction and localization by the remediating bacterium Shewanella oneidensis MR-1 by chemical and lifetime imaging. MR-1 has attracted wide interest from the research community because of its potential in reducing multiple chemical and metallic electron acceptors. While several biomolecular approaches to decode microbial reduction mechanisms exist, there is a considerable gap in the availability of sensor platforms to advance research from population-based studies to the single cell level. This study is one of the first attempts to incorporate SERS imaging to address this gap. First, we demonstrate that chromate-decorated nanoparticles can be taken up by cells using TEM and Fluorescence Lifetime imaging to confirm the internalization of gold nanoprobes. Second, we demonstrate the utility of a Raman chemical imaging platform to monitor chromate reduction and localization within single cells. Distinctive differences in Raman signatures of Cr(VI) and Cr(III) enabled their spatial identification within single cells from the Raman images. A comprehensive evaluation of toxicity and cellular interference experiments conducted revealed the inert nature of these probes and that they are non-toxic. Our results strongly suggest the existence of internal reductive machinery and that reduction occurs at specific sites within cells instead of at disperse reductive sites throughout the cell as previously reported. While chromate-decorated gold nanosensors used in this study provide an improved means for the tracking of specific chromate interactions within the cell and on the cell surface, we expect our single cell imaging tools to be extended to monitor the interaction of other toxic metal species.

Root exudates modify bacterial diversity of phenanthrene degraders in PAH-polluted soil but not phenanthrene degradation rates

To determine whether the diversity of phenanthrene-degrading bacteria in an aged polycyclic aromatic hydrocarbon (PAH) contaminated soil is affected by the addition of plant root exudates, DNA stable isotope probing (SIP) was used. Microcosms of soil with and without addition of ryegrass exudates and with ¹³C-labelled phenanthrene (PHE) were monitored over 12 days. PHE degradation was slightly delayed in the presence of added exudate after 4 days of incubation. After 12 days, 68% of added PHE disappeared both with and without exudate. Carbon balance using isotopic analyses indicated that a part of the ¹³C-PHE was not totally mineralized as ¹³CO₂ but unidentified ¹³C-compounds (i.e. ¹³C-PHE or ¹³C-labelled metabolites) were trapped into the soil matrix. Temporal thermal gradient gel electrophoresis (TTGE) analyses of 16S rRNA genes were performed on recovered ¹³C-enriched DNA fractions. 16S rRNA gene banding showed the impact of root exudates on diversity of PHE-degrading bacteria. With PHE as a fresh sole carbon source, Pseudoxanthomonas sp. and Microbacterium sp. were the major PHE degraders, while in the presence of exudates, Pseudomonas sp. and Arthrobacter sp. were favoured. These two different PHE-degrading bacterial populations were also distinguished through detection of PAH-ring hydroxylating dioxygenase (PAH-RHD(α)) genes by real-time PCR. Root exudates favoured the development of a higher diversity of bacteria and increased the abundance of bacteria containing known PAH-RHD(α) genes.

Bacteria with dual resistance to elevated concentrations of heavy metals and antibiotics in Nigerian contaminated systems

Samples of soil, water, and sediments from industrial estates in Lagos were collected and analyzed for heavy metals and physicochemical composition. Bacteria that are resistant to elevated concentrations of metals (Cd(2+), Co(2+), Ni(2+), Cr(6+), and Hg(2+)) were isolated from the samples, and they were further screened for antibiotic sensitivity. The minimum tolerance concentrations (MTCs) of the isolates with dual resistance to the metals were determined. The physicochemistry of all the samples indicated were heavily polluted. Twenty-two of the 270 bacterial strains isolated showed dual resistances to antibiotics and heavy metals. The MTCs of isolates to the metals were 14 mM for Cd(2+), 15 mM for Co(2+) and Ni(2+), 17 mM for Cr(6+), and 10 mM for Hg(2+). Five strains (Pseudomonas aeruginosa, Actinomyces turicensis, Acinetobacter junni, Nocardia sp., and Micrococcus sp.) resisted all the 18 antibiotics tested. Whereas Rhodococcus sp. and Micrococcus sp. resisted 15 mM Ni(2+), P. aeruginosa resisted 10 mM Co(2+). To our knowledge, there has not been any report of bacterial strains resisting such high doses of metals coupled with wide range of antibiotics. Therefore, dual expressions of antibiotics and heavy-metal resistance make the isolates, potential seeds for decommissioning of sites polluted with industrial effluents rich in heavy metals, since the bacteria will be able to withstand in situ antibiosis that may prevail in such ecosystems.

Bacterial community structure of sediments of the bizerte lagoon (Tunisia), a southern Mediterranean coastal anthropized lagoon

In order to estimate how pollution affects the bacterial community structure and composition of sediments, chemical and molecular approaches were combined to investigate eight stations around the Bizerte lagoon. Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified 16S rRNA genes revealed that each station was characterized by a specific bacterial community structure. The combination of this data with those of chemical analysis showed a correlation between the bacterial fingerprint and the pollutant content, principally with hydrocarbon pollution. The composition of the bacterial community of two contrasted stations related to the pollution revealed sequences affiliated to alpha, beta, gamma, delta, epsilon subclass of the Proteobacteria, Actinobacteria, and Acidobacteria in both stations although in different extent. Gamma and delta subclass of the Proteobacteria were dominant and represent 70% of clones in the heavy-metal-contaminated station and 47% in the polyaromatic hydrocarbon (PAH)-contaminated. Nevertheless, most of the sequences found were unaffiliated to cultured bacteria. The adaptation of the bacterial community mainly to PAH compounds demonstrated here and the fact that these bacterial communities are mainly unknown suggest that the Bizerte lagoon is an interesting environment to understand the capacity of bacteria to cope with some pollutants.

Assessing the correlation between anaerobic toluene degradation activity and bssA concentrations in hydrocarbon-contaminated aquifer material

The assessment of biodegradation activity in contaminated aquifers is critical to demonstrate the performance of bioremediation and natural attenuation and to parameterize models of contaminant plume dynamics. Real time quantitative PCR (qPCR) was used to target the catabolic bssA gene (coding for benzylsuccinate synthase) and a 16S rDNA phylogenetic gene (for total Bacteria) as potential biomarkers to infer on anaerobic toluene degradation rates. A significant correlation (P = 0.0003) was found over a wide range of initial toluene concentrations (1-100 mg/l) between toluene degradation rates and bssA concentrations in anaerobic microcosms prepared with aquifer material from a hydrocarbon contaminated site. In contrast, the correlation between toluene degradation activity and total Bacteria concentrations was not significant (P = 0.1125). This suggests that qPCR targeting of functional genes might offer a simple approach to estimate in situ biodegradation activity, which would enhance site investigation and modeling of natural attenuation at hydrocarbon-contaminated sites.

A combination method to study microbial communities and activities in zinc contaminated soil

Zinc (Zn) plays a special role in soil ecology and fertility because it can support the growth of soil organisms or inhibit their growth depending on its concentrations. In this work, the effects of different concentrations of Zn on soil microbial communities and activities were analyzed by loading five different doses of Zn (160-6000 microg g(-1)) into a wheat surface soil. The microbial metabolic process revealed a significant bimodal pattern at high concentrations of Zn (>1920 microg g(-1)). This phenomenon suggested that soil microorganisms were very sensitive to zincous poisoning. A variety of soil quality properties were also measured and assessed. The results showed slower bacterial growth in soil cultures polluted with high levels of Zn. In addition, two kinds of fungi were identified by morphology and glomalin-related soil protein content in the Zn-contaminated soil. The growth of the first kind was inhibited with increase in Zn concentration. By contrast, the second kind could survive and continue to grow with increasing doses of Zn at 160-1920 microg g(-1) and its growth began to decline with further increase in Zn concentration. Finally, the fungus could not survive at very high (6000 microg g(-1)) Zn concentration. In this work, we conclude that soil microbial communities and activities can adapt to Zn pollution to a certain extent.

High-level chromate resistance in Arthrobacter sp. strain FB24 requires previously uncharacterized accessory genes

Background

The genome of Arthrobacter sp. strain FB24 contains a chromate resistance determinant (CRD), consisting of a cluster of 8 genes located on a 10.6 kb fragment of a 96 kb plasmid. The CRD includes chrA, which encodes a putative chromate efflux protein, and three genes with amino acid similarities to the amino and carboxy termini of ChrB, a putative regulatory protein. There are also three novel genes that have not been previously associated with chromate resistance in other bacteria; they encode an oxidoreductase (most similar to malate:quinone oxidoreductase), a functionally unknown protein with a WD40 repeat domain and a lipoprotein. To delineate the contribution of the CRD genes to the FB24 chromate [Cr(VI)] response, we evaluated the growth of mutant strains bearing regions of the CRD and transcript expression levels in response to Cr(VI) challenge.

Results

A chromate-sensitive mutant (strain D11) was generated by curing FB24 of its 96-kb plasmid. Elemental analysis indicated that chromate-exposed cells of strain D11 accumulated three times more chromium than strain FB24. Introduction of the CRD into strain D11 conferred chromate resistance comparable to wild-type levels, whereas deletion of specific regions of the CRD led to decreased resistance. Using real-time reverse transcriptase PCR, we show that expression of each gene within the CRD is specifically induced in response to chromate but not by lead, hydrogen peroxide or arsenate. Higher levels of chrA expression were achieved when the chrB orthologs and the WD40 repeat domain genes were present, suggesting their possible regulatory roles.

Conclusion

Our findings indicate that chromate resistance in Arthrobacter sp. strain FB24 is due to chromate efflux through the ChrA transport protein. More importantly, new genes have been identified as having significant roles in chromate resistance. Collectively, the functional predictions of these additional genes suggest the involvement of a signal transduction system in the regulation of chromate efflux and warrants further study.

Inhibition of nitrate reduction by chromium (VI) in anaerobic soil microcosms

Chromium is often found as a cocontaminant at sites polluted with organic compounds. For nitrate-respiring microbes, Cr(VI) may be not only directly toxic but may also specifically interfere with N reduction. In soil microcosms amended with organic electron donors, Cr(VI), and nitrate, bacteria oxidized added carbon, but relatively low doses of Cr(VI) caused a lag and then lower rates of CO(2) accumulation. Cr(VI) strongly inhibited nitrate reduction; it occurred only after soluble Cr(VI) could not be detected. However, Cr(VI) additions did not eliminate Cr-sensitive populations; after a second dose of Cr(VI), bacterial activity was strongly inhibited. Differences in microbial community composition (assayed by PCR-denaturing gradient gel electrophoresis) driven by different organic substrates (glucose and protein) were smaller than when other electron acceptors had been used. However, the selection of bacterial phylotypes was modified by Cr(VI). Nine isolated clades of facultatively anaerobic Cr(VI)-resistant bacteria were closely related to cultivated members of the phylum Actinobacteria or Firmicutes. In Bacillus cereus GNCR-4, the nature of the electron donor (fermentable or nonfermentable) affected Cr(VI) resistance level and anaerobic nitrate metabolism. Our results indicate that carbon utilization and nitrate reduction in these soils were contingent upon the reduction of added Cr(VI). The amount of Cr(VI) required to inhibit nitrate reduction was 10-fold less than for aerobic catabolism of the same organic substrate. We speculate that the resistance level of a microbial process is directly related to the diversity of microbes capable of conducting it.

Enumeration of aromatic oxygenase genes to evaluate biodegradation during multi-phase extraction at a gasoline-contaminated site

Multi-phase extraction (MPE) is commonly used at petroleum-contaminated sites to volatilize and recover hydrocarbons from the vadose and saturated zones in contaminant source areas. Although primarily a physical treatment technology, the induced subsurface air flow can potentially increase oxygen supply and promote aerobic biodegradation of benzene, toluene, ethylbenzene, and xylenes (BTEX), the contaminants of concern at gasoline-contaminated sites. In this study, real-time PCR enumeration of aromatic oxygenase genes and PCR-DGGE profiles were used to elucidate the impact of MPE operation on the aquifer microbial community structure and function at a gasoline-contaminated site. Prior to system activation, ring-hydroxylating toluene monooxygenase (RMO) and naphthalene dioxygenase (NAH) gene copies were on the order of 10(6) to 10(10)copies L(-1) in groundwater samples obtained from BTEX-impacted wells. Aromatic oxygenase genes were not detected in groundwater samples obtained during continuous MPE indicating decreased populations of BTEX-utilizing bacteria. During periods of pulsed MPE, total aromatic oxygenase gene copies were not significantly different than prior to system activation, however, shifts in aromatic catabolic genotypes were noted. The consistent detection of RMO, NAH, and phenol hydroxylase (PHE), which catabolizes further oxidation of hydroxylated BTEX metabolites indicated the potential for aerobic biodegradation of dissolved BTEX during pulsed MPE.

Dynamics of microbial community during bioremediation of phenanthrene and chromium(VI)-contaminated soil microcosms

The combined effect of phenanthrene and Cr(VI) on soil microbial activity, community composition and on the efficiency of bioremediation processes has been studied. Biometer flask systems and soil microcosm systems contaminated with 2,000 mg of phenanthrene per kg of dry soil and different Cr(VI) concentrations were investigated. Temperature, soil moisture and oxygen availability were controlled to support bioremediation. Cr(VI) inhibited the phenanthrene mineralization (CO(2) production) and cultivable PAH degrading bacteria at levels of 500-2,600 mg kg(-1). In the bioremediation experiments in soil microcosms the degradation of phenanthrene, the dehydrogenase activity and the increase in PAH degrading bacteria counts were retarded by the presence of Cr(VI) at all studied concentrations (25, 50 and 100 mg kg(-1)). These negative effects did not show a correlation with Cr(VI) concentration. Whereas the presence of Cr(VI) had a negative effect on the phenanthrene elimination rate, co-contamination with phenanthrene reduced the residual Cr(VI) concentration in the water exchangeable Cr(VI) fraction (WEF) in comparison with the soil microcosm contaminated only with Cr(VI). Clear differences were found between the denaturing gradient gel electrophoresis (DGGE) patterns of each soil microcosm, showing that the presence of different Cr(VI) concentrations did modulate the community response to phenanthrene and caused perdurable changes in the structure of the microbial soil community.