Sediment biomarker, bacterial community characterization of high arsenic aquifers in Jianghan Plain, China

Arsenic inorganic exposure, metabolism, genetic biomarkers and its impact on human health: A mini-review

Inorganic arsenic species exist in the environment as a result of both natural sources, such as volcanic and geothermal activities, and geological formations, as well as anthropogenic activities, including smelting, exploration of fossil fuels, coal burning, mining, and the use of pesticides. These species deposit in water, rocks, soil, sediments, and the atmosphere. Arsenic-contaminated drinking water is a global public health issue because of its natural prevalence and toxicity. Therefore, chronic exposure to arsenic can have deleterious effect on humans, including cancer and other diseases. This work describes the mechanisms of environmental exposure to arsenic, molecular regulatory factors involved in its metabolism, genetic polymorphisms affecting individual susceptibility and the toxic effects of arsenic on human health (oxidative stress, DNA damage and cancer). We conclude that the role of single nucleotide variants affecting urinary excretion of arsenic metabolites are highly relevant and can be used as biomarkers of the intracellular retention rates of arsenic, showing new avenues of research in this field.

Comamonas-dominant microbial community in carbon poor aquitard sediments revealed by metagenomic-based growth rate investigation

The microbiological ecology of a low-nutrient shallow aquifer with high arsenic content in the Yinchuan Plain was investigated in this study. Amplicon sequencing data from five samples (depths: 1.5 m, 3.5 m, 11.2 m, 19.3 m, and 25.5 m) revealed diverse and adaptable microbial community. Among the microbial community, Comamonas was the most prominent, accounting for 10.52 % of the total. This genus displayed high growth rates, with a maximum growth rate of 12.06 d-1 and a corresponding doubling time of 1.38 days, as determined through an analysis of codon usage bias. Functional annotation of Metagenome-Assembled Genomes (MAGs) for samples at 1.5 m and 11.2 m depths revealed Comamonas' metabolic versatility, including various carbon pathways, assimilative sulfate reduction (ASR), and dissimilatory reduction to ammonium (DNRA). The TPM (Transcripts Per Kilobase of exon model per Million mapped reads) of MAGs at 11.2 m sample was 15.7 and 12.3. The presence of arsenic resistance genes in Comamonas aligns with sediment arsenic levels (65.8 mg/kg for 1.5 m depth, 32.8 mg/kg for 11.2 m depth). This study highlights the role of Comamonas as a 'generalist' bacteria in challenging oligotrophic sediments, emphasizing the significance of such organisms in community stability and ecological functions. ENVIRONMENTAL IMPLICATION: Low-biomass limits the microbial activity and biogeochemical study in oligotrophic environments, which is the typical condition for underground aquatic ecosystems. Facilitated by growth rate estimation, our research focuses on active functional microorganisms and their biogeochemical metabolic in oligotrophic aquifer sediments, revealing their impact on the environment and response to arsenic threats. Findings illuminate the metabolic advantage of a 'generalist life-style' in carbon-scarce environments and contribute to a broader understanding of bacterial ecosystems and environmental impacts in oligotrophic aquifer sediments worldwide.

Effects of simulated acid rain on hydrochemical factors and microbial community structure in red soil aquifers

Acid rain can lower the pH of groundwater and affect its hydrogeochemistry and microbial ecology. However, the effects of acid rain on the hydrogeochemistry and microbial ecology of red soil groundwater systems in southern China are poorly understood. Previous research had mainly investigated the sources and patterns of groundwater acidification, but not the microbial mechanisms that contribute to this process and their associations with hydrochemical factors. To address this knowledge gap, we conducted a soil column experiment to simulate the infiltration of acid rain through various filter materials (coarse, medium, and fine sand) and to examine the hydrochemical and microbial features of the infiltrate, which can reveal how simulated acid rain (pH 3.5-7.0) alters the hydrochemistry and microbial community composition in red soil aquifers. The results showed that the pH of the leachate decreased due to simulated acid rain, and that the leaching efficiency of nitrogen and metal ions was influenced by the particle size of the filter media. Illumina 16S rRNA gene sequencing revealed that the leachate was dominated by Proteobacteria, Patescibacteria, Actinobacteria, and Acidobacteria, with Proteobacteria accounting for 67.04-74.69% of the bacterial community and containing a high proportion of nitrifying and denitrifying bacteria. Additionally, several genera with heavy metal tolerance, such as Burkholderia-Caballeronia-Paraburkholderia, Delftia, Methylversatilis, Aquicella, and Ralstonia, were widely distributed in the leachate, indicating the strong adaptive capacity of the microbial population. A correlation analysis between the hydrochemical factors and the microbial community structure revealed that pH was the most influential factor, followed by NO2--N, Fe, Al, Cu, Mn, and others. These results indicate that acidification modifies the hydrochemical conditions of the aquifer, creating an environment that is unfavorable for microbial growth and survival. However, some microorganisms may acquire resistance genes to cope with environmental changes.

Elucidating Multiple Electron-Transfer Pathways for Metavanadate Bioreduction by Actinomycetic Streptomyces microflavus

While microbial reduction has gained widespread recognition for efficiently remediating environments polluted by toxic metavanadate [V(V)], the pool of identified V(V)-reducing strains remains rather limited, with the vast majority belonging to bacteria and fungi. This study is among the first to confirm the V(V) reduction capability of Streptomyces microflavus, a representative member of ubiquitous actinomycetes in environment. A V(V) removal efficiency of 91.0 ± 4.35% was achieved during 12 days of operation, with a maximum specific growth rate of 0.073 d-1. V(V) was bioreduced to insoluble V(IV) precipitates. V(V) reduction took place both intracellularly and extracellularly. Electron transfer was enhanced during V(V) bioreduction with increased electron transporters. The electron-transfer pathways were revealed through transcriptomic, proteomic, and metabolomic analyses. Electrons might flow either through the respiratory chain to reduce intracellular V(V) or to cytochrome c on the outer membrane for extracellular V(V) reduction. Soluble riboflavin and quinone also possibly mediated extracellular V(V) reduction. Glutathione might deliver electrons for intracellular V(V) reduction. Bioaugmentation of the aquifer sediment with S. microflavus accelerated V(V) reduction. The strain could successfully colonize the sediment and foster positive correlations with indigenous microorganisms. This study offers new microbial resources for V(V) bioremediation and improve the understanding of the involved molecular mechanisms.

Impact of exposure to arsenic on the bacterial microbiota associated with river biofilms in the Pampas region

Freshwater contamination by arsenic (As) is a worldwide problem. It may be found in Pampean streams of Argentina at concentrations higher than those recommended by international organizations and stipulated by national regulations. Exposure to high As concentrations causes serious consequences to both human health and the environment. The general objective of this work was to evaluate the effect of As on the biofilm microbiota structure from Naveira stream, Luján, Province of Buenos Aires (Coordinates: 34º34'02″ S 59º03'51″ W). The biofilm collected was cultivated in glass aquaria at different As III concentrations (0, 0.2 and 20 mg / L), inside incubation chambers under controlled conditions (16 h light: 8 h dark and 24 ± 1 °C) and constant aeration for 31 d, with partial water renewal every 9 d. We amplified the hypervariable regions V3 and V4 of the bacterial 16S rRNA gene from biofilm bacterial community samples to determine the diversity and abundance of the different taxa. The taxonomic composition of each sample, the alpha diversity of each treatment and the main metabolic pathways were analyzed. Principal Component Analysis of the present phyla and a Linear Discriminant Analysis of the metabolic pathways was also performed. Significant changes were observed in relation to the taxonomic composition of the bacterial community after exposure to the metalloid. However, this effect was not observed at the low concentration used (0.2 mg / L), which is the one that corresponds to ecologically relevant levels. The significantly affected phyla were Verrucomicrobiota, Acidobacteriota, Patescibacteria, Hydrogenedentes and WPS-2. The relative abundances of the Verrucomicrobiota, WPS-2 and Patescibacteria groups were notably decreased in the treatment with high As, while the Acidobacteria group was increased in both treatments with As. The stream samples showed greater bacterial diversity than those grown in the laboratory without As. Finally, it was possible to characterize the metabolic profile of the biofilm developed under natural conditions in the leaves of the aquatic plant Elodea canadensis in the Naveira stream. In addition, results showed that biosynthesis-related pathways were more abundant at the high As concentration treatment (20 mg / L).

Sediment microbiota in polyculture of shrimp and fish pattern is distinctive from those in monoculture intensive shrimp or fish ponds

Sediment microbial community plays a crucial role in aquaculture ecosystem. In aquaculture practice, rather than monoculture intensive shrimp (IS) or intensive fish (IF) patterns, polyculture of shrimp and fish (PolySF) pattern leads to a more reliable production. However, knowledge is still limited about the characteristics of sediment microbiota and its potential functions in the PolySF ponds compared to monoculture patterns (IS and IF). Herein, we collected sediment samples from these three patterns in seven cities to evaluate microbial variations among patterns. The highest oxidation reduction potential (ORP), total phosphate (TP) and total organic carbon (TOC) were detected in the PolySF pattern, representing a relatively less anoxic environment, while the highest iron (Fe) was detected in IS pattern. Proteobacteria was the most abundant phylum among three patterns, followed by Bacteroidetes and Chloroflexi. The microbial alpha diversity in the PolySF was higher than those in the IF, but lower than those in the IS. Microbial communities of these three patterns were significantly distinct from each other, and 23 distinguished taxa for each pattern were further characterized. In additional, the relative abundances of genes involved in nitrogen metabolism, fatty acid biosynthesis and carbon fixation pathways were markedly shifted. Moreover, ORP, TOC and Fe were the shaping factors for sediment microbiota, which significantly varied among three patterns. Collectively, these findings demonstrated that sediment microbial communities in the PolySF were distinctive from those in the IS and IF, which enlarged our understanding for the underlying mechanism of advances in the PolySF pattern from ecological perspective.

Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India

Rabindra Sarovar lake is an artificial freshwater lake in the arsenic infested eastern region of India. In this study, using the genome resolved metagenomics approach; we have deciphered the taxonomic diversity as well as the functional insights of the gene pools specific to this region. Initially, a total of 113 Metagenome Assembled Genomes (MAGs) were recovered from the two predominant seasons, that is, rainy (n = 50) and winter (n = 63). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Rainy season) were reconstructed. These MAGs were either of high-quality (n = 10) or of medium quality (n = 17) that was determined based on genome completeness and contamination. These 27 MAGs spanning across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Functional annotation across the MAGs suggested the existence of all known types of arsenic resistance and metabolism genes. Besides, important secondary metabolites such as zoocin_A, prochlorosin, and microcin were also abundantly present in these genomes. The metagenomic study of this lake provides the first insights into the microbiome composition and functional classification of the gene pools in two predominant seasons. The presence of arsenic metabolism and resistance genes in the recovered genomes is a sign of adaptation of the microbes to the arsenic contamination in this region. The presence of secondary metabolite genes in the lake microbiome has several implications including the potential use of these for the pharmaceutical industry.

Fractionation of carbon isotopes of dissolved organic matter adsorbed to goethite in the presence of arsenic to study the origin of DOM in groundwater

Natural dissolved organic matter (DOM) in groundwater plays a crucial role in mobilizing arsenic (As). The complex contribution of DOM sources makes it hard to predict how the variation of environmental conditions would affect the distribution of As concentrations. Identifying the carbon isotope fractionation of DOM is the key to quantify DOM sources based on stable carbon isotopes. To understand the magnitude and variability in the carbon isotopic fractionation of DOM in competitive adsorption with As(V), this study investigated the δ¹³C values of fulvic acid (FA) and DOM during adsorption to goethite in the presence of As(V), at a specific pH and temperature. The carbon isotopic enrichment factor (ε) of FA in the adsorption to goethite was 0.65 ± 2.11‰ at pH 4.1, 25 °C, suggesting that FA molecules containing ¹³C were more easily adsorbed to goethite. An increasing temperature increased ε_FA from 0.32 ± 1.17‰ to 0.82 ± 5.39‰ at 15-35 °C. For dissolved sediment organic matter (DSOM) cases, molecules containing ¹³C were more easily adsorbed to goethite. However, enrichment factors were not detected due to a reduction in DSOM adsorption and the diversity of natural humic substances or groups. The findings provide basic data for accurately ascertaining DOM sources through carbon isotopes, which is significant for predicting As fluctuation in aquifers affected by monsoon climate and/or human activities.

Impact process of the aquitard to regional arsenic accumulation of the underlying aquifer in Central Yangtze River Basin

The clayey aquitard has the potential to release geogenic poisonous chemicals such as arsenic (As) to the adjacent aquifer owing to complex hydrologic or biogeochemical processes. However, it remains unclear whether the aquitard has effect on As enrichment in the underlying aquifer in regions without extensive groundwater pumping, and the related processes have been poorly known. Based on piezometer water chemistry, stable water isotopes, sediment chemistry and reactive-transport model, this study aims to reveal the impact process of the aquitard to As accumulation of underlying aquifer from central Yangtze River Basin, a As-affected area without extensive groundwater pumping. On the whole, As migrated from top to bottom of the aquitard (especially the depth over 10 m) and significantly influenced the As accumulation in the underlying aquifer. Nonetheless, the results of three topical boreholes showed two different hydrogeological conditions affected As release in the aquitard and enrichment in the underlying aquifer. Different hydrogeological conditions could result in the input of different species organic carbon and then impact As concentrations in the aquifer. When the aquitard was near surface water bodies, the reductive dissolution of iron oxides was the main driver for As release and the aquitard had a significant influence on the enrichment of arsenic in the aquifer. At areas without surface water bodies nearby, the desorption of As(V) from minerals was the main source of As and the concentrations of As in pore water were quite low; this pattern had little effect on the enrichment of arsenic in the aquifer.

Effect of the natural arsenic gradient on the diversity and arsenic resistance of bacterial communities of the sediments of Camarones River (Atacama Desert, Chile)

Arsenic (As), a highly toxic metalloid, naturally present in Camarones River (Atacama Desert, Chile) is a great health concern for the local population and authorities. In this study, the taxonomic and functional characterization of bacterial communities associated to metal-rich sediments from three sites of the river (sites M1, M2 and M3), showing different arsenic concentrations, were evaluated using a combination of approaches. Diversity of bacterial communities was evaluated by Illumina sequencing. Strains resistant to arsenic concentrations varying from 0.5 to 100 mM arsenite or arsenate were isolated and the presence of genes coding for enzymes involved in arsenic oxidation (aio) or reduction (arsC) investigated. Bacterial communities showed a moderate diversity which increased as arsenic concentrations decreased along the river. Sequences of the dominant taxonomic groups (abundances ≥1%) present in all three sites were affiliated to Proteobacteria (range 40.3–47.2%), Firmicutes (8.4–24.8%), Acidobacteria (10.4–17.1%), Actinobacteria (5.4–8.1%), Chloroflexi (3.9–7.5%), Planctomycetes (1.2–5.3%), Gemmatimonadetes (1.2–1.5%), and Nitrospirae (1.1–1.2%). Bacterial communities from sites M2 and M3 showed no significant differences in diversity between each other (p = 0.9753) but they were significantly more diverse than M1 (p<0.001 and p<0.001, respectively). Sequences affiliated with Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi and Actinobacteria at M1 accounted for more than 89% of the total classified bacterial sequences present but these phyla were present in lesser proportions in M2 and M3 sites. Strains isolated from the sediment of sample M1, having the greatest arsenic concentration (498 mg kg^-1), showed the largest percentages of arsenic oxidation and reduction. Genes aio were more frequently detected in isolates from M1 (54%), whereas arsC genes were present in almost all isolates from all three sediments, suggesting that bacterial communities play an important role in the arsenic biogeochemical cycle and detoxification of arsenical compounds. Overall, results provide further knowledge on the microbial diversity of arsenic contaminated fresh-water sediments.

Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater

Microbial functional potential in high arsenic (As) groundwater ecosystems remains largely unknown. In this study, the microbial community functional composition of nineteen groundwater samples was investigated using a functional gene array (GeoChip 5.0). Samples were divided into low and high As groups based on the clustering analysis of geochemical parameters and microbial functional structures. The results showed that As related genes (arsC, arrA), sulfate related genes (dsrA and dsrB), nitrogen cycling related genes (ureC, amoA, and hzo) and methanogen genes (mcrA, hdrB) in groundwater samples were correlated with As, SO₄^2-, NH₄⁺ or CH₄ concentrations, respectively. Canonical correspondence analysis (CCA) results indicated that some geochemical parameters including As, total organic content, SO₄^2-, NH₄⁺, oxidation-reduction potential (ORP) and pH were important factors shaping the functional microbial community structures. Alkaline and reducing conditions with relatively low SO₄^2-, ORP, and high NH₄⁺, as well as SO₄^2- and Fe reduction and ammonification involved in microbially-mediated geochemical processes could be associated with As enrichment in groundwater. This study provides an overall picture of functional microbial communities in high As groundwater aquifers, and also provides insights into the critical role of microorganisms in As biogeochemical cycling.