Microbial community composition and PAHs removal potential of indigenous bacteria in oil contaminated sediment of Taean coast, Korea

The tidal flats near Sinduri beach in Taean, Korea, have been severely contaminated by heavy crude oils due to the Korea's worst oil spill accident, say the Hebei Spirit Oil Spill, in 2007. Crude oil compounds, including polycyclic aromatic hydrocarbons (PAHs), pose significant environmental damages due to their wide distribution, persistence, high toxicity, mutagenicity, and carcinogenicity. Microbial community of Sinduri beach sediments samples was analyzed by metagenomic data with 16S rRNA gene amplicons. Three phyla (Proteobacteria, Firmicutes, and Bacteroidetes) accounted for approximately ≥93.0% of the total phyla based on metagenomic analysis. Proteobacteria was the dominant phylum in Sinduri beach sediments. Cultivable bacteria were isolated from PAH-enriched cultures, and bacterial diversity was investigated through performing culture characterization followed by molecular biology methods. Sixty-seven isolates were obtained, comprising representatives of Actinobacteria, Firmicutes, α- and γ-Proteobacteria, and Bacteroidetes. PAH catabolism genes, such as naphthalene dioxygenase (NDO) and aromatic ring hydroxylating dioxygenase (ARHDO), were used as genetic markers to assess biodegradation of PAHs in the cultivable bacteria. The ability to degrade PAHs was demonstrated by monitoring the removal of PAHs using a gas chromatography mass spectrometer. Overall, various PAH-degrading bacteria were widely present in Sinduri beach sediments and generally reflected the restored microbial community. Among them, Cobetia marina, Rhodococcus soli, and Pseudoalteromonas agarivorans were found to be significant in degradation of PAHs. This large collection of PAH-degrading strains represents a valuable resource for studies investigating mechanisms of PAH degradation and bioremediation in oil contaminated coastal environment, elsewhere.

Enhancement of nutrients removal and biomass accumulation of Chlorella vulgaris in pig manure anaerobic digestate effluent by the pretreatment of indigenous bacteria

High concentrations of pollutants in pig manure anaerobic digestate effluent (PMADE) can severely inhibit microalgal growth. In this study, two types of PMADE (PMADE-1, PMADE-2) were pretreated with indigenous bacteria which were selected from PMADE to alleviate their inhibition for the growth of Chlorella vulgaris. Indigenous bacteria could decrease 34.04% and 47.80% of total phosphorus (TP) and turbidity in PMADE-1, and 80.81%, 43.27%, and 57.51% of COD, TP, and turbidity in PMADE-2, respectively. And no significant reduction of NH₄⁺-N in both PMADE after 5 days pretreatment occurred. C. vulgaris failed to grow in unpretreated PMADE-2. Pretreatment of PMADE with indigenous bacteria could remarkably promote nutrients removal and cell growth of C. vulgaris compared to the unpretreated PMADE. The order of abiotic stress in the studied PMADE was COD > NH₄⁺-N > turbidity, and it is appropriate to pretreat the PMADE with indigenous bacteria for 2-3 days.

Biodegradation of marine oil spill residues using aboriginal bacterial consortium based on Penglai 19-3 oil spill accident, China

Bioremediation, mainly by indigenous bacteria, has been regarded as an effective way to deal with the petroleum pollution after an oil spill accident. The biodegradation of crude oil by microorganisms co-incubated from sediments collected from the Penglai 19-3 oil platform, Bohai Sea, China, was examined. The relative susceptibility of the isomers of alkylnaphthalenes, alkylphenanthrenes and alkyldibenzothiophene to biodegradation was also discussed. The results showed that the relative degradation values of total petroleum hydrocarbon (TPH) are 43.56% and 51.29% for sediments with untreated microcosms (S-BR1) and surfactant-treated microcosms (S-BR2), respectively. TPH biodegradation results showed an obvious decrease in saturates (biodegradation rate: 67.85-77.29%) and a slight decrease in aromatics (biodegradation rate: 47.13-57.21%), while no significant difference of resins and asphaltenes was detected. The biodegradation efficiency of alkylnaphthalenes, alkylphenanthrenes and alkyldibenzothiophene for S-BR1 and S-BR2 samples reaches 1.28-84.43% and 42.56-86.67%, respectively. The efficiency of crude oil degradation in sediment with surfactant-treated microcosms cultures added Tween 20, was higher than that in sediment with untreated microcosms. The biodegradation and selective depletion is not only controlled by thermodynamics but also related to the stereochemical structure of individual isomer compounds. Information on the biodegradation of oil spill residues by the bacterial community revealed in this study will be useful in developing strategies for bioremediation of crude oil dispersed in the marine ecosystem.

Rapid degradation of long-chain crude oil in soil by indigenous bacteria using fermented food waste supernatant

The objective of this study is to explore how to stimulate soil indigenous bacteria for the degradation of long-chain crude oil by adding fermented food waste supernatant (FS). Four concentrations of FS (0 mL, 0.1 mL, 1 mL, and 3 mL) were added to two oil-contaminated soils S1 and S2 for 30 days of bioremediation experiments. The results showed that the biodegradation of long-chain alkanes (C₂₉ - C₂₄) could reach up to 1756 mg/kg (49.3%, S1) and 3937 mg/kg (43.9%, S2), which were 3.1 and 3.2 times that of the non-nutrient system. In addition, the logarithmic growth rate of the indigenous hydrocarbon degraders (IHD) reached 41.5%. The long-chain crude oil can be rapidly degraded by indigenous bacteria with FS added in a short time. The glucose and acetic acid accelerated the consumption of ammonia nitrogen (NH₄⁺-N) in the prophase of bioremediation and the molar ratio of consumed carbon (contained in glucose and acetic acid) to consumed NH₄⁺-N (C/N) was high by adding FS. Thus, the IHD can multiply rapidly. The analysis of microbial diversity revealed that the IHD (genera Acinetobacter and Aquabacterium) became the dominant bacteria. Long-chain alkanes became the main carbon sources for IHD after 14 days in soil S1 and 16 days in soil S2. Thus, the rapid biodegradation of long-chain crude oil was achieved. The genus Aquabacterium which was uncultivable on crude oil medium became the dominant bacteria. This study provides an environment-friendly and sustainable remediation technology for bioremediation of oil-contaminated soils.

Removal of polycyclic aromatic hydrocarbons (PAHs) and the response of indigenous bacteria in highly contaminated aged soil after persulfate oxidation

Integrated chemical-biological treatment is a promising alternative to remove PAHs from contaminated soil, wherein indigenous bacteria is the key factor for the biodegradation of residual PAHs after the application of chemical oxidation. However, systematical study on the impact of persulfate (PS) oxidation on indigenous bacteria as well as PAHs removal is still scarce. In this study, the influences of different PS dosages (1%, 3%, 6%, and 10% [w/w]), as well as various activation methods (native iron, H₂O₂, alkaline, ferrous iron, and heat) on PAHs removal and indigenous bacteria in highly contaminated aged soil were investigated. Apparent degradation of PAHs in the soil treated with PS oxidation was observed, and the removal efficiency of total PAHs in the soil ranged from 38.28% to 79.97%. The removal efficiency of total PAHs in the soil increased with increasing consumption of PS. However, the bacterial abundance in soil was negatively affected following oxidation for all of the treatments added with PS, with bacterial abundance in the soil decreased by 0.89-2.93 orders of magnitude compared to the untreated soil. Moreover, the number of total bacteria in the soil decreased as PS consumption increased. Different PS activation methods and PS dosages exhibited different influences on the bacterial community composition. Bacteria capable of degrading PAHs under anoxic conditions were composed predominantly by Proteobacteria and Firmicutes. The total amount of Proteobacteria and Firmicutes also decreased with increasing consumption of PS. The results of this study provide important insight for the design of PAHs contaminated soil remediation projects.

Assessment of heavy metal bioremediation potential of bacterial isolates from landfill soils

Indiscriminate disposal of wastes on landfills has led to increase in heavy metal contamination in landfill soils. However, the ability of the indigenous microorganisms to remediate the polluted environment can be of great influence in reclamation of such soils. The objectives of this study were to assess the bioremediation potential of the screened indigenous bacteria and evaluate the effects of carbon source and pH in the enhancement of the bioremediation process. Bacterial isolates from landfill sites were screened for their capability to utilize heavy metal (Cd and Pb). Nutrient Agar was supplemented with five different concentrations of each metal (25 to 600 mgL^-1). Viable counts of the isolates were taken four times at two days interval. Pseudomonas aeruginosa, Klebsiella edwardsii and Enterobacter cloacae were selected based on their tolerance to heavy metal for remediation process. Peptone broth was also supplemented using different concentrations of heavy metals. The remediation process was assessed by monitoring the growth of biomass using UV spectrophotometer at 600 nm and the residual heavy metal was evaluated after 8 days of incubation using AAS. Pseudomonas aeruginosa exhibited the highest bioremediation potential among the bacterial isolates with 58.80 and 33.67 remediation percentage in 50 mg Cd L^-1 and 300 mg Pb L^-1 . However, higher remediation percentage (79.87 and 92.41) was observed by Klebsiella edwardsii through addition of carbon source (5 g/L) and varying the pH (6) of the media in the heavy metal contaminated medium. The results of this study indicate that the effectiveness of the indigenous bacteria in remediation process can be enhanced through the addition of carbon source and increase pH for effective reclamation of contaminated soil.

Role of indigenous bacteria in dark fermentation of organic substrates

Hydrogen production by dark fermentation of complex organic substrates, such as biowaste, can naturally take place with indigenous bacteria or by adding an external microbial inoculum issued from various natural environments. This study aims to determine whether indigenous bacteria associated with thermal pretreatment could impact dark fermentation performances. Biochemical hydrogen potential tests were carried out on seven organic substrates. Results showed a strong influence of the indigenous bacteria which are as effective as thermally pretreated exogenous bacteria to produce H₂ and metabolites. High abundance in Clostridiales and/or Enterobacteriales was associated with high H₂ yield. This study shows that no inoculum nor pretreatment are required to achieve satisfactory dark fermentation performances from organic waste.

The potential role of fertilizer-derived exogenous bacteria on soil bacterial community assemblage and network formation

Manure fertilization contributes to crop production and sustainable agriculture by introducing large amounts of nutrients and exogenous microbes into soil. However, the contribution of exogenous microbes in shaping soil bacterial community and network structure after fertilization are still controversial. In this study, bacterial communities and network structure that received unsterilized (R + C) or sterilized (R + SC) manure fertilizers, as well as no fertilizer control (R), were characterized using high throughput sequencing. Results showed that the relative abundance of fertilizer-derived OTUs decreased from 10.4% to 4.6% after 90 days incubation, while the Bray-Curtis distance between the control and fertilization group (R + C and R + SC) gradually increased with the culture time. It can be supposed that manure fertilization altered soil bacterial communities by interfering the growth of indigenous bacteria rather than the colonization of fertilizer-derived bacteria. Network analysis showed that a subset of the fertilizer-derived OTUs identified as Xanthomonadales order and Promicromonospora, Constrictibacter genera acted as connectors between modules. They enhanced the interactions not only between soil-derived OTUs and fertilizer-derived OTUs, but also within indigenous bacteria, supported that the introduction of fertilizer-derived exogenous bacteria contributes large to soil bacterial network association. Moreover, fertilizer-derived OTUs presented to be positively correlated with soil pH, while majority soil-derived OTUs presented to be negatively correlated with various physicochemical variables (pH, DOC, NO₃^-, and LAP). Our study highlighted the critical role of fertilizer-derived bacteria in regulating indigenous soil microbial community and network formation after fertilization.

Feasibility of bioleaching of heavy metals from sediment with indigenous bacteria using agricultural sulfur soil conditioners

Sediment bioleaching using a sulfur substrate is a promising approach to the removal of heavy metals. Compared with commercial sulfur powder used as the sulfur substrate, agricultural sulfur soil conditioners may reduce secondary pollution and facilitate the reuse of sediment. This study explored the bioleaching effect of three agricultural sulfur soil conditioners, including sulfur-coated urea, bentonite sulfur, and bio-sulfur, and the bioleaching potential of the indigenous sediment bacteria. The results showed that the sulfur-coated urea had a comparable bioleaching effect with sulfur powder (Ni 35.35%, Cu 74.27%, Zn 69.92%) and the highest maximum bioleaching rate because of the additional nitrogen. The bentonite sulfur leached the least but increased the proportion of the residual state due to its adsorption of heavy metal. Similar changes to the microbial flora structure and bioleaching mechanism were found with the use of sulfur powder, sulfur-coated urea, and bentonite sulfur as the bioleaching substrate. There was no significant difference between the indigenous bacteria and the sludge-enriched bacteria in the bioleaching effect except for bio-sulfur, which only performed well with the sludge-enriched bacteria. In the absence of inoculum, the bio-sulfur hindered the bioleaching process due to high levels of organic matter. This study provides insights into the practical application of bioleaching heavy metal removal technology from the perspective of sulfur substrate selection.

Indigenous bacterial community and function in phenanthrene-polluted coastal wetlands: Potential for phenanthrene degradation and relation with soil properties

The Yellow River Delta, adjacent to Shengli Oilfield, has a potential risk of petroleum pollution. In this study, soil samples were collected from phenanthrene (PHE)-polluted (adjacent to abandoned oil well, Zone D) and non-polluted (far away from abandoned oil well, Zone E) coastal wetlands. The influence of PHE pollution on indigenous bacterial community and function, and their relationship with soil characteristics were investigated. The levels of PHE, salinity and NH₄⁺-N were higher in Zone D than in Zone E. PHE-degrading bacteria Achromobacter and Acinetobacter were mainly distributed in Zone E, whereas Halomonas, Marinobacter, and Roseovarius were highly abundant in Zone D. Halomonas and Marinobacter had the potential for denitrification and could achieve PHE degradation through mutual cooperation. PHE pollution could increase the abundance of functional bacteria but reduce the diversity of microbial community. PHE and salinity played key roles in shaping microbial community structure and function. High PHE level inhibited microbial metabolism but stimulated self-protection potential. PHE aerobic degradation associated with the catechol and phthalic acid pathways was found in Zone D, whereas the catechol pathway dominated in Zone E. Interestingly, PHE anaerobic degradation with nitrate reduction also dominated in Zone D, whereas the process coupled with multiple electron acceptors co-existed in Zone E, which was associated with tidal seawater carrying nutrients. This study illustrated the importance of comprehensive consideration of microbial community structure and function under PHE pollution, suggesting indigenous microorganisms as potential microbial consortium for bioremediation in coastal wetlands.

Imidacloprid biodegradation using novel bacteria Tepidibacillus decaturensis strain ST1 in batch and in situ microcosm study

Imidacloprid is one of the frequently used insecticides. Indiscriminate use of imidacloprid makes it perilous to non-target organisms as well as the environment, including soil and water sources, thus, making its elimination from the environment an irresistible concern. Bioremediation is a technique that uses the degrading capabilities of bacteria to create an economical and reliable method of pesticide abatement. In an attempt to solve the problem arising due to imidacloprid contamination, bacterial strains possessing the ability to degrade imidacloprid were isolated from contaminated agricultural soil samples in the present study. Imidacloprid-degrading isolate, identified as Tepidibacillus decaturensis strain ST1, could effectively degrade imidacloprid in liquid media, slurry, and soil microcosms. The microcosm studies using the isolate resulted in the degradation of around 77.5% and 85% of imidacloprid (200 ppm) in sterile and unsterile soils within 45 days. In addition to biodegradation, sorption of insecticide by the plants and natural reduction of insecticide over time has also been reported. The degradation in soil follows first-order kinetics. Hydrazinecarboxamide and hydroxyurea were identified as metabolites on conducting GC-MS analysis of the degraded samples.

Treatment of high-salinity chemical wastewater by indigenous bacteria--bioaugmented contact oxidation

A 90 m(3) biological contact oxidation system in chemical factory was bioaugmented with three strains of indigenous salt-tolerant bacteria. These three strains were screened from contaminative soil in situ. Their activity of growth and degradation was investigated with lab-scale experiments. Their salt-tolerant mechanism was confirmed to be compatible-solutes strategy for moderately halophilic bacteria, with amino acid and betaine playing important roles. The running conditions of the system were recorded for 150 days. The indigenous bacteria had such high suitability that the reactor got steady rapidly and the removal of COD maintained above 90%. It was introduced that biofilm fragments in sedimentation tank were inversely flowed to each reaction tank, and quantitative PCR demonstrated that this process could successfully maintain the bacterial abundance in the reaction tanks. In addition, the T-RFLP revealed that bioaugmented strains dominated over others in the biofilm.

Biodegradability and bioavailability of dissolved substances in aquaculture effluent: Performance of indigenous bacteria, cyanobacteria, and green microalgae

Aquaculture is a controlled aquatic farming sector and one of the most important human food sources. Fish farming is one of the predominant, fast-growing sectors that supply seafood products worldwide. Along with its benefits, aquaculture practices can discharge large quantities of nutrients into the environment through non-treated or poorly treated wastewater. This study aims to understand the nutrient composition of fish wastewater and the use of indigenous bacteria, cyanobacteria, and microalgae as an alternative biological treatment method. Wastewater samples from a local fish farming facility were collected and treated using six different species of cyanobacteria and microalgae include Chroococcus minutus, Porphyridium cruentum, Chlorella vulgaris, Microcystis aeruginosa, Chlamydomonas reinhardtii, and Fischerella muscicola. All the samples were incubated for 21 days, and the following parameters were measured weekly: Chemical oxygen demand (COD), phosphate, total dissolved nitrogen, and dissolved inorganic nitrogen. In addition, dissolved organic nitrogen (DON), bioavailable DON (ABDON), and biodegradable DON (BDON) were calculated from the mass-balance equations. Colorimetric and digestive methods were used for the parameter measurements. The results showed that C. reinhardtii reduced the soluble COD concentration by 74.6 %, DON by 94.3 %, and phosphorous by more than 99 %. Moreover, M. aeruginosa, and C. minutus significantly reduced inorganic nitrogen species (>99 %). This alternative fish wastewater treatment method was explored to gain insight into fish wastewater nutrient composition and to create a sustainable alternative to conventional fish wastewater treatment methods.

Spatial distribution and diversity of organohalide-respiring bacteria and their relationships with polybrominated diphenyl ether concentration in Taihu Lake sediments

It is acknowledged that organohalide-respiring bacteria (OHRB) can degrade polybrominated diphenyl ethers (PBDEs); however, very little is known about the distribution of OHRB or their response to PBDE contamination in natural sediments. We collected sediments from 28 sampling sites in Taihu Lake, China, and investigated the spatial distribution and diversity of OHRB, and the relationships between the PBDE contamination levels and the PBDE removal potential. The abundances of five typical OHRB genera, namely Dehalobacter, Dehalococcoides, Dehalogenimonas, Desulfitobacterium, and Geobacter, ranged from 0.34 × 10⁴ to 19.4 × 10⁷ gene copies g^-1 dry sediment, and varied significantly among different areas of Taihu Lake. OHRB were more abundant in sediments from Meiliang and Zhushan Bay, where the PBDE concentrations were higher, and the phylotype diversity of the OHRB belonging to the family Dehalococcoidaceae was lower, than reported for other areas. While the sulfate concentrations explained much of the spatial distribution of OHRB, PBDE concentrations were also a strong influence on the abundance and diversity of OHRB in the sediments. For Dehalococcoides, Dehalogenimonas and Geobacter, the abundance of each genus was positively related to its own potential to remove PBDEs. The dominant OHRB genus, Dehalogenimonas, may contribute most to in situ bioremediation of PBDEs in Taihu Lake.

Field-based evidence for the enrichment of intrinsic antibiotic resistome stimulated by plant-derived fertilizer in agricultural soil

Animal manures have been demonstrated to enhance antibiotic resistance in agricultural soils. However, little is known about the effects of plant-derived fertilizer on soil antibiotic resistome. Herein, metagenomic sequencing was used to investigate the effects of a plant-derived fertilizer processed from sugarcane and beet on soil antibiotic resistance genes (ARGs) in a soybean field along crop growth stages. ARG profiles in the soils amended by plant-derived fertilizer were compared with those in the soils amended by chicken manure. The abundance and diversity of total ARGs in the soils amended by plant-derived fertilizer were significantly (P < 0.05) elevated at the sprout stage, to a level comparable to that in the manured soils. Whereas, unlike chicken manure mainly introducing manure-borne ARGs to soil, the plant-derived fertilizer was indicated to mainly enrich multidrug resistance genes in soil by nourishing indigenous bacteria. ARGs with abundances in amended soils significantly (P < 0.05) higher than in unamended soils at the sprout stage of soybean were considered as enriched ARGs. Decrease in the abundance of the enriched ARGs was observed in both the amended soils from the sprout to the harvest. Network analysis further identified Proteobacteria and Bacteroidetes as the primary bacterial taxa involved in the temporal variation of the enriched ARGs in the soils amended by plant-derived fertilizer, while in manured soils were Firmicutes and Actinobacteria. As revealed by multivariate statistical analyses, variation of the enriched ARGs in the soils amended by plant-derived fertilizer was majorly attributed to the response of co-occurred bacteria to depleting nutrients, which was different from the failed establishment of manure-borne bacteria in the manured soils. Our study provided field-based evidence that plant-derived fertilizer stimulated the intrinsic antibiotic resistome, and proposed attention to the un-perceived risk since some clinically relevant ARGs originate and evolve from natural resistome.

Variation of Microbial Diversity in Catastrophic Oil Spill Area in Marine Ecosystem and Hydrocarbon Degradation of UCMs (Unresolved Complex Mixtures) by Marine Indigenous Bacteria

The study targeted an assessment of microbial diversity during oil spill in the marine ecosystem (Kaohsiung port, Taiwan) and screened dominant indigenous bacteria for oil degradation, as well as UCM weathering. DO was detected lower and TDS/conductivity was observed higher in oil-spilled area, compared to the control, where a significant correlation (R² = 1; P < 0.0001) was noticed between DO and TDS. The relative abundance (RA) of microbial taxa and diversities (> 90% similarity by NGS) were found higher in the boundary region of spilled-oily-water (site B) compared to the control (site C) and center of the oil spill area (site A) (B_RA/diversity > C_RA/diversity > A_RA/diversity). The isolated indigenous bacteria, such as Staphylococcus saprophyticus (CYCTW1), Staphylococcus saprophyticus (CYCTW2), and Bacillus megaterium (CYCTW3) degraded the C₁₀-C₃₀ including UCM of oil, where Bacillus sp. are exhibited more efficient, which are applicable for environmental cleanup of the oil spill area. Thus, the marine microbial diversity changes due to oil spill and the marine microbial community play an important role to biodegrade the oil, besides restoring the catastrophic disorders through changing their diversity by ecological selection and adaptation process.

DIVERISTY and enzymatic potential of indigenous bacteria from unexplored contaminted soils in Faisalabad

Bacteria residing in contaminated waste soil degrade and utilize organic and inorganic material as a source of nutrients as well as reduce environmental contamination through their enzymatic machinery. This enzymatic potential of indigenous bacteria can be exploited at industrial level through detailed screening, characterization, optimization and purification. In present study, diversity and enzymatic potential of indigenous bacteria was investigated through qualitative and quantitative screening methods from unexplored contaminated soil waste sites in Faisalabad. Shannon diversity (H') index revealed that twenty-eight soil samples from four contaminated sites were highly diverse of amylase, protease and lipase producing bacteria. Maximum protease producing bacteria were detected in fruit waste (1.929 × 10⁷), whereas amylase and lipase producing bacteria were found in industrial (1.475 × 10⁷) and (5.38 × 10⁶), in household waste soil samples. Most of the indigenous bacterial isolates showed potential for multiple enzymes. An isolate OC5 exhibited capability for amylase production and optimization at a wider range of cultural conditions; pH (6-8), temperature (25 °C, 37 °C, 45 °C), incubation time (24-72 h), and NaCl concentrations 0.5-13%, using (1%) starch and lactose as substrates. An isolate OC5 was identified by molecular identification and phylogenetic analysis showed 99% sequence similarity with Bacillus spp. ANOVA was used to analyzed all data statistically. This study enhances the importance of initial screening and reporting of industrially potent indigenous bacteria from unexplored contaminated waste soils. In future, indigenous bacteria in contaminated wastes may be good candidates to solve various environmental pollution problems.

Biomass acid pretreatment impacts on metabolic routes and bacterial composition of dark fermentation process

Complex organic matter represents a suitable substrate to produce hydrogen through dark fermentation (DF) process. To increase H2 yields, pretreatment technology is often required. The main objective of the present work was to investigate thermo-acid pretreatment impact on sugar solubilization and biotic parameters of DF of sorghum or organic fraction of municipal solid waste (OFMSW). Biochemical hydrogen potential tests were carried out without inoculum using raw or thermo-acid pretreated substrates. Results showed an improvement in sugar solubilization after thermo-acid pretreatments. Pretreatments led to similar DF performances (H2 and total metabolite production) compared to raw biomasses. Nevertheless, they were responsible for bacterial shifts from Enterobacteriales towards Clostridiales and Bacillales as well as metabolic changes from acetate towards butyrate or ethanol. The metabolic changes were attributed to the biomass pretreatment impact on indigenous bacteria as no change in the metabolic profile was observed after performing thermo-acid pretreatments on irradiated OFMSW (inactivated indigenous bacteria and inoculum addition). Consequently, acid pretreatments were inefficient to improve DF performances but led to metabolic and bacterial community changes due to their impact on indigenous bacteria.

Simultaneous removal of aliphatic and aromatic crude oil hydrocarbons by Pantoea agglomerans isolated from petroleum-contaminated soil in the west of Iran

Hydrocarbons are considered as one of the most common and harmful environmental pollutants affecting human health and the environment. Bioremediation as an environmentally friendly, highly efficient, and cost-effective method in remediating oil-contaminated environments has been interesting in recent decades. In this study, hydrocarbon degrader bacterial strains were isolated from the highly petroleum-contaminated soils in the Dehloran oil field in the west of Iran. Out of 37 isolates, 15 can grow on M9 agar medium that contains 1.5 g L-1 of crude oil as the sole carbon source. The morphological, biochemical, and 16SrRNA sequencing analyses were performed for the isolates. The choosing of the isolates as the hydrocarbon degrader was examined by evaluating the efficacy of their crude oil removal at a concentration of 10 g L-1 in an aqueous medium. The results showed that five isolates belonging to Pseudomonas sp., Pseudomonas oryzihabitans, Roseomonas aestuarii, Pantoea agglomerans, and Arthrobacter sp. had a hyper hydrocarbon-degrading activity and they could remove more than 85% of the total petroleum hydrocarbon (TPH) after 96 h. The highest TPH removal of about 95.75% and biodegradation rate of 0.0997 g L-1 h-1 was observed for P. agglomerans. The gas chromatography-mass spectroscopy (GC-MS) analysis was performed during the biodegradation process by P. agglomerans to detect the degradation intermediates and final products. The results confirmed the presence of intermediates such as alcohols and fatty acids in the terminal oxidation pathway of alkanes in this biodegradation process. A promising P. agglomerans NB391 strain can remove aliphatic and aromatic hydrocarbons simultaneously.

Algae and indigenous bacteria consortium in treatment of shrimp wastewater: A study for resource recovery in sustainable aquaculture system

Shrimp production facilities produce large quantities of wastewater, which consists of organic and inorganic pollutants. High concentrations of these pollutants in shrimp wastewater cause serious environmental problems and, therefore, a method of treating this wastewater is an important research topic. This study investigated the impact of algae and indigenous bacteria on treating shrimp wastewater. A total of four different microalgae cultures, including Chlorococcum minutus, Porphyridum cruentum, Chlorella vulgaris and Chlorella reinhardtii along with two cyanobacterial cultures, Microcystis aeruginosa and Fishcherella muscicola were used with indigenous bacterial cultures to treat shrimp wastewater. The highest soluble chemical oxygen demand (sCOD) removal rate (95%) was observed in the samples that were incubated using F. muscicola. Total dissolved nitrogen was degraded >90% in the C. vulgaris, M. aeruginosa, and C. reinhardtii seeded samples. Dissolved organic nitrogen removal was significantly higher for C. vulgaris (93%) as compared to other treatments. Similarly, phosphate degradation was very successful for all the algae-bacteria consortium (>99%). Moreover, the degradation kinetics were calculated, and the lowest half-life (t1/2) for sCOD (5 days) was recorded for the samples seeded with M. aeruginosa. Similarly, treatment with F. muscicola and C. reinhardtii showed the lowest t1/2 of NH3-N (2.9 days) and phosphate (2.7 days) values. Overall, the results from this study suggest that the symbiotic relationship between indigenous bacteria and algae significantly enhanced the process of shrimp wastewater treatment within 21 days of incubation. The outcome of this study supports resource recovery in the aquaculture sector and could be beneficial to treat a large-scale shrimp facility's wastewater worldwide.

Hydrocarbons removal and microbial community succession in petroleum-contaminated soil under hydrogen peroxide treatment

Chemical oxidation as a pretreatment step coupled with bioremediation for petroleum-contaminated soil may pose serious impacts on indigenous microorganisms and the available nutrients. Petroleum-contaminated soil were treated by hydrogen peroxide (H₂O₂) at initial concentrations of 105 mM (HH), 21 mM (HL), and 105 mM in three equal amounts (HT) without adding any external catalyst. The contents of total petroleum hydrocarbons (TPH) and dissolved nutrients (total organic compounds, nitrogen, and phosphate), and the indigenous bacteria community succession (analyzed by high-throughput sequencing of 16S rDNA) were investigated over 50 days. Compared to the control treatment without H₂O₂ addition, H₂O₂ treatments for the petroleum-contaminated soil significantly promoted the TPH removal especially in the first 4 days and impacted the contents of dissolved nutrients. Both of chemical oxidation and nutrients contributed to microbial community structure changes in alpha diversity. Although the soil microbial community structure had undergone significant changes after different chemical oxidation pretreatments, Firmicutes, Proteobacteria, Gemmatimonadetes, and Actinobacteria were the main bacterial phyla. Compared with adding H₂O₂ at one time, H₂O₂ added in stepwise was beneficial to indigenous bacterial diversity recovery and TPH removal. H₂O₂ oxidation treatments showed a great influence on the microbial community structures in the start-up stage, while recovery time rather than the oxidation treatments presented greater effects on the composition of the microbial community structure with the incubation time extended. Therefore, adding H₂O₂ as pretreatment for petroleum-contaminated soil showed little effect on the structure of soil indigenous microbial community from a long-term scale, and was conducive to the continuous removal of TPH by indigenous microorganisms.

Diurnal changes in bacterial settlement on the Peyer's patch and surrounding mucosa in the rat ileum and its effect against the intestinal immune system

Our previous study revealed the diurnal change in the indigenous bacteria settling on the terminal region of the rat ileum. In the present study, we investigated the diurnal change in indigenous bacteria on the most distal ileal Peyer's patch (PP) and surrounding ileal mucosa and explored how stimulation from indigenous bacteria for a day affects the intestinal immune system at the beginning of the light phase. Histological measurement revealed that bacteria adjacent to the follicle-associated epithelium of PP and to the villous epithelium of the surrounding ileal mucosa are more abundant at zeitgeber time (ZT)0 and ZT18 than at ZT12. On the other hand, tissue-section 16S rRNA amplicon sequencing revealed no significant difference between ZT0 and ZT12 in the bacterial composition on the ileal tissue including the PP. One-day treatment with an antibiotic (Abx) successfully impaired the settlement of bacteria around the ileal PP. In transcriptome analysis, 1-day Abx treatment led to the downregulation of several chemokines in both PP and ordinary ileal mucosa at ZT0. Histological analysis of the 1-day Abx group revealed decreases in both CD68⁺ macrophages in PP and naphthol AS-D chloroacetate esterase stain-positive mast cells in the ileal villi. Together, these findings suggest that the colonies of indigenous bacteria on the distal ileal PP and surrounding mucosa expand during the dark phase, which might lead to the expression of genes to regulate the intestinal immune system and contribute to the homeostasis of at least macrophages in PP and mast cells in the ileal mucosa.

Potential of indigenous bacteria driven U(VI) reduction under relevant deep geological repository (DGR) conditions

Understanding the biogeochemical U redox processes is crucial for controlling U mobility and toxicity under conditions relevant to deep geological repositories (DGRs). In this study, we examined the microbial reduction of aqueous hexavalent uranium U(VI) [U(VI)aq] by indigenous bacteria in U-contaminated groundwater. Three indigenous bacteria obtained from granitic groundwater at depths of 44-60 m (S1), 92-116 m (S2), and 234-244 m (S3) were used in U(VI)aq bioreduction experiments. The concentration of U(VI)aq was monitored to evaluate its removal efficiency for 24 weeks under anaerobic conditions with the addition of 20 mM sodium acetate. During the anaerobic reaction, U(VI)aq was precipitated in the form of U(IV)-silicate with a particle size >100 nm. The final U(VI)aq removal efficiencies were 37.7%, 43.1%, and 57.8% in S1, S2, and S3 sample, respectively. Incomplete U(VI)aq removal was attributed to the presence of a thermodynamically stable calcium uranyl carbonate complex in the U-contaminated groundwater. High-throughput 16S rRNA gene sequencing analysis revealed the differences in indigenous bacterial communities in response to the depth, which affected to the U(VI)aq removal efficiency. Pseudomonas peli was found to be a common bacterium related to U(VI)aq bioreduction in S1 and S2 samples, while two SRB species, Thermodesulfovibrio yellowstonii and Desulfatirhabdium butyrativorans, played key roles in the bioreduction of U(VI)aq in S3 sample. These results indicate that remediation of U(VI)aq is possible by stimulating the activity of indigenous bacteria in the DGR environment.

Ketoprofen promotes the conjugative transfer of antibiotic resistance among antibiotic resistant bacteria in natural aqueous environments

The emergence and spread of antibiotic resistance in the environment pose a serious threat to global public health. It is acknowledged that non-antibiotic stresses, including disinfectants, pharmaceuticals and organic pollutants, play a crucial role in horizontal transmission of antibiotic resistance genes (ARGs). Despite the widespread presence of non-steroidal anti-inflammatory drugs (NSAIDs), notably in surface water, their contributions to the transfer of ARGs have not been systematically explored. Furthermore, previous studies have primarily concentrated on model strains to investigate whether contaminants promote the conjugative transfer of ARGs, leaving the mechanisms of ARG transmission among antibiotic resistant bacteria in natural aqueous environments under the selective pressures of non-antibiotic contaminants remains unclear. In this study, the Escherichia coli (E. coli) K12 carrying RP4 plasmid was used as the donor strain, indigenous strain Aeromonas veronii containing rifampicin resistance genes in Taihu Lake, and E. coli HB101 were used as receptor strains to establish inter-genus and intra-genus conjugative transfer systems, examining the conjugative transfer frequency under the stress of ketoprofen. The results indicated that ketoprofen accelerated the environmental spread of ARGs through several mechanisms. Ketoprofen promoted cell-to-cell contact by increasing cell surface hydrophobicity and reducing cell surface charge, thereby mitigating cell-to-cell repulsion. Furthermore, ketoprofen induced increased levels of reactive oxygen species (ROS) production, activated the DNA damage-induced response (SOS), and enhanced cell membrane permeability, facilitating ARG transmission in intra-genus and inter-genus systems. The upregulation of outer membrane proteins, oxidative stress, SOS response, mating pair formation (Mpf) system, and DNA transfer and replication (Dtr) system related genes, as well as the inhibition of global regulatory genes, all contributed to higher transfer efficiency under ketoprofen treatment. These findings served as an early warning for a comprehensive assessment of the roles of NSAIDs in the spread of antibiotic resistance in natural aqueous environments.

Histological study of diurnal changes in bacterial settlement in the rat alimentary tract

The composition of fecal bacteria is reported to change throughout the day, whereas the circadian rhythmicity of indigenous bacteria that settle on the epithelium is mostly unknown. The present study aimed to clarify the diurnal changes in the settlement of indigenous bacteria in the rat alimentary tract using histological analysis. The settlement of indigenous bacteria on the mucosal epithelium throughout the day and the diurnal changes in settlement levels were observed in the esophagus, the nonglandular area of the stomach, and the ileum. The peak of zeitgeber time (ZT) in the settlement level differed by segment: ZT 12 in the esophagus, ZT 6 in the nonglandular area of the stomach, and ZT 0 in the ileum. Moreover, 16S rRNA amplicon sequencing using tissue sections revealed that the compositions of the indigenous bacteria in the ileum differed among ZT. In the intervillous spaces of the ileum, the formation level of the mucus layer, one of the most fundamental host defenses against bacteria, was lowest at ZT 0. Bacteria were preferentially adjacent to the villous epithelium in the area without coverage by the mucus layer at ZT 0. These findings collectively suggest that the settlement level and possibly the composition of the indigenous bacteria changed diurnally in various segments of the alimentary tract, and the formation of the mucus layer might be the most likely to lead to such diurnal changes in indigenous bacteria, at least in the ileum.