Spatial Pattern of Bacterial Community Diversity Formed in Different Groundwater Field Corresponding to Electron Donors and Acceptors Distributions at a Petroleum-Contaminated Site

Characterization the microbial diversity and functional genes in the multi-component contaminated groundwater in a petrochemical site

Microorganisms in groundwater at petroleum hydrocarbon (PHC)-contaminated sites are crucial for PHC natural attenuation. Studies mainly focused on the microbial communities and functions in groundwater contaminated by PHC only. However, due to diverse raw and auxiliary materials and the complex production processes, in some petrochemical sites, groundwater suffered multi-component contamination, but the microbial structure remains unclear. To solve the problem, in the study, a petrochemical enterprise site, where the groundwater suffered multi-component pollution by PHC and sulfates, was selected. Using hydrochemistry, 16S rRNA gene, and metagenomic sequencing analyses, the relationships among electron acceptors, microbial diversity, functional genes, and their interactions were investigated. Results showed that different production processes led to different microbial structures. Overall, pollution reduced species richness but increased the abundance of specific species. The multi-component contamination multiplied a considerable number of hydrocarbon-degrading and sulfate-reducing microorganisms, and the introduced sulfates might have promoted the biodegradation of PHC. PRACTITIONER POINTS: The compound pollution of the site changed the microbial community structure. Sulfate can promote the degradation of petroleum hydrocarbons by hydrocarbon-degrading microorganisms. The combined contamination of petroleum hydrocarbons and sulfates will decrease the species richness but increase the abundance of endemic species.

Insights into the characteristics of changes in dissolved organic matter fluorescence components on the natural attenuation process of toluene

Natural attenuation (NA) is of great significance for the remediation of contaminated groundwater, and how to identify NA patterns of toluene in aquifers more quickly and effectively poses an urgent challenge. In this study, the NA of toluene in two typical soils was conducted by means of soil column experiment. Based on column experiments, dissolved organic matter (DOM) was rapidly identified using fluorescence spectroscopy, and the relationship between DOM and the NA of toluene was established through structural equation modeling analysis. The adsorption rates of toluene in clay and sandy soil were 39 % and 26 %, respectively. The adsorption capacity and total NA capacity of silty clay were large. The occurrence of fluorescence peaks of protein-like components and specific products indicated the occurrence of biodegradation. Arenimonas, Acidovorax and Brevundimonas were the main degrading bacteria identified in Column A, while Pseudomonas, Azotobacter and Mycobacterium were the main ones identified in Column B. The pH, ORP, and Fe(II) were the most important factors affecting the composition of microbial communities, which in turn affected the NA of toluene. These results provide a new way to quickly identify NA of toluene.

Metagenomic analysis revealed highly diverse carbon fixation microorganisms in a petroleum-hydrocarbon-contaminated aquifer

As one of the ultimate products of hydrocarbon biodegradation, inorganic carbon always be used to evaluate hydrocarbon biodegradation rates in petroleum-hydrocarbon-contaminated (PHC) aquifers. The evaluation method was challenged because of the existence of carbon fixation microorganisms, which may uptake inorganic carbons and consequently cause the biodegradation rates to be underestimated. We wonder if there are carbon fixation microorganisms in PHC aquifers. Although an extremely limited number of carbon fixation microorganisms in PHC sites have been studied in previous studies, the vast majority of microorganisms that participate in carbon fixation have not been systematically identified. To systematically reveal carbon fixation microorganisms and their survival environmental conditions, high-throughput metagenomic sequencing technologies, which are characterized by culture-independent, unbiased, and comprehensive methods for the detection and taxonomic characterization of microorganisms, were introduced to analyze the groundwater samples collected from a PHC aquifer. Results showed that 1041 genera were annotated as carbon fixation microorganisms, which accounted for 49% of the total number of genera in the PHC aquifer. Carbon fixation genes involved in Calvin-Benson-Bassham (CBB), 3-hydroxy propionate (3HP), reductive tricarboxylic acid (rTCA), and Wood-Ljungdahl (WL) cycles accounted for 2%, 41%, 34%, and 23% of the total carbon fixation genes, respectively, and 3HP, rTCA, and WL can be deemed as the dominant carbon fixation pathways. Most of the identified carbon fixation microorganisms are potential hydrocarbon biodegraders, and the most abundant carbon fixation microorganisms, such as Microbacterium, Novosphingobium, and Reyranella, were just the most abundant microorganisms in the aquifer system. It's deduced that most of the microorganisms in the aquifer were facultative autotrophic, and undertaking the dual responsibilities of degrading hydrocarbons to inorganic carbon and uptaking inorganic carbon to biomass.

Natural attenuation of BTEX and chlorobenzenes in a formerly contaminated pesticide site in China: Examining kinetics, mechanisms, and isotopes analysis

Groundwater contamination from abandoned pesticide sites is a prevalent issue in China. To address this problem, natural attenuation (NA) of pollutants has been increasingly employed as a management strategy for abandoned pesticide sites. However, limited studies have focused on the long-term NA process of co-existing organic pollutants in abandoned pesticide sites by an integrated approach. In this study, the NA of benzene, toluene, ethylbenzene, and xylene (BTEX), and chlorobenzenes (CBs) in groundwater of a retired industry in China was systematically investigated during the monitoring period from June 2016 to December 2021. The findings revealed that concentrations of BTEX and CBs were effectively reduced, and their NA followed first-order kinetics with different rate constants. The sulfate-reducing bacteria, nitrate-reducing bacteria, fermenting bacteria, aromatic hydrocarbon metabolizing bacteria, and reductive dechlorinating bacteria were detected in groundwater. It was observed that distinct environmental parameters played a role in shaping both overall and key bacterial communities. ORP (14.72%) and BTEX (12.89%) were the main drivers for variations of the whole and key functional microbial community, respectively. Moreover, BTEX accelerated reductive dechlorination. Furthermore, BTEX and CBs exhibited significant enrichment of 13C, ranging from +2.9 to +27.3‰, demonstrating their significance in situ biodegradation. This study provides a scientific basis for site management.

Topographically Distinguished Microbiome Taxonomy and Stress-Response Genes of Royal Belum Rainforest and Raja Muda Musa Peat Swamp Revealed through Metagenomic Inquisition

Soil ecosystems are home to a diverse range of microorganisms, but they are only partially understood because no single-cell sequencing or whole-community sequencing provides a complete picture of these complex communities. Using one of such metagenomics approaches, we succeeded in monitoring the microbial diversity and stress-response gene in the soil samples. This study aims to test whether known differences in taxonomic diversity and composition are reflected in functional gene profiles by implementing whole gene sequencing (WGS) metagenomic analysis of geographically dispersed soils from two distinct pristine forests. The study was commenced by sequencing three rainforest soil samples and three peat swamp soil samples. Soil richness effects were assessed by exploring the changes in specific functional gene abundances to elucidate physiological constraints acting on different soil systems and identify variance in functional pathways relevant to soil biogeochemical cycling. Proteobacteria shows abundances of microbial diversity for 52.15% in Royal Belum Reserved Forest and 48.28% in Raja Musa; 177 out of 1,391,841 and 449 out of 3,586,577 protein coding represent acidic stress-response genes for Royal Belum and Raja Musa, respectively. Raja Musa indicates pH 2.5, which is extremely acidic. The analysis of the taxonomic community showed that Royal Belum soils are dominated by bacteria (98% in Sungai Kooi (SK), 98% in Sungai Papan (SP), and 98% in Sungai Ruok (SR), Archaea (0.9% in SK, 0.9% in SP, and 1% in SR), and the remaining were classed under Eukaryota and viruses. Likewise, the soils of Raja Muda Musa are also dominated by bacteria (95% in Raja Musa 1 (RM1), 98% in Raja Musa 2 (RM2), and 96% in Raja Musa 3 (RM3)), followed by Archaea (4% in RM1, 1% in RM2, and 3% in RM3), and the remaining were classed under Eukaryota and viruses. This study revealed that RBFR (Royal Belum Foresr Reserve) and RMFR (Raja Musa Forest Reserve) metagenomes contained abundant stress-related genes assigned to various stress-response pathways, many of which did not show any difference among samples from both sites. Our findings indicate that the structure and functional potential of the microbial community will be altered by future environmental potential as the first glimpse of both the taxonomic and functional composition of soil microbial communities.

Stress response characteristics of indigenous microorganisms in aromatic-hydrocarbons-contaminated groundwater in the cold regions of Northeast China

The resistance mechanism of microbial communities in contaminated groundwater under combined stresses of aromatic hydrocarbons (AHs), NH₄⁺, and Fe-Mn exceeding standard levels was studied in an abandoned oil depot in Northeast China. The response of environmental parameters and microbial communities under different pollution levels in the study area was discussed, and microscopic experiments were conducted using background groundwater with different AHs concentrations. The results showed that indigenous microbial community were significantly affected by environmental factors, including pH, TH, COD_Mn, TFe, Cr (VI), NH₄⁺, NO₃^-, and SO₄^2-. AHs likely had a limited influence on microbial communities, mainly causing indirect changes in the microbial community structure by altering the electron donor/acceptor (mainly Fe, Mn, NO₃^-, NO₂^-, NH₄⁺, and SO₄^2-) content in groundwater, and there was no linear effect of AHs content on the microbial community. In low- and medium-AHs-contaminated groundwater, the microbial diversity increased, whereas high AHs contents decreased the diversity of the microbial community. The microbial community had the strongest ability to metabolize AHs in the medium-AHs-contaminated groundwater. In the high-AHs-contaminated groundwater, microbial communities mainly degraded AHs through a complex co-metabolic mechanism due to the inhibitory effect caused by the high concentration of AHs, whereas in low-AHs-contaminated groundwater, microbial communities mainly caused a mutual transformation of inorganic electron donors/acceptors (mainly including N, S), and the microbial community's ability to metabolize AHs was weak. In the high-AHs-contaminated groundwater, the microbial community resisted the inhibitory effect of AHs mainly via a series of resistance mechanisms, such as regulating their life processes, avoiding unfavorable environments, and enhancing their feedback to the external environment under high-AHs-contaminated conditions.

Response of soil microbial communities to petroleum hydrocarbons at a multi-contaminated industrial site in Lanzhou, China

Total petroleum hydrocarbon (TPH) contamination poses threats to ecological systems and human health. Many studies have reported its negative impacts on soil microbes, but limited information is known about microbial change and response to multiple TPH contamination events. In this study, we investigated TPH contamination level, microbial community structure and functional genes at a multi-contaminated industrial site in Lanzhou, where a benzene spill accident caused the drinking water crisis in 2014. TPHs distribution in soils and groundwater indicated multiple TPH contamination events in history, and identified the spill location where high TPH level (6549 mg kg^-1) and high ratio of low-molecular-weight TPHs (>80%) were observed. In contrast, TPH level was moderate (349 mg kg^-1) and the proportion of low-molecular-weight TPHs was 44% in soils with a long TPH contamination history. After the spill accident, soil bacterial communities became significant diverse (p = 0.047), but the dominant microbes remained the same as Pseudomonadaceae and Comamonadaceae. The abundance of hydrocarbon-degradation related genes increased by 10-1000 folds at the site where the spill accident occurred in multi-contaminated areas and was significantly related to 2-ring PAHs. Such changes of microbial community and hydrocarbon-degradation related genes together indicated the resilience of soil indigenous microbes toward multiple contamination events. Our results proved the significant change of bacterial community and huge shift of hydrocarbon-degradation related genes after the spill accident (multiple contamination events), and provided a deep insight into microbial response at industrial sites with a long period of contamination history.

A new insight into the influencing factors of natural attenuation of chlorinated hydrocarbons contaminated groundwater: A long-term field study of a retired pesticide site

Natural attenuation of contaminants has been increasingly applied as a strategy to manage the retired pesticide manufacturing sites due to the increasing restrictions on the reuse of contaminated sites in China. However, the influencing factors to enhance natural attenuation for chlorinated hydrocarbons in retired pesticide sites were not well studied. In this paper, monitoring of pollutants, environmental factors and microbial community was conducted from 2016 to 2021 in a retired pesticide site in Jiangsu Province undergoing natural attenuation, where the groundwater was severely contaminated with chlorinated hydrocarbons. The spatial variation of main pollutants, including chlorinated ethenes and ethanes, indicated that the site could be divided into the source area, diffusion area, and the end of diffusion area, where organohalide-respiring bacteria (OHRB) were detected. Pollutants and environmental factors influenced the OHRB community structure, which explained 7.6% and 33.2% of the variation, respectively. The abundances of obligate and facultative OHRB were affected in opposite ways by pollutants and environmental factors. Dehalococcoides and Dehalogenimonas in obligate OHRB were significantly inhibited by sulfate (r = -0.448, p < 0.05). The spatial-temporal characteristics of pollutants and the reveal of microbial community structure and its restricting factors in different areas make the foundation for strengthening the implementation of natural attenuation.

Variation of bacterial community and alkane monooxygenase gene abundance in diesel n-alkane contaminated subsurface environment under seasonal water table fluctuation

n-Alkanes, the main component of diesel fuel, are common light non-aqueous phase liquids (LNAPLs) that threaten ecological security. The subsurface from vadose zone, through fluctuating zone, to saturated zone, is a critical multi-interface earth layer which significantly affects the biodegradation processes of n-alkanes. A pilot-scale diesel contaminated aquifer column experiment has been undertaken to investigate the variations of bacterial community and alkane monooxygenase (alkB) gene abundance in these zones due to water-table fluctuations. The n-alkanes formed a layer immediately above the water table, and when this was raised, they were carried upwards through the fluctuating zone into the vadose zone. Water content and n-alkanes component C10-C12 are main factors influencing bacterial community variation in the vadose zone, while C10-C12 is a key driving factor shaping bacterial community in the fluctuating zone. The most abundant bacterial phyla at all three zones were Proteobacteria, Firmicutes and Actinobacteria, but moisture-niche selection determined their relative abundance. The intermittent wetting cycle resulted in higher abundance of Proteobacteria, and lower abundance of Actinobacteria in the vadose and fluctuating zones in comparison to the control column with a static water-table. The abundances of the alkB gene variants were relatively uniform in different zones, probably because the bacterial populations harboring alkB gene are habituated to biogenic n-alkanes rather than responding to diesel fuel contamination. The variation in the bacterial populations with height due to moisture-niche selection had very little effect on the alkB gene abundance, possibly because numerous species in both phyla (Proteobacteria and Actinobacteria) carry an alkB gene variant. Nevertheless, the drop in the water table caused a short-term spike in alkB gene abundance in the saturated zone, which is most likely associated with transport of solutes or colloids from the fluctuating zone to bacteria species in the saturated zone, so a fluctuating water table could potentially increase n-alkane biodegradation function.

The Spatial Distribution of the Microbial Community in a Contaminated Aquitard below an Industrial Zone

The industrial complex Neot Hovav, in Israel, is situated above an anaerobic fractured chalk aquitard, which is polluted by a wide variety of hazardous organic compounds. These include volatile and non-volatile, halogenated, organic compounds. In this study, we characterized the indigenous bacterial population in 17 boreholes of the groundwater environment, while observing the spatial variations in the population and structure as a function of distance from the polluting source. In addition, the de-halogenating potential of the microbial groundwater population was tested through a series of lab microcosm experiments, thus exemplifying the potential and limitations for bioremediation of the site. In all samples, the dominant phylum was Proteobacteria. In the production plant area, the non-obligatory organo-halide respiring bacteria (OHRB) Firmicutes Phylum was also detected in the polluted water, in abundancies of up to 16 %. Non-metric multidimensional scaling (NMDS) analysis of the microbial community structure in the groundwater exhibited clusters of distinct populations following the location in the industrial complex and distance from the polluting source. Dehalogenation of halogenated ethylene was demonstrated in contrast to the persistence of brominated alcohols. Persistence is likely due to the chemical characteristics of brominated alcohols, and not because of the absence of active de-halogenating bacteria.

The Characterization of Microbial Communities Response to Shallow Groundwater Contamination in Typical Piedmont Region of Taihang Mountains in the North China Plain

Regional-scale nitrate and organic contaminants in the shallow groundwater were investigated in the Piedmont region of Taihang Mountains (PRTM), but the information of the microbial communities is limited. However, microorganisms provide a dominated contribution to indicate and degrade the contaminants in the aquifer. Therefore, this study investigates the microbial diversity and contamination microbial indicators of groundwater samples with different contaminated types to better understand the contamination in the PRTM. Seventy-six samples were collected between two rivers in the Tang-Dasha River Basin covering 4000 km2 in the PRTM. High-throughput sequencing was employed to determine the samples’ DNA sequences. The samples were divided into four groups: background (B), nitrate contamination (N), organic contamination (O) and organic-nitrate contamination (O_N) based on the cumulative probability distribution and the Chinese groundwater standard levels of NO3−, COD and DO concentrations. Then, the microbial diversity and contamination microbial indicators were studied in the four groups. The results showed that the O group exhibited lower diversity than other groups. Bacteria detected in these four groups covered 531 families, 987 genera, and 1881 species. Taxonomic assignment analysis indicated that Rhodobacter, Vogesella, Sphingobium dominated in the O_N group, N group, and O group, and accounted for 18.05%, 17.74%, 16.45% in each group at genus level, respectively. Furthermore, these three genera were identified as contamination microbial indicators to the three types of contamination, respectively. The results provide a potential molecular microbiological method to identity contamination in shallow groundwater, and established a strong foundation for further investigation and remediation in the PRTM.

Groundwater Contamination, Subsurface Processes, and Remediation Methods: Overview of the Special Issue of Water on Groundwater Contamination and Remediation

This special issue of Water brings together ten studies on groundwater contamination and remediation. Common themes include practical techniques for plume identification and delineation, the central role of subsurface processes, the pervasiveness of non-Fickian transport, and the importance of bacterial communities in the broader context of biogeochemistry.