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

Activated carbon as a strong DOM adsorbent mitigates antimony and arsenic release in flooded mining-impacted soils

In Southern China, the co-occurrence of arsenic (As) and antimony (Sb) contamination in soils around Sb mines presents an environmental challenge. During the flooding period of mining-impacted soils, anaerobic reduction of iron (Fe) oxides enhances the mobilization and bioavailability of Sb and As, further elevating the risk of Sb and As entering the food chain. To address this problem, activated carbon (AC) and biochar (BC) were applied to remediate flooded mining-impacted soils. Our results explored that AC can significantly decrease mobilization by 9-97 % for Sb and 9-67 % for As through inhibiting Fe(III) mineral reduction and dissolution in flooded soils. In contrast, there was no significant effect of BC. This was attributed to the strong adsorption of soil dissolved organic matter (DOM) by AC compared to BC, while DOM as electron shuttle is crucial for microbial Fe(III) reduction. Consequently, the DOM sequestration by AC effectively mitigates Sb and As leaching in contaminated mining soils.

Enriching electroactive microorganisms from ferruginous lake waters - Mind the sulfate reducers!

Electroactive microorganisms are pivotal players in mineral transformation within redox interfaces characterized by pronounced oxygen and dissolved metal gradients. Yet, their systematic cultivation from such environments remains elusive. Here, we conducted an anodic enrichment using anoxic ferruginous waters from a post-mining lake as inoculum. Weak electrogenicity (j = ∼5 µA cm-2) depended on electroactive planktonic cells rather than anodic biofilms, with a preference for formate as electron donor. Addition of yeast extract decreased the lag phase but did not increase current densities. The enriched bacterial community varied depending on the substrate composition but mainly comprised of sulfate- and nitrate-reducing bacteria (e.g., Desulfatomaculum spp. and Stenotrophomonas spp.). A secondary enrichment strategy resulted in different bacterial communities composed of iron-reducing (e.g., Klebsiella spp.) and fermentative bacteria (e.g., Paeniclostridium spp.). Secondary electron microscopy and energy-dispersive X-ray spectroscopy results indicate the precipitation of sulfur- and iron-rich organomineral aggregates at the anode surface, presumably impeding current production. Our findings indicate that (i) anoxic waters containing geogenically derived metals can be used to enrich weak electricigens, and (ii) it is necessary to specifically inhibit sulfate reducers. Otherwise, sulfate reducers tend to dominate over EAM during cultivation, which can lead to anode passivation due to biomineralization.

Effects of citric acid on arsenic transformation and microbial communities in different paddy soils

Root exudate is a major source of soil organic matter and can significantly affect arsenic (As) migration and transformation in paddy soils. Citric acid is the main component of rice root exudate, however, the impacts and rules of citric acid on As bioavailability and rhizobacteria in different soils remains unclear. This study investigated the effects of citric acid on As transformation and microbial community in ten different paddy soils by flooded soil culture experiments. The results showed that citric acid addition increased total As and arsenate (As(V)) in the soil porewater by up to 41-fold and 65-fold, respectively, after 2-h incubation. As(V) was the main As species in soil porewater within 10 days with the addition of citric acid. Non-specifically sorbed As of soils, total Fe and total As were the main environmental factors affecting the soil microbial communities. High-throughput sequencing analysis demonstrated that citric acid addition significantly altered the soil microbial community structure, shifting the Proteobacteria-related reducing bacteria to Firmicutes-related reducing bacteria in different paddy soils. The relative abundance of Firmicutes was promoted by 174-196%. Clostridium-related bacteria belonging to Firmicutes became the dominant genera, which is believed to regulate As release through the reductive dissolution of iron oxides or the direct reduction of As(V) to arsenite (As(III)). However, citric acid addition significantly decreased the relative abundance of Geobacter and Anaeromyxobacter, which are also typical active As(V)- and ferric-reducing bacteria. Real-time quantitative polymerase chain reaction (qPCR) also revealed that the addition of citric acid significantly decreased the relative abundances of Geobacter in the different soils by 8-28 times while the relative abundances of Clostridium increased by 2-5 times. These results provide significant insight on As transformation in different types of rice rhizospheric soils and guidance for the application of rice varieties with low citric acid exuding to restrict As accumulation.

A combined strategy to mitigate the accumulation of arsenic and cadmium in rice (Oryza sativa L.)

Arsenic and cadmium in rice grain are of growing concern in the global food supply chain. Paradoxically, the two elements have contrasting behaviors in soils, making it difficult to develop a strategy that can concurrently reduce their uptake and accumulation by rice plant. This study examined the combined impacts of watering (irrigation) schemes, different fertilizers and microbial populations on the bioaccumulation of arsenic and cadmium by rice as well as on rice grain yield. Compared to drain-flood and flood-drain treatments, continuously flooded condition significantly reduced the accumulation of cadmium in rice plant but the level of arsenic in rice grain remained above 0.2 mg/kg, which exceeded the China national food safety standard. Application of different fertilizers under continuously flooded condition showed that compared to inorganic fertilizer and biochar, manure addition effectively reduced the accumulation of arsenic over three to four times in rice grain and both elements were below the food safety standard (0.2 mg/kg) while significantly increasing the rice yield. Soil Eh was the critical factor in the bioavailability of cadmium, while the behavior of arsenic in rhizosphere was associated with the iron cycle. The results of the multi-parametric experiments can be used as a roadmap for low-cost and in-situ approach for producing safe rice without compromising the yield.

The key role of biogenic arsenic sulfides in the removal of soluble arsenic and propagation of arsenic mineralizing communities

Biogeochemical processes govern the transport and availability of arsenic in sediments. However, little is known about the transition from indigenous communities to cultivable consortia when exposed to high arsenic concentrations. Such cultivable communities could be exploited for arsenic bioremediation of waste streams and polluted sites. Thus, it is crucial to understand the dynamics and selective pressures that shape the communities during the development of customized bacterial consortia. First, from the arsenic partitioning of two sediments with high arsenic concentrations, we found that up to 55% of arsenic was bioavailable because it was associated with the soluble, carbonate, and ionically exchangeable fractions. Next, we prepared sediment enrichment cultures under arsenate- and sulfate-reducing conditions to precipitate arsenic sulfide biominerals and analyze the communities. The produced biominerals were used as the inoculum to develop bacterial consortia via successive transfers. Tracking of the 16S rRNA gene in the fresh sediments, sediment enrichments, biogenic minerals, and bacterial consortia revealed differences in the bacterial communities. Removing the sediment caused a substantial decrease in diversity and shifts toward the dominance of the Firmicutes phylum to the detriment of Proteobacteria. In agreement with the 16S rRNA gene results, the sequencing of the arrA gene confirmed the presence of phylotypes closely related to Desulfosporosinus sp. Y5 (100% similarity), highlighting the pivotal role of this genus in the removal of soluble arsenic. Here, we demonstrated for the first time that besides being important as arsenic sinks, the biogenic arsenic sulfide minerals are reservoirs of arsenic resistant/respiring bacteria and can be used to culture them.

Manure application facilitated electrokinetic remediation of antibiotic-arsenic co-contaminated paddy soil

The co-existence of antibiotics and heavy metals in soil with manure application poses high risk to both environment and human health, and thus effective remediation methods are in urgent need. This study investigated the synergistic effects of electrokinetic remediation (EKR) on antibiotic resistance and arsenic (As) in co-contaminated paddy soils. EKR treatments in soil amended with pig manure (EKR-PD) showed better remediation efficiency compared with that without pig manure. In detail, the content of available As and the abundance of antibiotic-resistant bacteria (ARB) decreased by 25.2 %-41.4 % and 9.5 %-21.1 % after 7-d remediation, respectively, due to a relatively higher current density for EKR-PD. The role of the electric field contributed to 33.9 % of antibiotic degradation. Antibiotic resistance genes (ARGs) with ribosomal-protection and enzymatic-deactivation types were easier to remove, with the removal ratio of 37.8 %-41.6 % in EKR-PD. Brevundimonas was the most significantly different species during remediation. Bacillus and Clostridium_ sensu_stricto_1 were potential host bacteria of ARGs in the electric field. Membrane transport might be an effective strategy for microorganisms to respond to the stress of both electric field and co-contaminated environments. This study supports the potential role of EKR in the co-contamination of heavy metals and antibiotic resistance under manure application.

Rhizosphere bacteria regulated arsenic bioavailability and accumulation in the soil-Chinese cabbage system

The accumulation of arsenic (As) in Chinese cabbage (Brassica rapa ssp. pekinensis) has recently been a source of concern for a potential risk to human health. It is unknown whether natural variations of As accumulation in different genotypes of Chinese cabbage are related to rhizobacterial characteristics. Experiments were conducted to investigate the mechanisms of rhizobacteria involving in As fates in a soil-Chinese cabbage system using various genotypes using high-throughput sequencing and quantitative PCR. There were significant differences in As accumulation in cabbage leaves between 32 genotypes, and genotypes of low-As-accumulation (LSA) and high-As-accumulation (HSA) were identified. The As concentrations in the shoots of LSA were 23.25 %, 24.19 %, 15.05 %, and 70.69 % lower than those of HSA in seedling stage (SS), rosette stage (RS), heading stage (HS), and mature stage (MS), respectively. Meanwhile, the relative abundances of phyla Patescibacteria (in RS), Acidobacteria and Rokubacteria (in HS) in the rhizosphere of LSA were 60.18 %, 28.19 %, and 45.38 % less than those of HSA, respectively. Additionally, both shoot-As and As translocation factor had significantly positive or negative correlations with the relative abundances of Rokubacteria or Actinobacteria. In LSA rhizosphere, the relative abundances of genera Flavobacterium (in SS), Ellin6055 and Sphingomonas (in HS) were 128.12 %, 83.69 % and 79.50 % higher than those of HSA, respectively. This demonstrated that rhizobacteria contribute to the accumulation and translocation of As in HSA and LSA. Furthermore, the gene copies of aioA and arsM in LSA rhizosphere were 25.54 % and 16.13 % higher than those of HSA, respectively, whereas the gene copies of arsC in LSA rhizosphere were 26.36 % less than those of HSA in MS, indicating that rhizobacteria are involved in As biotransformation in the soil. These results provide a comprehensive understanding of the relationship between characteristics of rhizobacterial communities and As variations in Chinese cabbage genotypes.

Soil ridge cultivation maintains grain As and Cd at low levels and inhibits As methylation by changing arsM-harboring bacterial communities in paddy soils

The simultaneous mitigation of toxic arsenic (As) and cadmium (Cd) in rice grain remains a global challenge. The over-accumulation of husk dimethylarsinic acid (DMAs) induces the rice straight-head disease, which threatens rice production worldwide. In this study, we investigated various soil ridge height treatments with Eh ranging from - 225-87 mV and pH ranging from 6.3 to 4.1. Soil ridge cultivation can maintain grain As and Cd at low levels for slightly co-contaminated paddy soils, especially when the ridge height is 11 cm (Eh of 43 mV and pH of 4.6), where grain inorganic As decreased-at maximum-by 48% and DMAs by 55%. Grain Cd (0.14 mg kg^-1) increased but was still below the limit (0.2 mg kg^-1) in China, and the cost of ridging is acceptable. There were definite correlations among porewater As, Cd, Fe, S, and Mn contents across various Eh and pH values. Soil ridge cultivation significantly (P < 0.05) diminished the copy number of As-reducing (harboring arsC and arrA), As-methylating (harboring arsM), and sulfate-reducing (harboring dsrA) bacteria. Moreover, soil ridge cultivation shifted the arsM-harboring microbiota. In response to ridge height increase, the abundance of the bacterial biomarker phylum Euryachaeota declined and the families Halorubrum and Planctomyces were gradually replaced by Sandaracinus in paddy soil.

Biotic Process Dominated the Uptake and Transformation of Ag+ by Shewanella oneidensis MR-1

Silver ions (Ag⁺) directly emitted from industrial sources or released from manufactured Ag nanoparticles (AgNPs) in biosolid-amended soils have raised concern about the risk to ecosystems. However, our knowledge of Ag⁺ toxicity, internalization, and transformation mechanisms to bacteria is still insufficient. Here, we combine the advanced technologies of hyperspectral imaging (HSI) and single-particle inductively coupled plasma mass spectrometry to visualize the potential formed AgNPs inside the bacteria and evaluate the contributions of biological and non-biological processes in the uptake and transformation of Ag⁺ by Shewanella oneidensis MR-1. The results showed a dose-dependent toxicity of Ag⁺ to S. oneidensis MR-1 in the ferrihydrite bioreduction process, which was primarily induced by the actively internalized Ag. Moreover, both HSI and cross-section high-resolution transmission electron microscopy results confirmed that Ag inside the bacteria existed in the form of particulate. The Ag mass distribution in and around live and inactivated cells demonstrated that the uptake and transformation of Ag⁺ by S. oneidensis MR-1 were mainly via biological process. The bioaccumulation of Ag⁺ may be lethal to bacteria. A better understanding of the uptake and transformation of Ag⁺ in bacteria is central to predict and monitor the key factors that control Ag partitioning dynamics at the biointerface, which is critical to develop practical risk assessment and mitigation strategies.

The chemical-microbial release and transformation of arsenic induced by citric acid in paddy soil

Citric acid (CA) is the major exudate of rice roots, yet the effects of CA on arsenic (As) transformation and microbial community in flooded paddy soil have not been clearly elucidated. In this study, microcosms were established by amending CA to As contaminated paddy soils, mimicking the rhizosphere environment. Results showed that 0.5% CA addition significantly enhanced As mobilization after one-hour incubation, increased total As in porewater by about 20-fold. CA addition induced arsenate release into porewater, and subsequently formed ternary complex of As, iron and organic matters, inhibiting further As transformation (including arsenate reduction and arsenite methylation). Furthermore, the results of linear discriminant analysis (LDA) effect size (LEfSe) and network analysis revealed that CA addition significantly enriched bacteria associated with arsenic and iron reductions, such as Clostridium (up to 35-fold) and Desulfitobacterium (up to 4-fold). Our results suggest that CA exhibits robust ability to mobilize As through both chemical and microbial processes, increasing the risk of As accumulation by rice. This study sheds light on our understanding of As mobilization and transformation in rhizosphere soil, potentially providing effective strategies to restrict As accumulation in food crops by screening or cultivating varieties with low CA exuding.

Influence of tetracycline on arsenic mobilization and biotransformation in flooded soils

This study examined the effect of tetracycline addition on arsenic (As) mobilization and biotransformation in two contrasting soils (upland soil and paddy soil) under flooded conditions. The soils with added tetracycline (0-50 mg kg^-1) were incubated for 30 days, and soil properties and microbial functional genes over time were quantified. Tetracycline significantly promoted As reduction and As release into porewater in both soils. The enhancement had resulted from an increase in the concentration of dissolved organic carbon and a decrease in soil redox potential. Tetracycline also increased the abundances of As-reducing genes (arsC and arrA) and the relative abundances of As-reducing bacteria Streptomyces, Bacillus, Burkholderia, Clostridium and Rhodococcus, all of which have been found resistant to tetracycline. These genera play a key part in stimulating As reduction in the presence of tetracycline. The study indicated the significance of tetracycline in the biochemical behavior of As in flooded soils and provided new insights into the potential effects of tetracycline on the quality and safety of agricultural products in the future.

Diversity and arsenic-metabolizing gene clusters of indigenous arsenate-reducing bacteria in high arsenic groundwater of the Hetao Plain, Inner Mongolia

Dissimilatory arsenate reduction from arsenic (As)-bearing minerals into highly mobile arsenite is one of the key mechanisms of As release into groundwater. To detect the microbial diversity and As-metabolizing gene clusters of indigenous arsenate-reducing bacteria in high As groundwater in the Hetao Plain of Inner Mongolia, China, three anaerobic arsenate-reducing bacteria were isolated and arrA and arsC gene-based clone libraries of four in situ groundwater samples were constructed. The strains IMARCUG-11(G-11), IMARCUG-C1(G-C1) and IMARCUG-12(G-12) were phylogenetically belonged to genera Paraclostridium, Citrobacter and Klebsiella, respectively. They could reduce >99% of 1 mM arsenate under anoxic conditions with lactate as a carbon source in 60 h, 72 h and 84 h, respectively. As far as we know, this was the first report of arsenate reduction by genus Paraclostridium. Compared with strain G-11 (arsC) and G-C1 (arsRBC), strain G-12 contained two incomplete ars operons (operon1: arsABC, operon2: arsBC), indicating that these strains might present different strategies to resist As toxicity. Phylogenetic analysis illuminating by the arrA genes showed that in situ arsenate-reducing bacterial communities were diverse and mainly composed of Desulfobacterales (53%, dominated by Geobacter), Betaproteobacteria (12%), and unidentified groups (35%). Based on the arsC gene analysis, the indigenous arsenate-reducing bacterial communities were mainly affiliated with Omnitrophica (88%) and Deltaproteobacteria (11%, dominated by Geobacter and Syntrophobacterales). Results of this study expanded our understanding of indigenous arsenic-reducing bacteria in high As groundwater aquifers.

Arsenic mobilization affected by extracellular polymeric substances (EPS) of the dissimilatory iron reducing bacteria isolated from high arsenic groundwater

The factors that control arsenic (As) mobilization by dissimilatory iron reduction (DIR) are complicated. The association between As mobilization and extracellular polymeric substance (EPS) of dissimilatory iron reducing bacteria (DIRB) remained unclear. In this study, three DIRB were isolated from high arsenic groundwater to understand the effects of EPS on As mobilization. In the laboratory settings, strain Klebsiella oxytoca IR-ZA released As into aqueous phase from As-bearing ferrihydrite, while strain Shewanella putrefaciens IAR-S1 and S. xiamenensis IR-S2 re-sequestrated As by forming secondary minerals during ferrihydrite reduction. Characterization of EPS contents with Fourier Transform Infrared Spectroscopy and high-performance liquid chromatography suggested that mannan and succinic acid were the main different EPS contents of the DIRB. The biomineralization processes were tightly regulated by EPS compositions. Mannan secreted by IAR-S1 and IR-S2 promoted while succinic acid secreted by IR-ZA suppressed the biomineralization and As immobilization. Energy-dispersive X-ray Spectroscopy mapping indicated that As in the secondary minerals was wrapped with EPS. X-ray diffraction and room temperature Mössbauer spectroscopy showed these secondary minerals were vivianite and magnetite, respectively. The amount of As mobilized into aqueous phase was strongly affected by available anions (H₂PO₄^- and HCO₃^-). Our results indicated that the EPS of DIRB significantly influenced As mobilization.

The characterization of arsenic biotransformation microbes in paddy soil after straw biochar and straw amendments

Straw biochar and straw application to paddy soil dramatically altered arsenic (As) biogeochemical cycling in soil-rice system, but it remains unknown how As biotransformation microbes (ABMs) contribute to these processes. In this study, rice pot experiments combining terminal restriction fragment length polymorphism (T-RFLP) analysis and clone library were performed to characterize ABMs. Through linear discriminant analysis (LDA) effect size (LEfSe) and correlation analysis, results revealed that arrA-harbouring iron-reducing bacteria (e.g., Geobacter and Shewanella) and arsC-harbouring Gammaproteobacteria (e.g., fermentative hydrogen-producing and lignin-degrading microorganisms) potentially mediated arsenate [As(V)] reduction under biochar and straw amendments, respectively. Methanogens and sulfate-reducing bacteria (SRB) carrying arsM gene might regulate methylated As concentration in soil-rice system. Network analysis demonstrated that the association among ABMs in rhizosphere was significantly stronger than that in bulk soil. Arsenite [As(III)] methylators carrying arsM gene exhibited much stronger co-occurrence pattern with arsC-harbouring As(V) reducers than with arrA-harbouring As(V) reducers. This study would broaden our insights for the dramatic variation of As biogeochemical cycling in soil-rice system after straw biochar and straw amendments through the activities of ABMs, which could contribute to the safe rice production and high rice yield in As-contaminated fields.

Linking microbial community composition to hydrogeochemistry in the western Hetao Basin: Potential importance of ammonium as an electron donor during arsenic mobilization

Various functional groups of microorganisms and related biogeochemical processes are likely to control arsenic (As) mobilization in groundwater systems. However, spatially-dependent correlations between microbial community composition and geochemical zonation along groundwater flow paths are not fully understood, especially with respect to arsenic mobility. The western Hetao Basin was selected as the study area to address this limitation, where groundwater flows from a proximal fan (geochemical-group I: low As, oxidizing), through a transition area (geochemical-group II: moderate As, moderately-reducing) and then to a flat plain (geochemical-group III: high As, reducing). High-throughput Illumina 16S rRNA gene sequencing showed that the microbial community structure in the proximal fan included bacteria affiliated with organic carbon degradation and nitrate-reduction or even nitrate-dependant Fe(II)-oxidation, mainly resulting in As immobilization. In contrast, for the flat plain, high As groundwater contained Fe(III)- and As(V)-reducing bacteria, consistent with current models on As mobilization driven via reductive dissolution of Fe(III)/As(V) mineral assemblages. However, Spearman correlations between hydrogeochemical data and microbial community compositions indicated that ammonium as a possible electron donor induced reduction of Fe oxide minerals, suggesting a wider range of metabolic pathways (including ammonium oxidation coupled with Fe(III) reduction) driving As mobilization in high As groundwater systems.

Characterization and application of an anaerobic, iron and sulfate reducing bacterial culture in enhanced bioremediation of acid mine drainage impacted soil

Development of an appropriate bioremediation strategy for acid mine drainage (AMD) impacted environment is imperative for sustainable mining but remained critically challenged due to the paucity of knowledge on desired microbiological factors and their nutrient requirements. The present study was conducted to utilize the potential of an anaerobic, acid-tolerant, Fe³⁺ and SO₄^2- reducing microbial consortium for in situ remediation of highly acidic (pH 3.21), SO₄^2- rich (6285 mg/L) mine drainage impacted soil (AIS). A microbial consortium enriched from AMD system and composed of Clostridiales and Bacillales members was characterized and tested for in situ application through microcosms. A combination of bioaugmentation (enriched consortium) and biostimulation (cellulose) allowed 97% reduction in dissolved sulfate and rise in pH up to 7.5. 16S rRNA gene-based amplicon sequencing confirmed that although the bioaugmented community could survive in AIS, availability of carbon source was necessary for superior iron- and sulfate- reduction. Quantitative PCR of dsrB gene confirmed the role of carbon source in boosting the SO₄^2- reduction activities of sulfate reducers. This study demonstrated that native AIS harbored limited catabolic activities required for the remediation but addition of catabolically active microbial populations along with necessary carbon and energy source facilitate the bioremediation of AIS.

Dissolution and final fate of arsenic associated with gypsum, calcite, and ferrihydrite: Influence of microbial reduction of As(V), sulfate, and Fe(III)

Several studies have demonstrated that gypsum (CaSO₄·2H₂O) and calcite (CaCO₃) can be important hosts of arsenic in contaminated hydrogeological systems. However, the extent to which microbial reducing processes contribute to the dissolution and transformation of carbonate and sulfate minerals and, thereby, to arsenic mobilization is poorly understood. These processes are likely to have a strong impact on arsenic mobility in iron-poor environments and in reducing aquifers where iron oxyhydroxides become unstable. Anoxic batch bioassays with arsenate (As(V)) coprecipitated with calcite, gypsum, or ferrihydrite (Fe(OH)₃) were conducted in the presence of sulfate or molybdate to examine the impact of bioprocesses (i.e. As(V), sulfate, and Fe(III)-reduction) on arsenic dissolution, speciation, and eventual remineralization. Microbial reduction of As(V)-bearing calcite caused an important dissolution of arsenite, As(III), which remained in solution up to the end of the experiment (30 days). The reduction of As(V) from gypsum-As(V) also led to the release of As(III), which was subsequently remineralized, possibly as arsenic sulfides. The presence of sulfate triggered arsenic dissolution in the bioassays with ferrihydrite-As(V). This study showed that although gypsum and calcite have a lower capacity to bind arsenic, compared to iron oxides, they can play a critical role in the biogeochemical cycle of arsenic in natural calcareous and gypsiferous systems depleted of iron since they can be a source of electron acceptors for reducing bioprocesses.

Redox transformation of soil minerals and arsenic in arsenic-contaminated soil under cycling redox conditions

Changes in the saturation degree of aquifers control the geochemical reactions of redox-sensitive elements such as iron (Fe), sulfur (S), and arsenic (As). In this study, the effects of redox conditions and the presence of Fe and S on the behavior of As in a soil environment were investigated by observation in a batch experimental system. Arsenic was stable on Fe(III) solid surface in an oxidizing environment but was easily released into the aqueous phase following the reductive dissolution of Fe during an anoxic period. The alternating redox cycles led to a change in the concentrations of Fe, S, and As in both the aqueous and solid phases. The composition of Fe minerals changed to a less crystalline phase while that of solid phase As changed to a more reduced phase in both the As-contaminated natural soil and FeS-amended soil batch systems. This tendency was more prominent in the batch containing higher amounts of total Fe and S. These results show that a redox cycle can increase the possibility of As contamination of groundwater during dissolution and reprecipitation of Fe minerals and simultaneous microbial reduction of S and/or As species.

Arsenic mobilization in a high arsenic groundwater revealed by metagenomic and Geochip analyses

Microbial metabolisms of arsenic, iron, sulfur, nitrogen and organic matter play important roles in arsenic mobilization in aquifer. In this study, microbial community composition and functional potentials in a high arsenic groundwater were investigated using integrated techniques of RNA- and DNA-based 16S rRNA gene sequencing, metagenomic sequencing and functional gene arrays. 16S rRNA gene sequencing showed the sample was dominated by members of Proteobacteria (62.3-75.2%), such as genera of Simplicispira (5.7-6.7%), Pseudomonas (3.3-5.7%), Ferribacterium (1.6-4.4%), Solimonas (1.8-3.2%), Geobacter (0.8-2.2%) and Sediminibacterium (0.6-2.4%). Functional potential analyses indicated that organics degradation, assimilatory sulfate reduction, As-resistant pathway, iron reduction, ammonification, nitrogen fixation, denitrification and dissimilatory nitrate reduction to ammonia were prevalent. The composition and function of microbial community and reconstructed genome bins suggest that high level of arsenite in the groundwater may be attributed to arsenate release from iron oxides reductive dissolution by the iron-reducing bacteria, and subsequent arsenate reduction by ammonia-producing bacteria featuring ars operon. This study highlights the relationship between biogeochemical cycling of arsenic and nitrogen in groundwater, which potentially occur in other aquifers with high levels of ammonia and arsenic.

Micro-colonization of arsenic-resistant Staphylococcus sp. As-3 on arsenopyrite (FeAsS) drives arsenic mobilization under anoxic sub-surface mimicking conditions

We investigated the subsurface biomatrix of the most abundant As-mineral, arsenopyrite (FeAsS), and meticulously studied a potential biogenic arsenic mobilization phenomenon. An arsenic-resistant [up to 7.5 mM As(III) and 200 mM As(V)] and arsenate-reducing bacterial strain (Staphylococcus sp. As-3) was isolated from a sediment core sample taken from the Budai borehole, on the southwestern coast of Taiwan. Isolate As-3 could reduce 5 mM As(V) to 3.04 mM in 96 h, generating 1.6 mM As(III) under anoxic conditions. Isolate As-3, which adsorbed As(V) up to 19.02 mg g^-1 (cdw) and As(III) up to 0.46 mg g^-1 (cdw), demonstrated effective As-bioaccumulating ability, as corroborated by a TEM-EDS analysis. Under anaerobic batch conditions, isolate As-3 micro-colonies could grow on as well as interact with arsenopyrite (FeAsS), mobilizing arsenic into soluble phase as As(III) and As(V). Using synchrotron radiation-based FTIR micro-spectroscopy, various functional group signatures and critical chemical bonds enabling a direct interaction with arsenopyrite were underpinned, such as a potential P-OFe bond involved in facilitating bacteria-mineral interaction. Using atomic force microscopy, we analyzed the scattered bacterial cell arrangement and structure and measured various biomechanical properties of micro-colonized Staphylococcus sp. As-3 cells on arsenopyrite. We suggest that the release of organic acids from As-3 drives soluble arsenic release in the aqueous phase under anoxic conditions through oxidative dissolution. Furthermore, arsC-encoding putative cytoplasmic arsenic reductase sequencing and transcript characterization indicated that arsC plays a possible role in the reduction of moderately soluble As(V) to highly soluble toxic As(III) under anoxic conditions. Thus, we suggest that firmicutes such as Staphylococcus sp. As-3 may play an important role in microbially-mediated arsenic mobilization, leading to arsenic release in the sub-surface niche.

Iron limitation effects on nitrogen-fixing organisms with possible implications for cyanobacterial blooms

Cyanobacteria-dominated harmful algal blooms are increasing in occurrence. Many of the taxa contributing to these blooms are capable of fixing atmospheric nitrogen and should be favored under conditions of low nitrogen availability. Yet, synthesizing nitrogenase, the enzyme responsible for nitrogen fixation, is energetically expensive and requires substantial concentrations of iron. Phosphorus addition to nitrogen poor streams should promote nitrogen fixation, but experimental results so far have been inconclusive, suggesting that other factors may be involved in controlling this process. With iron potentially limited in many streams, we examined the influence of phosphorus-iron colimitation on the community structure of nitrogen-fixing organisms. In stream microcosms, using microscopic and molecular sequence data, we observed: (i) the greatest abundance of heterocyst forming nitrogen-fixing cyanobacteria in low nitrogen treatments with high phosphorus and iron and (ii) greater abundance of non-photosynthetic nitrogen-fixing bacteria in treatments with nitrogen compared to those without it. We also found that comparisons between molecular results and those obtained from microscopic identification provided complementary information about cyanobacterial communities. Our investigation indicates the potential for phosphorus-iron colimitation of stream nitrogen-fixing organisms.

Impact of soil salinity on the microbial structure of halophyte rhizosphere microbiome

The rhizosphere microbiome plays a significant role in the life of plants in promoting plant survival under adverse conditions. However, limited information is available about microbial diversity in saline environments. In the current study, we compared the composition of the rhizosphere microbiomes of the halophytes Urochloa, Kochia, Salsola, and Atriplex living in moderate and high salinity environments (Khewra salt mines; Pakistan) with that of the non-halophyte Triticum. Soil microbiomes analysis using pyrosequencing of 16S rRNA gene indicated that Actinobacteria were dominant in saline soil samples whereas Proteobacteria predominated in non-saline soil samples. Firmicutes, Acidobacteria, Bacteriodetes and Thaumarchaeota were predominant phyla in saline and non-saline soils, whereas Cyanobacteria, Verrucomicrobia, Gemmatimonadetes and the unclassified WPS-2 were less abundant. Sequences from Euryarchaeota, Ignavibacteriae, and Nanohaloarchaeota were identified only from the rhizosphere of halophytes. Dominant halophilic bacteria and archaea identified in this study included Agrococcus, Armatimonadetes gp4, Halalkalicoccus, Haloferula and Halobacterium. Our analysis showed that increases in soil salinity correlated with significant differences in the alpha and beta diversity of the microbial communities across saline and non-saline soil samples. Having a complete inventory of the soil bacteria from different saline environments in Pakistan will help in the discovery of potential inoculants for crops growing on salt-affected land.

Diversity of Bacillus-like bacterial community in the rhizospheric and non-rhizospheric soil of halophytes (Salsola stocksii and Atriplex amnicola), and characterization of osmoregulatory genes in halophilic Bacilli

Salinity is one of the major abiotic stresses; a total of 3% of the world’s land mass is affected by salinity. Approximately 6.3 million hectares of land in Pakistan is affected by salinity to varying degrees, and most of the areas are arid to semiarid with low annual precipitation. The aim of the present study is to identify and characterize Bacillus and Bacillus-derived bacterial genera from the rhizospheric and non-rhizospheric soil samples from the Khewra Salt Mine, Pakistan, by using culture-independent and -dependent methods. Seven Bacillus-like bacterial genera, Bacillus, Halobacillus, Virgibacillus, Brevibacillus, Paenibacillus, Tumebacillus, and Lysinibacillus, were detected by using pyrosequencing analysis, whereas only four genera, Bacillus, Halobacillus, Oceanobacillus, and Virgibacillus, were identified by culture-dependent methods. Most of the Bacillus-like isolates identified in this study were moderately halophilic, alkaliphilic, and mesophilic bacteria and were considered a good source of hydrolytic enzymes because of their ability to degrade proteins, carbohydrates, and lipids. Eight Bacillus-like strains from the genera Bacillus, Halobacillus, Oceanobacillus, and Virgibacillus showed positive results for the presence of ectABC gene cluster (ectoine), six strains could synthesize betaine from choline, and six strains tested positive for the synthesis of proline from either glutamate or ornithine by using proline dehydrogenase enzyme.

Simultaneous influence of indigenous microorganism along with abiotic factors controlling arsenic mobilization in Brahmaputra floodplain, India

In the dynamic cycling of oxic and anoxic aqueous alluvial aquifer environments, varying Arsenic (As) concentrations are controlled by both abiotic and biotic factors. Studies have shown a significant form of toxic As (III) being released through the reductive dissolution of iron-oxy/hydroxide minerals and microbial reduction mechanisms, which leads to a serious health concern. The present study was performed in order to assess the abiotic and biotic factors influencing As release into the alluvial aquifer groundwater in Brahmaputra floodplain, India. The groundwater chemistry, characterization of the sediments, isolation, identification and characterization of prominent As releasing indigenous bacterium were conducted. The measured solid and liquid phases of total As concentration were ranged between 0.02 and 17.2 mg kg^-1 and 8 to 353 μg L^-1, respectively. The morphology and mineralogy showed the presence of detrital and authigenic mineral assemblages whereas primary and secondary As bearing Realgar and Claudetite minerals were identified, respectively. Furthermore, significant non-labile As fraction was found associated with the amorphous oxides of Fe, Mn and Al. The observed groundwater chemistry and sediment color, deduced a sub-oxic reducing aquifer conditions in As-contaminated regions. In addition, 16S rDNA sequencing results of the isolated bacterium showed the prominent Pseudomonas aeruginosa responsible for the mobilization of As, reducing condition, biomineralization and causing grey color to the sediments at the shallower and deeper aquifers in the study area. These findings suggest that microbial metabolic activities are equally responsible in iron-oxy/hydroxide reductive dissolution, controlling As mobilization in dynamic fluvial flood plains.

Microbe mediated arsenic release from iron minerals and arsenic methylation in rhizosphere controls arsenic fate in soil-rice system after straw incorporation

Arsenic (As) contamination is a global problem. Straw incorporation is widely performed in As contaminated paddy fields. To understand how straw and straw biochar incorporation affect As transformation and translocation in the soil-microbe-rice system, a pot experiment was carried out with different dosages of rice straw and straw biochar application. Results showed that both straw biochar and straw application significantly increased As mobility. Straw biochar mobilized As mainly through increasing soil pH and DOM content. Straw incorporation mainly through enhancing As release from iron (Fe) minerals and arsenate (As(V)) reduction to arsenite (As(III)). Straw biochar didn't significantly affect As methylation, while straw incorporation significantly enhanced As methylation, elevated dimethylarsenate (DMA) concentration in soil porewater and increased As volatilization. Straw biochar didn't significantly change total As accumulation in rice grains, but decreased As(III) accumulation by silicon (Si) inhibition. Straw incorporation significantly increased DMA, but decreased As(III) concentration in rice grains. After biochar application, dissolved As was significantly positively correlated with the abundance of Bacillus, indicating that Bacillus might be involved in As release, and As(III) concentration in polished grains was negatively correlated with Si concentration. The significant positive correlation between dissolved As with Fe and the abundance of iron-reducing bacteria suggested the coupling of As and Fe reduction mediated by iron-reducing bacteria. The significant positive correlation between DMA in rice grains and the abundance of methanogenic bacteria indicated that methanogenic bacteria could be involved in As methylation after straw application. The results of this study would advance the understanding how rice straw incorporation affects As fate in soil-microbe-rice system, and provide some guidance to straw incorporation in As contaminated paddy soil. This study also revealed a wealth of microorganisms in the soil environment that dominate As mobility and transformation after straw incorporation.

Effect of microbially mediated iron mineral transformation on temporal variation of arsenic in the Pleistocene aquifers of the central Yangtze River basin

Significant seasonal variation of groundwater arsenic (As) concentrations in shallow aquifers of the Jianghan Plain, central Yangtze River Basin has been reported recently, but the underlying mechanisms remain not well understood. To elaborate biogeochemical processes responsible for the observed As concentration variation, 42-day incubation experiments were done using sediment samples collected respectively from the depth of 26, 36 and 60m of the As-affected aquifer which were labeled respectively as JH26, JH36, JH60. Where JH denotes Jianghan Plain, and the number indicates the depth of the sediment sample. The results indicated that As could be mobilized from the sediments of 26m and 36m depth under the stimulation of exogenous organic carbon, with the maximum As release amount of 1.60 and 1.03mgkg^-1, respectively, while the sediments at 60m depth did not show As mobilization. The microbially mediated reductive dissolution of amorphous iron oxides and reduction of As(V) to As(III) could account for the observed As mobilization. The 16S rRNA high-throughput sequencing results indicated that the variation of microbial community correlated with the released As concentration (R=0.7, P<0.05) and the iron-reducing bacteria, including Pseudomonas, Clostridium and Geobacter, were the main drivers for the As mobilization from the sediments at 26m and 36m depth. The increase of arsC gene abundance (up to 1.4×10⁵ copies g^-1) during As release suggested that As reduction was mediated by the resistant reduction mechanism. By contrast, in the 60m sediments where the Fe and As release was absent, the iron-reducing bacteria accounted for a very minor proportion and sulfate-reducing bacteria were predominant in the microbial community. In addition, after 30days of incubation, the released As in the 26m sediments was immobilized via co-precipitation with or adsorption onto the Fe-sulfide mineral newly-formed by the bacterial sulfate reduction. These results are consistent with the results of our previous field monitoring, indicating that the bacterial sulfate reduction could lead to the temporal decrease in groundwater As concentrations. This study provides insights into the mechanism for As mobilization and seasonal As concentration variation in the Pleistocene aquifers from alluvial plains.

Retrieved 16S rRNA and nifH sequences reveal co-dominance of Bradyrhizobium and Ensifer (Sinorhizobium) strains in field-collected root nodules of the promiscuous host Vigna radiata (L.) R. Wilczek

In the present study, the relative distribution of endophytic rhizobia in field-collected root nodules of the promiscuous host mung bean was investigated by sequencing of 16S ribosomal RNA (rRNA) and nifH genes, amplified directly from the nodule DNA. Co-dominance of the genera Bradyrhizobium and Ensifer was indicated by 32.05 and 35.84% of the total retrieved 16S rRNA sequences, respectively, and the sequences of genera Mesorhizobium and Rhizobium comprised only 0.06 and 2.06% of the recovered sequences, respectively. Sequences amplified from rhizosphere soil DNA indicated that only a minor fraction originated from Bradyrhizobium and Ensifer strains, comprising about 0.46 and 0.67% of the total retrieved sequences, respectively. 16S rRNA gene sequencing has also identified the presence of several non-rhizobial endophytes from phyla Proteobacteria, Actinobacteria, Bacteroides, and Firmicutes. The nifH sequences obtained from nodules also confirmed the co-dominance of Bradyrhizobium (39.21%) and Ensifer (59.23%) strains. The nifH sequences of the genus Rhizobium were absent, and those of genus Mesorhizobium comprised only a minor fraction of the sequences recovered from the nodules and rhizosphere soil samples. Two bacterial isolates, identified by 16S rRNA gene sequence analysis as Bradyrhizobium strain Vr51 and Ensifer strain Vr38, successfully nodulated the original host (mung bean) plants. Co-dominance of Bradyrhizobium and Ensifer strains in the nodules of mung bean indicates the potential role of the host plant in selecting specific endophytic rhizobial populations. Furthermore, successful nodulation of mung bean by the isolates showed that strains of both the genera Bradyrhizobium and Ensifer can be used for production of inoculum.

Isolation, identification and characterization of arsenic transforming exogenous endophytic Citrobacter sp. RPT from roots of Pteris vittata

The aim of the present study was to assess the arsenic (As) transformation potential of endophytic bacteria isolated from roots of Pteris vittata plant. The endophytic bacterium was tested for minimal inhibitory concentration (MIC) against As. The endophytic strain RPT exhibited the highest resistance to As(V) (400 mg/l). Phylogenetic analysis of the 16S rRNA sequence suggested that strain RPT was a member of genus Citrobacter. The As transformation assay revealed As(III) oxidation and As(V) reduction potential of Citrobacter sp. RPT. The As resistance mechanism was further confirmed by amplification of arsC and aoxB genes. The growth kinetics of strain RPT was altered slightly in the presence of different concentration (100-400 mg/l) of As stress. Temperature and pH influenced the As removal rate. The maximum As removal was observed at pH 7.0 (74%) and 37 °C (70.9%). The results suggest that strain RPT can survive under the As stress and has been identified as a potential candidate for application in bioremediation of As in contaminated environments.

Dehalococcoides and general bacterial ecology of differentially trichloroethene dechlorinating flow-through columns

The diversity of Dehalococcoides mccartyi (Dhc) and/or other organohalide respiring or associated microorganisms in parallel, partial, or complete trichloroethene (TCE) dehalogenating systems has not been well described. The composition of Dhc populations and the associated bacterial community that developed over 7.5 years in the top layer (0-10 cm) of eight TCE-fed columns were examined using pyrosequencing. Columns biostimulated with one of three carbon sources, along with non-stimulated controls, developed into complete (ethene production, whey amended), partial (cis-dichloroethene (DCE) and VC, an emulsified oil with nonionic surfactant), limited (<5 % cis-DCE and 95 % TCE, an emulsified oil), and non- (controls) TCE dehalogenating systems. Bioaugmentation of one column of each treatment with Bachman Road enrichment culture did not change Dhc populations nor the eventual degree of TCE dehalogenation. Pyrosequencing revealed high diversity among Dhc strains. There were 13 OTUs that were represented by more than 1000 sequences each. Cornell group-related populations dominated in complete TCE dehalogenating columns, while Pinellas group related Dhc dominated in all other treatments. General microbial communities varied with biostimulation, and three distinct microbial communities were established: one each for whey, oils, and control treatments. Bacterial genera, including Dehalobacter, Desulfitobacterium, Sulfurospirillum, Desulfuromonas, and Geobacter, all capable of partial TCE dehalogenation, were abundant in the limited and partial TCE dehalogenating systems. Dhc strain diversity was wider than previously reported and their composition within the community varied significantly depending on the nature of the carbon source applied and/or changes in the Dhc associated partners that fostered different biogeochemical conditions across the columns.

New Arsenate Reductase Gene (arrA) PCR Primers for Diversity Assessment and Quantification in Environmental Samples

The extent of arsenic contamination in drinking water and its potential threat to human health have resulted in considerable research interest in the microbial species responsible for arsenic reduction. The arsenate reductase gene (arrA), an important component of the microbial arsenate reduction system, has been widely used as a biomarker to study arsenate-reducing microorganisms. A new primer pair was designed and evaluated for quantitative PCR (qPCR) and high-throughput sequencing of the arrA gene, because currently available PCR primers are not suitable for these applications. The primers were evaluated in silico and empirically tested for amplification of arrA genes in clones and for amplification and high-throughput sequencing of arrA genes from soil and groundwater samples. In silico, this primer pair matched (≥90% DNA identity) 86% of arrA gene sequences from GenBank. Empirical evaluation showed successful amplification of arrA gene clones of diverse phylogenetic groups, as well as amplification and high-throughput sequencing of independent soil and groundwater samples without preenrichment, suggesting that these primers are highly specific and can amplify a broad diversity of arrA genes. The arrA gene diversity from soil and groundwater samples from the Cache Valley Basin (CVB) in Utah was greater than anticipated. We observed a significant correlation between arrA gene abundance, quantified through qPCR, and reduced arsenic (AsIII) concentrations in the groundwater samples. Furthermore, we demonstrated that these primers can be useful for studying the diversity of arsenate-reducing microbial communities and the ways in which their relative abundance in groundwater may be associated with different groundwater quality parameters.

IMPORTANCE

Arsenic is a major drinking water contaminant that threatens the health of millions of people worldwide. The extent of arsenic contamination and its potential threat to human health have resulted in considerable interest in the study of microbial species responsible for the reduction of arsenic, i.e., the conversion of AsV to AsIII In this study, we developed a new primer pair to evaluate the diversity and abundance of arsenate-reducing microorganisms in soil and groundwater samples from the CVB in Utah. We observed significant arrA gene diversity in the CVB soil and groundwater samples, and arrA gene abundance was significantly correlated with the reduced arsenic (AsIII) concentrations in the groundwater samples. We think that these primers are useful for studying the ecology of arsenate-reducing microorganisms in different environments.

Microbial communities involved in arsenic mobilization and release from the deep sediments into groundwater in Jianghan plain, Central China

It was shown that groundwater in Jianghan Plain was severely contaminated by arsenic; however, little is known about the mechanism by which the mineral arsenic was mobilized and released into groundwater from the high-arsenic sediments in this area. Here, we collected sediment samples from the depths of 5-230m in Jianghan Plain. Although all of the samples contain high contents of total arsenic, the soluble arsenic was only detectable in few of the shallow sediments, but was readily detectable in all of the deep sediments at the depths of 190-230m. Analysis of the genes of arsenate-respiring reductases indicated that they were not present in all of the shallow sediments from the depths of 5-185m, but were detectable in all of the deep sediments from the depths of 190-230m; all of the identified reductase genes are new or new-type, and they display unique diversity. Microcosm assay indicated that the microbial communities from the deep sediments were able to reduce As(V) into As(III) using lactate, formate, pyruvate or acetate as an electron donor under anaerobic condition. Arsenic release assay demonstrated that these microbial communalities efficiently catalyzed the mobilization and release of the mineral arsenic into aqueous phase. We also isolated a novel cultivable dissimilatory As(V)-respiring bacterium Aeromonas sp. JH155 from the sediments. It is able to completely reduce 2.0mM As(V) into As(III) in 72h, and efficiently promote the reduction and release of the mineral arsenic into aqueous phase. Analysis of the 16S rRNA genes indicated that the deep sediments contain diversities of microbial communities, which were shaped by the environmental factors, such as As, SO₄^2-, NO₃^-, Fe and pH value. These data suggest that the microorganisms in the deep sediments in Jianghan Plain played key roles in the mobilization and release of insoluble arsenic into the groundwater.

Comparison of arsenate reduction and release by three As(V)-reducing bacteria isolated from arsenic-contaminated soil of Inner Mongolia, China

Arsenic (As) contamination has become a worldwide environmental problem: arsenite (As(Ⅲ)) especially has posed a major threat to human health. Here, we report the first three isolates of anaerobic As(Ⅴ)-reducing bacterial strains (strains JQ, DJ-3 and DJ-4) from a soil sample containing 48.7% of total As in the form of As(III) collected in Chifeng, Inner Mongolia, China. Strains JQ, DJ-3 and DJ-4 were phylogenetically closely related to Bacillus, Desulfitobacterium and Exiguobacterium, respectively. Among these strains, JQ and DJ-3 have the arsC gene, DJ-4 possesses the arrA gene. The three strains could all resist and reduce high concentrations of As(Ⅴ) under anoxic conditions. The order of resistance to As(Ⅴ) was DJ-3 > JQ > DJ-4. Strain DJ-3 not only possesses the strongest resistance to As(Ⅴ) but could also reduce 53% of the As(Ⅴ) to As(III) in the treatment of 60 mM As(Ⅴ) in 5 d. All three strains could release As from goethite; strain DJ-4 has the highest ability to promote the release of As (90.5%) from goethite. These results suggested that strains JQ, DJ-3 and DJ-4 may play an important role in the mobilization and transformation of As in soil.

Enhanced bioreduction of iron and arsenic in sediment by biochar amendment influencing microbial community composition and dissolved organic matter content and composition

Biochar derived from the pyrolysis at 500 °C with fresh biogas slurry and residue, was conducted to investigate its potential role in mediating the speciation and mobilization of As(V) and Fe(III) from arsenic-contaminated tailing mine sediment, with consideration of the changes in microbial populations and dissolved organic matter (DOM). The reduction of As(V) (10-13%) and Fe(III) (12-17%) were partly in response to biochar abiotically causing desorption and reduction effect, but were predominantly (87-90% and 83-88% for As(V) and Fe(III)) attributed to biochar stimulating biological reduction. The level of As(III) released from sediment upon biochar amendment (656.35±89.25 μg L(-1)) was significantly higher than the level released without biochar amendment (98.06±19.38 μg L(-1)) after 49 days incubation. Although a low level of Fe(II) (0.81±0.07 mg L(-1)) was determined in the solution when amending with biochar, most of released Fe(II) (166.25±40.25 mg L(-1)) was formed as biochar-Fe(II)minerals composite. More importantly, biochar stimulated the DOM bioavailability in association with bacterial activities mediating As(V) and Fe(III) reduction. High-throughput sequencing results indicated biochar application shifted the soil microbial community and increased the relative abundance of As(V)-/Fe(III)-reducing bacteria, mostly Geobacter, Anaeromyxobacter, Desulfosporosinus and Pedobacter. The discovery of biochar-bacteria-DOM consortium may broaden new understanding into speciation and mobilization of metals, which arouses attention to exploit feasible bioremediation for metal-contaminated sediment.

Effects of microbially induced transformations and shift in bacterial community on arsenic mobility in arsenic-rich deep aquifer sediments

Elevated concentration of arsenic (As) prevailed in deep aquifers of Chianan Plain, Taiwan. Arsenic release in relation to microbially induced transformations and shift in bacterial communities in deep aquifer sediments of Budai, southwestern Taiwan were investigated using microcosm experiments and substrate amendments over 90 days of anaerobic incubation. The results revealed that As reduction was independent of Fe reduction and a modest rate of sedimentary As release into aqueous phase occurred at the expense of the native organic carbon. Addition of lactate resulted in a parallel increase in As(III) (3.7-fold), Fe(II) (6.2-fold) and Mn (3.5 fold) in aqueous phase compared to un-amended slurries and the enrichment of sequences related to mostly Bacillus, Flavisolibacter, and Geobacter spp, suggesting the important role of these bacteria in As enrichment through reductive dissolution of As-bearing Fe and Mn minerals. The increase in phosphate-extractable As in solid phase with concomitant rise in As in aqueous phase over the course of incubation further attested to the importance of reductive dissolution in promoting As release. Furthermore, the increase in arrA gene abundance with addition of labile carbon suggests that dissimilatory As reduction also may contribute to As enrichment in the water of the deep aquifer of Budai.

Association of plant growth-promoting Serratia spp. with the root nodules of chickpea

Serratia species-affiliated DNA sequences have recently been discovered in the root nodules of two chickpea cultivars; however, little is known about their potential influence on chickpea plant growth. All Serratia-affiliated sequences (1136) could be grouped into two clusters at 98% DNA similarity. The major cluster, represented by 96% of sequences, was closely associated with Serratia marcescens sequences from GenBank. In the current study, we isolated two Serratia strains, 5D and RTL100, from root nodules of a field-grown Desi cultivar from Faisalabad and Thal areas, respectively. In vitro, strain 5D showed significantly higher phosphate (P) solubilization and lactic acid production than RTL100, whereas a comparable concentration of phytohormone was produced by both isolates. The application of Serratia strain 5D as an inoculum resulted in 25.55% and 30.85% increases in the grain yield of crops grown on fertile soil in irrigated areas and nutrient-deficient soil in rainfed areas, respectively, compared to the non-inoculated control. Results of plant inoculations indicated that Serratia sp. 5D and RTL100 can serve as effective microbial inoculants, particularly in nutrient-deficient soils in rainfed areas, where chickpea is the only major crop grown during the entire year.

Impact of Arsenite on the Bacterial Community Structure and Diversity in Soil

The impact of arsenite (As[III]) on the bacterial community structure and diversity in soil was determined by incubating soil slurries with 50, 500, and 5,000 μM As(III). As(III) was oxidized to arsenate (As[V]), and the microbial contribution to As(III) oxidation was 70–100%. PCR-denaturing gradient gel electrophoresis revealed that soil bacterial diversity decreased in the presence of As(III). Bacteria closely related to the family Bacillaceae were predominant in slurry spiked with 5,000 μM As(III). The population size of culturable As(III)-resistant bacteria was 37-fold higher in this slurry than in unspiked slurry (p < 0.01), indicating that high levels of As(III) stimulate the emergence of As(III)-resistant bacteria. As(III)-resistant bacteria isolated from slurry spiked with 5,000 μM As(III) were mainly affiliated with the genus Bacillus; however, no strains showed As(III)-oxidizing capacity. An As(III)-oxidizing bacterial community analysis based on As(III) oxidase gene (aioA) sequences demonstrated that diversity was the lowest in slurry spiked with 5,000 μM As(III). The deduced AioA sequences affiliated with Alphaproteobacteria accounted for 91–93% of all sequences in this slurry, among which those closely related to Bosea spp. were predominant (48–86%). These results suggest that exposure to high levels of As(III) has a significant impact on the composition and diversity of the soil bacterial community, including the As(III)-oxidizing bacterial community. Certain As(III)-oxidizing bacteria with strong As(III) resistance may be enriched under high As(III) levels, while more sensitive As(III) oxidizers are eliminated under these conditions.

Indigenous arsenic(V)-reducing microbial communities in redox-fluctuating near-surface sediments of the Mekong Delta

Arsenic (As) cycling within soils and sediments of the Mekong Delta of Cambodia is affected by drastic redox fluctuations caused by seasonal monsoons. Extensive flooding during monsoon seasons creates anoxic soil conditions that favor anaerobic microbial processes, including arsenate [As(V)] respiration-a process contributing to the mobilization of As. Repeated oxidation and reduction in near-surface sediments, which contain 10-40 mg kg(-1) As, lead to the eventual downward movement of As to the underlying aquifer. Amplification of a highly conserved functional gene encoding dissimilatory As(V) reductase, arrA, can be used as a molecular marker to detect the genetic potential for As(V) respiration in environmental samples. However, few studies have successfully amplified arrA from sediments without prior enrichment, which can drastically shift community structure. In the present study, we examine the distribution and diversity of arrA genes amplified from multiple sites within the Cambodian Mekong Delta as a function of near-surface depth (10, 50, 100, 200, and 400 cm), where sediments undergo seasonal redox fluctuations. We report successful amplification of 302 arrA gene sequences (72 OTUs) from near-surface Cambodian soils (without prior enrichment or stimulation with carbon amendments), where a large majority (>70%) formed a well-supported clade that is phylogenetically distinct from previously reported sequences from Cambodia and other South and Southeast Asian sediments, with highest sequence similarity to known Geobacter species capable of As(V) respiration, further supporting the potentially important role of Geobacter sp. in arsenic mobilization in these regions.

Arsenate reduction and mobilization in the presence of indigenous aerobic bacteria obtained from high arsenic aquifers of the Hetao basin, Inner Mongolia

Intact aquifer sediments were collected to obtain As-resistant bacteria from the Hetao basin. Two strains of aerobic As-resistant bacteria (Pseudomonas sp. M17-1 and Bacillus sp. M17-15) were isolated from the aquifer sediments. Those strains exhibited high resistances to both As(III) and As(V). Results showed that both strains had arr and ars genes, and led to reduction of dissolved As(V), goethite-adsorbed As(V), scorodite As(V) and sediment As(V), in the presence of organic carbon as the carbon source. After reduction of solid As(V), As release was observed from the solids to solutions. Strain M17-15 had a higher ability than strain M17-1 in reducing As(V) and promoting the release of As. These results suggested that the strains would mediate As(V) reduction to As(III), and thereafter release As(III), due to the higher mobility of As(III) in most aquifer systems. The processes would play an important role in genesis of high As groundwater.

Isolation of an arsenate-respiring bacterium from a redox front in an arsenic-polluted aquifer in West Bengal, Bengal Basin

Natural pollution of groundwater by arsenic adversely affects the health of tens of millions of people worldwide, with the deltaic aquifers of SE Asia being particularly polluted. The pollution is caused primarily by, or as a side reaction of, the microbial reduction of sedimentary Fe(III)-oxyhydroxides, but the organism(s) responsible for As release have not been isolated. Here we report the first isolation of a dissimilatory arsenate reducer from sediments of the Bengal Basin in West Bengal. The bacterium, here designated WB3, respires soluble arsenate and couples its reduction to the oxidation of acetate; WB3 is therefore implicated in the process of arsenic pollution of groundwater, which is largely by arsenite. The bacterium WB3 is also capable of reducing dissolved Fe(III) citrate, solid Fe(III)-oxyhydroxide, and elemental sulfur, using acetate as the electron donor. It is a member of the Desulfuromonas genus and possesses a dissimilatory arsenate reductase that was identified using degenerate polymerase chain reaction primers. The sediment from which WB3 was isolated was brown, Pleistocene sand at a depth of 35.2 m below ground level (mbgl). This level was some 3 cm below the boundary between the brown sands and overlying reduced, gray, Holocene aquifer sands. The color boundary is interpreted to be a reduction front that releases As for resorption downflow, yielding a high load of labile As sorbed to the sediment at a depth of 35.8 mbgl and concentrations of As in groundwater that reach >1000 μg/L.

Diverse arsenic- and iron-cycling microbial communities in arsenic-contaminated aquifers used for drinking water in Bangladesh

Subsurface removal of arsenic by injection with oxygenated groundwater has been proposed as a viable technology for obtaining 'safe' drinking water in Bangladesh. While the oxidation of ferrous iron to solid ferric iron minerals, to which arsenic adsorbs, is assumed to be driven by abiotic reactions, metal-cycling microorganisms may potentially affect arsenic removal. A cultivation-independent survey covering 24 drinking water wells in several geographical regions in Bangladesh was conducted to obtain information on microbial community structure and diversity in general, and on specific functional groups capable of the oxidation or reduction of arsenic or iron. Each functional group, targeted by either group-specific 16S rRNA or functional gene amplification, occurred in at least 79% of investigated samples. Putative arsenate reducers and iron-oxidizing Gallionellaceae were present at low diversity, while more variation in potentially arsenite-oxidizing microorganisms and iron-reducing Desulfuromonadales was revealed within and between samples. Relations between community composition on the one hand and hydrochemistry on the other hand were in general not evident, apart from an impact of salinity on iron-cycling microorganisms. Our data suggest widespread potential for a positive contribution of arsenite and iron oxidizers to arsenic removal upon injection with oxygenated water, but also indicate a potential risk for arsenic re-mobilization by anaerobic arsenate and iron reducers once injection is halted.