Biodegradation of polycyclic aromatic hydrocarbons, phenol and sodium sulfate by Nocardia species isolated and characterized from Iranian ecosystems

Impact mechanisms of various surfactants on the biodegradation of phenanthrene in soil: Bioavailability and microbial community responses

The present study was conducted to systematically explore the mechanisms underlying the impact of various surfactants (CTAB, SDBS, Tween 80 and rhamnolipid) at different doses (10, 100 and 1000 mg/kg) on the biodegradation of a model polycyclic aromatic hydrocarbon (PAH) by indigenous soil microorganisms, focusing on bioavailability and community responses. The cationic surfactant CTAB inhibited the biodegradation of phenanthrene within the whole tested dosage range by decreasing its bioavailability and adversely affecting soil microbial communities. Appropriate doses of SDBS (1000 mg/kg), Tween 80 (100, 1000 mg/kg) and rhamnolipid at all amendment levels promoted the transformation of phenanthrene from the very slow desorption fraction (Fvslow) to bioavailable fractions (rapid and slow desorption fractions, Frapid and Fslow), assessed via Tenax extraction. However, only Tween 80 and rhamnolipid at these doses significantly improved both the rates and extents of phenanthrene biodegradation by 22.1-204.3 and 38.4-76.7 %, respectively, while 1000 mg/kg SDBS had little effect on phenanthrene removal. This was because the inhibitory effects of anionic surfactant SDBS, especially at high doses, on the abundance, diversity and activity of soil microbial communities surpassed the bioavailability enhancement in dominating biodegradation. In contrast, the nonionic surfactant Tween 80 and biosurfactant rhamnolipid enhanced the bioavailability of phenanthrene for degradation and also that to specific degrading bacterial genera, which stimulated their growth and increased the abundance of the related nidA degradation gene. Moreover, they promoted the total microbial/bacterial biomass, community diversity and polyphenol oxidase activity by providing available substrates and nutrients. These findings contribute to the design of suitable surfactant types and dosages for mitigating the environmental risk of PAHs and simultaneously benefiting microbial ecology in soil through bioremediation.

Bioremediation of petroleum refinery wastewater using Bacillus subtilis IH-1 and assessment of its toxicity

Environmental contamination from petroleum refinery operations has increased due to the rapid population growth and modernization of society, necessitating urgent repair. Microbial remediation of petroleum wastewater by prominent bacterial cultures holds promise in circumventing the issue of petroleum-related pollution. Herein, the bacterial culture was isolated from petroleum-contaminated sludge samples for the valorization of polyaromatic hydrocarbons and biodegradation of petroleum wastewater samples. The bacterial strain was screened and identified as Bacillus subtilis IH-1. After six days of incubation, the bacteria had degraded 25.9% of phenanthrene and 20.3% of naphthalene. The treatment of wastewater samples was assessed using physico-chemical and Fourier-transform infrared spectroscopy analysis, which revealed that the level of pollutants was elevated and above the allowed limits. Following bacterial degradation, the reduction in pollution parameters viz. EC (82.7%), BOD (87.0%), COD (80.0%), total phenols (96.3%), oil and grease (79.7%), TKN (68.8%), TOC (96.3%) and TPH (52.4%) were observed. The reduction in pH and heavy metals were also observed after bacterial treatment. V. mungo was used in the phytotoxicity test, which revealed at 50% wastewater concentration the reduction in biomass (30.3%), root length (87.7%), shoot length (93.9%), and seed germination (30.0%) was observed in comparison to control. When A. cepa root tips immersed in varying concentrations of wastewater samples, the mitotic index significantly decreased, suggesting the induction of cytotoxicity. However, following the bacterial treatment, there was a noticeable decrease in phytotoxicity and cytotoxicity. The bacterial culture produces lignin peroxidase enzyme and has the potential to degrade the toxic pollutants of petroleum wastewater. Therefore the bacterium may be immobilised or directly used at reactor scale or pilot scale study to benefit the industry and environmental safety.

Microcystin influence on soil-plant microbiota: Unraveling microbiota modulations and assembly processes in the rhizosphere of Vicia faba

Microcystins (MCs) are frequently detected in cyanobacterial bloom-impacted waterbodies and introduced into agroecosystems via irrigation water. They are widely known as phytotoxic cyanotoxins, which impair the growth and physiological functions of crop plants. However, their impact on the plant-associated microbiota is scarcely tackled and poorly understood. Therefore, we aimed to investigate the effect of MCs on microbiota-inhabiting bulk soil (BS), root adhering soil (RAS), and root tissue (RT) of Vicia faba when exposed to 100 μg L-1 MCs in a greenhouse pot experiment. Under MC exposure, the structure, co-occurrence network, and assembly processes of the bacterial microbiota were modulated with the greatest impact on RT-inhabiting bacteria, followed by BS and, to a lesser extent, RAS. The analyses revealed a significant decrease in the abundances of several Actinobacteriota-related taxa within the RT microbiota, including the most abundant and known genus of Streptomyces. Furthermore, MCs significantly increased the abundance of methylotrophic bacteria (Methylobacillus, Methylotenera) and other Proteobacteria-affiliated genera (e.g., Paucibacter), which are supposed to degrade MCs. The co-occurrence network of the bacterial community in the presence of MCs was less complex than the control network. In MC-exposed RT, the turnover in community composition was more strongly driven by deterministic processes, as proven by the beta-nearest taxon index. Whereas in MC-treated BS and RAS, both deterministic and stochastic processes can influence community assembly to some extent, with a relative dominance of deterministic processes. Altogether, these results suggest that MCs may reshape the structure of the microbiota in the soil-plant system by reducing bacterial taxa with potential phytobeneficial traits and increasing other taxa with the potential capacity to degrade MCs.

Characterizing the development of biofilm in polyethylene pipes in the non-chlorinated Danish drinking-water distribution system

In newly commissioned drinking-water polyethylene (PE) pipes, biofilm develops on the inner pipe surface. The microbial community composition from colonization to the establishment of mature biofilms is less known, including the effect on the distributed water quality. Biofilm development was followed through 1.5 years in PE-pipe side streams at two locations of a full-scale, non-chlorinated drinking-water distribution system (leaving a waterworks versus 5-6 km from a waterworks) along with inlet and outlet water quality. Mature biofilms were established after ∼8-9 months, dominated by Proteobacteria, Actinobacteria and Saccharibacteria (61-93% relative abundance), with a higher diversity (OTUs/Shannon Index/16S rRNA gene amplicon sequencing) in pipes in the far end of the distribution system. Comamonadaceae, and specifically Aquabacterium (>30% of reads), dominated young (∼1.5-month-old) biofilms. Young biofilms were linked to increased microbiological counts in drinking water (HPC/ATP/qPCR), while the establishment of mature biofilms led to a drop in HPC and benefited the water quality, highlighting the importance of optimizing commissioning procedures for rapidly achieving mature and stable biofilms.

Fifteen years of phenotypic and genotypic surveillance and antibiotic susceptibility pattern of Actinomycetes (Mycobacterium, Nocardia, Rhodococcus, etc.) in clinical and environmental samples of Iran

Actinomycetes, ubiquitous in the natural world, have been known to inflict infections upon both immunocompromised and healthy individuals. Interestingly enough, these species are oftentimes found residing within the microbiota of humans and animals alike. Unfortunately, these infections are frequently misdiagnosed as more sinister ailments such as malignancy or tuberculosis. Due to this issue, this review deals with 15 years of study on clinical and environmental samples to determine Actinomycetes' prevalence, isolation, identification, and antibiotic susceptibility pattern in Iran by Davood Azadi et al. According to the Davood Azadi framework, we searched the following databases: PubMed/MEDLINE, Embase, Scopus, Web of Science, SID, and Google Scholar in the period from 2007 to 2023. This review aimed to provide an overview of the most recent techniques for collecting environmental samples, cultivating them, and identifying the Actinomycetes group's members. The isolation of Actinomycetes from clinical and ecological sources is becoming more prevalent and should be a concern for health authorities in developing countries. Health centers should take action to increase awareness of diagnostic criteria and management guidelines for actinomycete diseases. Improvements in national and regional reference laboratories may also aid in accurately diagnosing these diseases.

Deconstructed Plastic Substrate Preferences of Microbial Populations from the Natural Environment

Over half of the world's plastic waste is landfilled, where it is estimated to take hundreds of years to degrade. Given the continued use and disposal of plastic products, it is vital that we develop fast and effective ways to utilize plastic waste. Here, we explore the potential of tandem chemical and biological processing to process various plastics quickly and effectively. Four samples of compost or sediment were used to set up enrichment cultures grown on mixtures of compounds, including disodium terephthalate and terephthalic acid (monomers of polyethylene terephthalate), compounds derived from the chemical deconstruction of polycarbonate, and pyrolysis oil derived from high-density polyethylene plastics. Established enrichment communities were also grown on individual substrates to investigate the substrate preferences of different taxa. Biomass harvested from the cultures was characterized using 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing. These data reveal low-diversity microbial communities structured by differences in culture inoculum, culture substrate source plastic type, and time. Microbial populations from the classes Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Acidobacteriae were significantly enriched when grown on substrates derived from high-density polyethylene and polycarbonate. The metagenomic data contain abundant aromatic and aliphatic hydrocarbon degradation genes relevant to the biodegradation of deconstructed plastic substrates used here. We show that microbial populations from diverse environments are capable of growth on substrates derived from the chemical deconstruction or pyrolysis of multiple plastic types and that paired chemical and biological processing of plastics should be further developed for industrial applications to manage plastic waste. IMPORTANCE The durability and impermeable nature of plastics have made them a popular material for numerous applications, but these same qualities make plastics difficult to dispose of, resulting in massive amounts of accumulated plastic waste in landfills and the natural environment. Since plastic use and disposal are projected to increase in the future, novel methods to effectively break down and dispose of current and future plastic waste are desperately needed. We show that the products of chemical deconstruction or pyrolysis of plastic can successfully sustain the growth of low-diversity microbial communities. These communities were enriched from multiple environmental sources and are capable of degrading complex xenobiotic carbon compounds. This study demonstrates that tandem chemical and biological processing can be used to degrade multiple types of plastics over a relatively short period of time and may be a future avenue for the mitigation of rapidly accumulating plastic waste.

Accelerated PAH Transformation in the Presence of Dye Industry Landfill Leachate Combined with Fungal Membrane Lipid Changes

The ascomycete fungus Nectriella pironii, previously isolated from soil continuously contaminated by dye industry waste, was used for the biodegradation of phenanthrene (PHE), benz[a]anthracene (B[a]A), and benz[a]pyrene (B[a]P). The degradation of polycyclic aromatic hydrocarbons (PAHs) by N. pironii was accelerated in the presence of landfill leachate (LL) collected from the area of fungus isolation. The rate of cometabolic elimination of PHE and B[a]P in the presence of LL was, respectively, 75% and 94% higher than in its absence. LC-MS/MS analysis revealed that PAHs were converted to less-toxic derivatives. The parallel lipidomic study showed changes in membrane lipids, including a significant increase in the content of phosphatidylcholine (PC) (almost double) and saturated phospholipid fatty acids (PLFAs) and a simultaneous reduction (twofold) in the content of phosphatidylethanolamine (PE) and unsaturated PLFAs, which may have promoted the fungus to PHE + LL adaptation. In the presence of PHE, an intense lipid peroxidation (fivefold) was observed, confirming the stabilization of the cell membrane and its extended integrity. Determining the course of elimination and adaptation to harmful pollutants is essential for the design of efficient bioremediation systems in the future.

Structural, metabolic, and functional characteristics of soil microbial communities in response to benzo[a]pyrene stress

Understanding the characteristics of soil microbes responding to benzo[a]pyrene (BaP) helps to deepen the knowledge of the risks of BaP to soil ecosystem. In this study, the structural, metabolic, and functional responses of soil microbial communities to BaP (8.11 mg kg^-1) were investigated. Analysis of microbial community structure based on 16 S rRNA and ITS gene sequencing indicated that BaP addition enriched microbes associated with aromatic compound degradation (Sphingomonas, Bacilli, Fusarium) and oligotrophs (Blastocatellaceae, Rokubacteriales), but inhibited Cyanobacteria involved in nitrogen-fixing process. Network analysis showed that the bacterial community enhanced intraspecific cooperation, while fungal community mainly altered the keystone taxa under BaP stress. Biolog EcoPlate assay demonstrated that microbial metabolism of carbon sources, especially nitrogen-containing sources, was stimulated by BaP addition. Functional analysis based on enzyme activity tests, functional gene quantification, and function annotation showed that nitrogen-cycling processes, especially nitrogen fixation, were significantly inhibited. These results suggest that BaP-tolerant microbes may establish cooperative relationships and compete for resources and ecological niches with sensitive microbes, especially those associated with nitrogen cycling, ultimately leading to enhanced carbon source utilization and restricted nitrogen cycling. This study clearly elucidates the adaptation strategies and functional shifts of soil microbial communities to BaP contamination.

Poly-cis-isoprene Degradation by Nocardia sp. BSTN01 Isolated from Industrial Waste

The natural and synthetic rubber (NR and SR) products are made up of poly-cis-isoprene which are estimated as one of the major solid-wastes and need to be cleared through bacterial bioremediation. The present research reports isolation and characterization of a gram-positive, non-spore forming, filamentous actinomycete Nocardia sp. BSTN01 from the waste of a rubber processing industry. We found NR- and SR-dependent growth of BSTN01 over a period of time. BSTN01 has been found to degrade NR by 55.3% and SR by 45.9% in 6 weeks. We have found an increase in the total protein of BSTN01 cells up to 623.6 and 573.9 µg/ml for NR and SR, respectively, after 6 weeks of growth in rubber-supplemented MSM medium. Scanning electron microscopy revealed adhesive growth of BSTN01 on the surface of NR and SR. Formation of aldehyde groups due to the degradation was indicated by Schiff's test and confirmed by FTIR-ATR analysis. The genome sequence of BSTN01 revealed the gene responsible for rubber degradation. The presence of lcp gene and structural analysis of the latex clearing protein further confirmed the reliability. Studies on quantification of rubber degradation capability by the isolated strain prove it to be an efficient degrader of NR and SR. This study revealed the genome sequence and structural analysis of the proteins responsible for degradation of rubber. A new fast-growing Nocardia strain can degrade both NR and SR with higher efficiency and have future potential for rubber solid-waste management either alone or in consortia.

Enhanced degradation of phenol by a novel biomaterial through the immobilization of bacteria on cationic straw

As phenol possesses a threat to human health, there is a great demand to search for fast and efficient methods for it to be discharged. In this study, a novel biomaterial was prepared by the immobilization of bacteria on a cationic straw carrier, and the remediation ability of the biomaterial on phenol-containing wastewater was investigated. The free bacteria could degrade 1,000 mg/L phenol within 240 h, while the prepared biomaterial was 192 h, shortening by 48 h that of free bacteria. In addition, the degradation tolerance of biomaterial increased from 1,000 mg/L to 1,200 mg/L than the free bacteria, within 216 h, which shortened by 24 h the degradation time of 1,000 mg/L phenol by free bacteria (240 h). Further, under different pH conditions, the degradation efficiency of phenol by prepared biomaterial was much higher than that of free bacteria. Especially for the lower pH 5, the degradation efficiency of biomaterial was nearly twice that of the free bacteria. This investigation demonstrates that this biomaterial has great potential in the field of remediation of organic pollution.

Assessment of the Suitability of Melilotus officinalis for Phytoremediation of Soil Contaminated with Petroleum Hydrocarbons (TPH and PAH), Zn, Pb and Cd Based on Toxicological Tests

The article presents issues related to the possibility of using toxicological tests as a tool to monitor the progress of soil treatment contaminated with petroleum substances (TPH, PAH), Zn, Pb and Cd in bio-phytoremediation processes. In order to reduce the high content of petroleum pollutants (TPH = 56,371 mg kg⁻¹ dry mass, PAH = 139.3 mg kg⁻¹ dry mass), the technology of stepwise soil treatment was applied, including basic bioremediation and inoculation with biopreparations based of indigenous non-pathogenic species of bacteria, fungi and yeasts. As a result of basic bioremediation in laboratory conditions (ex-situ method), the reduction of petroleum pollutants TPH by 33.9% and PAH by 9.5% was achieved. The introduction of inoculation with biopraparation-1 prepared on the basis of non-pathogenic species of indigenous bacteria made it possible to reduce the TPH content by 86.3%, PAH by 40.3%. The use of a biopreparation-1 enriched with indigenous non-pathogenic species of fungi and yeasts in the third series of inoculation increased to an increase in the degree of biodegradation of aliphatic hydrocarbons with long carbon chains and PAH by a further 28.9%. In the next stage of soil treatment after biodegradation processes, which was characterized by an increased content of heavy metals (Zn, Pb, Cd) and naphthalene, chrysene, benzo(a)anthracene and benzo(ghi)perylene belonging to polycyclic aromatic hydrocarbons, phytoremediation with the use of Melilotus officinalis was applied. After the six-month phytoremediation process, the following was achieved: Zn content by 25.1%, Pb by 27.9%, Cd by 23.2% and TPH by 42.2% and PAH by 49.9%. The rate of removal of individual groups of hydrocarbons was in the decreasing order: C₁₂–C₁₈ > C₆–C₁₂ > C₁₈–C₂₅ > C₂₅–C₃₆. PAHs tended to be removed in the following order: chrysene > naphthalene > benzo(a)anthracene > benzo(ghi)perylene. The TF and BCF coefficients were calculated to assess the capacity of M. officinalis to accumulate metal in tissues, uptake from soil and transfer from roots to shoots. The values of TF translocation coefficients were, respectively, for Zn (0.44), Pb (0.12), Cd (0.40). The calculated BCF concentration factors (BCF_roots > BCF_shoots) show that heavy metals taken up by M. officinalis are mainly accumulated in the root tissues in the following order Zn > Pb > Cd, revealing a poor metal translocation from the root to the shoots. This process was carried out in laboratory conditions for a period of 6 months. The process of phytoremediation of contaminated soil using M. officinalis assisted with fertilization was monitored by means of toxicological tests: Microtox, Ostracodtoxkit F^TM, MARA and Phytotoxkit^TM. The performed phytotoxicity tests have indicated variable sensitivity of the tested plants on contaminants occurring in the studied soils, following the sequence: Lepidium sativum < Sorghum saccharatum < Sinapis alba. The sensitivity of toxicological tests was comparable and increased in the order: MARA < Ostracodtoxkit F^TM < Microtox. The results of the toxicological monitoring as a function of the time of soil treatment, together with chemical analyses determining the content of toxicants in soil and biomass M. officinalis, clearly confirmed the effectiveness of the applied concept of bioremediation of soils contaminated with zinc, lead and cadmium in the presence of petroleum hydrocarbons.

Biodegradation of chlorpyrifos using isolates from contaminated agricultural soil, its kinetic studies

Extensive pesticides use is negatively disturbing the environment and humans. Pesticide bioremediation with eco-friendly techniques bears prime importance. This study evaluates the bioremediation of chlorpyrifos in soil using indigenous Bacillus cereus Ct3, isolated from cotton growing soils. Strains were identified through ribotyping (16s rRNA) by Macrogen (Macrogen Inc. Geumchen-gu, South Korea). Bacillus cereus Ct3 was resistant up to 125 mg L⁻¹ of chlorpyrifos and successfully degraded 88% of chlorpyfifos in 8 days at pH 8. Bacillus cereus Ct3 tolerated about 30–40 °C of temperature, this is a good sign for in situ bioremediation. Green compost, farmyard manure and rice husk were tested, where ANOVA (P < 0.05) and Plackett–Burman design, results indicated that the farm yard manure has significant impact on degradation. It reduced the lag phase and brought maximum degradation up to 88%. Inoculum size is a statistically significant (P < 0.05) factor and below 10⁶ (CFU g⁻¹) show lag phase of 4–6 days. Michaelis–Menten model results were as follows; R² = 0.9919, V_max = 18.8, K_s = 121.4 and V_max/K_s = 0.1546. GC–MS study revealed that chlorpyrifos first converted into diethylthiophosphoric acid and 3,5,6-trichloro-2-pyridinol (TCP). Later, TCP ring was broken and it was completely mineralized without any toxic byproduct. Plackett–Burman design was employed to investigate the effect of five factors. The correlation coefficient (R²) between experimental and predicted value is 0.94. Central composite design (CBD) was employed with design matrix of thirty one predicted and experimental values of chlorpyrifos degradation, having “lack of fit P value” of “0.00”. The regression coefficient obtained was R² = 0.93 which indicate that the experimental vales and the predicted values are closely fitted. The most significant factors highlighted in CBD/ANOVA and surface response plots were chlorpyrifor concentration and inoculum size. Bacillus cereus Ct3 effectively degraded chlorpyrifos and can successfully be used for bioremediation of chlorpyrifos contaminated soils.

Isolation and Characterization of Nocardiae Associated with Foaming Coastal Marine Waters

Nocardiosis is an infectious disease caused by Nocardia species that occurs worldwide, albeit more prevalently in tropical/subtropical regions. It can appear as either acute, subacute or as a chronic infection mostly with those with a compromised/weakened immune system. Inhalation of spores and or mycelium fragments is the main transmission route for developing pulmonary nocardiosis. In contrast, cutaneous nocardiosis usually occurs via direct contact. In the subtropical region of the Sunshine Coast in Australia foaming events with thick and persistent and orange-brown color foam have been observed during summer seasons in the near shore marine environments. This study reports the existence of nocardiae in these near shore marine environments by the use of a novel isolation method which used the gas requirements of nocardiae as a selective battery. A total of 32 nocardiae were isolated with the use of this novel method and subsequently conducted molecular identification methods confirmed that the isolates belonged to the genus Nocardia. Twenty-one isolates out of the 32 were closely related to N. nova strains MGA115 and one was related to CBU 09/875, in addition when compared with human pathogenic nocardiae twenty of the isolates were found to be related to N. nova strain JCM 6044. Isolates displayed varied resistance against some of the antibiotics tested when interpretation threshold recommended the Comite de L'Antibiogramme de la Societe Francaise de Microbiologie were used. The highest level of resistance against cefotaxime (n = 27) and ceftriaxone (n = 24). Some of the isolates (n = 6) that displayed resistance to selected antibiotics also possessed potential human pathogenic characteristics such as adherence and translocation through human long epithelial cells as well as displaying phage resistance (n = 26). They might thus present a potential public health risk if frequently encountered through exposure to aerosols generated by the foam as well as direct contact through a wound. Preventative measures to control the growth of nocardiae in such environments such as the control of pollutants, might prevent potential infections that might be caused by these bacteria in humans as well as in marine animals.