Response characteristics of indigenous microbial community in polycyclic aromatic hydrocarbons (PAHs) contaminated aquifers under polyethylene microplastics stress: A microcosmic experimental study

To understand the response characteristics of indigenous microbial community in PAH-contaminated aquifers to the coexistence of microplastics. In this paper, we constructed a groundwater microecosystem using lithologic media collected from the field and subjected it to the stress of a polyethylene microplastics (PE-MPs) concentration gradient. By conducting adsorption experiments and 16S rRNA sequencing, we revealed the growth, structure, metabolism, and resistance mechanisms of the indigenous microbial community in the aquifer lithologic media exposed to varying levels of co-stress from PE-MPs and phenanthrene. Our findings suggest that the adsorption capacity of aquifer lithologic media for phenanthrene is significantly weaker than that of PE-MPs. Additionally, our observations indicated that small particle lithologic media had a greater adsorption capacity for phenanthrene than large particle lithologic media. The presence of PE-MPs was found to increase both the abundance and diversity of microbial communities, although the relationship was not linear with the content of PE-MPs. When exposed to the combined stress of PE-MPs and phenanthrene, the relative abundance of Proteobacteria decreased while that of Bacteroidetes increased. Several genera belonging to Proteobacteria (Aeromonas, Desulfovibrio, Klebsiella, Pantoea, and Microvirgula) and Bacteroidetes (Macellibacteroides and Bacteroides) occupied a central position in the microbial community interaction network and showed significant correlations with other genera. Furthermore, an increase in the proportion of genera capable of degrading various refractory organics was observed. The presence of PE-MPs increased the phenanthrene content in the aquifer lithologic media, thereby intensifying the inhibitory effect on indigenous microbial community in this environment. Despite an increase in the phenanthrene content of aquifer lithologic media due to the presence of PE-MPs, indigenous microbial community in this environment exhibited resistance to the combined inhibition of PE-MPs and phenanthrene through a series of resistance mechanisms. These mechanisms included strengthening the N-cycle process, enhancing metabolic capacity for phenanthrene, improving perception, response, and adaptation to changes in the external environment or intracellular state, modifying the transmembrane transport of the cell membrane to the substrate, and regulating life processes.

A starch-based controlled-release targeted nutrient agent to stimulate the activity of volatile chlorinated hydrocarbon-degrading indigenous microflora present in groundwater

Volatile chlorinated hydrocarbons (VCHs) contaminated groundwater has a low indigenous microorganism population, and lack of nutrient substrates involved in degradation reactions, resulting in a weak natural remediation ability of groundwater ecosystems. In this study, based on the principle of degradation of VCHs by indigenous microorganisms in groundwater, and combined with biostimulation and controlled-release technology, we developed a starch-based encapsulated targeted bionutrient (YH-1) with easy uptake, good stability, controllable slow-release migration, and long timeliness for the remediation of groundwater contaminated by VCHs by indigenous microorganisms. The results showed that YH-1 is easily absorbed by microorganisms and can rapidly initiate itself to stimulate the microbial degradation of VCHs, and the degradation rate of various VCH components within 7 days was 82.38-92.38 %. The release rate of nutrient components in YH-1 increases with increasing VCH concentrations in groundwater; this could effectively prolong the action time of nutrient components, while also improving the degradation efficiency of pollutants with a sustained effect of more than 15 days. Simultaneously, owing to the fluidity, water solubility, and biodegradability of YH-1 in lithologic media, YH-1 injection did not cause blockage of the lithologic media in the aquifer. Through YH-1 stimulation, indigenous microorganisms grew rapidly in the underground environment, the diversity of microbial communities and the total number of species increased, and the correlation between genera strengthened. Simultaneously, YH-1 improved the ability of microbial community to convert inorganic electron donors/acceptors, thereby strengthening the co-metabolic mechanism between microorganisms. Additionally, there was a significant increase in the percentage of many microorganisms (e.g., Sphingomonas, Janthinobacterium, Duganella, etc.) that mediated the reductive dechlorination process and were redox inorganic electron donors/acceptors. This was conducive to the reductive dechlorination process of VCHs and achieved the efficient degradation of VCHs.

Linking microbial community composition to farming pattern in selenium-enriched region: Potential role of microorganisms on Se geochemistry

Selenium (Se) is an essential micronutrient for lives. Indigenous microbial communities play an important role on Se geochemistry in soils. In this study, the microbial community composition and functions of 53 soil samples were investigated using high-throughput sequencing. Samples were divided into 3 groups with different farming types based on the measured geochemical parameters and microbial functional structures. Results indicated that putative Se related bacteria Bacillus, Dyella, Paenibacillus, Burkholderia and Brevibacillus were dominant in dryland plantation soils which were characterized with higher available Se and low contents of H₂O, total organic carbon (TOC), NH₄⁺ and NO₂^-. In contrast, the putative denitrifier Pseudomonas dominated in flooded paddy soils with higher TOC, NO₃^- and organic Se, whereas genera Rhizobium, Nitrosospira, and Geobacter preferred woodland soils with higher oxidation-reduction potential (ORP), pH, NH₄⁺ and Fe. Farming patterns resulted in distinct geochemical parameters including moisture, pH, ORP, TOC, and contents of soluble Fe, NO₂^- and NH₄⁺, shaping the microbial communities, which in turn affected Se forms in soils. This study provides a valuable insight into understanding of Se biogeochemistry in soils and prospective strategy for Se-rich agriculture production.

In situ remediation of Cr(VI) contaminated groundwater by ZVI-PRB and the corresponding indigenous microbial community responses: a field-scale study

The performance of a permeable reactive barrier (PRB) for the in situ remediation of hexavalent chromium [Cr(VI)] contaminated groundwater, and the resulted responses in the indigenous microbial community, were investigated in a field-scale study. The PRB consisted of a mixture of zero-valent iron (ZVI), gravel and sand. The results showed that the PRB segment with 20% active reaction medium (ZVI) was able to successfully reduce Cr(VI) via chemical reduction from 27.29-242.65 mg/L to below the clean-up goal of 0.1 mg/L, and can be scaled-up under field conditions. It was found that the ZVI induced significant changes in the indigenous microbial community structure and compositions in the area of the PRB and those areas downgradient. The competitive growth among Cr(VI)-reducing bacteria (the reduced abundance of Hydrogenophaga, Pseudomonas, Exiguobacterium and Rhodobacter, along with the enrichment of Rivibacter and Candidatus_Desulforudis) were observed in PRB. In addition, Cr(VI)-reducing bacteria (Hydrogenophaga, Pseudomonas, Exiguobacterium and Rhodobacter) were enriched in the downgradient of PRB, indicating that Cr(VI) can be further bio-reduced to Cr(III). The Cr(VI) bio-reduction could serve as a secondary mechanism for further removal of Cr(VI) from contaminated groundwater, suggesting that the actual lifetime of a PRB can be prolonged, which is important for the design and economic assessment of a PRB. Further analysis revealed that pH, dissolved oxygen, Cr(VI) level, the oxidation-reduction potential, and temperature were the main environmental factors influencing the subsurface microbial community compositions.

Enhanced biostimulation coupled with a dynamic groundwater recirculation system for Cr(VI) removal from groundwater: A field-scale study

A large gap exists between laboratory findings and successful implementation of bioremediation technologies for the treatment of chromium (Cr)-contaminated sites. This work conducted the enhanced bioremediation of Cr(VI) in situ via the addition of organic carbon (ethanol) coupled with a dynamic groundwater recirculation (DGR)-based system in a field-scale study. The DGR system was applied to successfully (1) remove Cr(VI) from groundwater via enhanced flushing by the recirculation system and (2) deliver the biostimulant to the heterogeneous subsurface environment, including a sand/cobble aquifer and a fractured bedrock aquifer. The results showed that the combined extraction and bioreduction of Cr(VI) were able to reduce Cr(VI) concentrations from 1000 to 2000 mg/L to below the clean-up goal of 0.1 mg/L within the operation period of 52 days. The effectiveness of Cr(VI) bioremediation and the relationship between microbial communities and geochemical parameters were evaluated. Multiple-line of evidence demonstrated that the introduction of ethanol significantly stimulated a variety of bacteria, including those responsible for denitrification, sulfate reduction and reduction of Cr(VI), which contributed to the establishment of reducing conditions in both aquifers. Cr(VI) was removed from groundwater via combined mechanisms of physical removal through the DGR system and the bioreduction of Cr(VI) followed by precipitation. In particular, it was found competitive growth among Cr(VI)-reducing bacteria (such as the enrichment of Geobacter, along with the reduced relative abundance of Acinetobacter and Pseudomonas) was induced by ethanol injection. Furthermore, Cr(VI), total organic carbon, NO₂^-, and SO₄^2- played important roles in shaping the composition of the microbial community and its functions.

Insights into the mechanisms underlying efficient Rhizodegradation of PAHs in biochar-amended soil: From microbial communities to soil metabolomics

The combined effects of biochar amendment and the rhizosphere on the soil metabolic microbiome during the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil remain unknown. In this study, we attempted to characterize a PAH degradation network by coupling the direct PAH degradation with soil carbon cycling. From microbial community structure and functions to metabolic pathways, we revealed the modulation strategies by which biochar and the rhizosphere benefited PAH degradation in soil. Firstly, some PAH degraders were enriched by biochar and the rhizosphere, and their combination promoted the cooperation among these PAH degraders. Simultaneously, under the combined effects of biochar and the rhizosphere, the functional genes participating in upstream PAH degradation were greatly upregulated. Secondly, there were strong co-occurrences between soil microbial community members and metabolites, in particular, some PAH degraders and the metabolites, such as PAH degradation products or common carbon resources, were highlighted in the networks. It shows that the overall downstream carbon metabolism of PAH degradation was also greatly upregulated by the combined effects of biochar and plant roots, showing good survival of the soil microbiome and contributing to PAH biodegradation. Taken together, both soil carbon metabolism and direct contaminant biodegradation are likely to be modulated by the combined effects of biochar and plant roots, jointly benefitting to PAH degradation by soil microbiome. Our study is the first to link PAH degradation with native carbon metabolism by coupling sequencing and soil metabolomics technology, providing new insights into a systematic understanding of PAH degradation by indigenous soil microbiome and their networks.

The plasticity of indigenous microbial community in a full-scale heavy oil-produced water treatment plant

Indigenous microbial communities are main and promising performers for bioremediation due to their excellent adaptability, degradation capability, and inherent plasticity. Treating heavy oil-produced water (HOPW) is a challenge owing to the high recalcitrance and heterogeneity of chemicals it contains. A full-scale HOPW treatment plant was built at a capacity of 10,000 m³/d with the indigenous microbial community. After the treatment, the outlet water reached the design standard. The microbial community structures in all treatment stages were analyzed by using Illumina MiSeq 16S rRNA gene sequencing. The composition of microbial community changed greatly with the changes in environmental conditions, especially with the only artificially regulated parameter of dissolved oxygen. In the anaerobic stage, the community converted the recalcitrant chemical oxygen demand to biological oxygen demand (BOD), and played a major role in enhancing the biodegradability of HOPW. During the aerobic stage, the community mainly mineralized BOD. These results suggest that the structures of indigenous microbial community differed in different treatment stages to accomplish the corresponding functions. Based on these findings, it is proposed that exploiting the plasticity of microbial communities for bioremediation is feasible, especially treating wastewater with varied components.

Synergistic antimicrobial activity of caprylic acid in combination with citric acid against both Escherichia coli O157:H7 and indigenous microflora in carrot juice

The identification of novel, effective, and non-thermal decontamination methods is imperative for the preservation of unpasteurized and fresh vegetable juices. The aim of this study was to examine the bactericidal effects of caprylic acid + citric acid against the virulent pathogen Escherichia coli O157:H7 and the endogenous microflora in unpasteurized fresh carrot juice. Carrot juice was treated with either caprylic acid, citric acid, or a combination of caprylic acid + citric acid at mild heating temperature (45 °C or 50 °C). The color of the treated carrot juice as well as microbial survival was examined over time. Combined treatment was more effective than individual treatment in terms of both color and microbial survival. Caprylic acid + citric acid treatment (each at 5.0 mM) at 50 °C for 5 min resulted in 7.46 and 3.07 log CFU/ml reductions in the E. coli O157:H7 and endogenous microflora populations, respectively. By contrast, there was no apparent reduction in either population following individual treatment. A validation assay using a low-density E. coli O157:H7 inoculum (3.31 log CFU/ml) showed that combined treatment with caprylic acid (5.0 mM) + citric acid (2.5 mM) at 50 °C for >5 min or with caprylic acid + citric acid (both at 5.0 mM) at either 45 °C or 50 °C for >5 min completely destroyed the bacteria. Combined treatment also increased the redness of the juice, which is a perceived indication of quality. Taken together, these results indicate that combined treatment with low concentrations of caprylic acid and citric acid, which are of biotic origin, can eliminate microorganisms from unpasteurized carrot juice.