Naphthalene Degradation Research Articles

Genomic characterization of a polyvalent hydrocarbonoclastic bacterium Pseudomonas sp. strain BUN14

Bioremediation offers a viable alternative for the reduction of contaminants from the environment, particularly petroleum and its recalcitrant derivatives. In this study, the ability of a strain of Pseudomonas BUN14 to degrade crude oil, pristane and dioxin compounds, and to produce biosurfactants, was investigated. BUN14 is a halotolerant strain isolated from polluted sediment recovered from the refinery harbor on the Bizerte coast, north Tunisia and capable of producing surfactants. The strain BUN14 was assembled into 22 contigs of 4,898,053 bp with a mean GC content of 62.4%. Whole genome phylogeny and comparative genome analyses showed that strain BUN14 could be affiliated with two validly described Pseudomonas Type Strains, P. kunmingensis DSM 25974T and P. chloritidismutans AW-1T. The current study, however, revealed that the two Type Strains are probably conspecific and, given the priority of the latter, we proposed that P. kunmingensis DSM 25974 is a heteronym of P. chloritidismutans AW-1T. Using GC-FID analysis, we determined that BUN14 was able to use a range of hydrocarbons (crude oil, pristane, dibenzofuran, dibenzothiophene, naphthalene) as a sole carbon source. Genome analysis of BUN14 revealed the presence of a large repertoire of proteins (154) related to xenobiotic biodegradation and metabolism. Thus, 44 proteins were linked to the pathways for complete degradation of benzoate and naphthalene. The annotation of conserved functional domains led to the detection of putative genes encoding enzymes of the rhamnolipid biosynthesis pathway. Overall, the polyvalent hydrocarbon degradation capacity of BUN14 makes it a promising candidate for application in the bioremediation of polluted saline environments.

Isolation and identification of naphthalene degrading bacteria and their degradation characteristics under rainwater environment in heavily polluted areas

This study is screened for naphthalene degrading strains from a heavily polluted area with high naphthalene concentration in the rainwater for the effective removal of naphthalene from rainwater. Recently, naphthalene biodegradation has been achieved in water. However, the influences of organics and inorganics in the rainwater on the biodegradation of naphthalene remains unclear. The naphthalene degrading strain Klebsiella sp. (WJ-1) was identified from sewage sludge. The effects of temperature, pH, inoculum size, and rotation speed on the degradation ability of WJ-1 were studied. The results showed that the naphthalene degradation rates of WJ-1 in rainwater were higher than those in aqueous solution at different experimental conditions. The optimal conditions were 30 °C, 10% inoculum size, pH 7.0, and a rotation speed of 150 rpm. The substances in rainwater might be important co-metabolites of naphthalene degradation. Based on intermediate metabolites detected by gas chromatography–mass spectrometer (GC-MS), the naphthalene biodegradation pathway was identified, as being similar to the phthalic acid pathway. These results suggest WJ-1 as a good candidate for the efficient bioremediation of naphthalene from rainwater in heavily polluted areas.

Carbon textiles electrodes modified with RGO and Pt nanoparticles used for electrochemical treatment of azo dye

• The use of a dimensionally versatile textile electrode permits efficient wastewater decolorization. • TC–RGO–Pt electrodes permit naphthalene degradation after electrolysis. • The stability of TC–RGO–Pt anodes have been proved after the electrolysis. • Very low energy consumption is needed for dye electrochemical degradation. • High mineralization of organic matter is obtained with chloride addition. • These electrodes are a valuable alternative for textile wastewater remediation. The efficiency of Orange G (OG) azo dye degradation using an electrochemical method under potentiostatic conditions has been comparatively studied in two electrolytic cells (divided and undivided cells) in the presence or absence of chloride ions with Pt-modified textile electrodes. The morphology of the carbon-based electrodes with nanoparticles of platinum electrochemically dispersed on their surface was analyzed using field emission scanning electron microscopy (FESEM) and EDX analysis. The FESEM analyses confirmed that the textile surface was coated by Pt nanoparticles. According to the experimental results obtained, when the same solutions are comparatively treated with the two cells, the undivided cell always gives a quicker decolorization than the divided cell – and the decrease in total organic carbon (TOC), chemical oxygen demand (COD), and total nitrogen (TN) confirms this result. The degree of OG removal was monitored by spectroscopic methods and high-performance liquid chromatography (HPLC). The results indicate that that full best dye removal is obtained at a loaded charge of around 0.17 Ah L −1 which is associated with an electrical energy per order (EEO) of 0.189 kW h m −3 order −1 . Based on the results obtained, the electrochemical process with TC-RGO-Pt electrodes could be useful as a pretreatment technique or treatment for decolorizing wastewaters containing dyes.

Microbial Degradation of Naphthalene and Substituted Naphthalenes: Metabolic Diversity and Genomic Insight for Bioremediation.

Low molecular weight polycyclic aromatic hydrocarbons (PAHs) like naphthalene and substituted naphthalenes (methylnaphthalene, naphthoic acids, 1-naphthyl N-methylcarbamate, etc.) are used in various industries and exhibit genotoxic, mutagenic, and/or carcinogenic effects on living organisms. These synthetic organic compounds (SOCs) or xenobiotics are considered as priority pollutants that pose a critical environmental and public health concern worldwide. The extent of anthropogenic activities like emissions from coal gasification, petroleum refining, motor vehicle exhaust, and agricultural applications determine the concentration, fate, and transport of these ubiquitous and recalcitrant compounds. Besides physicochemical methods for cleanup/removal, a green and eco-friendly technology like bioremediation, using microbes with the ability to degrade SOCs completely or convert to non-toxic by-products, has been a safe, cost-effective, and promising alternative. Various bacterial species from soil flora belonging to Proteobacteria (Pseudomonas, Pseudoxanthomonas, Comamonas, Burkholderia, and Novosphingobium), Firmicutes (Bacillus and Paenibacillus), and Actinobacteria (Rhodococcus and Arthrobacter) displayed the ability to degrade various SOCs. Metabolic studies, genomic and metagenomics analyses have aided our understanding of the catabolic complexity and diversity present in these simple life forms which can be further applied for efficient biodegradation. The prolonged persistence of PAHs has led to the evolution of new degradative phenotypes through horizontal gene transfer using genetic elements like plasmids, transposons, phages, genomic islands, and integrative conjugative elements. Systems biology and genetic engineering of either specific isolates or mock community (consortia) might achieve complete, rapid, and efficient bioremediation of these PAHs through synergistic actions. In this review, we highlight various metabolic routes and diversity, genetic makeup and diversity, and cellular responses/adaptations by naphthalene and substituted naphthalene-degrading bacteria. This will provide insights into the ecological aspects of field application and strain optimization for efficient bioremediation.

Identification of marine sponges-symbiotic bacteria and their application in degrading polycyclic aromatic hydrocarbons

Abstract. Marzuki I, Kamaruddin M, Ahmad R. 2021. Identification of marine sponges-symbiotic bacteria and their application in degrading polycyclic aromatic hydrocarbons. Biodiversitas 22: 1481-1488. Diverse and abundant microbial species that occupy marine sponges may make important contributions to host metabolism. Sponges are filter feeders and devour microorganisms from the seawater around them. Each microbe that endures the sponges’ digestive and immune responses are related symbiotically. Marine sponges symbiont bacteria can comprise as much as 40% of sponge tissue volume, and these are known to exhibit a great potential on polycyclic aromatic hydrocarbons (PAHs) degradation. However, the potential use of marine sponges symbiont bacteria is unexplored. Therefore, we designed and conducted a study to identify bacterial isolates obtained from sponges. For this, we collected sponges samples (Hyrtios erectus, Clathria (Thalysias) reinwardti), Niphates sp., and Callyspongia sp.) from the Spermonde islands in Indonesia. We successfully found eight bacterial isolates from four sponges, as molecular identification based on 16S rRNA approach revealed bacterial isolates of SpAB1, SpAB2, SpBB1, SpDB1, and SpDB2 from three sponges (Hyrtios erectus, Clathria (Thalysias) reinwardti), Niphates sp.). Interestingly, these were closely related to Pseudomonas, and a bacterial isolate from Callyspongia sp. (SpCB1) showed similarity to Bacillus. Bacillus and Pseudomonas bacteria isolated from hydrocarbon-contaminated sponges exhibited degradation of naphthalene and pyrene PAHs.

Naphthalene degradation studies using Pseudomonas sp. strain SA3 from Alang-Sosiya ship breaking yard, Gujarat

Polycyclic aromatic hydrocarbons (PAHs) remediation has received considerable attention due to their significant health concern and environmental pollution. However, PAHs contaminated sites also contain indigenous microbes that can potentially degrade naphthalene. Therefore, this study aimed to isolate, characterise and optimise process parameters for efficient naphthalene degradation. A total of 50 naphthalene degrading bacteria were isolated from Alang-Sosiya ship breaking yard, Bhavnagar, Gujarat and screened for their naphthalene degrading capacity. The selected isolate, Pseudomonas sp. strain SA3 was found to degrade 98.74 ± 0.00% naphthalene at a concentration of 500 ppm after 96 h. Further, optimisation of environmental parameters using one factor at a time approach using different inoculum sizes (v/v), pH, salinity, temperature, carbon and nitrogen source greatly accelerated the degradation process attaining 98.6 ± 0.46% naphthalene degradation after 72 h. The optimised parameters for maximum naphthalene degradation were pH 8, 0.1% peptone as nitrogen source, 8% salinity and 1% (v/v) inoculum size.

Naphthalene degradation in aqueous solution by Fe(II) activated persulfate coupled with citric acid

More and more attention has been paid to polycyclic aromatic hydrocarbons (PAHs) contaminated sites caused by coking industries and chemical manufactures. In this study, the degradation performance of naphthalene (NAP), one of the typical pollutants in PAHs contaminated sites, in persulfate (PS) oxidation system activated by Fe(II) coupled with citric acid (CA) was investigated. The effects of PS, CA, and Fe(II) dosages on NAP were evaluated. 97.5% removal of NAP was obtained at the molar ratio of 15/5/1/1 of PS/Fe(II)/CA/NAP within 120 min, demonstrating that the addition of CA could significantly strengthen NAP degradation. The results of probe tests, EPR detection and scavenging experiments suggested that HO• played a predominant role in the degradation of NAP. The effect of surfactants including tween-80 (TW-80) and sodium dodecyl sulfate (SDS) on NAP degradation was explored. Moreover, the major degradation intermediates of NAP were determined by GC–MS and the possible degradation pathways of NAP were proposed. Finally, the effectiveness of PS/Fe(II)/CA process for NAP degradation in the actual groundwater demonstrated that this technique has a remarkable preponderance and prospect in NAP contaminated groundwater remediation.

Enhancement of photocatalytic activity of TiO2 by immobilization on activated carbon for degradation of aquatic naphthalene under sunlight irradiation

Remediating and controlling PAHs (Polyaromatic Hydrocarbons) contamination in the environment is essential all over the world. Nano-TiO2 immobilized on large surface area adsorbent is a kind of emerging endeavor to enhance the photo-catalysis performance. In this paper, activated carbon samples (ACs) were synthesized by using a kind of subtropical macroalgae, i.e., Sargassum Horneri (S.H.) as raw material. ACs activated by FeCl3, ZnCl2, a composite activators mixture of FeCl3 and ZnCl2 (CA) were selected to immobilize nano-TiO2 in aquatic environment, and naphthalene degradation performance of these materials was systematically assessed. The results showed that ACs could provide more activated space for naphthalene photocatalytic reaction, in which Zn2+ helped to hold relative high specific surface area, Fe3+ helped to extend the valid light responsive wavelength, and CA could take advantage of both metal ions, with the largest whole volume and surface functional groups. The highest naphthalene degradation efficiency of TiO2/AC-CA under simulated sunlight could arrive to 77.5%, while those of TiO2/AC-FeCl3 and TiO2/AC-ZnCl2 were 65.0%, 54.5%, respectively. Meanwhile, the pH-resistance and reusing capability of TiO2/AC-CA are better than those of other TiO2/ACs. The results helped to clarify the synergistic mechanism of AC and TiO2 in photo-catalysis, especially the metal ions’ role in combining the two materials, and showed the industrial potential of S.H. in PAHs contamination.

Photocatalysis of naphthalene by Fe3O4/Oxone/UV: Simultaneous radical and non-radical pathways

Naphthalene (Nap) degradation by photocatalysis of Fe3O4/Oxone/UV was studied. The system eliminated Nap in 30 min and the kinetics is described by a novel mixed order model with adsorption and decay dominant rate constants, representing non-radical and radical pathways respectively. The reaction is dominated by catalysis in acidic pHs as Oxone anions are adsorbed onto the protonated Fe3O4 surface for activation; In alkaline solution, the adsorption of Nap to the deprotonated Fe3O4 surface is the main removal pathway. The catalyst was reused for 5 cycles and the performance was enhanced after reuse. XPS study confirmed that the surface Fe content of Fe3O4 remained stable after reusing due to the effective UV-assisted ≡FeII—≡FeIII catalytic cycle. An additional C‒O bond on Fe3O4 surface was detected after reuse, which is proposed to be an OH bond on catalyst as an extra adsorption site and for radical generation.

Root exudates enhance the PAH degradation and degrading gene abundance in soils

Root exudates could influence the bioavailability of polycyclic aromatic hydrocarbons (PAHs), provide nutrients for soil microorganisms, and affect PAH biodegradation. However, it remains unclear how a bacterial community and its PAH-degrading genes play crucial roles in PAH biodegradation and respond to root exudates. In this study, a 32-day soil microcosm study was conducted to explore the impacts of artificial and actual root exudates on PAH degradation, degrading genes, and bacterial community structure. The results showed that 10–100 mg DOC/kg artificial and actual root exudates promoted the degradation of naphthalene, phenanthrene, and pyrene in soils, and their percent removal increased initially and then decreased with the increasing root exudates. Quantitative polymerase chain reaction analysis and 16S rRNA gene high-throughput sequencing suggested that the artificial root exudates significantly promoted the Nocardioides and Arthrobacter genera, which may harbor the nidA gene (the representative PAH-degrading gene from Gram-positive bacteria). In contrast, actual root exudates significantly stimulated the Pseudomonas genus that may harbor the nahAc gene (the representative PAH-degrading gene from Gram-negative bacteria). The correlation analysis further indicated that the absolute abundance of PAH degraders and degrading genes had strong correlations with PAH degradation efficiency. Therefore, these findings suggest that root exudates enhanced PAH biodegradation probably due to increases in abundance of both PAH-degraders and their degrading genes.

Function and Molecular Ecology Significance of Two Catechol-Degrading Gene Clusters in Pseudomonas putida ND6.

Many bacteria metabolize aromatic compounds via catechol as a catabolic intermediate, and possess multiple genes or clusters encoding catechol-cleavage enzymes. The presence of multiple isozyme-encoding genes is a widespread phenomenon that seems to give the carrying strains a selective advantage in the natural environment over those with only a single copy. In the naphthalene-degrading strain Pseudomonas putida ND6, catechol can be converted into intermediates of the tricarboxylic acid cycle via either the ortho- or meta-cleavage pathways. In this study, we demonstrated that the catechol ortho-cleavage pathway genes (catBICIAI and catBIICIIAII) on the chromosome play an important role. The catI and catII operons are co-transcribed, whereas catAI and catAII are under independent transcriptional regulation. We examined the binding of regulatory proteins to promoters. In the presence of cis-cis-muconate, a well-studied inducer of the cat gene cluster, CatRI and CatRII occupy an additional downstream site, designated as the activation binding site. Notably, CatRI binds to both the catI and catII promoters with high affinity, while CatRII binds weakly. This is likely caused by a T to G mutation in the G/T-N11-A motif. Specifically, we found that CatRI and CatRII regulate catBICIAI and catBIICIIAII in a cooperative manner, which provides new insights into naphthalene degradation.

Diversity and functional prediction of microbial communities involved in the first aerobic bioreactor of coking wastewater treatment system.

The pre-aerobic process of coking wastewater treatment has strong capacity of decarbonization and detoxification, which contribute to the subsequent dinitrogen of non-carbon source/heterotrophic denitrification. The COD removal rate can reach > 90% in the first aerobic bioreactor of the novel O/H/O coking wastewater treatment system during long-term operation. The physico-chemical characteristics of influent and effluent coking wastewater in the first aerobic bioreactor were analyzed to examine how they correlated with bacterial communities. The diversity of the activated sludge microbial community was investigated using a culture-independent molecular approach. The microbial community functional profiling and detailed pathways were predicted from the 16S rRNA gene-sequencing data by the PICRUSt software and the KEGG database. High-throughput MiSeq sequencing results revealed a distinct microbial composition in the activated sludge of the first aerobic bioreactor of the O/H/O system. Proteobacteria, Bacteroidetes, and Chlorobi were the decarbonization and detoxification dominant phyla with the relative abundance of 84.07 ± 5.45, 10.89 ± 6.31, and 2.96 ± 1.12%, respectively. Thiobacillus, Rhodoplanes, Lysobacter, and Leucobacter were the potential major genera involved in the crucial functional pathways related to the degradation of phenols, cyanide, benzoate, and naphthalene. These results indicated that the comprehensive understanding of the structure and function diversity of the microbial community in the bioreactor will be conducive to the optimal coking wastewater treatment.

Biodegradation of selected hydrocarbons by novel bacterial strains isolated from contaminated Arabian Gulf sediment

Three strains of novel bacteria were isolated from oil-contaminated sediment from the Arabian Gulf (Brevibacillus brevis T2C2008, Proteus mirabilis T2A12001, and Rhodococcus quinshengi TA13008). The isolated strains were tested for their degrading efficacy of low and high molecular hydrocarbon (naphthalene and pyrene). The efficacy of the two-hydrocarbon degradation by the isolates bacterial was determined at a temperature of 25 °C and 37 °C and pH of 5.0 and 9.0. In inoculated media at 37 °C, Rhodococcus qinshengi fully metabolized naphthalene and degrade 56% of pyrene. Brevibacillus brevis break down over 80% of naphthalene at room temperatures (25 °C). However, it was found that P. mirabilis and R. qinshengi biodegraded nearly 94% of naphthalene in the incubated media. The capacity for pyrene and naphthalene degradation in varying pH and temperature conditions was shown to be significant in Rhodococcus qinshengi because of its mineralization exceeding 50% across the tested pH and temperature. This implies that the isolated strains are ideal for biodegradation of contaminated sediment with naphthalene and pyrene.

Degradation of naphthalene and pyrene by several biofilm-forming photosynthesis purple bacterial strains

Aromatic hydrocarbons such as naphthalene, pyrene are recalcitrant compounds found in oil contaminated areas including petroleum storage tanks, oil exploiting companies. These components are difficult to be degraded/transformed in the lack of oxygen conditions. Among anaerobic and micro-aerobic microorganisms, photosynthetic purple bacteria are the dominant group. Photosynthetic purple bacteria (PPB) are considered as aquatic organisms which are able to grow in anaerobic conditions by photosynthesis but without oxygen. This bacterial group has flexible metabolic types depending on living conditions, then they are widely distributed in nature. There are numerous publications on planktonic PPB which could use naphthalene and pyrene as carbon and energy sources. However, there is no publication on biofilm formed by PPB to degrade their aromatic compounds. In this research, 4 biofilm-forming PPB strains including DQ41, PY2, PY6 and DG12 were screened and estimated their pyrene and napthalene degradation capacity. These organisms demonstrated high biofilm forming ability. As biofilm types, their utilization efficiencies were upper 79% with the initial concentrations of naphthalene and pyrene of 200 and 250 ppm, respectively. These results may contribute to enlarge the number of biofilm-forming microorganisms to degrade/transform aromatic hydrocarbons in polluted area treatment in Vietnam.

Isolation and Molecular Characterization of Polycyclic Aromatic Hydrocarbon Degrading Bacteria from Effluent Water from Weras River Park, Sri Lanka

The present study records the detection of PAHs such as naphthalene and anthracene and isolation of PAHs degrading bacteria from a restaurant site, Weras River Park, in Boralesgamuwa, Sri Lanka. Water samples were collected in seven locations of the study area. Water temperature (oC), pH, and electric conductivity (EC) were measured at the site itself using standard meters. Nitrogen nitrate (N-NO3-) and total phosphate (TP) were measured at the laboratory following the standard methods. Following the extraction of PAHs in collected water samples, detection was carried out using the PDA-HPLC diode array method. PAH degrading bacteria were identified using microplate assay. The selected bacteria strains were subjected to degradation kinetic studies following molecular identification by 16S rRNA analysis. Phylogenetic analysis identified Achromobacter spanius as potential naphthalene degrading bacteria, where Alcaligens faecalis was recorded as an anthracene degrader. Degradation study confirmed that A. spanius efficiently degraded naphthalene at the rate of 0.145±0.002 ppm/day, whereas A. faecalis degraded anthracene at the rate of 0.181±0.036 ppm/day, respectively. Degradation of structures of the Naphthalene and Anthracene by A. spanius and A. faecalis was further analyzed by Fourier Transform Infrared Spectroscopy (FTIR). This is the first record on naphthalene degradation by the bacterium A. spanius.

The effects of adsorptive materials on microbial community composition and PAH degradation at the sediment cap–water interface

Capping with layers of inert or adsorptive materials is used to control the release of polycyclic aromatic hydrocarbons (PAH) in sediment but little is known about microbial degradation processes in these materials. A rich native microbial community inhabits the sediment bed, and capping media can influence enrichment and biodegradation activity of benthic microorganisms. The aim of this study was to evaluate the effects of capping media (sand, organoclay, and powdered activated carbon [PAC]) on microbial communities under oxic conditions typical of the cap–water interface, where naphthalene degradation (model PAH) is likely to be maximized. Bench scale experiments compared naphthalene concentrations, nahAc biomarker abundance, microbial community composition, and cellular attachment in systems amended with adsorptive and non-adsorptive capping materials. Results indicate that activated carbon promoted and enhanced bioactivity; PAC treatments showed high biodegradation rates, nahAc biomarker levels, and attached biological growth consistent with enrichment of the PAH-degrading genus Pseudomonae. In contrast, sand did not enhance biological activity compared to media-free systems. Naphthalene strongly influenced microbial community composition at the species level in all treatments except organoclay, which promoted biological signatures commonly associated with impeding degradation activity. Data overall suggest that adsorptive capping materials can both promote (PAC) and inhibit (organoclay) bioactivity in the surficial layer of caps, indicating that media selection is critical to the design of bioactive capping systems.

Adapting the algal microbiome for growth on domestic landfill leachate

We aimed to improve algal growth rate on leachate by optimising the algal microbiome. An algal-bacterial consortium was enriched from landfill leachate and subjected to 24 months of adaptive laboratory evolution, increasing the growth rate of the dominant algal strain, Chlorella vulgaris, almost three-fold to 0.2 d−1. A dramatic reduction in nitrate production suggested a shift in biological utilisation of ammoniacal-N, supported by molecular 16S rRNA taxonomic analyses, where Nitrosomonas numbers were not detected in the adapted consortium. A PICRUSt approach predicted metagenomic functional content and revealed a high number of sequences belonging to bioremediation pathways, including degradation of aromatic compounds, benzoate and naphthalene, as well as pathways known to be involved in algal-bacterial symbiosis. This study enhances our understanding of beneficial mechanisms in algal-bacterial associations in complex effluents, and ultimately enables the bottom-up design of optimised algal microbiomes for exploitation within industry.

Naphthalene catabolism by biofilm forming marine bacterium Pseudomonas aeruginosa N6P6 and the role of quorum sensing in regulation of dioxygenase gene.

This study aims to establish the role of quorum sensing (QS) system on the regulation of naphthalene ring cleaving gene ndo (encoding naphthalene dioxygenase) in biofilm forming marine bacterium Pseudomonas aeruginosa N6P6 for naphthalene degradation. Total cell count of P. aeruginosa N6P6 during biofilm mode of growth was slightly higher (7·3×108 CFU per ml) than its planktonic mid-exponential phase culture (4·7×108 CFU per ml). Naphthalene degradation in 20h by biofilm (48-h old) and planktonic culture was 99·4±0·002% and 77±3·25%, respectively. Pseudomonas aeruginosa N6P6 was able to degrade 64·3± 4·7% naphthalene in sterile soil microcosm in 24h. The bacterium showed the presence of 136bp ndo gene which was upregulated in a dose-dependent manner in presence of naphthalene. QS inhibitor (QSI) tannic acid downregulated the expression of ndo gene, naphthalene 1, 2-dioxygenase (N12O) enzyme activity and naphthalene degradation (by biofilm culture). P. aeruginosa N6P6 shows chemotaxis towards naphthalene and adapts well in terrestrial environment for naphthalene degradation. This study provides the information that the QS plays crucial role in biofilm formation in P. aeruginosa N6P6 and QS regulatory genes subsequently control the ndo gene for enzymatic degradation of naphthalene.

Microplastics contamination in the protected agricultural soils and its effects on bacterial community diversity

<p indent="0mm">Mircroplastics (MPs) are defined as plastic particles or fibers of size ˂<sc>5 mm</sc> and have been of concern in terrestrial ecosystems for several years. Protected agricultural soils have been assumed to be potentially contaminated with MPs because of the use of large amounts of plastic films and annual compost inputs. However, there is little published information on MP contamination of protected agricultural soils and its ecological effects on soil biota remain unknown. Here, a total of 54 surface <sc>(0−10 cm</sc> depth) soils were sampled from intensively managed protected agricultural soils around Hangzhou Bay, east China. MPs were extracted from the soil samples using continuous air flotation followed by density separation. Stereomicroscopy and micro-Fourier transform infrared spectroscopy (μ-FTIR) were used for identification after the extracted MPs were pre-sorted based on their shapes. In addition, a 29-d soil incubation experiment was conducted to observe the changes in microbial community diversity due to MP contamination. Soils were spiked with 1% and 5% (w/w) low density polyethylene (LDPE) MPs (average size <sc>678 μm)</sc> and sampled at an intervals of 1, 15 and<sc>29 d</sc> in an incubation experiment. The soil bacterial community in these samples was analyzed using high-throughput sequencing technology. A field survey of the protected agricultural soils indicates that soil MP abundance ranged from 20 to 1560 pieces kg⁻¹ with an average of 443 pieces kg⁻¹. Fragments dominated the MP types which comprised films, fragments and fibers, likely originating from compost applications to the soils. LDPE MPs occurred mainly in MP films and were widely distributed in soil samples from mulched soils. Soil MP was also influenced by the type of plastic mulching film used. Relatively high MP abundance was found in soils covered with black mulching film compared with other types of film. Soil MP contamination was found to affect soil microorganisms in the incubation experiment. The Chao1 index (which indicates the richness of the bacterial community) decreased initially and then increased in both PE-spiked and PE-free soils during incubation for <sc>29 d.</sc> However, larger decreases and smaller increases in Chao1 were observed in PE-spiked than PE-free soils, indicating that the presence of PE in the soil might inhibit the recovery of the bacterial community richness. The 16S rRNA high-throughput sequencing results indicate that changes in bacterial community diversity were not proportional to the PE microplastic contents of the soils. Larger changes occurred in soils spiked with 1% PE than in those spiked with 5% PE. After addition of PE MPs a significant (<italic>P</italic>&lt;0.05) increase in the relative abundance of the bacterial orders Sphingomonadales, Xanthomonadales, Propionibacteriales, Chitinophagales, Sphingobacteriales and Flavobacteriales was observed but the relative abundance of the orders unclassified Actinobacteria, Betaproteobacteriales, Myxococcales and Gemmatimonadales decreased significantly (<italic>P</italic>&lt;0.05). Functional profiling of the bacterial communities was predicted using KEGG pathways. A total of seven KEGG pathways showed significant difference between the 1% PE spiked and PE-free soils. For example, the biosynthesis of secondary metabolites such as isoflavonoids will be impacted and naphthalene degradation will be promoted after addition of PE microplastics. Further studies are planned on the transformation of soil nutrients and xenobiotic pollutants by the selection of functional genes.

Microbial communities in field-scale oil-polluted soil remediation using 16S rRNA amplicon sequencing

ABSTRACT This investigation employed 16S rRNA amplicon sequencing to understand microbial dynamics during a 2-month field-scale oil-impacted soil remediation in the Niger Delta. Surface soil (0.0–0.5 m) had extractable total petroleum hydrocarbons (ETPH) concentrations of 6231 mg/kg and subsurface samples from 1.0 m, 1.5 m and 2.0 m depths had 4836 mg/kg, 9112 mg/kg and 7273 mg/kg, respectively. Proteobacteria dominated the bacterial community of the oil-polluted soil and comprised mainly Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. Alpha diversity analysis revealed the presence of hydrocarbons reduced microbial diversity. Principal coordinate analysis indicated that the community structure continually changed following variations in the ETPH concentrations. Mycobacterium, Burkholderia, Methylobacterium and Bacillus were among the core operational taxonomic units (OTUs) detected during remediation. Significant variation in predicted pathway abundance, particularly pathways for fatty acid metabolism, propanoate, benzoate, polycyclic aromatic hydrocarbons, naphthalene and xenobiotics degradation, was more apparent in samples obtained during remediation than in the reference control.