Characterization of the bacterial archaeal diversity in hydrocarbon-contaminated soil

Stoichiometric analysis and control strategy of partial nitrification for treating dewatering liquid from food-waste methane fermentation

Methane fermentation is critical for food-waste management; however, effective treatment of its high-ammonium dewatering liquid remains a major challenge. Anammox, a promising candidate for liquid treatment, requires effective pretreatment, such as partial nitrification (PN), to reduce ammonium and generate sufficient nitrite to optimize efficiency. In this study, an airlift reactor was employed to process the dewatering liquid from food-waste methane fermentation. Stable operation for over 360 days demonstrated its feasibility under high-load conditions. By implementing precise aeration control strategy to stabilize the ammonium removal efficiency (ARE = 50.2-57.1 %), a detailed summary of the optimal operational parameter ranges (consumed inorganic carbon [ΔIC] 1000-1160 mg C/L, effluent [Eff.] IC 282-378 mg C/L, pH 8.05-8.17, Eff. Alkalinity 1000-1350 mg CaCO3/L, free ammonia 61.9-82.5 mg/L, and free nitrous acid 47.6-71.1 μg/L) were provided under the ideal NO2⁻/NH4⁺ ratio of 1.1-1.3. Additionally, variations in ammonium oxidizing bacteria activity with temperature and pH were analyzed by the Arrhenius, cardinal temperature model with inflection, and Haldane models, with R2 values of 0.998, 0.975, and 0.999, respectively. Results suggest that the optimal conditions for partial nitrification were identified as a temperature range of 20-40 °C and a pH range of 7.5-8.5. Microbial sequencing reveals Nitrosomonas markedly enriched during operation, with its abundance rising from 3.67 % to 9.76 % as the NLR increased. Notably, NOB was nearly undetectable throughout the entire process. Additionally, an advanced aeration-based control mechanism with a positive feedback loop were proposed, which allows the airlift PN reactor to effectively treat high-ammonia dewatering liquid, thereby providing a suitable influent for subsequent anammox and offering crucial theoretical insights for future controlling pilot-scale system operation.

Biodegradation characterization and mechanism of low-density polyethylene by the enriched mixed-culture from plastic-contaminated soil

Plastic pollution poses significant ecological and health risks. In this study, we enriched microbial consortia from plastic-contaminated soil capable of degrading low-density polyethylene (LDPE) film over a 28-day incubation period. Using two kinds of enriched cultures, the mean film weight loss rate (WLR) of 0.27 ± 0.04 % (p < 0.01) was 9 times higher than the control. Scanning electron microscopy (SEM) revealed a average hole occurrence area of 0.67 ± 0.11 μm2 in the topmost sample, while the control had no change. Fourier transform infrared (FTIR) revealed specific changes in hydrophilicity (increased by 5.70 ± 0.02 times) and crystallinity (decreased by 15.73 ± 3.26 %). Meanwhile, FTIR analyses including peak occurrence at 3741 cm-1, carbonyl index and Lambert-Beer law calculations revealed moisture infiltration and predominant aldehyde carbonyl formation (88.69 % in total carbonyl). The results of high-throughput sequencing indicated Brevibacillus, Bacillus and Sporosarcina were dominate genera in the mixed-cultures, and PICRUSt2 implied they could use LDPE as the sole carbon source. Our study aims to provided theoretical basis driving plastic degradation and to mitigate plastic pollution based on microbial resource development.

Depletion of hydrocarbons and concomitant shift in bacterial community structure of a diesel-spiked tropical agricultural soil

Bacterial community of a diesel-spiked agricultural soil was monitored over a 42-day period using the metagenomic approach in order to gain insight into key phylotypes impacted by diesel contamination and be able to predict end point of bioattenuation. Soil physico-chemical parameters showed significant differences (P < 0.05) between the Polluted Soil (PS) and the Unpolluted control (US)across time points. After 21 days, the diesel content decreased by 27.39%, and at the end of 42 days, by 57.11%. Aromatics such as benzene, anthanthrene, propylbenzene, phenanthrenequinone, anthraquinone, and phenanthridine were degraded to non-detected levels within 42 days, while some medium range alkanes and polyaromatics such as acenaphthylene, naphthalene, and anthracene showed significant levels of degradation. After 21 days (LASTD21), there was a massive enrichment of the phylum Proteobacteria (72.94%), a slight decrease in the abundance of phylum Actinobacteriota (12.74%), and > 500% decrease in the abundance of the phylum Acidobacteriodota (5.26%). Day 42 (LASTD42) saw establishment of the dominance of the Proteobacteria (34.95%), Actinobacteriota, (21.71%), and Firmicutes (32.14%), and decimation of phyla such as Gemmatimonadota, Planctomycetota, and Verrucromicrobiota which play important roles in the cycling of elements and soil health. Principal component analysis showed that in PS moisture contents, phosphorus, nitrogen, organic carbon, had greater impacts on the community structure in LASTD21, while acidity, potassium, sodium, calcium and magnesium impacted the control sample. Recovery time of the soil based on the residual hydrocarbons at Day 42 was estimated to be 229.112 d. Thus, additional biostimulation may be required to achieve cleanup within one growing season.

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

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

Microbial functional heterogeneity induced in a petroleum-polluted soil profile

Microbial taxonomic diversity declines with increasing stress caused by petroleum pollution. However, few studies have tested whether functional diversities vary similarly to taxonomic diversity along the stress gradient. Here, we investigated soil microbial communities in a petrochemically polluted site in China. Total petroleum hydrocarbon (TPH) concentrations were higher in the middle (2-3 m) and deep soil layer (3-5 m) than in the surface soil layer (0-2 m). Accordingly, microbial taxonomic α-diversity was decreased by 44% (p < 0.001) in the middle and deep soil layers, compared to the surface soil layer. In contrast, functional α-diversity decreased by 3% (p < 0.001), showing a much better buffering capacity to environmental stress. Differences in microbial taxonomic and functional β-diversities were enlarged in the middle and deep soil layers, extending the Anna Karenina Principle (AKP) that a community adapts to stressful environments in its own way. Consistent with the stress gradient hypothesis, we revealed a higher degree of network connectivity among microbial species and genes in the middle and deep soil layers compared to the surface soil layer. Together, we demonstrate that microbial functionality is more tolerant to stress than taxonomy, both of which were amenable to AKP and the stress gradient hypothesis.

Diverse hydrocarbon degradation genes, heavy metal resistome, and microbiome of a fluorene-enriched animal-charcoal polluted soil

Environmental compartments polluted with animal charcoal from the skin and hide cottage industries are rich in toxic heavy metals and diverse hydrocarbon classes, some of which are carcinogenic, mutagenic, and genotoxic, and thus require a bio-based eco-benign decommission strategies. A shotgun metagenomic approach was used to decipher the microbiome, hydrocarbon degradation genes, and heavy metal resistome of a microbial consortium (FN8) from an animal-charcoal polluted site enriched with fluorene. Structurally, the FN8 microbial consortium consists of 26 phyla, 53 classes, 119 orders, 245 families, 620 genera, and 1021 species. The dominant phylum, class, order, family, genus, and species in the consortium are Proteobacteria (51.37%), Gammaproteobacteria (39.01%), Bacillales (18.09%), Microbulbiferaceae (11.65%), Microbulbifer (12.21%), and Microbulbifer sp. A4B17 (19.65%), respectively. The microbial consortium degraded 57.56% (28.78 mg/L) and 87.14% (43.57 mg/L) of the initial fluorene concentration in 14 and 21 days. Functional annotation of the protein sequences (ORFs) of the FN8 metagenome using the KEGG GhostKOALA, KofamKOALA, NCBI's conserved domain database, and BacMet revealed the detection of hydrocarbon degradation genes for benzoate, aminobenzoate, polycyclic aromatic hydrocarbons (PAHs), chlorocyclohexane/chlorobenzene, chloroalkane/chloroalkene, toluene, xylene, styrene, naphthalene, nitrotoluene, and several others. The annotation also revealed putative genes for the transport, uptake, efflux, and regulation of heavy metals such as arsenic, cadmium, chromium, mercury, nickel, copper, zinc, and several others. Findings from this study have established that members of the FN8 consortium are well-adapted and imbued with requisite gene sets and could be a potential bioresource for on-site depuration of animal charcoal polluted sites.

Insight into the evolution of microbial communities and resistance genes induced by sucralose in partial nitrification system with triclosan pre-exposure

Sucralose (SUC), an artificial sweetener widely used in food, beverages and pharmaceuticals, is frequently detected in various environmental matrices. Triclosan (TCS) is commonly used as a disinfectant and often co-exists with SUC in sewage environments. This study investigated the effects of SUC (0.1-10 mg/L) on the transmission of intracellular and extracellular antibiotic resistance genes (ARGs) in the partial nitrification systems with and without TCS pre-exposure. The reactors operated for 150 days, and SUC did not affect ammonia oxidation performance, while TCS led to the maintenance of partial nitrification. The types and abundances of extracellular ARGs in sludge and free ARGs in water increased significantly after TCS pre-exposure when faced SUC stress, which might be caused by a decrease in α-Helix/(β-Sheet + Random coil). SUC was more easily to enrich ARGs in partial nitrification systems with TCS pre-exposure, exacerbating the risk of ARGs transmission. The microbial community showed stronger relationships to cope with the direct stress of SUC, and the functional bacteria (Thauera and Nitrosomonas) in TCS pre-exposure system might be potential hosts of ARGs. This study might provide insights for better understanding the fates of SUC in partial nitrification systems and the ecological risks in wastewater containing TCS and SUC. ENVIRONMENTAL IMPLICATION: Sucralose (SUC) is often detected in the environment and considered as an emerging contaminant due to its soaring consumption and environmental persistence. Triclosan (TCS) is an antibacterial agent that often co-exists with SUC in personal care products and sewage environments. During 150 d, two partial nitrification reactors with and without TCS pre-exposure were established to study the effects of SUC on nitrification performance, antibiotic resistance genes (ARGs) and microbial communities. This study showed the refractory nature of SUC, and SUC led to the transmission of extracellular ARGs in partial nitrification system with TCS pre-exposure, exacerbating the risk of ARGs dissemination.

The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean

To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 5 to 200 m at 22 stations in the photic zone of the Western North Pacific Ocean. Total 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods, and 295 of them were positive for nitrate reduction. These nitrate-reducing bacteria belonged to 19 genera and 29 species and among them, Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. Twenty-nine nitrate-reducing strains representing different species were selected for further the study of nitrogen, sulfur, and carbon metabolism. All 29 nitrate-reducing isolates contained genes encoding dissimilatory nitrate reduction or assimilatory nitrate reduction. Six nitrate-reducing isolates can oxidize thiosulfate based on genomic analysis and activity testing, indicating that nitrate-reducing thiosulfate-oxidizing bacteria exist in the photic zone. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Collectively, these results reveal culturable nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, sulfur, and carbon in the oligotrophic marine photic zone.

An overview of bioelectrokinetic and bioelectrochemical remediation of petroleum-contaminated soils

The global problem of petroleum contamination in soils seriously threatens environmental safety and human health. Current studies have successfully demonstrated the feasibility of bioelectrokinetic and bioelectrochemical remediation of petroleum-contaminated soils due to their easy implementation, environmental benignity, and enhanced removal efficiency compared to bioremediation. This paper reviewed recent progress and development associated with bioelectrokinetic and bioelectrochemical remediation of petroleum-contaminated soils. The working principles, removal efficiencies, affecting factors, and constraints of the two technologies were thoroughly summarized and discussed. The potentials, challenges, and future perspectives were also deliberated to shed light on how to overcome the barriers and realize widespread implementation on large scales of these two technologies.

Impacts of Arctic diesel contamination on microbial community composition and degradative gene abundance during hydrocarbon biodegradation with and without nutrients: A case study of seven sub-Arctic soils

Although a number of studies have assessed hydrocarbon degradation or microbial responses in petroleum contaminated soils, few have examined both and/or assessed impacts in multiple soils simultaneously. In this study petroleum hydrocarbon biodegradation and microbial activity was monitored in seven sub-Arctic soils at similar levels (∼3500-4000 mg/kg) of Arctic diesel (DSL), amended with moisture and nutrients (70 mg-N/kg, 78 mg-P/kg), and incubated at site-representative summer temperatures (∼7 °C) under water unsaturated conditions. Total petroleum hydrocarbon (TPH) biodegradation extents (42.7-85.4 %) at 50 days were slightly higher in nutrient amended (DSL + N,P) than unamended (DSL) systems in all but one soil. Semi-volatile (C₁₀-C₁₆) hydrocarbons were degraded to a greater extent (40-80 %) than non-volatile (C₁₆-C₂₄) hydrocarbons (20-40 %). However, more significant shifts in microbial diversity and relative abundance of genera belonging to Actinobacteria and Proteobacteria phyla were observed in DSL + N,P than in DSL systems in all soils. Moreover, higher abundance of the alkane degrading gene alkB were observed in DSL + N,P systems than in DSL systems for all soils. The more significant microbial community response in the DSL + N,P systems indicate that addition of nutrients may have influenced the microbial community involved in degradation of carbon sources other than the diesel compounds, such as the soil organic matter or degradation intermediates of diesel compounds. Nocardioides, Arthrobacter, Marmoricola, Pseudomonas, Polaromonas, and Massilia genera were present in high relative abundance in the DSL systems suggesting those genera contained hydrocarbon degraders. Overall, the results suggest that the extents of microbial community shifts or alkB copy number increases may not be closely correlated to the increase in hydrocarbon biodegradation and thus bioremediation performance between various treatments or across different soils.

Draft genome sequences of hydrocarbon degrading Haloferax sp. AB510, Haladaptatus sp. AB618 and Haladaptatus sp. AB643 isolated from the estuarine sediments of Sundarban mangrove forests, India

The present study reports the draft genomes of three hydrocarbon-degrading haloarchaeal strains Haloferax sp. AB510, Haladaptatus sp. AB618 and Haladaptatus sp. AB643 that were isolated from the estuarine sediments of Sundarban mangrove forests, India. All three genomes had a high GC content of around 60%, characteristic of the haloarchaea. The Haloferax sp. AB510 genome was around 3.9 Mb in size and consisted of 4567 coding sequences and 54 RNAs. The Haladaptatus sp. AB618 and Haladaptatus sp. AB643 genomes were comparatively larger and around 4.8 Mb each. The AB618 and AB643 genomes comprised 5279 and 5304 coding sequences and 60 and 59 RNAs, respectively. All three of the genomes encoded several genes that attributed to their survival in the presence of hydrocarbons in their native habitats. Functional annotation and curation of the sequenced genomes suggested that the Haloferax sp. AB510 strain utilized the gentisate pathway of aromatic compound degradation. While the Haladaptatus sp. AB618 and Haladaptatus sp. AB643 strains possessed the freedom of utilizing both the gentisate and the catechol pathways for degrading aromatic hydrocarbons.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03273-5.

Bacterial communities in peat swamps reflect changes associated with catchment urbanisation

Like many peat wetlands around the world, Temperate Highland Peat Swamps on Sandstone (THPSS), located in the Sydney Basin, Australia, have been impacted by urban development. In this paper, we used Illumina 16S rRNA DNA amplicon sequencing to characterise and compare the bacterial communities of surface (top 0–2 cm) and deep (50 cm) sediments in peat swamps that occur in both urbanised and non-urbanised catchments. Proteobacteria (32.2% of reads), Acidobacteria (23.6%) and Chloroflexi (10.7%) were the most common phyla of the dataset. There were significant differences in the bacterial community structure between catchment types and depths apparent at the phyla level. Proteobacteria, Bacteroidetes, Actinobacteria and Verrucomicrobia made up a greater proportion of the reads in the surface sediments than the deeper sediments, while Chloroflexi and Nitrospirae were relatively more common in the deeper than the surface sediment. By catchment type, Acidobacteria were more common in swamps occurring in non-urbanised catchments, while Nitrospirae, Bacteroidetes and Actinobacteria were more common in those in urbanised catchments. Microbial community structure was significantly correlated with sediment pH, as was the relative abundance of several phyla, including Acidobacteria (negative correlation) and Bacteroidetes (positive correlation). As an indicator of trophic shift from oligotrophic to copiotrophic conditions associated with urbanised catchment, we found significant differences ratios of β-Proteobacteria to Acidobacteria and Bacteriodetes to Acidobacteria between the catchment types. Based on SIMPER results we suggest the relative abundance of Nitrosomonadaceae family as a potential indicator of urban degradation. As the first study to analyse the bacterial community structure of THPSS using sequencing of 16S rDNA, we reveal the utility of such analyses and show that urbanisation in the Blue Mountains is impacting the microbial ecology of these important peatland ecosystems.

Metagenomic analysis for taxonomic and functional potential of Polyaromatic hydrocarbons (PAHs) and Polychlorinated biphenyl (PCB) degrading bacterial communities in steel industrial soil

Iron and steel industries are the major contributors to persistent organic pollutants (POPs). The microbial community present at such sites has the potential to remediate these contaminants. The present study highlights the metabolic potential of the resident bacterial community of PAHs and PCB contaminated soil nearby Bhilai steel plant, Chhattisgarh (India). The GC-MS/MS analysis of soil samples MGB-2 (sludge) and MGB-3 (dry soil) resulted in identification of different classes of POPs including PAHs {benzo[a]anthracene (nd; 17.69%), fluorene (15.89%, nd), pyrene (nd; 18.7%), benzo(b)fluoranthene (3.03%, nd), benzo(k)fluoranthene (11.29%; nd), perylene (5.23%; nd)} and PCBs (PCB-15, PCB-95, and PCB-136). Whole-genome metagenomic analysis by Oxford Nanopore GridION Technology revealed predominance of domain bacteria (97.4%; 97.5%) followed by eukaryote (1.4%; 1.5%), archaea (1.2%; 0.9%) and virus (0.02%; 0.04%) in MGB-2 and MGB-3 respectively. Proteobacteria (44.3%; 50.0%) to be the prominent phylum followed by Actinobacteria (22.1%; 19.5%) in MBG-2 and MBG-3, respectively. However, Eukaryota microbial communities showed a predominance of phylum Ascomycota (20.5%; 23.6%), Streptophyta (18.5%, 17.0%) and unclassified (derived from Eukaryota) (12.1%; 12.2%) in MGB-2 and MGB-3. The sample MGB-3 was richer in macronutrients (C, N, P), supporting high microbial diversity than MGB-2. The presence of reads for biphenyl degradation, dioxin degradation, PAH degradation pathways can be further correlated with the presence of PCB and PAH as detected in the MGB-2 and MGB-3 samples. Further, taxonomic vis-à-vis functional analysis identified Burkholderia, Bradyrhizobium, Mycobacterium, and Rhodopseudomonas as the keystone degrader of PAH and PCB. Overall, our results revealed the importance of metagenomic and physicochemical analysis of the contaminated site, which improves the understanding of metabolic potential and adaptation of bacteria growing under POP contaminated environments.

Isotope fractionation (δ13C, δ15N) and microbial community response in degradation of petroleum hydrocarbons by biostimulation in contaminated soil

This study investigated the isotope effects of δ¹³C and δ¹⁵N and microbial response during biodegradation of hydrocarbons by biostimulation with nitrate or compost in the petroleum-contaminated soil. Compost and KNO₃ amendments promoted the total petroleum hydrocarbon (TPH) removal accompanied by a significant increase of Actinobacteria and Firmicutes phyla. Soil alpha diversity decreased after 90 days of biostimulation. An inverse significant carbon isotope effect (ε_c = 16.6 ± 0.8‰) and strong significant nitrogen isotope effect (ε_N = -24.20 ± 9.54‰) were shown by the KNO₃ supplementation. For compost amendment, significant carbon and nitrogen isotope effect were ε_c = 38.8 ± 1.1‰ and ε_N = -79.49 ± 16.41‰, respectively. A clear difference of the carbon and nitrogen stable isotope fractionation was evident by KNO₃ or compost amendment, which indicated that the mechanisms of petroleum degradation by adding compost or KNO₃ may be different.

Salicylate or Phthalate: The Main Intermediates in the Bacterial Degradation of Naphthalene

Polycyclic aromatic hydrocarbons (PAHs) are widely presented in the environment and pose a serious environmental threat due to their toxicity. Among PAHs, naphthalene is the simplest compound. Nevertheless, due to its high toxicity and presence in the waste of chemical and oil processing industries, naphthalene is one of the most critical pollutants. Similar to other PAHs, naphthalene is released into the environment via the incomplete combustion of organic compounds, pyrolysis, oil spills, oil processing, household waste disposal, and use of fumigants and deodorants. One of the main ways to detoxify such compounds in the natural environment is through their microbial degradation. For the first time, the pathway of naphthalene degradation was investigated in pseudomonades. The salicylate was found to be a key intermediate. For some time, this pathway was considered the main, if not the only one, in the bacterial destruction of naphthalene. However, later, data emerged which indicated that gram-positive bacteria in the overwhelming majority of cases are not capable of the formation/destruction of salicylate. The obtained data made it possible to reveal that protocatechoate, phthalate, and cinnamic acids are predominant intermediates in the destruction of naphthalene by rhodococci. Pathways of naphthalene degradation, the key enzymes, and genetic regulation are the main subjects of the present review, representing an attempt to summarize the current knowledge about the mechanism of the microbial degradation of PAHs. Modern molecular methods are also discussed in the context of the development of “omics” approaches, namely genomic, metabolomic, and proteomic, used as tools for studying the mechanisms of microbial biodegradation. Lastly, a comprehensive understanding of the mechanisms of the formation of specific ecosystems is also provided.

Hydrocarbon transformation pathways and soil organic carbon stability in the biostimulation of oil-contaminated soil: Implications of 13C natural abundance

Mineralization, assimilation, and humification are key processes to detoxify oil-contaminated soil by biostimulation remediation strategies, and these processes are affected by stimulants. In this study, we investigated the effects of either inorganic salts or organic stimulants (organic compost and sawdust) on hydrocarbon transformation. Total petroleum hydrocarbons (TPH) and hydrocarbon components were determined by gravimetry and gas chromatography, and the ¹³C of CO₂, microbial biomass carbon (MBC), and humus were measured by stable isotope mass spectrometry. The results showed that organic compost was the most beneficial for the dissipation of hydrocarbons. After 60 days of remediation, the removal rates of TPH, saturates, aromatics, C7-C30 n-alkanes, and 16 PAHs were 35.7%, 39.6%, 15.9%, 80.5%, and 8.8%, respectively. A total of 84.7%-88.5% of the removed hydrocarbons were mineralized in all the treatments. The hydrocarbon degradation pathway in the control soil (without stimulant addition) was "assimilation → humification → mineralization". The hydrocarbon transformation pathways in the biostimulation treatments were "assimilation → mineralization → humification". The soil organic carbon (SOC) stability decreased during remediation, which was attributed to the enhanced microbial activity and the removal of recalcitrant hydrocarbons.

Response of bacterial and fungal communities to high petroleum pollution in different soils

Petroleum pollution of soils is a major environmental problem. Soil microorganisms can decompose a significant fraction of petroleum hydrocarbons in soil at low concentrations (1-5%). This characteristic can be used for soil remediation after oil pollution. Microbial community dynamics and functions are well studied in cases of moderate petroleum pollution, while cases with heavy soil pollution have received much less attention. We studied bacterial and fungal successions in three different soils with high petroleum contents (6 and 25%) in a laboratory experiment. The proportion of aliphatic and aromatic compounds decreased by 4-7% in samples with 6% pollution after 120 days of incubation but remained unchanged in samples with 25% hydrocarbons. The composition of the microbial community changed significantly in all cases. Oil pollution led to an increase in the relative abundance of bacteria such as Actinobacteria and the candidate TM7 phylum (Saccaribacteria) and to a decrease in that of Bacteroidetes. The gene abundance (number of OTUs) of oil-degrading bacteria (Rhodococcus sp., candidate class TM7-3 representative) became dominant in all soil samples, irrespective of the petroleum pollution level and soil type. The fungal communities in unpolluted soil samples differed more significantly than the bacterial communities. Nonmetric multidimensional scaling revealed that in the polluted soil, successions of fungal communities differed between soils, in contrast to bacterial communities. However, these successions showed similar trends: fungi capable of lignin and cellulose decomposition, e.g., from the genera Fusarium and Mortierella, were dominant during the incubation period.

Microbial community responses to soil parameters and their effects on petroleum degradation during bio-electrokinetic remediation

This study evaluated the interactions among total petroleum hydrocarbons (TPH), soil parameters, and microbial communities during the bio-electrokinetic (BIO-EK) remediation process. The study was conducted on a petroleum-contaminated saline-alkali soil inoculated with petroleum-degrading bacteria with a high saline-alkali resistance. The results showed that the degradation of TPH was better explained by second-order kinetics, and the efficacy and sustainability of the BIO-EK were closely related to soil micro-environmental factors and microbial community structures. During a 98-d remediation process, the removal rate of TPH was highest in the first 35 d, and then decreased gradually in the later period, which was concurrent with changes in the soil physicochemical properties (conductivity, inorganic ions, pH, moisture, and temperature) and subsequent shifts in the microbial community structures. According to the redundancy analysis (RDA), TPH, soil temperature, and electric conductivity, as well as SO₄^2-, Cl^-, and K⁺ played a better role in explaining the changes in the microbial community at 0-21 d. However, pH and NO₃^- better explained the changes in the microbial community at 63-98 d. In particular, the dominant genera, Marinobacter and Bacillus, showed a positive correlation with TPH, conductivity, and SO₄^2-, Cl^-, and K⁺, but a negative relationship with pH and NO₃. Rhodococcus was positively correlated with soil temperature. The efficacy and sustainability of the BIO-EK remediation process is likely to be improved by controlling these properties.

Remarkable shift in structural and functional properties of an animal charcoal-polluted soil accentuated by inorganic nutrient amendment

Background

Soils polluted with animal charcoal from skin and hide cottage industries harbour extremely toxic and carcinogenic hydrocarbon pollutants and thus require a bio-based eco-friendly strategy for their depuration. The effects of carbon-free mineral medium (CFMM) amendment on hydrocarbon degradation and microbial community structure and function in an animal charcoal-polluted soil was monitored for 6 weeks in field moist microcosms consisting of CFMM-treated soil (FN4) and an untreated control (FN1). Hydrocarbon degradation was monitored using gas chromatography-flame ionization detector (GC-FID), and changes in microbial community structure were monitored using Kraken, while functional annotation of putative open reading frames (ORFs) was done using KEGG KofamKOALA and NCBI’s conserved domain database (CDD).

Results

Gas chromatographic analysis of hydrocarbon fractions revealed the removal of 84.02% and 82.38% aliphatic and 70.09% and 70.14% aromatic fractions in FN4 and FN1 microcosms in 42 days. Shotgun metagenomic analysis of the two metagenomes revealed a remarkable shift in the microbial community structure. In the FN4 metagenome, 92.97% of the population belong to the phylum Firmicutes and its dominant representative genera Anoxybacillus (64.58%), Bacillus (21.47%) and Solibacillus (2.39%). In untreated FN1 metagenome, the phyla Proteobacteria (56.12%), Actinobacteria (23.79%) and Firmicutes (11.20%), and the genera Xanthobacter (9.73%), Rhizobium (7.49%) and Corynebacterium (7.35%), were preponderant. Functional annotation of putative ORFs from the two metagenomes revealed the detection of degradation genes for aromatic hydrocarbons, benzoate, xylene, chlorocyclohexane/chlorobenzene, toluene and several others in FN1 metagenome. In the FN4 metagenome, only seven hydrocarbon degradation genes were detected.

Conclusion

This study revealed that though CFMM amendment slightly increases the rate of hydrocarbon degradation, it negatively impacts the structural and functional properties of the animal charcoal-polluted soil. It also revealed that intrinsic bioremediation of the polluted soil could be enhanced via addition of water and aeration.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-020-00089-9.

Design, Operation and Optimization of Constructed Wetland for Removal of Pollutant

Constructed wetlands (CWs) are affordable and reliable green technologies for the treatment of various types of wastewater. Compared to conventional treatment systems, CWs offer an environmentally friendly approach, are low cost, have fewer operational and maintenance requirements, and have a high potential for being applied in developing countries, particularly in small rural communities. However, the sustainable management and successful application of these systems remain a challenge. Therefore, after briefly providing basic information on wetlands and summarizing the classification and use of current CWs, this study aims to provide and inspire sustainable solutions for the performance and application of CWs by giving a comprehensive review of CWs' application and the recent development of their sustainable design, operation, and optimization for wastewater treatment. To accomplish this objective, thee design and management parameters of CWs, including macrophyte species, media types, water level, hydraulic retention time (HRT), and hydraulic loading rate (HLR), are discussed. Besides these, future research on improving the stability and sustainability of CWs are highlighted. This article provides a tool for researchers and decision-makers for using CWs to treat wastewater in a particular area. This paper presents an aid for informed analysis, decision-making, and communication. The review indicates that major advances in the design, operation, and optimization of CWs have greatly increased contaminant removal efficiencies, and the sustainable application of this treatment system has also been improved.

Supplementing resuscitation-promoting factor (Rpf) enhanced biodegradation of polychlorinated biphenyls (PCBs) by Rhodococcus biphenylivorans strain TG9T

The biodegradation of polychlorinated biphenyls (PCBs) occurs slowly when the degrading bacteria enter a low activity state, such as a viable but nonculturable (VBNC) state, under unfavorable environmental conditions. The introduction of resuscitation-promoting factor (Rpf) can re-activate VBNC bacteria. This study tested the feasibility of enhancing PCB biodegradation via supplementing Rpf in liquid culture and soil microcosms inoculated with Rhodococcus biphenylivorans strain TG9^T. Exogenous Rpf resuscitated TG9^T cells that had previously entered the VBNC state after 90 d of nutrient starvation, resulting in the significantly enhanced degradation of PCB by 24.3% over 60 h in liquid medium that originally contained 50 mg L^-1 Aroclor 1242. In soil microcosms containing 50 mg kg^-1 Aroclor 1242 and inoculated with VBNC TG9^T cells, after 49 d of supplementation with Rpf, degradation efficiency of PCB reached 34.2%, which was significantly higher than the control. Our results confirmed that exogenous Rpf resuscitated VBNC TG9^T cells by stimulating endogenous expression of rpf gene orthologs. The enhanced PCB-degrading capability was likely due to the increased cell numbers and the strong expression of PCB catabolic genes. This study demonstrated the role of Rpf in enhancing PCB degradation via resuscitating PCB-degrading bacteria, indicating a promising approach for the remediation of PCB contamination.

Perylene pigment wastewater treatment by fenton-enhanced biological process

Polycyclic aromatic hydrocarbons (PAHs) are regarded as priority pollutants owing to their toxic, mutagenic and carcinogenic characteristics. Perylene is a kind of 5-ring PAH with biological toxicity, and classified as a class III carcinogen by the World Health Organization (WHO). Nowadays, some of its derivatives are often used as industrial pigments. Hence, urgent attention is highly needed to develop new and improved techniques for PAHs and their derivatives removal from the environment. In this study, Fenton oxidation process was hybridized with the biological (anaerobic and aerobic) treatments for the removal of perylene pigment from wastewater. The experiments were carried out by setting Fenton treatment system before and between the biological treatments. The biological results showed that COD removal efficiency reached 60% during 24 h HRT with an effluent COD concentration of 1567.78 mg/L. After the HRT increased to 48 h, the COD removal efficiency was slightly increased (67.9%). However, after combining Fenton treatment with biological treatment (Anaerobic-Fenton-Aerobic), the results revealed over 85% COD removal efficiency and the effluent concentration less than 600 mg/L which was selected as the better treatment configuration for the biological and chemical combined system. The microbial community analysis of activated sludge was carried out with high-throughput Illumina sequencing platform and results showed that Pseudomonas, Citrobacter and Methylocapsa were found to be the dominant genera detected in aerobic and anaerobic reactors. These dominant bacteria depicted that the community composition of the reactors for treating perylene pigments wastewater were similar to that of the soil contaminated by PAHs and the activated sludge from treating PAHs wastewater. Economic analysis results revealed that the reagent cost was relatively cheap, amounting to 10.64 yuan per kilogram COD. This study vividly demonstrated that combining Fenton treatment with biological treatment was efficient and cost-effective.

Distribution Characteristics of Bacterial Communities and Hydrocarbon Degradation Dynamics During the Remediation of Petroleum-Contaminated Soil by Enhancing Moisture Content

Microorganisms are the driver of petroleum hydrocarbon degradation in soil micro-ecological systems. However, the distribution characteristics of microbial communities and hydrocarbon degradation dynamics during the remediation of petroleum-contaminated soil by enhancing moisture content are not clear. In this study, polymerase chain reaction and high-throughput sequencing of soil microbial DNA were applied to investigate the compositions of microorganisms and alpha diversity in the oil-polluted soil, and the hydrocarbon removal also being analyzed using ultrasonic extraction and gravimetric method in a laboratory simulated ex-situ experiment. Results showed the distribution of petroleum hydrocarbon degrading microorganisms in the petroleum-contaminated loessal soil mainly was Proteobacteria phylum (96.26%)-Gamma-proteobacteria class (90.03%)-Pseudomonadales order (89.98%)-Pseudomonadaceae family (89.96%)-Pseudomonas sp. (87.22%). After 15% moisture content treatment, Actinobacteria, Proteobacteria, and Firmicutes still were the predominant phyla, but their relative abundances changed greatly. Also Bacillus sp. and Promicromonospora sp. became the predominant genera. Maintaining 15% moisture content increased the relative abundance of Firmicutes phylum and Bacillus sp. As the moisture-treated time increases, the uniformity and the richness of the soil bacterial community were decreased and increased respectively; the relative abundance of Pseudomonas sp. increased. Petroleum hydrocarbon degradation by enhancing soil moisture accorded with the pseudo-first-order reaction kinetic model (correlation coefficient of 0.81; half-life of 56 weeks). The richness of Firmicutes phylum and Bacillus sp. may be a main reason for promoting the removal of 18% petroleum hydrocarbons responded to 15% moisture treatment. Our results provided some beneficial microbiological information of oil-contaminated soil and will promote the exploration of remediation by changing soil moisture content for increasing petroleum hydrocarbon degradation efficiency.

Microbial communities from subglacial water of naled ice bodies in the forefield of Werenskioldbreen, Svalbard

We assessed the structure of microbial communities in the subglacial drainage system of the Werenskioldbreen glacier, Svalbard, which consists of three independent channels. Dome-shaped naled ice bodies that had been forming and releasing subglacial water in the glacial forefield during accumulations season were used to study glacial microbiome. We tested the hypothesis that the properties of the water transported by these channels are site-dependent and influence bacterial diversity. We therefore established the phylogenetic structure of the subglacial microbial communities using next generation sequencing (NGS) of the 16S rRNA gene and performed bioinformatics analyses. A total of 1409 OTUs (operational taxonomic units) belonged to 40 phyla; mostly Proteobacteria, Gracilibacteria, Bacteroidetes, Actinobacteria and Parcubacteria were identified. Sites located on the edge of Werenskioldbreen forefield (Angell, Kvisla) were mainly dominated by Betaproteobacteria. In the central site (Dusan) domination of Epsilonproteobacteria class was observed. Gracilibacteria (GN02) and Gammaproteobacteria represented the dominant taxa only in the sample Kvisla 2. Principal Coordinate Analysis (PCoA) of beta diversity revealed that phylogenetic profiles grouped in three different clusters according to the sampling site. Moreover, higher similarity of bacterial communities from Angell and Kvisla compared to Dusan was confirmed by cluster analysis and Venn diagrams. The highest alpha index values was measured in Dusan. Richness and phylogenetic diversity indices were significantly (p < .05) and positively correlated with pH values of subglacial water and negatively with concentration of Cl^-, Br^-, and NO₃^- anions. These anions negatively impacted the values of richness indices but positively correlated with abundance of some microbial phyla. Our results indicated that subglacial water from naled ice bodies offer the possibility to study the glacial microbiome. In the studied subglacial water, the microbial community structure was sampling site specific and dependent on the water properties, which in turn were probably influenced by the local bedrock composition.

Molecular and culture-based surveys of metabolically active hydrocarbon-degrading archaeal communities in Sundarban mangrove sediments

Archaea remain important players in global biogeochemical cycles worldwide, including in the highly productive mangrove estuarine ecosystems. In the present study, we have explored the diversity, distribution, and function of the metabolically active fraction of the resident archaeal community of the Sundarban mangrove ecosystem, using both culture-independent and culture-dependent approaches. To evaluate the diversity and distribution pattern of the active archaeal communities, RNA based analysis of the 16S rRNA gene was performed on an Illumina platform. The active Crenarchaeal community was observed to remain constant while active Euryarchaeal community underwent considerable change across the sampling sites depending on varying anthropogenic factors. Haloarchaea were the predominant group in hydrocarbon polluted sediments, leading us to successfully isolate eleven p-hydroxybenzoic acid degrading haloarchaeal species. The isolates could also survive in benzoic acid, naphthalene, and o-phthalate. Quantitative estimation of p-hydroxybenzoic acid degradation was studied on select isolates, and their ability to reduce COD of polluted saline waters of Sundarban was also evaluated. To our knowledge, this is the first ever study combining culture-independent (Next Generation sequencing and metatranscriptome) and culture-dependent analyses for an assessment of archaeal function in the sediment of Sundarban.

Kinetic modelling of total petroleum hydrocarbon in spent lubricating petroleum oil impacted soil under different treatments

The integration of first and second order kinetic model in parameter estimation for the degradation pattern of total petroleum hydrocarbon (TPH) in spent lubricating petroleum oil (SLPO) over a four-month period was the subject of the present investigation. Study design considered four treatment microcosms notably; sewage sludge (SB), monitored natural recovery (MNR), surfactant (SA) and control (SO). The rate of TPH degradation using sewage sludge as amendment material depicted effective TPH removal within ten weeks. A maximum allowable concentration of residual TPH (4300 mg kg^-1) was obtained through an amendment with sewage sludge. Degradation constant (k) produced by both first and second order rates significantly demonstrated the performance of sewage sludge biomass over the other three treatments applied, however, experimental data adequately fitted into the first order kinetics (k = 0.27 d^-1, t½ = 3.0 d). TPH removal efficiency of sewage sludge and detergent were 96.0% and 81.0% respectively. The use of sewage sludge biomass significantly (p < .05) improved soil biological characteristics and produced optimum dehydrogenase activity (DHA ≥ 8.8 TPFg^-1 d), germination index (%IG ≥ 88%), and chlorophyll content (chl ≥ 100 µg cm^-2), thus, recommended for field scale application in soil hydrocarbon pollution remediation.

Characterizations of microbial diversity and machine oil degrading microbes in machine oil contaminated soil

Microbial diversity in machine oil contaminated soil was determined by high-throughput amplicon sequencing technology. The diversity of culturable microbes in the contaminated soil was further characterized using polymerase chain reaction method. Proteobacteria and Bacteroidetes were the most dominant phyla and occupied 52.73 and 16.77%, respectively, while the most abundant genera were Methylotenera (21.62%) and Flavobacterium (3.06%) in the soil. In the culturable microbes, the major phyla were Firmicutes (46.15%) and Proteobacteria (37.36%) and the most abundant genera were Bacillus (42.86%) and Aeromonas (34.07%). Four isolated microbes with high machine oil degradation efficiency were selected to evaluate their characteristics on the oil degradation. All of them reached their highest oil degradation rate after 7 days of incubation. Most of them significantly increased their oil degradation rate by additional carbon or organic nitrogen source in the incubation medium. The oil degradation rate by combination of the four microbes at the same inoculation level was also higher than the rate from each individual microbe. The protocol and findings of this study are very useful for developing micro-bioremediation method to eliminate machine oil contaminants from soil.

Oil degradation potential of microbial communities in water and sediment of Baltic Sea coastal area

Two long-term potentially oil exposed Baltic Sea coastal sites near old oil refineries and harbours were compared to nearby less exposed sites in terms of bacterial, archaeal and fungal microbiomes and oil degradation potential. The bacterial, archaeal and fungal diversities were similar in oil exposed and less exposed sampling sites based on bacterial and archaeal 16S rRNA gene and fungal 5.8S rRNA gene amplicon sequencing from both DNA and RNA fractions. The number of genes participating in alkane degradation (alkB) or PAH-ring hydroxylation (PAH–RHDα) were detected by qPCR in all water and sediment samples. These numbers correlated with the number of bacterial 16S rRNA gene copies in sediment samples but not with the concentration of petroleum hydrocarbons or PAHs. This indicates that both the clean and the more polluted sites at the Baltic Sea coastal areas have a potential for petroleum hydrocarbon degradation. The active community (based on RNA) of the coastal Baltic Sea water differed largely from the total community (based on DNA). The most noticeable difference was seen in the bacterial community in the water samples were the active community was dominated by Cyanobacteria and Proteobacteria whereas in total bacterial community Actinobacteria was the most abundant phylum. The abundance, richness and diversity of Fungi present in water and sediment samples was in general lower than that of Bacteria and Archaea. Furthermore, the sampling location influenced the fungal community composition, whereas the bacterial and archaeal communities were not influenced. This may indicate that the fungal species that are adapted to the Baltic Sea environments are few and that Fungi are potentially more vulnerable to or affected by the Baltic Sea conditions than Bacteria and Archaea.

Comparative assessment of autochthonous bacterial and fungal communities and microbial biomarkers of polluted agricultural soils of the Terra dei Fuochi

Organic and inorganic xenobiotic compounds can affect the potential ecological function of the soil, altering its biodiversity. Therefore, the response of microbial communities to environmental pollution is a critical issue in soil ecology. Here, a high-throughput sequencing approach was used to investigate the indigenous bacterial and fungal community structure as well as the impact of pollutants on their diversity and richness in contaminated and noncontaminated soils of a National Interest Priority Site of Campania Region (Italy) called "Terra dei Fuochi". The microbial populations shifted in the polluted soils via their mechanism of adaptation to contamination, establishing a new balance among prokaryotic and eukaryotic populations. Statistical analyses showed that the indigenous microbial communities were most strongly affected by contamination rather than by site of origin. Overabundant taxa and Actinobacteria were identified as sensitive biomarkers for assessing soil pollution and could provide general information on the health of the environment. This study has important implications for microbial ecology in contaminated environments, increasing our knowledge of the capacity of natural ecosystems to develop microbiota adapted to polluted soil in sites with high agricultural potential and providing a possible approach for modeling pollution indicators for bioremediation purposes.

Bioavailability of weathered hydrocarbons in engine oil-contaminated soil: Impact of bioaugmentation mediated by Pseudomonas spp. on bioremediation

Heavier fraction hydrocarbons (C₁₅-C₃₆) formed in soil after biotic and abiotic weatherings of engine oil are the continuing constraints in the bioremediation strategy, and their bioavailability remains a poorly quantified regulatory factor. In a microcosm study, we used two strains of Pseudomonas, P. putida TPHK-1 and P. aeruginosa TPHK-4, in strategies of bioremediation, viz., natural attenuation, biostimulation and bioaugmentation, for removal of weathered total petroleum hydrocarbons (TPHs) in soil contaminated long-term with high concentrations of engine oil (39,000-41,000 mg TPHs kg^-1 soil). Both the bacterial strains exhibited a great potential in remediating weathered hydrocarbons of engine oil. Addition of inorganic fertilizers (NPK), at recommended levels for bioremediation, resulted in significant inhibition in biostimulation/enhanced natural attenuation as well as bioaugmentation. The data on dehydrogenase activity clearly confirmed those of bioremediation strategies used, indicating that this enzyme assay could serve as an indicator of bioremediation potential of oil-contaminated soil. Extraction of TPHs from engine oil-contaminated soil with hydroxypropyl-β-cyclodextrin (HPCD), but not 1-butanol, was found reliable in predicting the bioavailability of weathered hydrocarbons. Also, 454 pyrosequencing data were in accordance with those of bioremediation strategies used in the present microcosm study, suggesting the possible use of pyrosequencing in designing approaches for bioremediation.

Diversity and Niche of Archaea in Bioremediation

Bioremediation is the use of microorganisms for the degradation or removal of contaminants. Most bioremediation research has focused on processes performed by the domain Bacteria; however, Archaea are known to play important roles in many situations. In extreme conditions, such as halophilic or acidophilic environments, Archaea are well suited for bioremediation. In other conditions, Archaea collaboratively work alongside Bacteria during biodegradation. In this review, the various roles that Archaea have in bioremediation is covered, including halophilic hydrocarbon degradation, acidophilic hydrocarbon degradation, hydrocarbon degradation in nonextreme environments such as soils and oceans, metal remediation, acid mine drainage, and dehalogenation. Research needs are addressed in these areas. Beyond bioremediation, these processes are important for wastewater treatment (particularly industrial wastewater treatment) and help in the understanding of the natural microbial ecology of several Archaea genera.

Characterization of bacterial community structure in a hydrocarbon-contaminated tropical African soil

The bacterial community structure in a hydrocarbon-contaminated Mechanical Engineering Workshop (MWO) soil was deciphered using 16S rRNA gene clone library analysis. Four hundred and thirty-seven clones cutting across 13 bacterial phyla were recovered from the soil. The representative bacterial phyla identified from MWO soil are Proteobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, Firmicutes, Actinobacteria, Verrucomicrobia, Planctomycetes, Ignavibacteriae, Spirochaetes, Chlamydiae, Candidatus Saccharibacteria and Parcubacteria. Proteobacteria is preponderant in the contaminated soil (51.2%) with all classes except Epsilonproteobacteria duly represented. Rarefaction analysis indicates 42%, 52% and 77% of the clone library is covered at the species, genus and family/class delineations with Shannon diversity (H') and Chao1 richness indices of 5.59 and 1126, respectively. A sizeable number of bacterial phylotypes in the clone library shared high similarities with strains previously described to be involved in hydrocarbon biodegradation. Novel uncultured genera were identified that have not been previously reported from tropical African soil to be associated with natural attenuation of hydrocarbon pollutants. This study establishes the involvement of a wide array of physiologically diverse bacterial groups in natural attenuation of hydrocarbon pollutants in soil.

Removal of artificial sweeteners and their effects on microbial communities in sequencing batch reactors

Concern is growing over contamination of the environment with artificial sweeteners (ASWs) because of their widespread existence in wastewater treatment plants (WWTPs). To evaluate ASWs removal and the effect on activated sludge, acesulfame (ACE), sucralose (SUC), cyclamate (CYC) and saccharin (SAC) were introduced individually or in mixture to sequencing batch reactors (SBRs) in environmentally relevant concentrations (100 ppb) for 100 days. Comparisons between ACE removal in a full-scale WWTP and in lab-scale SBRs were conducted. Results showed that CYC and SAC were completely removed, whereas SUC was persistent. However, ACE removal in lab-scale SBRs was significantly greater than in the full-scale WWTP. In SBRs, chemical oxygen demand (COD), ammonia nitrogen (NH₄⁺-N) and total nitrogen (TN) removal appeared unchanged after adding ASWs (p > 0.05). Adenosine triphosphate (ATP) concentrations and triphenyl tetrazolium chloride-dehydrogenase activity (TTC-DHA) declined significantly (p < 0.05). The mixed ASWs had more evident effects than the individual ASWs. Microbial community analyses revealed that Proteobacteria decreased obviously, while Bacteroidetes, Chloroflexi and Actinobacteria were enriched with the addition of ASWs. Redundancy Analysis (RDA) indicated ACE had a greater impact on activated sludge than the other ASWs.

Anaerobic degradation of 1-methylnaphthalene by a member of the Thermoanaerobacteraceae contained in an iron-reducing enrichment culture

An anaerobic culture (1MN) was enriched with 1-methylnaphthalene as sole source of carbon and electrons and Fe(OH)₃ as electron acceptor. 1-Naphthoic acid was produced as a metabolite during growth with 1-methylnaphthalene while 2-naphthoic acid was detected with naphthalene and 2-methylnaphthalene. This indicates that the degradation pathway of 1-methylnaphthalene might differ from naphthalene and 2-methylnaphthalene degradation in sulfate reducers. Terminal restriction fragment length polymorphism and pyrosequencing revealed that the culture is mainly composed of two bacteria related to uncultured Gram-positive Thermoanaerobacteraceae and uncultured gram-negative Desulfobulbaceae. Stable isotope probing showed that a ¹³C-carbon label from ¹³C₁₀-naphthalene as growth substrate was mostly incorporated by the Thermoanaerobacteraceae. The presence of putative genes involved in naphthalene degradation in the genome of this organism was confirmed via assembly-based metagenomics and supports that it is the naphthalene-degrading bacterium in the culture. Thermoanaerobacteraceae have previously been detected in oil sludge under thermophilic conditions, but have not been shown to degrade hydrocarbons so far. The second member of the community belongs to the Desulfobulbaceae and has high sequence similarity to uncultured bacteria from contaminated sites including recently proposed groundwater cable bacteria. We suggest that the gram-positive Thermoanaerobacteraceae degrade polycyclic aromatic hydrocarbons while the Desulfobacterales are mainly responsible for Fe(III) reduction.

Metagenomic insights into effects of spent engine oil perturbation on the microbial community composition and function in a tropical agricultural soil

Analyzing the microbial community structure and functions become imperative for ecological processes. To understand the impact of spent engine oil (SEO) contamination on microbial community structure of an agricultural soil, soil microcosms designated 1S (agricultural soil) and AB1 (agricultural soil polluted with SEO) were set up. Metagenomic DNA extracted from the soil microcosms and sequenced using Miseq Illumina sequencing were analyzed for their taxonomic and functional properties. Taxonomic profiling of the two microcosms by MG-RAST revealed the dominance of Actinobacteria (23.36%) and Proteobacteria (52.46%) phyla in 1S and AB1 with preponderance of Streptomyces (12.83%) and Gemmatimonas (10.20%) in 1S and Geodermatophilus (26.24%), Burkholderia (15.40%), and Pseudomonas (12.72%) in AB1, respectively. Our results showed that soil microbial diversity significantly decreased in AB1. Further assignment of the metagenomic reads to MG-RAST, Cluster of Orthologous Groups (COG) of proteins, Kyoto Encyclopedia of Genes and Genomes (KEGG), GhostKOALA, and NCBI's CDD hits revealed diverse metabolic potentials of the autochthonous microbial community. It also revealed the adaptation of the community to various environmental stressors such as hydrocarbon hydrophobicity, heavy metal toxicity, oxidative stress, nutrient starvation, and C/N/P imbalance. To the best of our knowledge, this is the first study that investigates the effect of SEO perturbation on soil microbial communities through Illumina sequencing. The results indicated that SEO contamination significantly affects soil microbial community structure and functions leading to massive loss of nonhydrocarbon degrading indigenous microbiota and enrichment of hydrocarbonoclastic organisms such as members of Proteobacteria and Actinobacteria.

Changes in the microbial community during bioremediation of gasoline-contaminated soil

We aimed to verify the changes in the microbial community during bioremediation of gasoline-contaminated soil. Microbial inoculants were produced from successive additions of gasoline to municipal solid waste compost (MSWC) previously fertilized with nitrogen-phosphorous. To obtain Inoculant A, fertilized MSWC was amended with gasoline every 3 days during 18 days. Inoculant B received the same application, but at every 6 days. Inoculant C included MSWC fertilized with N–P, but no gasoline. The inoculants were applied to gasoline-contaminated soil at 10, 30, or 50 g/kg. Mineralization of gasoline hydrocarbons in soil was evaluated by respirometric analysis. The viability of the inoculants was evaluated after 103 days of storage under refrigeration or room temperature. The relative proportions of microbial groups in the inoculants and soil were evaluated by FAME. The dose of 50 g/kg of inoculants A and B led to the largest CO₂ emission from soil. CO₂ emissions in treatments with inoculant C were inversely proportional to the dose of inoculant. Heterotrophic bacterial counts were greater in soil treated with inoculants A and B. The application of inoculants decreased the proportion of actinobacteria and increased of Gram-negative bacteria. Decline in the density of heterotrophic bacteria in inoculants occurred after storage. This reduction was bigger in inoculants stored at room temperature. The application of stored inoculants in gasoline-contaminated soil resulted in a CO₂ emission twice bigger than that observed in uninoculated soil. We concluded that MSWC is an effective material for the production of microbial inoculants for the bioremediation of gasoline-contaminated soil.

Depletion of pentachlorophenol in soil microcosms with Byssochlamys nivea and Scopulariopsis brumptii as detoxification agents

Pentachlorophenol (PCP) is a toxic compound which is widely used as a wood preservative product and general biocide. It is persistent in the environment and has been classified as a persistent organic pollutant to be reclaimed in many countries. Fungal bioremediation is an emerging approach to rehabilitating areas fouled by recalcitrant xenobiotics. In the present study, we isolated two fungal strains from an artificially PCP-contaminated soil during a long-term bioremediation study and evaluated their potential as bioremediation agents in depletion and detoxification of PCP in soil microcosms. The two fungal strains were identified as: Byssochlamys nivea (Westling, 1909) and Scopulariopsis brumptii (Salvanet-Duval, 1935). PCP removal and toxicity were examined during 28 days of incubation. Bioaugmented microcosms revealed a 60% and 62% PCP removal by B. nivea and S. brumptii, respectively. Co-inoculation of B. nivea and S. brumptii showed a synergetic effect on PCP removal resulting in 95% and 80% PCP decrease when initial concentrations were 12.5 and 25 mg kg^-1, respectively. Detoxification in bioaugmented soil and the efficient role of fungi in the rehabilitation of PCP contaminated soil were experimentally proven by toxicity assays. A decrease in inhibition of bioluminescence of Escherichia coli HB101 pUCD607 and an increase of germination index of mustard (Brassica alba) seeds were observed in the decontaminated soils.

Characterization of Crude Oil Degrading Bacteria Isolated from Contaminated Soils Surrounding Gas Stations

A total of twenty bacterial cultures were isolated from hydrocarbon contaminated soil. Of the 20 isolates, RAM03, RAM06, RAM13, and RAM17 were specifically chosen based on their relatively higher growth on salt medium amended with 4 % crude oil, emulsion index, surface tension, and degradation percentage. These bacterial cultures had 16S rRNA gene sequences that were most similar to Ochrobactrum cytisi (RAM03), Ochrobactrum anthropi (RAM06 and RAM17), and Sinorhizobium meliloti (RAM13) with 96 %, 100 % and 99 %, and 99 % similarity. The tested strains revealed a promising potential for bioremediation of petroleum oil contamination as they could degrade >93 % and 54 % of total petroleum hydrocarbons (TPHs) in a liquid medium and soil amended with 4 % crude oil, respectively, after 30 day incubation. These bacteria could effectively remove both aliphatic and aromatic petroleum hydrocarbons. In conclusion, these strains could be considered as good prospects for their application in bioremediation of hydrocarbon contaminated environment.

Stimulation of Microbially Mediated Arsenic Release in Bangladesh Aquifers by Young Carbon Indicated by Radiocarbon Analysis of Sedimentary Bacterial Lipids

The sources of reduced carbon driving the microbially mediated release of arsenic to shallow groundwater in Bangladesh remain poorly understood. Using radiocarbon analysis of phospholipid fatty acids (PLFAs) and potential carbon pools, the abundance and carbon sources of the active, sediment-associated, in situ bacterial communities inhabiting shallow aquifers (<30 m) at two sites in Araihazar, Bangladesh, were investigated. At both sites, sedimentary organic carbon (SOC) Δ(14)C signatures of -631 ± 54‰ (n = 12) were significantly depleted relative to dissolved inorganic carbon (DIC) of +24 ± 30‰ and dissolved organic carbon (DOC) of -230 ± 100‰. Sediment-associated PLFA Δ(14)C signatures (n = 10) at Site F (-167‰ to +20‰) and Site B (-163‰ to +21‰) were highly consistent and indicated utilization of carbon sources younger than the SOC, likely from the DOC pool. Sediment-associated PLFA Δ(14)C signatures were consistent with previously determined Δ(14)C signatures of microbial DNA sampled from groundwater at Site F indicating that the carbon source for these two components of the subsurface microbial community is consistent and is temporally stable over the two years between studies. These results demonstrate that the utilization of relatively young carbon sources by the subsurface microbial community occurs at sites with varying hydrology. Further they indicate that these young carbon sources drive the metabolism of the more abundant sediment-associated microbial communities that are presumably more capable of Fe reduction and associated release of As. This implies that an introduction of younger carbon to as of yet unaffected sediments (such as those comprising the deeper Pleistocene aquifer) could stimulate microbial communities and result in arsenic release.

Diversity of active microbial communities subjected to long-term exposure to chemical contaminants along a 40-year-old sediment core

In estuarine ecosystems, metallic and organic contaminants are mainly associated with fine grain sediments which settle on mudflats. Over time, the layers of sediment accumulate and are then transformed by diagenetic processes mainly controlled by microbial activity, recording the history of the estuary's chemical contamination. In an environment of this specific type, we investigated the evolution of the chemical contamination and the structure of both total and active microbial communities, based on PhyloChip analysis of a 4.6-m core corresponding to a 40-year sedimentary record. While the archaeal abundance remained constant along the core, a decrease by one order of magnitude in the bacterial abundance was observed with depth. Both total and active microbial communities were dominated by Proteobacteria, Actinobacteria, and Firmicutes in all sediment samples. Among Proteobacteria, alpha-Proteobacteria dominated both total (from 37 to 60 %) and metabolically active (from 19.7 to 34.6 %) communities, including the Rhizobiales, Rhodobacter, Caulobacterales, and Sphingomonadales orders. Co-inertia analysis revealed a relationship between polycyclic aromatic hydrocarbons, zinc and some polychlorobiphenyls concentrations, and the structure of total and active microbial communities in the oldest and most contaminated sediments (from 1970 to 1975), suggesting that long-term exposure to chemicals shaped the structure of the microbial community.

Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes

Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs) were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. The heatmap plot depicted the relative percentage of each bacterial family within each sample and clustered five samples into two groups. For the samples, bacteria in the soils varied at different periods of oil exposure. The oil pollution exerted strong selective pressure to propagate many potentially petroleum degrading bacteria. Redundancy analysis (RDA) indicated that organic matter was the highest determinant factor for explaining the variations in community compositions. This suggests that compared to clean soils, oil-polluted soils support more diverse bacterial communities and soil bacterial community shifts were mainly controlled by organic matter and exposure time. These results provide some useful information for bioremediation of petroleum contaminated soil in the future.

Abundance and diversity of soil petroleum hydrocarbon-degrading microbial communities in oil exploring areas

Alkanes and polycyclic aromatic hydrocarbons (PAHs) are the commonly detected petroleum hydrocarbon contaminants in soils in oil exploring areas. Hydrocarbon-degrading genes are useful biomarks for estimation of the bioremediation potential of contaminated sites. However, the links between environmental factors and the distribution of alkane and PAH metabolic genes still remain largely unclear. The present study investigated the abundances and diversities of soil n-alkane and PAH-degrading bacterial communities targeting both alkB and nah genes in two oil exploring areas at different geographic regions. A large variation in the abundances and diversities of alkB and nah genes occurred in the studied soil samples. Various environmental variables regulated the spatial distribution of soil alkane and PAH metabolic genes, dependent on geographic location. The soil alkane-degrading bacterial communities in oil exploring areas mainly consisted of Pedobacter, Mycobacterium, and unknown alkB-harboring microorganisms. Moreover, the novel PAH-degraders predominated in nah gene clone libraries from soils of the two oil exploring areas. This work could provide some new insights towards the distribution of hydrocarbon-degrading microorganisms and their biodegradation potential in soil ecosystems.

Phytoremediation of hydrocarbon contaminants in subantarctic soils: an effective management option

Accidental fuel spills on world heritage subantarctic Macquarie Island have caused considerable contamination. Due to the island's high latitude position, its climate, and its fragile ecosystem, traditional methods of remediation are unsuitable for on-site clean up. We investigated the tolerance of a subantarctic native tussock grass, Poa foliosa (Hook. f.), to Special Antarctic Blend (SAB) diesel fuel and its potential to reduce SAB fuel contamination via phytoremediation. Toxicity of SAB fuel to P. foliosa was assessed in an 8 month laboratory growth trial under growth conditions which simulated the island's environment. Single seedlings were planted into 1 L pots of soil spiked with SAB fuel at concentrations of 1000, 5 000, 10,000, 2000 and 40,000 mg/kg (plus control). Plants were harvested at 0, 2, 4 and 8 months and a range of plant productivity endpoints were measured (biomass production, plant morphology and photosynthetic efficiency). Poa foliosa was highly tolerant across all SAB fuel concentrations tested with respect to biomass, although higher concentrations of 20,000 and 40,000 mg SAB/kg soil caused slight reductions in leaf length, width and area. To assess the phytoremediation potential of P. foliosa (to 10 000 mg/kg), soil from the planted pots was compared with that from paired unplanted pots at each SAB fuel concentration. The effect of the plant on SAB fuel concentrations and the associated microbial communities found within the soil (total heterotrophs and hydrocarbon degraders) were compared between planted and unplanted treatments at the 0, 2, 4 and 8 month harvest periods. The presence of plants resulted in significantly less SAB fuel in soils at 2 months and a return to background concentration by 8 months. Microbes did not appear to be the sole driving force behind the observed hydrocarbon loss. This study provides evidence that phytoremediation using P. foliosa is a valuable remediation option for use at Macquarie Island, and may be applicable to the management of fuel spills in other cold climate regions.