Indigenous Microbial Communities Research Articles

Polymetallic contamination drives indigenous microbial community assembly dominated by stochastic processes at Pb-Zn smelting sites

Indigenous microbial communities in smelting areas are crucial for maintaining fragile ecosystem functions. However, the community assembly process and their responses to polymetallic pollution are poorly understood, especially the taxa in each bin from the amplicons that contributed to the assembly process. Herein, microbial diversity, co-occurrence patterns, assembly process and the intrinsic mechanisms across contamination gradients at a typical PbZn smelting site were systematically unravelled by high-throughput sequencing. The results showed a consistent compositional profile among the indigenous communities across sampling sites, wherein genera KD4–96 from Chloroflexi and Sphingomonas from Proteobacteria emerged as the most abundant taxa. Network modularity of the high- and middle-contaminated communities at Pb and Zn smelting sites was >0.44, indicating that community populations were clustered into modules to resist high heavy metal stress. Stochastic processes dominated the community assembly, with the greatest contribution from drift (DR), which was significantly correlated with Pb, Zn, Cr and Cu contents. What's particular was that the DR-controlled bins were dominated by Proteobacteria (typical r-strategists), while the HoS-controlled bins were by Chloroflexi (typical K-strategists). Furthermore, the proportion of DR in the bins dominated by Sphingomonadaceae (phylum Proteobacteria) increased gradually with the increase of heavy metal contents. These discoveries provide essential insights for community control in restoring and mitigating soil degradation at PbZn smelting sites.

Research on Microbial Community Structure in Different Blocks of Alkaline–Surfactant–Polymer Flooding to Confirm Optimal Stage of Indigenous Microbial Flooding

The microbial communities associated with alkaline–surfactant–polymer (ASP)-flooded reservoirs have rarely been investigated. In this study, high-throughput sequencing was used to analyse the indigenous microbial communities in two different blocks, the water flooding after the alkaline–surfactant–polymer flooding block and the alkaline–surfactant–polymer flooding block, and to ascertain the optimal stage for the implementation of indigenous microbial oil recovery technology. The different displacement blocks had significant effects on the indigenous microbial community at the genus level according to an alpha diversity analysis and community composition. In water flooding after alkaline–surfactant–polymer flooding, the dominant genus of Pseudomonas exceeded 30%, increasing to 52.1% in alkaline–surfactant–polymer flooding, but alpha diversity decreased. Through a co-occurrence network analysis, it was found that the complexity of the water flooding after alkaline–surfactant–polymer flooding was higher than that of alkaline–surfactant–polymer flooding. This means that the water flooding ecosystem after alkaline–surfactant–polymer flooding was more stable and less susceptible to external environmental influences. In addition, there were significant differences in the functional redundancy of microbial communities in different blocks. In summary, the optimal stage for implementing local microbial oil recovery technology may be water flooding after alkaline–surfactant–polymer flooding.

Synthesis of iron-manganese bimetallic materials supported by activated carbon and application of activated persulfate in the degradation of soil contaminated by crude oil

Heterogeneous catalytic processes based on zero-valent iron (ZVI) have been developed to treat soil and wastewater pollutants. However, the agglomeration of ZVI reduces its ability to activate persulfate (PS). In this study, a new Fe-Mn@AC activated material was prepared to activated PS to treat oil-contaminated soil, and using the microscopic characterization of Fe-Mn@AC materials, the electron transfer mode during the Fe-Mn@AC activation of PS was clarified. Firstly, the petroluem degradation rate was optimized. When the PS addition amount was 8%, Fe-Mn@AC addition amount was 3% and the water to soil ratio was 3:1, the petroluem degradation rate in the soil reached to the maximum of 85.69% after 96 hours of reaction. Then it was illustrated that sulfate and hydroxyl radicals played major roles in crude oil degradation, while singlet oxygen contributed slightly. Finally, the indigenous microbial community structures remaining after restoring the Fe-Mn@AC/PS systems were analyzed. The proportion of petroleum degrading bacteria in soil increased by 23% after oxidation by Fe-Mn@AC/PS system. Similarly, the germination rate of wheat seeds revealed that soil toxicity was greatly reduced after applying the Fe-Mn@AC/PS system. After the treatment with Fe-Mn@AC/PS system, the germination rate, root length and bud length of wheat seed were increased by 54.05%, 7.98 mm and 6.84 mm, respectively, compared with the polluted soil group. These results showed that the advanced oxidation system of Fe-Mn@AC activates PS and can be used in crude oil-contaminated soil remediation.

Interspecific barrier effect driven by heavy metals makes soil bacterial functional assembly more stochastic

Residual heavy metals in soils will destroy microbial community stability and influence its aggregation. However, exploring microbial ecology under heavy-metal stress still requires a conjoint analysis of bacterial interspecies communication and the community diversity maintenance mechanism. In this study, soil samples were collected from a heavy-metal-contaminated site in China to investigate the ecological response of indigenous microbial communities through high-throughput sequencing. Results showed that bacterial taxa and functions generated unusual decoupling phenomena. There were no significant differences in the diversity of species with the increase in concentration of heavy metals (Hg, Se, and Cr), but the functional diversity was lost. Also, the average niche breadth of bacterial species increased from 1.70 to 2.28, but community stability declined and the species assembly was always a deterministic process (NST <0.5). After the bacterial functional assembly changed from a stochastic process to a deterministic process (NST <0.5), it was transformed into a stochastic process (NST >0.5) again under the stress of high-concentration heavy metals, indicating that the collective stress resistance of bacterial communities changed from positive mutation into passive functional propagation. The research results can provide new insight into understanding the adaptive evolution of communities and ecosystem restoration under the stress of soil heavy metals.

Optimal conditions for nano-emulsified vegetable oil synthesis for the biostimulation of 1,1,2-trichloroethane and vinyl chloride contaminated groundwater in bioreactors

Contamination of groundwater with chlorinated aliphatic hydrocarbons (CAHs) has become increasingly widespread. Enhanced reductive dechlorination (ERD) by emulsified vegetable oil (EVO) is an environmentally friendly, low-carbon and sustainable technology that effectively eliminates the threat from CAHs. To improve the permeability and bioavailability of EVO in the low-permeability substratum, nano-emulsified vegetable oil (nanoEVO) can be synthesized using a modified phase inversion composition method (MPIC) by increasing the emulsification temperature that reduces the shear force required for the formation of nanodroplets and the interfacial tension between the mixed phase and water. The emulsification temperature of 60 °C, the water content of 40–70%, the droplet diameter (DD) of nanoEVO prepared by MPIC is ∼200 nm, and had good monodispersion (≤0.2). The high molecular weight and low solubility of vegetable oil, and similar size of droplet make nanoEVO remains homogeneous after storage for > one year. NanoEVO can effectively biostimulate indigenous bacteria in CAHs-contaminated groundwater to dechlorinate 1,1,2-trichloroethane (1,1,2-TCA) to ethene via vinyl chloride (VC). The maximum dihaloelimination rate of 1,1,2-TCA was ∼66.06 μM·Cl−·day−1 and the maximum hydrogenolysis rate of VC was ∼35.67 μM·Cl−·day−1. NanoEVO effectively increased the relative abundance of Dehalococcoides from <0.10 to 9.61%. The abundances of Dhc 16S rRNA gene and dehalogenase gene vcrA increased by 102 and 103, respectively. Biostimulation shaped the structure of microbial communities and promoted hydrolytic acidification and anaerobic fermentation. Moreover, the syntrophic VFA-oxidizing bacteria participated in secondary fermentation and were closely correlated with H2 consumption metabolism. By providing carbon sources and maintaining an anaerobic environment with stable pH and ORP, nanoEVO biostimulated the hydrolytic acidification led by fermentative bacteria, secondary fermentation with syntrophic VFA-oxidizing bacteria and reductive dechlorination carried out by dechlorinator, thus greatly increasing the CAH-dechlorinating ability of indigenous microbial communities.

Analyzing microbial communities and metabolic functions in estuaries affected by human activity to uncover bioelectrochemical system potential

In the context of bioelectrochemical systems (BES), a profound understanding of the taxonomic composition within indigenous microbial communities is crucial. Their metabolic versatility assumes a foundational role in dictating the functionality of BES, yielding diverse applications for bioenergy production and bioremediation in anthropogenically impacted estuaries. Employing high-throughput sequencing of the V3-V4 region of 16S rRNA and predictive metagenomic analyses of three different estuaries samples (eutrophicated urban reservoir, mud volcano impacted river, and its river mouth), this study delves into the intricate interplay between these communities and their metabolic functions in response to human-induced perturbations, with a specific focus on their applicability to BES. Our findings illuminate remarkable distinctions among the three samples, manifesting in variations in microbial composition and functional metabolic pathways within the respective ecosystems. The mud volcano-affected river, characterized by the highest microbial diversity, exhibited the most diverse array of functional metabolic processes, prominently dominated by chemoheterotrophy (67.43%). In contrast, the river mouth displayed a distinct penchant for autotrophy (33.33%). The eutrophicated urban reservoir showcased a balanced coexistence of chemoheterotrophy (41.18%) and autotrophy (35.29%). Regarding metabolic potential for BES application, most of metabolism potential were associated with anodic activity, while cathodic activity was restricted to autotrophy and its relatives. The results suggested that the microbial communities anthropogenically impacted estuaries were potentially used for anodic and cathodic reactions in BES as electrogens to generate bioelectricity and reduce of pollutants.

Investigating the activity of indigenous microbial communities from Italian depleted gas reservoirs and their possible impact on underground hydrogen storage.

H2 produced from renewable energies will play a central role in both greenhouse gas reduction and decarbonization by 2050. Nonetheless, to improve H2 diffusion and utilization as a fuel, large storage capacity systems are needed. Underground storage of natural gas in depleted reservoirs, aquifers and salt caverns is a well-established technology. However, new challenges arise when it comes to storing hydrogen due to the occurrence and activity of indigenous microbial populations in deep geological formations. In a previous study, four Italian natural gas reservoirs were characterized both from a hydro-chemical and microbiological point of view, and predictive functional analyses were carried out with the perspective of underground hydrogen storage (UHS). In the present work, formation waters from the same reservoirs were used as inoculant during batch cultivation tests to characterize microbial activity and its effects on different gas mixtures. Results evidence a predominant acidogenic/acetogenic activity, whilst methanogenic and sulfate reducing activity were only marginal for all tested inoculants. Furthermore, the microbial activation of tested samples is strongly influenced by nutrient availability. Obtained results were fitted and screened in a computational model which would allow deep insights in the study of microbial activity in the context of UHS.

The effect of anaerobic digestate as an organic soil fertilizer on the diversity and structure of the indigenous soil microbial and nematode communities.

Anaerobic digestate is a popular soil additive which can promote sustainability and transition toward a circular economy. This study addresses how anaerobic digestate modifies soil health when combined with a common chemical fertilizer. Attention was given to soil microbes and, a neglected but of paramount importance soil taxonomic group, soil nematodes. A mesocosm experiment was set up in order to assess the soil's microbial and nematode community. The results demonstrated that the microbial diversity was not affected by the different fertilization regimes, although species richness increased after digestate and mixed fertilization. The composition and abundance of nematode community did not respond to any treatment. Mixed fertilization notably increased potassium (K) and boron (B) levels, while nitrate (NO3-) levels were uniformly elevated across fertilized soils, despite variations in nitrogen input. Network analysis revealed that chemical fertilization led to a densely interconnected network with mainly mutualistic relationships which could cause ecosystem disruption, while digestate application formed a more complex community based on bacterial interactions. However, the combination of both orchestrated a more balanced and less complex community structure, which is more resilient to random disturbances, but on the downside, it is more likely to collapse under targeted perturbations.

Assessing the impacts of oil contamination on microbial communities in a Niger Delta soil

Oil spills are a global challenge, contaminating the environment with organics and metals known to elicit toxic effects. Ecosystems within Nigeria's Niger Delta have suffered from prolonged severe spills for many decades but the level of impact on the soil microbial community structure and the potential for contaminant bioremediation remains unclear. Here, we assessed the extent/impact of an oil spill in this area 6 months after the accident on both the soil microbial community/diversity and the distribution of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHDGNα) genes, responsible for encoding enzymes involved in the degradation of PAHs, across the impacted area. Analyses confirmed the presence of oil contamination, including metals such as Cr and Ni, across the whole impacted area and at depth. The contamination impacted on the microbial community composition, resulting in a lower diversity in all contaminated soils. Gamma-, Delta-, Alpha- proteobacteria and Acidobacteriia dominated 16S rRNA gene sequences across the contaminated area, while Ktedonobacteria dominated the non-contaminated soils. The PAH-RHDαGN genes were only detected in the contaminated area, highlighting a clear relationship with the oil contamination/hydrocarbon metabolism. Correlation analysis indicated significant positive relationships between the oil contaminants (organics, Cr and Ni), PAH-RHDαGN gene, and the presence of bacteria/archaea such as Anaerolinea, Spirochaetia Bacteroidia Thermoplasmata, Methanomicrobia, and Methanobacteria indicating that the oil contamination not only impacted the microbial community/diversity present, but that the microbes across the impacted area and at depth were potentially playing an important role in degrading the oil contamination present. These findings provide new insights on the level of oil contamination remaining 6 months after an oil spill, its impacts on indigenous soil microbial communities and their potential for in situ bioremediation within a Niger Delta's ecosystem. It highlights the strength of using a cross-disciplinary approach to assess the extent of oil pollution in a single study.

One-step bioremediation of hypersaline and nutrient-rich food industry process water with a domestic microbial community containing diatom Halamphora coffeaeformis

Proper treatment of hypersaline and nutrient-rich food industry process water (FIPW) is challenging in conventional wastewater plants. Insufficient treatment leads to serious environmental hazards. However, bioremediation of FIPW with an indigenous microbial community can not only recover nutrients but generate biomass of diverse applications. In this study, monoculture of Halamphora coffeaeformis, together with synthetic bacteria isolated from a local wastewater plant, successfully recovered 91% of NH4+-N, 78% of total nitrogen, 95% of total phosphorus as well as 82% of total organic carbon from medium enriched with 10% FIPW. All identified organic acids and amino acids, except oxalic acid, were completely removed after 14 days treatment. A significantly higher biomass concentration (1.74 g L−1) was achieved after 14 days treatment in the medium with 10% FIPW than that in a nutrient-replete lab medium as control. The harvested biomass could be a potential feedstock for high-value biochemicals and fertilizer production, due to fucoxanthin accumulation (3 mg g−1) and a fantastic performance in P assimilation. Metagenomic analysis revealed that bacteria community in the algal system, dominated by Psychrobacter and Halomonas, also contributed to the biomass accumulation and uptake of nutrients. Transcriptomic analysis further disclosed that multiple pathways, involved in translation, folding, sorting and degradation as well as transport and catabolism, were depressed in H. coffeaeformis grown in FIPW-enriched medium, as compared to the control. Collectively, the proposed one-step strategy in this work offers an opportunity to achieve sustainable wastewater management and a way towards circular economy.

Phage-Dependent Alteration of Rhizosphere Microbiota in Tomato Plants

Bacteriophages (phages) that infect bacterial pathogens are an alternative means of controlling bacterial diseases in humans, animals, and plants. However, the effects of targeted phage therapy on indigenous microbial communities are not fully understood. In this study, we hypothesized that phages infecting plant pathogenic bacteria play a role in modulating the microbial community in the plant rhizosphere. To explore this, we used the soil-borne plant bacterial pathogen Ralstonia pseudosolanacearum as the host bacterium and its phages as a model system in the tomato rhizosphere. The effect of phages on the microbiota was examined using a narrow host range phage RpY1 and a combination of two phages (RpY2 and RpT1, termed the phage combo) with a broad host range under the natural rhizosphere microbiota of tomato plants. Both RpY1 and the phage combo altered the tomato rhizosphere microbiota. The phage combo displayed phage effects mostly in the presence of R. pseudosolanacearum. However, RpY1 affected the rhizosphere microbiota even in the absence of the host bacterium. The effect of phage RpY1 on the microbiota was further investigated in the tomato rhizosphere using a synthetic community (SynCom) mimicking the natural tomato rhizosphere microbiota. Phage RpY1 affected the microbial community structure of the SynCom in the tomato rhizosphere in the absence of the host bacterium. Analyses of the natural microbiota and SynCom in the tomato rhizosphere indicated an indirect effect of phage RpY1 on the microbiota. This study suggests that phage application modulates the indigenous microbiota through unknown interactions with nonhost bacterial members in the plant rhizosphere. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Response of TCE biodegradation to elevated H2 and O2: Implication for electrokinetic-enhanced bioremediation

The study investigated the influences of pure H2 and O2 introduction, simulating gases produced from the electrokinetic-enhanced bioremediation (EK-Bio), on TCE degradation, and the dynamic changes of the indigenous microbial communities. The dissolved hydrogen (DH) and oxygen (DO) concentrations ranged from 0.2 to 0.7 mg/L and 2.6 to 6.6 mg/L, respectively. The biological analysis was conducted by 16S rRNA sequencing and functional gene analyses. The results showed that the H2 introduction enhanced TCE degradation, causing a 90.4% TCE removal in the first 4 weeks, and 131.1 μM was reduced eventually. Accordingly, cis-dichloroethylene (cis-DCE) was produced as the only product. The following three ways should be responsible for this promoted TCE degradation. Firstly, the high DH rapidly reduced the oxidation-reduction potential (ORP) value to around −500 mV, beneficial to TCE microbial dechlorination. Secondly, the high DH significantly changed the community and promoted the enrichment of TCE anaerobic dechlorinators, such as Sulfuricurvum, Sulfurospirillum, Shewanella, Geobacter, and Desulfitobacterium, and increased the abundance of dechlorination gene pceA. Thirdly, the high DH promoted preferential TCE dechlorination and subsequent sulfate reduction. However, TCE bio-remediation did not occur in a high DO environment due to the reduced aerobic function or lack of functional bacteria or co-metabolic substrate. The competitive dissolved organic carbon (DOC) consumption and unfriendly microbe-microbe interactions also interpreted the non-degradation of TCE in the high DO environment. These results provided evidence for the mechanism of EK-Bio. Providing anaerobic obligate dechlorinators, and aerobic metabolic bacteria around the electrochemical cathodes and anodes, respectively, or co-metabolic substrates to the anode can be feasible methods to promote remediation of TCE-contaminated shallow aquifer under EK-Bio technology.

Salinity-induced succession of phototrophic communities in a southwestern Siberian soda lake during the solar activity cycle

A variety of lakes located in the dry steppe area of southwestern Siberia are exposed to rapid climatic changes, including intra-century cycles with alternating dry and wet phases driven by solar activity. As a result, the salt lakes of that region experience significant fluctuations in water level and salinity, which have an essential impact on the indigenous microbial communities. But there are few microbiological studies that have analyzed this impact, despite its importance for understanding the functioning of regional water ecosystems. This work is a retrospective study aimed at analyzing how solar activity-related changes in hydrological regime affect phototrophic microbial communities using the example of the shallow soda lake Tanatar VI, located in the Kulunda steppe (Altai Region, Russia, southwestern Siberia). The main approach used in this study was the comparison of hydrochemical and microscopic data obtained during annual field work with satellite and solar activity data for the 12-year observation period (2011–2022). The occurrence of 33 morphotypes of cyanobacteria, two key morphotypes of chlorophytes, and four morphotypes of anoxygenic phototrophic bacteria was analyzed due to their easily recognizable morphology. During the study period, the lake surface changed threefold and the salinity changed by more than an order of magnitude, which strongly correlated with the phases of the solar activity cycles. The periods of high (2011–2014; 100–250 g/L), medium (2015–2016; 60 g/L), extremely low (2017–2020; 13–16 g/L), and low (2021–2022; 23–34 g/L) salinity with unique biodiversity of phototrophic communities were distinguished. This study shows that solar activity cycles determine the dynamics of the total salinity of a southwestern Siberian soda lake, which in turn determines the communities and microorganisms that will occur in the lake, ultimately leading to cyclical changes in alternative states of the ecosystem (dynamic stability).

Role of indigenous microbial communities in the mobilization of potentially toxic elements and rare-earth elements from alkaline mine waste

This study aims to evaluate the role of indigenous microorganisms in the mobilization of potentially toxic elements (PTE) and rare-earth elements (REE), the influence of the bioavailability of carbon sources that might boost microbial leaching, and the generation of neutral/alkaline mine drainage from alkaline tailings. These tailings, with significant concentrations of total organic carbon (TOC), were mainly colonized by bacteria belonging to the genera Sphingomonas, Novosphingobium and Solirubrobacter, and fungi of the genera Alternaria, Sarocladium and Aspergillus. Functionality analysis suggests the capability of these microorganisms to leach PTE and REE. Bio-/leaching tests confirmed the generation of neutral mine drainage, the influence of organic substrate, and the leaching of higher concentrations of PTE and REE due to the production of organic acids and siderophores by indigenous microorganisms. In addition, this study offers some insights into a sustainable alternative for reprocessing PMC alkaline tailings to recover REE.

Fate, behaviour and microbial response of diluted bitumen and conventional crude spills in a simulated warm freshwater environment

Diluted bitumen (DB), one of the most transported unconventional crude oils in Canada's pipelines, raises public concerns due to its potential spillage into freshwater environments. This study aimed to compare the fate and behaviour of DB versus conventional crude (CC) in a simulated warm freshwater environment. An equivalent of 10 L of either DB or CC was spilled into 1200 L of North Saskatchewan River (NSR) water containing natural NSR sediment (2.4 kg) in a mesoscale spill tank and its fate and behaviour at air/water temperatures of 18 °C/24 °C were monitored for 56 days. Oil mass distribution analysis showed that 42.3 wt % of CC and 63.6 wt% of DB resided in the oil slicks at the end of 56-day tests, consisting mainly high molecular weight (HMW) compounds (i.e., resins and asphaltenes). The lost oil contained mainly low molecular weight (LMW) compounds (i.e., light saturates and some aromatics) into the atmosphere, water column, and sediment through collective weathering processes. Notably, weathered CC emulsified with water and remained floating until the end, while the weathered DB mat started to lose its buoyancy after 24 days under quiescent conditions and resurfaced once waves were applied. Analysis of the microbial communities of water pre- and post-spills revealed the replacement of indigenous microbial communities with hydrocarbon-degrading species. Exposure to CC reduced the microbial diversity by 12%, while exposure to DB increased the diversity by 10%. During the early stages of the spill (up to Day 21), most dominant species were positively correlated with the benzene, toluene, ethylbenzene, and xylenes (BTEX) content or polycyclic aromatic hydrocarbon (PAH) content of the water column, while the dominant species at the later stages (Days 21–56) of the spill were negatively correlated with BTEX or PAH content and positively correlated with the total organic carbon (TOC) content in waters.

Biosynthesized zinc oxide nanoparticles modulate the phytoremediation potential of Pennisetum giganteum and its rhizocompartments associated microbial community structure

The accumulation of cadmium (Cd) in agricultural products and the potential danger of its incursion into the food chain pose serious implications for public health. To address soil Cd-contamination, a combination of biogenic zinc oxide nanoparticles (ZnO.NPs) and Pennisetum giganteum was employed for remediation. Phytoextraction potential of P. giganteum plants was assessed in Cd-contaminated soil (40 mg/kg) by facilitating with low (50 mg/kg) and high (100 mg/kg) dosages of ZnO.NPs and its impact was assessed on the indigenous microbial community associated with its rhizocompartments. ZnO.NPs substantially enhanced the tolerance and ability of plant to accumulate Cd in plant shoot (1.48–1.72-fold) and root (1.6–2.1-fold) system as compared with control. Moreover, an improvement in the antioxidative response was observed, which effectively mitigated oxidative stress at a low concentration of ZnO.NPs, as evidenced by leaf ultrastructural analysis. Beyond that, soil enzyme activities such as acid phosphatase (1.33 and1.43-fold), urease (1.42 and 1.57-fold) catalase (2.3 and 1.9-fold) and saccharase (1.2 and 1.3-fold) were augmented by low and high doses, respectively. In addition, we opted to examine the plant rhizocompartments-associated bacterial community structure which likely affected by the modifications in soil enzymes influenced by ZnO.NPs. Multivariate analysis demonstrated that root associated bacterial community was prominently differed in control, low and high levels of ZnO.NPs. Nevertheless, the bacterial community structure's richness and evenness did not show significant differences, while diversity was found to be negatively affected only by high concentrations of ZnO.NPs. It is worth noting that, Thiobacillus, Stenotrophomonas, Chloroflexi, Cellvibro and Phenylobacterium were significantly enriched only in low ZnO.NPs supplemented plants. In-depth analysis of indicator genera also indicated differences (LDA score >2.0, p < 0.05) in plants rhizocompartments under different treatments. The results from this study highlight significant changes in several plant-based endpoints, particularly at low concentration, by improving the phytoremediation potential, overall plant performance and rhizocompartments-associated bacterial community structure.

Comparing the response of the indigenous microbial community to crude oil amendment in oxic versus hypoxic conditions

IntroductionThe Caspian Sea is the world’s largest landlocked saline lake which lies between Europe and Asia. This region is particularly known for its large-scale oil reserves, pipelines, and drilling activities, which have contributed to the environmental decline of this lake. In addition to pollution from the petroleum industry, drainage from various river basins brings an influx of residential, industrial, and agricultural effluents that induce eutrophication and hypoxic conditions in deeper, colder waters, creating an oxygen gradient. The temperature and oxygen stratification in this environment has presented a unique opportunity to investigate the potential of the biodegradative processes carried out by the indigenous microbial community. We believe these indigenous microbes possess different metabolic capabilities to degrade oil as they adapted to declining oxygen concentrations and temperatures with increasing depths over a prolonged period. Hence, community structure and composition will vary with depth.MethodsMicrocosms were set up to observe the indigenous microbial reaction after a 60 ppm native crude oil amendment over 115 days. Surface water microcosms were incubated at 28ºC and aerated while deep water microcosms were incubated at 8ºC under anaerobic conditions. These two environmental conditions represent the temperature and oxygen extremes along the gradient and were selected as we try to simulate the indigenous community’s response to this oil contamination. DNA was extracted and amplified from these microcosms and sequenced. Bioinformatic analysis was performed to track changes in the abundance of taxa present and biodiversity over different time points to show the progression of community structure.ResultsAll microcosms showed the presence of hydrocarbon-degrading phyla, whose presence is consistent with other reports from oil-enriched environments. However, distinct communities were observed in oxic versus hypoxic microcosms.ConclusionOrders of Bacteria related to sulfate and nitrogen cycling were found in hypoxic microcosms, indicating a possible mechanism for the anaerobic biodegradation of crude oil. GC-MS analysis of initial and final microcosms also provided evidence of degradation of hydrocarbon fractions in both warm, oxic and cold, hypoxic conditions.

A study on microbial mechanism in response to different nano-plastics concentrations in constructed wetland and its carbon footprints analysis

The increasing accumulation of environmental nano-plastics (NPs) poses significant environmental risk. While constructed wetlands (CWs) have proven effective in treating NPs, and most research efforts primarily emphasize on denitrification capacities. However, there are still knowledge gaps concerning the carbon footprints characteristics within CWs as well as the response mechanisms of microbial communities to perturbations caused by NPs. To evaluate these effects, a 360-day CWs microcosm experiment was conducted with nano-plastic treatments of 0 μg/L, 1 μg/L, 10 μg/L, and 100 μg/L. Results showed that COD removal efficiencies were 28.42 % for the CK, decreasing significantly to 11.92 % at 100 μg/L concentrations. TN removal efficiencies for the 1 μg/L, 10 μg/L, and 100 μg/L treatments showed average reductions of 8.65 %, 11.05 % and 13.47 %, respectively, in comparison to the control, which had a mean TN removal efficiency of 22.82 %. Simultaneously, the concentration of NPs had a direct impact on greenhouse gas (GHG) emissions from CWs, which increased from 5326.60 CO2-eq/m3·y to 30109.47 g CO2-eq/m3·y as NP concentration increased, and the contribution of microorganisms to CWs decreased from 23.28 % to 19.56 %. These phenomena could be attributed to the following reasons: as NPs concentration increased, the abundance of genes associated with nitrogen and methanogenesis metabolism (amo and cdh) decreased, resulting in a decline in COD and TN removal rates. Concurrently, the genes abundance related to methane formation (mtr and mcr) increased, leading to higher emissions of methane gas as a result of the consumption of accumulated CH-H4MPT and CH2-H4MPT intracellularly. Through this research, we gain fresh insights into sustained structural and functional adaptations of indigenous microbial communities in response to NPs. These findings serve as a theoretical foundation for future engineering enhancement of CWs geared towards more effective NPs treatment.

Responses of composition and metabolism of microbial communities during the remediation of black and odorous water using bioaugmentation and aeration

This study elucidated the effect patterns of aeration and bioaugmentation on indigenous microbial communities, metabolites, and metabolic pathways in the remediation of black and odorous water. This is crucial for the precise formulation and targeted development of effective microbial consortia, as well as for tracking and forecasting the bioremediation of black and odorous water. The results confirmed that combining bioaugmentation with aeration markedly enhanced the degradation of COD, NH4+-N, and TN and the conversion of Fe and Mn. Aeration significantly increased the relative abundance of Flavobacterium and Diaphorobacter, and the positive interbacterial interaction in the effective microbial consortia EM31 gave the constituent strain Klebsiella and Bacillus a dominant niche in the bioaugmentation. Furthermore, bioaugmentation improved the capacity of the indigenous microbial consortia to utilize basic carbon source, particularly the utilization of L-glycerol, I-erythritol, glucose-1-phosphate, and the catabolism of cysteine and methionine. Moreover, during the remediation of black and odorous water by aeration and bioaugmentation, Glucosinolate biosynthesis (map00966), Steroid hormone biosynthesis (map00140), Folate biosynthesis (map00790), One carbon pool by folate (map00670), and Tyrosine metabolism (map00350) were identified as key functional metabolic pathways in microbial communities.

Machine Learning Modeling Based on Microbial Community for Prediction of Natural Attenuation in Groundwater.

Natural attenuation is widely adopted as a remediation strategy, and the attenuation potential is crucial to evaluate whether remediation goals can be achieved within the specified time. In this work, long-term monitoring of indigenous microbial communities as well as benzene, toluene, ethylbenzene, and xylene (BTEX) and chlorinated aliphatic hydrocarbons (CAHs) in groundwater was conducted at a historic pesticide manufacturing site. A machine learning approach for natural attenuation prediction was developed with random forest classification (RFC) followed by either random forest regression (RFR) or artificial neural networks (ANNs), utilizing microbiological information and contaminant attenuation rates for model training and cross-validation. Results showed that the RFC could accurately predict the feasibility of natural attenuation for both BTEX and CAHs, and it could successfully identify the key genera. The RFR model was sufficient for the BTEX natural attenuation rate prediction but unreliable for CAHs. The ANN model showed better performance in the prediction of the attenuation rates for both BTEX and CAHs. Based on the assessments, a composite modeling method of RFC and ANN was proposed, which could reduce the mean absolute percentage errors. This study reveals that the combined machine learning approach under the synergistic use of field microbial data has promising potential for predicting natural attenuation.