Abundance and diversity of functional genes involved in the degradation of aromatic hydrocarbons in Antarctic soils and sediments around Syowa Station

The bioremediation of the typical persistent organic pollutants (POPs) by microalgae-bacteria consortia: A systematic review

With industrialisation and the rapidly growing agricultural demand, many organic compounds have been leaked into the environment, causing serious damage to the biosphere. Persistent organic pollutants (POPs) are a type of toxic chemicals that are resistant to degradation through normal chemical, biological or photolytic approaches. With their stable chemical structures, POPs can be accumulated in the environment, and transported through wind and water, causing global environmental issues. Many researches have been conducted to remediate POPs contamination using various kinds of biological methods, and significant results have been seen. Microalgae-bacteria consortium is a newly developed concept for biological technology in contamination treatment, with the synergetic effects between microalgae and bacteria, their potential for pollutants degradation can be further released. In this review, two types of POPs (polychlorinated biphenyls and polycyclic aromatic hydrocarbons) are selected as the targeted pollutants to give a systematic analysis of the biodegradation through microalgae and bacteria, including the species selection, the identification of dominant enzymes, as well as the real application performance of the consortia. In the end, some outlooks and suggestions are given to further guide the development of applying microalgae-bacteria consortia in remediating POPs contamination. In general, the coculturing of microalgae and bacteria is a novel and efficient way to fulfil the advanced treatment of POPs in soil or liquid phase, and both monooxygenase and dioxygenase belonging to oxygenase play a vital role in the biodegradation of PCBs and PAHs. This review provides a general guide in the future investigation of biological treatment of POPs.

Construction of an effective method combining in situ capping with electric field-enhanced biodegradation for treating PAH-contaminated soil at abandoned coking sites

The simultaneous application of in situ capping and electro-enhanced biodegradation may be a suitable method for ensuring the feasibility and safety of reusing abandoned coking sites. However, the capping layer type and applied electric field pattern may affect the efficiency of sequestering and removing pollutants. This study investigated changes in electric current, soil moisture content and pH, polycyclic aromatic hydrocarbon (PAH) concentration, bacterial number, and microbial community structure and metabolic function during soil remediation at abandoned coking plant sites under different applied electric field patterns and barrier types. The results indicated that polarity-reversal electric field was more conducive to maintaining electric current, soil properties, resulting in higher microbial number, community diversity, and functional gene abundance. At 21d, the mean PAH concentrations in contaminated soil, the capping layer's clean soil and barrier were 78.79, 7.56, and 1.57 mg kg-1 lower than those with a unidirectional electric field, respectively. The mean degradation rate of PAHs in the bio-barrier was 10.12 % higher than that in the C-Fe barrier. In the experiment combining a polarity-reversal electric field and a bio-barrier, the mean PAH concentrations in contaminated soil and the capping layer were 706.68 and 27.15 mg kg-1 lower than those in other experiments, respectively, and no PAHs were detected in the clean soil, demonstrating that the combination of the polarity-reversal electric field and the bio-barrier was effective in treating soil at abandoned coking plant sites. The established method of combining in situ capping with electro-enhanced biodegradation will provide technical support for the treatment and reuse of heavily PAH-contaminated soil at abandoned coking plant sites.

Biosurfactants-based mixed polycyclic aromatic hydrocarbon degradation: From microbial community structure toward non-targeted metabolomic profile determination

Biosurfactants-based bioremediation is considered an efficient technology to eliminate environmental pollutants including polycyclic aromatic hydrocarbons (PAHs). However, the precise role of rhamnolipids or lipopeptide-biosurfactants in mixed PAH dissipation, shaping microbial community structure, and influencing metabolomic profile remained unclear. In this study, results showed that the maximum PAH degradation was achieved in lipopeptide-assisted treatment (SPS), where the pyrene and phenanthrene were substantially degraded up to 74.28 % and 63.05 % respectively, as compared to rhamnolipids (SPR) and un-aided biosurfactants (SP). Furthermore, the high throughput sequencing analysis revealed a significant change in the PAH-degrading microbial community, with Proteobacteria being the predominant phylum (>98 %) followed by Bacteroidota and Firmicutes in all the treatments. Moreover, Pseudomonas and Pannonibacter were found as highly potent bacterial genera for mixed PAH degradation in SPR, SPS, and SP treatments, nevertheless, the abundance of the genus Pseudomonas was significantly enhanced (>97 %) in SPR treatment groups. On the other hand, the non-targeted metabolomic profile through UHPLC-MS/MS exhibited a remarkable change in the metabolites of amino acids, carbohydrates, and lipid metabolisms by the input of rhamnolipids or lipopeptide-biosurfactants whereas, the maximum intensities of metabolites (more than two-fold) were observed in SPR treatment. The findings of this study suggested that the aforementioned biosurfactants can play an indispensable role in mixed PAH degradation as well as seek to offer new insights into shifts in PAH-degrading microbial communities and their metabolic function, which can guide the development of more efficient and targeted strategies for complete removal of organic pollutants such as PAH from the contaminated environment.

Insight into the role of niche concept in deciphering the ecological drivers of MPs-associated bacterial communities in mangrove forest

Myriad inherent and variable environmental features are controlling the assembly and succession of bacterial communities colonizing on mangrove microplastics (MPs). However, the mechanisms governing mangrove MPs-associated bacterial responses to environmental changes still remain unknown. Here, we assessed the dissimilarities of MPs-associated bacterial composition, diversity and functionality as well as quantified the niche variations of each taxon on plastispheres along river-mangrove-ocean and mangrove landward-to-seaward gradients in the Beibu Gulf, China, respectively. The bacterial richness and diversity as well as the niche breadth on mangrove sedimentary MPs dramatically decreased from landward to seaward regions. Characterizing the niche variations linked the difference of ecological drivers of MPs-associated bacterial populations and functions between river-mangrove-ocean (microplastic properties) and mangrove landward-to-seaward plastispheres (sediment physicochemical properties) to the trade-offs between selective stress exerted by inherent plastic substrates and microbial competitive stress imposed by environmental conditions. Notably, Rhodococcus erythropolis was predicted to be the generalist species and closely associated to biogeochemical cycles of mangrove plastispheres. Our work provides a reliable pathway for tackling the hidden mechanisms of environmental factors driving MPs-associated microbe from perspectives of niches and highlights the spatial dynamic variations of mangrove MPs-associated bacteria.

Comparative genomics reveals evidence of polycyclic aromatic hydrocarbon degradation in the moderately halophilic genus Pontibacillus

Polycyclic aromatic hydrocarbons (PAHs) are a common class of persistent organic pollutants (POPs) that are widely distributed in various environments and pose significant threats to both environmental and human health. The genus Pontibacillus, a type of moderately halophilic bacteria, has demonstrated potential for biodegrading aromatic compounds in high-salinity environments. However, no previous study has comprehensively investigated the PAH degradation mechanisms and environmental adaptability in the genus Pontibacillus. In this study, we sequenced the whole genome of the PAH-degrading strain Pontibacillus chungwhensis HN14 and conducted a comparative genomics analysis of genes associated with PAH degradation, as well as salt and arsenic tolerance using ten other Pontibacillus sp. strains. Here, we elucidated potential degradation pathways for benzo[a]pyrene and phenanthrene, which were initiated by cytochrome P450 monooxygenases, in most Pontibacillus strains. Moreover, four Pontibacillus strains were selected to investigate the biodegradation of benzo[a]pyrene and phenanthrene under high-salt (5% NaCl) stress, and all four strains exhibited exceptional degradation abilities. The results of comparative genomics and phenotypic analyses demonstrate that the genus Pontibacillus have the potential to degrade polycyclic aromatic hydrocarbons in high-salinity environments, thus providing valuable insights for biodegradation in extreme environments.

Effect of electric fields strength on soil factors and microorganisms during electro-bioremediation of benzo[a]pyrene-contaminated soil

Electro-bioremediation is a promising technology for remediating soils contaminated with polycyclic aromatic hydrocarbons (PAHs). However, the resulting electrokinetic effects and electrochemical reactions may inevitably cause changes in soil factors and microorganism, thereby reducing the remediation efficiency. To avoid negative effect of electric field on soil and microbes and maximize microbial degradability, it is necessary to select a suitable electric field. In this study, artificial benzo [a]pyrene (BaP)-contaminated soil was selected as the object of remediation. Changes in soil factors and microorganisms were investigated under the voltage of 1.0, 2.0, and 2.5 V cm-1 using chemical analysis, real-time PCR, and high-throughput sequencing. The results revealed noticeable changes in soil factors (pH, moisture, electrical conductivity [EC], and BaP concentration) and microbes (PAHs ring-hydroxylating dioxygenase [PAHs-RHDα] gene and bacterial community) after the application of electric field. The degree of change was related to the electric field strength, with a suitable strength being more conducive to BaP removal. At 70 d, the highest mean extent of BaP removal and PAHs-RHDα gene copies were observed in EK2.0 + BIO, reaching 3.37 and 109.62 times those in BIO, respectively, indicating that the voltage of 2.0 V cm-1 was the most suitable for soil microbial growth and metabolism. Changes in soil factors caused by electric fields can affect microbial activity and community composition. Redundancy analysis revealed that soil pH and moisture had the most significant effects on microbial community composition (P < 0.05). The purpose of this study was to determine the appropriate electric field that could be used for electro-bioremediation of PAH-contaminated soil by evaluating the effects of electric fields on soil factors and microbial communities. This study also provides a reference for efficiency enhancement and successful application of electro-bioremediation of soil contaminated with PAHs.

Role of Microbes in the degradation of organic semivolatile compounds in polar ecosystems: A review

The Arctic and the Antarctic Continent correspond to two eco-regions with extreme climatic conditions. These regions are exposed to the presence of contaminants resulting from human activity (local and global), which, in turn, represent a challenge for life forms in these environments. Anthropogenic pollution by semi-volatile organic compounds (SVOCs) in polar ecosystems has been documented since the 1960s. Currently, various studies have shown the presence of SVOCs and their bioaccumulation and biomagnification in the polar regions with negative effects on biodiversity and the ecosystem. Although the production and use of these compounds has been regulated, their persistence continues to threaten biodiversity and the ecosystem. Here, we summarize the current literature regarding microbes and SVOCs in polar regions and pose that bioremediation by native microorganisms is a feasible strategy to mitigate the presence of SVOCs. Our systematic review revealed that microbial communities in polar environments represent a wide reservoir of biodiversity adapted to extreme conditions, found both in terrestrial and aquatic environments, freely or in association with vegetation. Microorganisms adapted to these environments have the potential for biodegradation of SVOCs through a variety of genes encoding enzymes with the capacity to metabolize SVOCs. We suggest that a comprehensive approach at the molecular and ecological level is required to mitigate SVOCs presence in these regions. This is especially patent when considering that SVOCs degrade at slow rates and possess the ability to accumulate in polar ecosystems. The implications of SVOC degradation are relevant for the preservation of polar ecosystems with consequences at a global level.

Utilization of-Omic technologies in cold climate hydrocarbon bioremediation: a text-mining approach

Hydrocarbon spills in cold climates are a prominent and enduring form of anthropogenic contamination. Bioremediation is one of a suite of remediation tools that has emerged as a cost-effective strategy for transforming these contaminants in soil, ideally into less harmful products. However, little is understood about the molecular mechanisms driving these complex, microbially mediated processes. The emergence of -omic technologies has led to a revolution within the sphere of environmental microbiology allowing for the identification and study of so called 'unculturable' organisms. In the last decade, -omic technologies have emerged as a powerful tool in filling this gap in our knowledge on the interactions between these organisms and their environment in vivo. Here, we utilize the text mining software Vosviewer to process meta-data and visualize key trends relating to cold climate bioremediation projects. The results of text mining of the literature revealed a shift over time from optimizing bioremediation experiments on the macro/community level to, in more recent years focusing on individual organisms of interest, interactions within the microbiome and the investigation of novel metabolic degradation pathways. This shift in research focus was made possible in large part by the rise of omics studies allowing research to focus not only what organisms/metabolic pathways are present but those which are functional. However, all is not harmonious, as the development of downstream analytical methods and associated processing tools have outpaced sample preparation methods, especially when dealing with the unique challenges posed when analyzing soil-based samples.

Treatment of PAHs contaminated soil in abandoned industrial site using combined method of improved in situ capping and electrokinetic enhanced-bioremediation

In situ capping and bioremediation are common technologies for treating contaminated soil at industrial sites. However, these two technologies have some shortcomings for treating soil heavily contaminated with organic matter, such as the limited adsorption in capping layer and the low biodegradation efficiency. This study proposed the method of an improved in situ capping combined with electrokinetic enhanced-bioremediation, and investigated its feasibility for treating heavily polycyclic aromatic hydrocarbons (PAHs) contaminated soil at an abandoned industrial site. By analyzing the changes in soil properties, PAHs concentration, and microbial community in experiments with voltages of 0, 0.8, 1.2, and 1.6 V cm^-1, it was found that improved in situ capping could effectively sequester PAHs migration by adsorption and biodegradation, and electric field could enhance PAHs removal from contaminated soil and bio-barrier. In the experiments with electric field, soil environment under the voltage of 1.2 V cm^-1 was more favorable for the growth and metabolism of microorganisms, and the residual PAHs concentrations (19.47 ± 0.76 mg kg^-1 and 619.38 ± 20.05 mg kg^-1) in the bio-barrier and contaminated soil of experiment with 1.2 V cm^-1 were the lowest, which indicated that optimization of the electric field conditions could lead to better effects.

Effects of different carbon substrates on PAHs fractions and microbial community changes in PAHs-contaminated soils

Different types of carbon substrates were widely used in soil remediation. However, differences of their impacts and related mechanisms on degradation of polycyclic aromatic hydrocarbons (PAHs) and microbial community structures in contaminated soil still remain unclear. Here, we investigated the effects of corn straw (S), glucose (G), straw combined with glucose (SG), and sodium azide (N, as an abiotic control) on PAHs fractions and bacterial communities in soil. After 70 days' microcosm experiments, total PAHs concentrations were significantly reduced by 30.9%, 19.5% and 44.6% under S, G and SG treatments. Water soluble, acid soluble and residual PAHs under all treatments were significantly decreased after 70 days of incubation, while organically bound PAHs were increased by 11.4%, 22.7% and 36.1% under G, S and SG treatments. Additionally, straw and glucose application increased relative abundance related PAHs-degrading bacteria and the copy numbers of gram-negative (PAHs-RHDα GN) and gram-positive genes (PAHs-RHDα GP) in the contaminated soil. Redundancy analysis (RDA) and Random Forest (RF) indicated that PAHs fractions are crucial factors for biodegradation of PAHs in PAHs-contaminated soils amended with carbon substrates. These suggested that carbon substrates contributed to PAHs conversion from residual PAHs (nonlabile fractions) to organically bound PAHs and thus increased the potential for PAHs conversion to water-soluble and organic acid-soluble PAHs, which were more easy to be utilized by soil microorganisms. This study revealed the new insights of different carbon substrates on degradation and dynamic changes of PAHs fractions and the better potential of combined application of straw and glucose in enhancing degradation of PAHs in PAHs-contaminated soils.

Ecological risk assessment and identification of the distinct microbial groups in heavy metal-polluted river sediments

To assess the health of river ecosystems, it is essential to quantify the ecological risk of heavy metals in river sediments and the structure of microbial communities. As important tributaries of the Tuo River in the upper reaches of the Yangtze River, the Mianyuan River and the Shiting River, are closely related to the economic development and human daily life in the region. This study assessed the ecological risks of heavy-metal-polluted river sediments, the heavy-metal-driven bacterial communities were revealed, and the relationships between the ecological risks and the identical bacterial communities were discussed. The Cd content was significantly greater than the environmental background value, leading to a serious pollution and very high ecological risk at the confluence of the two rivers and the upper reaches of the Mianyuan River. Microbial community analysis showed that Rhodobacter, Nocardioides, Sphingomonas, and Pseudarthrobacter were the dominant bacterial genera in the sediments of the Shiting River. However, the dominant bacterial genera in the Mianyuan River were Kouleothrix, Dechloromonas, Gaiella, Pedomicrobium, and Hyphomicrobium. Mantel test results showed (r = 0.5977, P = 0.005) that the Cd, As, Zn, Pb, Cr, and Cu were important factors that influenced differences in the distribution of sediment bacterial communities Mianyuan and Shiting rivers. A correlation heatmap showed that heavy metals were negatively correlated for most bacterial communities, but some bacterial communities were tolerant and showed a positive correlation. Overall, the microbial structure of the river sediments showed a diverse spatial distribution due to the influence of heavy metals. The results will improve the understanding of rivers contaminated by heavy metals and provide theoretical support for conservation and in situ ecological restoration of river ecosystems.

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.

Unravelling the genetic potential for hydrocarbon degradation in the sediment microbiome of Antarctic islands

Hydrocarbons may have a natural or anthropogenic origin and serve as a source of carbon and energy for microorganisms in Antarctic soils. Herein, 16S rRNA gene and shotgun sequencing were employed to characterize taxonomic diversity and genetic potential for hydrocarbon degradation of the microbiome from sediments of sites located in two Antarctic islands subjected to different temperatures, geochemical compositions, and levels of presumed anthropogenic impact, named: Crater Lake/Deception Island (pristine area), Whalers Bay and Fumarole Bay/Deception Island (anthropogenic-impacted area), and Hannah Point/Livingston Island (anthropogenic-impacted area). Hydrocarbon concentrations were measured for further correlation analyses with biological data. The majority of the hydrocarbon-degrading genes were affiliated to the most abundant bacterial groups of the microbiome: Proteobacteria and Actinobacteria. KEGG annotation revealed 125 catabolic genes related to aromatic hydrocarbon (styrene, toluene, ethylbenzene, xylene, naphthalene, and polycyclic hydrocarbons) and aliphatic (alkanes and cycloalkanes) pathways. Only aliphatic hydrocarbons, in low concentrations, were detected in all areas, thus not characterizing the areas under study as anthropogenically impacted or nonimpacted. The high richness and abundance of hydrocarbon-degrading genes suggest that the genetic potential of the microbiome from Antarctic sediments for hydrocarbon degradation is driven by natural hydrocarbon occurrence.

Effects of Salinity on the Biodegradation of Polycyclic Aromatic Hydrocarbons in Oilfield Soils Emphasizing Degradation Genes and Soil Enzymes

The biodegradation of organic pollutants is the main pathway for the natural dissipation and anthropogenic remediation of polycyclic aromatic hydrocarbons (PAHs) in the environment. However, in the saline soils, the PAH biodegradation could be influenced by soil salts through altering the structures of microbial communities and physiological metabolism of degradation bacteria. In the worldwide, soils from oilfields are commonly threated by both soil salinity and PAH contamination, while the influence mechanism of soil salinity on PAH biodegradation were still unclear, especially the shifts of degradation genes and soil enzyme activities. In order to explain the responses of soils and bacterial communities, analysis was conducted including soil properties, structures of bacterial community, PAH degradation genes and soil enzyme activities during a biodegradation process of PAHs in oilfield soils. The results showed that, though low soil salinity (1% NaCl, w/w) could slightly increase PAH degradation rate, the biodegradation in high salt condition (3% NaCl, w/w) were restrained significantly. The higher the soil salinity, the lower the bacterial community diversity, copy number of degradation gene and soil enzyme activity, which could be the reason for reductions of degradation rates in saline soils. Analysis of bacterial community structure showed that, the additions of NaCl increase the abundance of salt-tolerant and halophilic genera, especially in high salt treatments where the halophilic genera dominant, such as Acinetobacter and Halomonas. Picrust2 and redundancy analysis (RDA) both revealed suppression of PAH degradation genes by soil salts, which meant the decrease of degradation microbes and should be the primary cause of reduction of PAH removal. The soil enzyme activities could be indicators for microorganisms when they are facing adverse environmental conditions.

Metagenomic analysis of microbial communities across a transect from low to highly hydrocarbon-contaminated soils in King George Island, Maritime Antarctica

Soil samples from a transect from low to highly hydrocarbon-contaminated soils were collected around the Brazilian Antarctic Station Comandante Ferraz (EACF), located at King George Island, Antarctica. Quantitative PCR (qPCR) analysis of bacterial 16S rRNA genes, 16S rRNA gene (iTag), and shotgun metagenomic sequencing were used to characterize microbial community structure and the potential for petroleum degradation by indigenous microbes. Hydrocarbon contamination did not affect bacterial abundance in EACF soils (bacterial 16S rRNA gene qPCR). However, analysis of 16S rRNA gene sequences revealed a successive change in the microbial community along the pollution gradient. Microbial richness and diversity decreased with the increase of hydrocarbon concentration in EACF soils. The abundance of Cytophaga, Methyloversatilis, Polaromonas, and Williamsia was positively correlated (p-value = <.05) with the concentration of total petroleum hydrocarbons (TPH) and/or polycyclic aromatic hydrocarbons (PAH). Annotation of metagenomic data revealed that the most abundant hydrocarbon degradation pathway in EACF soils was related to alkyl derivative-PAH degradation (mainly methylnaphthalenes) via the CYP450 enzyme family. The abundance of genes related to nitrogen fixation increased in EACF soils as the concentration of hydrocarbons increased. The results obtained here are valuable for the future of bioremediation of petroleum hydrocarbon-contaminated soils in polar environments.

Microbial community analysis of biopiles in Antarctica provides evidence of successful hydrocarbon biodegradation and initial soil ecosystem recovery

Microorganisms comprise the bulk of biodiversity and biomass in Antarctic terrestrial ecosystems. To effectively protect and manage the Antarctic environment from anthropogenic impacts including contamination, the response and recovery of microbial communities should be included in soil remediation efficacy and environmental risk assessments. This is the first investigation into the microbial dynamics associated with large scale bioremediation of hydrocarbon contaminated soil in Antarctica. Over five years of active management, two significant shifts in the microbial community were observed. The initial shift at 12-24 months was significantly correlated with the highest hydrocarbon degradation rates, increased microbial loads, and significant increases in alkB gene abundances. ANCOM analysis identified bacterial genera most likely responsible for the bulk of degradation including Alkanindiges, Arthrobacter, Dietzia and Rhodococcus. The second microbial community shift occurring from 36 to 60 months was associated with further reductions in hydrocarbons and a recovery of amoA nitrification genes, but also increasing pH, accumulation of nitrite and a reduction of oligotrophic bacterial species. Over time, the addition of inorganic fertilisers altered the soil chemistry and led to a disruption of the nitrogen cycle, most likely decoupling ammonia oxidisers from nitrite oxidisers, resulting in nitrite accumulation. The results from this study provide key insights to the long-term management of hydrocarbon bioremediation in Antarctic soils.

Variation of the mangrove sediment microbiomes and their phenanthrene biodegradation rates during the dry and wet seasons

Mangrove sediment is a major sink for phenanthrene in natural environments. Consequently, this study investigated the effects of seasonal variation on the biodegradation rates of low (150 mg kg^-1), moderate (600 mg kg^-1), and high (1200 mg kg^-1) phenanthrene-contaminated mangrove sediments using a microcosm study and identified potential key phenanthrene-degrading bacteria using high throughput sequencing of 16 S rRNA gene and quantitative-PCR of the PAH-ring hydroxylating dioxygenase (PAH-RHD_α) genes. The biodegradation rates of phenanthrene in all treatments were higher in the wet-season sediments (11.58, 14.51, and 8.94 mg kg^-1 sediment day^-1) than in the dry-season sediments (3.51, 12.56, and 5.91 mg kg^-1 sediment day^-1) possibly due to higher nutrient accumulation caused by rainfall and higher diversity of potential phenanthrene-degrading bacteria. The results suggested that the mangrove sediment microbiome significantly clustered according to season. Although Gram-negative phenanthrene-degrading bacteria (i.e., Anaerolineaceae, Marinobacter, and Rhodobacteraceae) played a key role in both dry and wet seasons, distinctly different phenanthrene-degrading bacterial taxa were observed in each season. Halomonas and Porticoccus were potentially responsible for the degradation of phenanthrene in the dry and wet seasons, respectively. The knowledge gained from this study contributes to the development of effective and rationally designed microbiome innovations for oil removal.

Bacterial and archaeal diversity in oil fields and reservoirs and their potential role in hydrocarbon recovery and bioprospecting

Hydrocarbon is a primary source of energy in the current urbanized society. Considering the increasing demand, worldwide oil productions are declining due to maturity of oil fields and because of difficulty in discovering new oil fields to substitute the exploited ones. To meet current and future energy demands, further exploitation of oil resources is highly required. Microorganisms inhabiting in these areas exhibit highly diverse catabolic activities to degrade, transform, or accumulate various hydrocarbons. Enrichment of hydrocarbon-utilizing bacteria in oil basin is caused by continuous long duration and low molecular weight hydrocarbon microseepage which plays a very important role as an indicator for petroleum prospecting. The important microbial metabolic processes in most of the oil reservoir are sulfate reduction, fermentation, acetogenesis, methanogenesis, NO3- reduction, and Fe (III) and Mn (IV) reduction. The microorganisms residing in these sites have critical control on petroleum composition, recovery, and production methods. Physical characteristics of heavy oil are altered by microbial biotransformation and biosurfactant production. Considering oil to be one of the most vital energy resources, it is important to have a comprehensive understanding of petroleum microbiology. This manuscript reviews the recent research work referring to the diversity of bacteria in oil field and reservoir sites and their applications for enhancing oil transformation in the target reservoir and geomicrobial prospecting scope for petroleum exploration.

Diversity and Composition of Microbial Communities in an Eelgrass (Zostera marina) Bed in Tokyo Bay, Japan

Zostera marina (eelgrass) is a widespread seagrass species that forms diverse and productive habitats along coast lines throughout much of the northern hemisphere. The present study investigated the microbial consortia of Z. marina growing at Futtsu clam-digging beach, Chiba prefecture, Japan. The following environmental samples were collected: sediment, seawater, plant leaves, and the root-rhizome. Sediment and seawater samples were obtained from three sampling points: inside, outside, and at the marginal point of the eelgrass bed. The microbial composition of each sample was analyzed using 16S ribosomal gene amplicon sequencing. Microbial communities on the dead (withered) leaf surface markedly differed from those in sediment, but were similar to those in seawater. Eelgrass leaves and surrounding seawater were dominated by the bacterial taxa Rhodobacterales (Alphaproteobacteria), whereas Rhodobacterales were a minor group in eelgrass sediment. Additionally, we speculated that the order Sphingomonadales (Alphaproteobacteria) acts as a major degrader during the decomposition process and constantly degrades eelgrass leaves, which then spread into the surrounding seawater. Withered eelgrass leaves did not accumulate on the surface sediment because they were transported out of the eelgrass bed by wind and residual currents unique to the central part of Tokyo Bay.

Plasmid-mediated catabolism for the removal of xenobiotics from the environment

The large-scale application of xenobiotics adversely affects the environment. The genes that are present in the chromosome of the bacteria are considered nonmobile, whereas the genes present on the plasmids are considered mobile genetic elements. Plasmids are considered indispensable for xenobiotic degradation into the contaminated environment. In the contaminated sites, bacteria with plasmids can transfer the mobile genetic element into another strain. This mechanism helps in spreading the catabolic genes into the bacterial population at the contaminated sites. The indigenous microbial strains with such degradative plasmids are important for the bioremediation of xenobiotics. Environmental factors play a critical role in the conjugation efficiency, which is involved in the bioremediation of the xenobiotics at the contaminated sites. However, there is still a need for more research to fill in the gaps regarding plasmids and their impact on bioremediation. This review explores the role of bacterial plasmids in the bioremediation of xenobiotics from contaminated environments.

Soil indigenous microorganisms weaken the synergy of Massilia sp. WF1 and Phanerochaete chrysosporium in phenanthrene biodegradation

Biodegradation is a promising way to reduce phenanthrene (PHE) in environment. PHE biodegradation by bioaugmentation of axenic and mixed cultures of Massilia sp. WF1 (a highly efficient PHE-degrading bacteria) and Phanerochaete chrysosporium (P. chrysosporium, an extensively researched model fungus in organic pollutant bioremediation) was investigated in aqueous and autoclaved/un-autoclaved soil cultures. In the liquid cultures, the strain WF1 could use PHE (ca. 10 mg L^-1) as the sole carbon source, and the presence of d-fructose (500 mg L^-1) had no obvious effect on its PHE degradation; while the opposite was observed for P. chrysosporium. The bioaugmentation of strain WF1 and P. chrysosporium co-culture showed the highest PHE-degradation efficiency, especially in the aqueous and the autoclaved soil (PHE, ca. 50 mg kg^-1) cultures, indicating a synergistic interaction of the co-culture during PHE dissipation. It was further observed that the indigenous microorganisms (mainly the Gram-positive bacteria) played a dominant role during PHE biodegradation and showed an antagonistic action against the strain WF1-P. chrysosporium co-culture, which weakened the synergistic action of the co-culture in the un-autoclaved soil. Besides, the abundances of PAH-RHDα GP and nidA genes were negatively correlated with residual PHE in the soil. Our findings provide the scientific support for bioremediation of PAHs in environment.

Enhanced phytoremediation of PAHs and cadmium contaminated soils by a Mycobacterium

This study investigated Fire Phoenix (Festuca L.) and Echinacea purpurea (L.) Moench inoculated with a Mycobacterium strain N12 in remediation of soils contaminated with both polycyclic aromatic hydrocarbons (PAHs) and cadmium (Cd). Plant growth and PAH and Cd removal were monitored in 60, 120, and 150 days after transplanting. Results showed that Fire Phoenix plants grown in soil containing 200 mg/kg PAHs and 15 mg/kg Cd inoculated with N12 were able to remove 76.3% PAHs compared to removal of 68.3% of PAHs by the plants without N12 inoculation. On day 150, the underground biomass of Fire Phoenix plants grown in soil inoculated with N12 increased 59.40% compared to that without N12 inoculation. The enhanced removal of PAH by Fire Phoenix and N12 was related to the improved rhizosphere microbial activities. However, inoculation of N12 to E. purpurea grown soil did not significantly improve the removal of PAHs and Cd. Our results showed that phytoremediation of PAHs and Cd can be enhanced by a Mycobacterium strain N12, especially when PLFA concentrations of bacteria and fungi exceeded 60% of the initial concentrations, but the enhancement is plant species dependent.

Changes in the fluorescence intensity, degradability, and aromaticity of organic carbon in ammonium and phenanthrene-polluted aquatic ecosystems

Mixed cultures were established by a sediment to investigate the changes in organic carbon (C) in a combined ammonium and phenanthrene biotransformation process in aquatic ecosystems. The microorganisms in the sediment demonstrated significant ammonium-N and phenanthrene biotransformation capacity with removal efficiencies of 99.96% and 99.99%, respectively. The changes in the organic C characteristics were evaluated by the fluorescence intensity, degradability (humification index (HIX) and UV absorbance at 254 nm (A₂₅₄)), aromaticity (specific UV absorbance at 254 nm (SUVA₂₅₄) and fluorescence index (FI)). Compared with C2 (the second control), the lower values of fluorescence intensity (after the 15^th d), HIX (after the 8^th d), A₂₅₄ (after the 11^th d), and SUVA₂₅₄ (after the 8^th d) and the higher FI value (after the 8^th d) in ammonium and phenanthrene-fed mixed cultures (N_PHE) suggest that aromatic structures and some condensed molecules were easier to break down in N_PHE. Similar results were obtained from Fourier transformation infrared spectroscopy (FTIR) and nuclear magnetic resonance (¹H NMR) spectra. Changes in organic C characteristics may be due to two key organisms Massilia and Azohydromonas. The biodiversity also suggested that the selective pressure of ammonium and phenanthrene is the decisive factor for changes in organic C characteristics. This study will shed light on theoretical insights into the interaction of N and aromatic compounds in aquatic ecosystems.

Mixed cultures were established by a sediment to investigate the changes in organic carbon (C) in a combined ammonium and phenanthrene biotransformation process in aquatic ecosystems.

The combination of biochar and plant roots improves soil bacterial adaptation to PAH stress: Insights from soil enzymes, microbiome, and metabolome

Polycyclic aromatic hydrocarbon (PAH) contamination in agricultural soils poses serious stress to the soil microbiome. With the broad application of biochar, however, the co-effects of biochar and plant roots on the bacterial responses to PAH stress remain unclear. Here, the effects of biochar and the rhizosphere on bacterial community structure and functions were analyzed by coupling enzyme activity tests, high-throughput sequencing, and soil metabolomics. The contents of available nutrients and dissolved organic carbon, enzyme activities, and carbon metabolism functions were improved by biochar and plant roots. With the combined effects of biochar and plant roots, sucrose and starch metabolism was mainly impacted, and the soil metabolite diversity decreased. There was a strong co-occurrence network among soil properties, bacterial members, and metabolites in the biochar-amended and rhizosphere soils, favoring bacterial resistance to PAH stress, and consequently, PAH removal. In light of the above results, we suggest that biochar application can efficiently improve bacterial functions in rhizosphere soil, and our results facilitate the development of in situ remediation programs in soil contaminated with PAHs.

Insights into the mechanisms underlying efficient Rhizodegradation of PAHs in biochar-amended soil: From microbial communities to soil metabolomics

The combined effects of biochar amendment and the rhizosphere on the soil metabolic microbiome during the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil remain unknown. In this study, we attempted to characterize a PAH degradation network by coupling the direct PAH degradation with soil carbon cycling. From microbial community structure and functions to metabolic pathways, we revealed the modulation strategies by which biochar and the rhizosphere benefited PAH degradation in soil. Firstly, some PAH degraders were enriched by biochar and the rhizosphere, and their combination promoted the cooperation among these PAH degraders. Simultaneously, under the combined effects of biochar and the rhizosphere, the functional genes participating in upstream PAH degradation were greatly upregulated. Secondly, there were strong co-occurrences between soil microbial community members and metabolites, in particular, some PAH degraders and the metabolites, such as PAH degradation products or common carbon resources, were highlighted in the networks. It shows that the overall downstream carbon metabolism of PAH degradation was also greatly upregulated by the combined effects of biochar and plant roots, showing good survival of the soil microbiome and contributing to PAH biodegradation. Taken together, both soil carbon metabolism and direct contaminant biodegradation are likely to be modulated by the combined effects of biochar and plant roots, jointly benefitting to PAH degradation by soil microbiome. Our study is the first to link PAH degradation with native carbon metabolism by coupling sequencing and soil metabolomics technology, providing new insights into a systematic understanding of PAH degradation by indigenous soil microbiome and their networks.

Sphingomonas: from diversity and genomics to functional role in environmental remediation and plant growth

The species belonging to the Sphingomonas genus possess multifaceted functions ranging from remediation of environmental contaminations to producing highly beneficial phytohormones, such as sphingan and gellan gum. Recent studies have shown an intriguing role of Sphingomonas species in the degradation of organometallic compounds. However, the actual biotechnological potential of this genus requires further assessment. Some of the species from the genus have also been noted to improve plant-growth during stress conditions such as drought, salinity, and heavy metals in agricultural soil. This role has been attributed to their potential to produce plant growth hormones e.g. gibberellins and indole acetic acid. However, the current literature is scattered, and some of the important areas, such as taxonomy, phylogenetics, genome mapping, and cellular transport systems, are still being overlooked in terms of elucidation of the mechanisms behind stress-tolerance and bioremediation. In this review, we elucidated the prospective role and function of this genus for improved utilization during environmental biotechnology.

Petroleum Hydrocarbon Contamination in Terrestrial Ecosystems-Fate and Microbial Responses

Petroleum hydrocarbons represent the most frequent environmental contaminant. The introduction of petroleum hydrocarbons into a pristine environment immediately changes the nature of that environment, resulting in reduced ecosystem functionality. Natural attenuation represents the single, most important biological process which removes petroleum hydrocarbons from the environment. It is a process where microorganisms present at the site degrade the organic contaminants without the input of external bioremediation enhancers (i.e., electron donors, electron acceptors, other microorganisms or nutrients). So successful is this natural attenuation process that in environmental biotechnology, bioremediation has developed steadily over the past 50 years based on this natural biodegradation process. Bioremediation is recognized as the most environmentally friendly remediation approach for the removal of petroleum hydrocarbons from an environment as it does not require intensive chemical, mechanical, and costly interventions. However, it is under-utilized as a commercial remediation strategy due to incomplete hydrocarbon catabolism and lengthy remediation times when compared with rival technologies. This review aims to describe the fate of petroleum hydrocarbons in the environment and discuss their interactions with abiotic and biotic components of the environment under both aerobic and anaerobic conditions. Furthermore, the mechanisms for dealing with petroleum hydrocarbon contamination in the environment will be examined. When petroleum hydrocarbons contaminate land, they start to interact with its surrounding, including physical (dispersion), physiochemical (evaporation, dissolution, sorption), chemical (photo-oxidation, auto-oxidation), and biological (plant and microbial catabolism of hydrocarbons) interactions. As microorganism (including bacteria and fungi) play an important role in the degradation of petroleum hydrocarbons, investigations into the microbial communities within contaminated soils is essential for any bioremediation project. This review highlights the fate of petroleum hydrocarbons in tertial environments, as well as the contributions of different microbial consortia for optimum petroleum hydrocarbon bioremediation potential. The impact of high-throughput metagenomic sequencing in determining the underlying degradation mechanisms is also discussed. This knowledge will aid the development of more efficient, cost-effective commercial bioremediation technologies.

Soil bacterial community dynamics following surfactant addition and bioaugmentation in pyrene-contaminated soils

Because of their toxic properties, polycyclic aromatic hydrocarbons (PAHs) are designated as priority pollutants. The low solubility and strong sorption of PAHs in soil often limits bioremediation. To increase PAH bioavailability and enhance microbial degradation, surfactants are often added to contaminated soils. However, the effects of surfactants on the PAH degradation capacities of soil microbes are generally neglected. In this study, 16S rRNA gene high-throughput sequencing was used to evaluate changes in the soil microbial community after the application of rhamnolipid biosurfactant or Brij-35 surfactant and Mycobacterium vanbaalenii PYR-1 bioaugmentation over a 50-d mineralization study in two soils contaminated with pyrene at 10 mg kg^-1. The introduction of pyrene in both soils resulted in an increase in Firmicutes and a decrease in microbial richness and Shannon diversity index. Amendment of rhamnolipid at 1,400 μg g^-1 to the native clay soil resulted in a decrease in Bacillus from 48% to 2%, which was accompanied with an increase in Mycoplana that accounted for 67% of the total genera relative abundance. Phylogenetic investigation of communities by reconstruction of unobserved states was used to predict the activity of functional genes involved in the PAH degradation KEGG pathway and determined that M. vanbaalenii PYR-1 bioaugmentation resulted in an increased number of functional genes utilized in PAH biodegradation. Results of this study provide a better understanding of the soil microbial dynamics in response to surfactant amendments in addition to bioaugmentation of a PAH-degrading microbe. This knowledge contributes to successful and efficient surfactant-enhanced bioremediation of PAH-contaminated soils.

Mitigation of environmental pollution by genetically engineered bacteria - Current challenges and future perspectives

Industries are the paramount driving force for the economic and technological development of society. However, the flourishing industrialization and unimpeded growth of current production unit's result in widespread environmental pollution due to increased discharge of wastes loaded with baleful, hazardous, and carcinogenic contaminants. Physicochemical-based remediation means are costly, create a secondary disposal problem and remain inadequate for pollution mitigating because of the continuous emergence of new recalcitrant pollutants. Due to eco-friendly, social acceptance, and lesser health hazards, microbial bioremediation has received considerable global attention for pollution abatement. Moreover, with the recent advancement in biotechnology and microbiology, genetically engineered bacteria with high ability to remove environmental pollutants are widely used in the fields of environmental restoration, resulting in the bioremediation in a more viable and eco-friendly way. This review summarized the advantages of genetically engineered bacteria and their application in the treatment of a wide variety of environmental contaminants such as synthetic dyestuff, heavy metal, petroleum hydrocarbons, polychlorinated biphenyls, phenazines and agricultural chemicals which will include herbicides, pesticides, and fertilizers. Considering the risk of genetic material exchange by using genetically engineered bacteria, the challenges and limitations associated with the application of recombinant bacteria on contaminated sites are also discussed. An integrated microbiological, biological and ecological acquaintance accompanied by field engineering designs are the desired features for effective in situ bioremediation of hazardous waste polluted sites by recombinant bacteria.

Influence of bacterial community composition and soil factors on the fate of phenanthrene and benzo[a]pyrene in three contrasting farmland soils

The fate of polycyclic aromatic hydrocarbons (PAHs) determines their potential risk in soil, which may be directly affected by abiotic conditions and indirectly through the changes in decomposer communities. In comparison, the indirect effects on the fate remain largely elusive. In this study, the fate of phenanthrene and benzo[a]pyrene and the corresponding bacterial changes were investigated in three contaminated farmland soils using a ¹⁴C tracer method and Miseq sequencing. The results showed that most benzo[a]pyrene was consistently extractable with dichloromethane (DCM) after the 60-day incubation (60.4%-78.2%), while phenanthrene was mainly mineralized to CO₂ during the 30-day incubation (40.4%-58.7%). Soils from Guangzhou (GZ) showed a different distribution pattern of ¹⁴C-PAHs exemplified by low mineralization and disparate bound residue formation. The PAH fate in the Shenyang (SY) and Nanjing (NJ) soils were similar to each other than to that in the GZ soil. The fate in the GZ soil seemed to be linked to the distinct edaphic properties, such as organic matter content, however soil microbial community could have influenced the distribution pattern of PAHs. This potential role of microorganisms was reflected by the unique changes in the copy numbers of Gram positive RHD_α gene, and by the distinct shifts in bacterial community composition during the incubation. A quite different shift in bacterial communities was found in the GZ microcosms which may influence PAH mineralization and non-extractable residue (NER) formation.

Combined effects of maize straw biochar and oxalic acid on the dissipation of polycyclic aromatic hydrocarbons and microbial community structures in soil: A mechanistic study

Whether the rhizodegradation of organic contaminants occurs in biochar- amended soil and its potential mechanisms have rarely been reported. Therefore, a study was conducted to investigate the combined effects of root exudates and biochar on the dissipation of polycyclic aromatic hydrocarbons (PAHs) and on the microbial community structures in soil. As a major component of the root exudates of ryegrass, oxalic acid (OA) significantly enhanced the dissipation of high- and low-ring PAHs in the studied soil with or without maize straw biochar amendment (p < 0.05). However, biochar alone enhanced only the dissipation of high-ring PAHs. The activities of three enzymes (urease, polyphenol oxidase and dehydrogenase) were the highest in soil amended with both maize straw biochar and 0.5 mg kg^-1 of OA. Moreover, soil microbial biomass and the abundances of genera and genes associated with PAH degradation were significantly enhanced with the tandem application of biochar and OA (p < 0.05). These changes led to a synergetic effect of biochar and OA on the shifts in microbial community structures and on the dissipation of PAHs, especially for high-ring PAHs. The results in this study suggested that a combined biochar-rhizosphere approach should be a feasible remediation strategy for PAH-contaminated soil.

Biostimulation potentials of corn steep liquor in enhanced hydrocarbon degradation in chronically polluted soil

The effects of corn steep liquor (CSL) on hydrocarbon degradation and microbial community structure and function was evaluated in field-moist soil microcosms. Chronically polluted soil treated with CSL (AB4) and an untreated control (3S) was compared over a period of 6 weeks. Gas chromatographic fingerprints of residual hydrocarbons revealed removal of 95.95% and 94.60% aliphatic and aromatic hydrocarbon fractions in AB4 system with complete disappearance of nC₁-nC₈, nC₁₀, nC₁₅, nC₂₀-nC₂₃ aliphatics and aromatics such as naphthalene, acenaphthylene, fluorene, phenanthrene, pyrene, benzo(a)anthracene, and indeno(123-cd)pyrene in 42 days. In 3S system, there is removal of 61.27% and 66.58% aliphatic and aromatic fractions with complete disappearance of nC₂ and nC₂₁ aliphatics and naphthalene, acenaphthylene, fluorene, phenanthrene, pyrene, and benzo(a)anthracene aromatics in 42 days. Illumina shotgun sequencing of the DNA extracted from the two systems showed the preponderance of Actinobacteria (31.46%) and Proteobacteria (38.95%) phyla in 3S and AB4 with the dominance of Verticillium (22.88%) and Microbacterium (8.16%) in 3S, and Laceyella (24.23%), Methylosinus (8.93%) and Pedobacter (7.73%) in AB4. Functional characterization of the metagenomic reads revealed diverse metabolic potentials and adaptive traits of the microbial communities in the two systems to various environmental stressors. It also revealed the exclusive detection of catabolic enzymes in AB4 system belonging to the aldehyde dehydrogenase superfamily. The results obtained in this study showed that CSL is a potential resource for bioremediation of hydrocarbon-polluted soils.

Distribution of bacterial polycyclic aromatic hydrocarbon (PAH) ring-hydroxylating dioxygenases genes in oilfield soils and mangrove sediments explored by gene-targeted metagenomics

PAH ring-hydroxylating dioxygenases (PAH-RHDα) gene, a useful biomarker for PAH-degrading bacteria, has been widely used to examine PAH-degrading bacterial community in different contaminated sites. However, the distribution of PAH-RHDα genes in oilfield soils and mangrove sediments and their relationship with environmental factors still remain largely unclear. In this study, gene-targeted metagenomics was first used to investigate the diversity of PAH-degrading bacterial communities in oilfield soils and mangrove sediments. The results showed that higher diversity of PAH-degrading bacteria in the studied samples was revealed by gene-targeted metagenomics than traditional clone library analysis. Pseudomonas, Burkholderia, Ralstonia, Polymorphum gilvum, Mycobacterium, Sciscionella marina, Rhodococcus, and potential new degraders were prevailed in the oilfield area. For mangrove sediments, novel PAH degraders and Mycobacterium were predominated. The spatial distribution of PAH-RHDα gene was dependent on geographical location and regulated by local environmental variables. PAH content played a key role in shaping PAH-degrading bacterial communities in the studied samples, which would enrich PAH-degrading bacterial population and decrease PAH-degrading bacterial diversity. This work brings a more comprehensive and some new insights into the distribution and biodegradation potential of PAH-degrading bacteria in soil and sediments ecosystems.

Bioremediation of Polluted Soil Sites with Crude Oil Hydrocarbons Using Carrot Peel Waste

The biostimulation potentials of carrot peel waste and carob kibbles for bioremediation of crude petroleum-oil polluted soil were investigated. Temperature, pH, moisture, total petroleum hydrocarbon (TPH), and changes in microbial counts during 45 days were monitored when 4 mL of carrot peel waste or carob kibbles media were added to 200 g of crude oil polluted soil samples. Gas chromatography-flame ionization detection (GC-FID) was used to compare hydrocarbon present in the crude oil polluted soil and in pure fuel, composition of crude oil polluted soil was analyzed by X-ray diffraction (XRD), and the TPH was measured by distillation using distiller mud. The results showed that, at the end of experiments, the concentration of TPH decreased in crude oil polluted soil containing carrot peel waste with a percentage of 27 ± 1.90% followed by crude oil polluted soil containing carob kibbles (34 ± 1.80%) and in the unamended control soil (36 ± 1.27%), respectively. The log [Colony Forming Unit (CFU)/g] of total heterotrophic bacteria in the crude oil polluted soil increased from 10.46 ± 0.91 to 13.26 ± 0.84 for carrot peel waste, from 11.01 ± 0.56 to 11.99 ± 0.77 for carob kibbles and from 8.18 ± 0.39 to 8.84 ± 0.84 for control, respectively. Such results demonstrated that carrot peel could be used to enhance activities of the microbial hydrocarbon-degrading bacteria during bioremediation of crude petroleum-oil polluted soil.

Efficiency of surfactant-enhanced bioremediation of aged polycyclic aromatic hydrocarbon-contaminated soil: Link with bioavailability and the dynamics of the bacterial community

Shifts in the bacterial-community dynamics, bioavailability, and biodegradation of polycyclic aromatic hydrocarbons (PAHs) of chronically contaminated soil were analyzed in Triton X-100-treated microcosms at the critical micelle concentration (T-CMC) and at two sub-CMC doses. Only the sub-CMC-dose microcosms reached sorbed-PAH concentrations significantly lower than the control: 166±32 and 135±4mgkg^-1 dry soil versus 266±51mgkg^-1; consequently an increase in high- and low-molecular-weight PAHs biodegradation was observed. After 63days of incubation pyrosequencing data evidenced differences in diversity and composition between the surfactant-modified microcosms and the control, with those with sub-CMC doses containing a predominance of the orders Sphingomonadales, Acidobacteriales, and Gemmatimonadales (groups of known PAHs-degrading capability). The T-CMC microcosm exhibited a lower richness and diversity index with a marked predominance of the order Xanthomonadales, mainly represented by the Stenotrophomonas genus, a PAHs- and Triton X-100-degrading bacterium. In the T-CMC microcosm, whereas the initial surface tension was 35mNm^-1, after 63days of incubation an increase up to 40mNm^-1 was registered. The previous observation and the gas-chromatography data indicated that the surfactant may have been degraded at the CMC by a highly selective bacterial community with a consequent negative impact on PAHs biodegradation. This work obtained strong evidence for the involvement of physicochemical and biologic influences determining the different behaviors of the studied microcosms. The results reported here contribute significantly to an optimization of, surfactant-enhanced bioremediation strategies for chronically contaminated soil since the application of doses below the CMC would reduce the overall costs.

Mechanisms of biochar reducing the bioaccumulation of PAHs in rice from soil: Degradation stimulation vs immobilization

This study aimed to elucidate the mechanisms by which biochar reduces the bioaccumulation of polycyclic aromatic hydrocarbons (PAHs) in rice under anaerobic conditions. Corn straw- or bamboo-derived biochar pyrolyzed at 300 °C and 700 °C (CB300 or BB700), respectively, was amended into flooded PAH-contaminated soil. After harvest, 2% CB300, 0.5% BB700 or 2% BB700 amendments reduced the bioaccumulation of PAHs in rice root, especially that of high-molecular-weight PAHs (p < .05). Total PAH concentrations were higher, and their bioavailable concentrations were lower in BB700-amended soils than the control. The stimulation of PAH desorption from BB by low-molecular-weight organic acids (LMWOAs) was gentle and did not significantly retard the adsorption of PAHs on BB700, indicating that BB700 reduced PAH bioavailability primarily via immobilization. The total and bioavailable concentrations of PAHs were both lower in the 2% CB300-treated soils than the control. LMWOAs facilitated PAH release from CB300-amended soils, thus increasing the bioavailability of immobilized PAHs. The relative abundances of the bacteria, functional genes, and methanogens involved in PAH anaerobic degradation were significantly higher in the 2% CB300 treatment than other treatments. Fast PAH dissipation in soil amended with 2% CB300 may be attributed to the increased bioavailability of immobilized PAHs and enhanced biodegradation, both of which were induced by LMWOAs and CB. In summary, biochar types and root presence jointly affected the mechanisms by which biochar reduced the bioaccumulation of PAHs in rice under anaerobic conditions.

Autochthonous Bioaugmentation-Modified Bacterial Diversity of Phenanthrene Degraders in PAH-Contaminated Wastewater as Revealed by DNA-Stable Isotope Probing

To reveal the mechanisms of autochthonous bioaugmentation (ABA) in wastewater contaminated with polycyclic aromatic hydrocarbons (PAHs), DNA-stable-isotope-probing (SIP) was used in the present study with the addition of an autochthonous microorganism Acinetobacter tandoii LJ-5. We found LJ-5 inoculum produced a significant increase in phenanthrene (PHE) mineralization, but LJ-5 surprisingly did not participate in indigenous PHE degradation from the SIP results. The improvement of PHE biodegradation was not explained by the engagement of LJ-5 but attributed to the remarkably altered diversity of PHE degraders. Of the major PHE degraders present in ambient wastewater ( Rhodoplanes sp., Mycobacterium sp., Xanthomonadaceae sp. and Enterobacteriaceae sp.), only Mycobacterium sp. and Enterobacteriaceae sp. remained functional in the presence of strain LJ-5, but five new taxa Bacillus, Paenibacillus, Ammoniphilus, Sporosarcina, and Hyphomicrobium were favored. Rhodoplanes, Ammoniphilus, Sporosarcina, and Hyphomicrobium were directly linked to, for the first time, indigenous PHE biodegradation. Sequences of functional PAH-RHD_α genes from heavy fractions further proved the change in PHE degraders by identifying distinct PAH-ring hydroxylating dioxygenases between ambient degradation and ABA. Our findings indicate a new mechanism of ABA, provide new insights into the diversity of PHE-degrading communities, and suggest ABA as a promising in situ bioremediation strategy for PAH-contaminated wastewater.

Goethite promoted biodegradation of 2,4-dinitrophenol under nitrate reduction condition

Iron oxide may interact with other pollutants in the aquatic environments and further influence their toxicity, transport and fate. The current study was conducted to investigate the biodegradation of 2,4-dinitrophenol (2,4-DNP) in the presence of iron oxide of goethite under anoxic condition using nitrate as the electron acceptor. Experiment results showed that the degradation rate of 2,4-DNP was improved by goethite. High performance liquid chromatography-mass spectra analysis results showed that goethite promoted degradation and transformation of 2,4-diaminophenol and 2-amino-4-nitrophenol (2-nitro-4-aminophenol). Microbial community analysis results showed that the abundance of Actinobacteria, which have the potential ability to degrade PAHs, was increased when goethite was available. This might partially explain the higher degradation of 2,4-DNP. Furthermore, another bacterium of Desulfotomaculum reducens which could reduce soluble Fe(III) and nitrate was also increased. Results further confirmed that nanomaterials in the aquatic environment will influence the microbial community and further change the transformation process of toxic pollutants.

Identification of biphenyl 2, 3-dioxygenase and its catabolic role for phenazine degradation in Sphingobium yanoikuyae B1

Phenazines are important nitrogen-containing secondary metabolites that display a range of biological functionalities. However, these compounds have shown lethal effects on humans and, the fate of phenazine in the ecosystem remains uncertain. In this study, we investigated that Sphingobium yanoikuyae B1 could utilize phenazine as a sole carbon source for growth. Intermediate produced during phenazine degradation was purified and identified as 1, 2-dihydrogen 1, 2-dihydroxy phenazine. Biphenyl 2, 3-dioxygenase was determined to be the initial dioxygenase for phenazine degradation through gene cloning and whole cell transformation techniques. Phenazine was converted to 1, 2-dihydrogen 1, 2-dihydroxy phenazine through hydrogenation and hydroxylation, which then transformed to 2-hydroxy phenazine through spontaneous dehydration. ThebphA1fA2f, were evidenced to be the only genes encoding the initial dioxygenase for phenazine degradation. BphB (dihydrodiol dehydrogenase) and BphC (2,3-dihydroxybiphenyl 1,2-dioxygenase) did not exhibit any 1, 2-dihydrogen 1, 2-dihydroxy phenazine and 1, 2-dihydroxy phenazine degradation capability, suggesting no contribution in phenazine degradation. Phylogenetic analysis of the dioxygenases demonstrated enormous biodegradation potential in strain B1. In conclusion, this study opens up new possibilities in better understanding the phenazine degradation in the environment.

Biochar reduces the bioaccumulation of PAHs from soil to carrot (Daucus carota L.) in the rhizosphere: A mechanism study

The aim of this study was to reveal the mechanisms on how biochar reduces bioaccumulation of polycyclic aromatic hydrocarbons (PAHs) in tuberous vegetables. Corn straw-derived biochar pyrolyzed at 300°C (CB300) or bamboo-derived biochar pyrolyzed at 700°C (BB700) was amended into PAH-contaminated soil planted with carrot (Daucus carota L.). After 150days, 2% CB300 or 2% BB700 amendments significantly reduced the bioaccumulation of PAHs in carrot root (p<0.05), especially for high-molecular-weight PAHs. In the non-rhizosphere, either CB300 or BB700 suppressed PAH dissipation and decreased the bioavailability via adsorption processes. Compared to the control, the total concentration of PAHs in the rhizosphere was higher in the 2% BB700 treatment but the bioavailable concentration was lower. This indicates that BB700 decreased the bioavailability of PAHs primarily via immobilization (adsorption processes). By contrast, the total and bioavailable PAH concentrations were both lower in the 2% CB300 treatment than those in the control. The abundance of bacteria such as Arthrobacter and Flavobacterium and the total number of genes playing important roles in microbial PAH degradation processes increased significantly (p<0.05), which were likely responsible for the rapid dissipation of PAHs in the 2% CB300 treatment in the rhizosphere. These results indicate that CB300 decreased the PAH bioavailability primarily via increasing degradation of PAHs by indigenous microorganisms. The two biochars both showed better effectiveness at reducing the bioavailability of high-molecular-weight PAHs than the low-molecular-weight PAHs in the rhizosphere. Therefore, the mechanisms on how biochar reduces the PAH uptake into carrot are dependent on the type of biochar (e.g., pyrolysis temperature and feedstock) and root presence.

Diversity and temporal shifts of the bacterial community associated with a toxic cyanobacterial bloom: An interplay between microcystin producers and degraders

The biodegradation of microcystins (MCs) by bacteria constitutes an important process in freshwater ecosystems to prevent the accumulation of toxins. However, little is known about the diversity and the seasonal dynamics of the bacterial community composition (BCC) involved in the degradation of MCs in nature. To explore these BCC shifts, high-throughput sequencing was used to analyse the 16S rRNA, mcyE and mlrA genes during a year in a freshwater reservoir with a toxic cyanobacterial bloom episode. The analysis of the mcyE and mlrA genes from water samples revealed the coexistence of different MC-producing and MC-degrading genotypes, respectively. The patchy temporal distribution of the mlrA genotypes (from the families Sphingomonadaceae and Xanthomonadaceae) suggests their dissimilar response to environmental conditions and the influence of other factors besides the MCs that may control their presence and relative abundance. During the maximum toxic cyanobacterial biomass and cell lysis, other bacterial taxa that lack mlr genes increased their relative abundance. Among these bacteria, those with a recognized role in the degradation of xenobiotic and other complex organic compounds (e.g., orders Myxococcales, Ellin6067, Spirobacillales and Cytophagales) were the most representative and suggest their possible involvement in the removal of MCs in the environment.

Indigenous 14C-phenanthrene biodegradation in "pristine" woodland and grassland soils from Norway and the United Kingdom

In this study, the indigenous microbial mineralisation of ¹⁴C-phenanthrene in seven background soils (four from Norwegian woodland and three from the UK (two grasslands and one woodland)) was investigated. ∑PAHs ranged from 16.39 to 285.54 ng g^-1 dw soil. Lag phases (time before ¹⁴C-phenanthrene mineralisation reached 5%) were longer in all of the Norwegian soils and correlated positively with TOC, but negatively with ∑PAHs and phenanthrene degraders for all soils. ¹⁴C-phenanthrene mineralisation in the soils varied due to physicochemical properties. The results show that indigenous microorganisms can adapt to ¹⁴C-phenanthrene mineralisation following diffuse PAH contamination. Considering the potential of soil as a secondary PAH source, these findings highlight the important role of indigenous microflora in the processing of PAHs in the environment.

Distribution of Anaerobic Hydrocarbon-Degrading Bacteria in Soils from King George Island, Maritime Antarctica

Anaerobic diesel fuel Arctic (DFA) degradation has already been demonstrated in Antarctic soils. However, studies comparing the distribution of anaerobic bacterial groups and of anaerobic hydrocarbon-degrading bacteria in Antarctic soils containing different concentrations of DFA are scarce. In this study, functional genes were used to study the diversity and distribution of anaerobic hydrocarbon-degrading bacteria (bamA, assA, and bssA) and of sulfate-reducing bacteria (SRB-apsR) in highly, intermediate, and non-DFA-contaminated soils collected during the summers of 2009, 2010, and 2011 from King George Island, Antarctica. Signatures of bamA genes were detected in all soils analyzed, whereas bssA and assA were found in only 4 of 10 soils. The concentration of DFA was the main factor influencing the distribution of bamA-containing bacteria and of SRB in the analyzed soils, as shown by PCR-DGGE results. bamA sequences related to genes previously described in Desulfuromonas, Lautropia, Magnetospirillum, Sulfuritalea, Rhodovolum, Rhodomicrobium, Azoarcus, Geobacter, Ramlibacter, and Gemmatimonas genera were dominant in King George Island soils. Although DFA modulated the distribution of bamA-hosting bacteria, DFA concentration was not related to bamA abundance in the soils studied here. This result suggests that King George Island soils show functional redundancy for aromatic hydrocarbon degradation. The results obtained in this study support the hypothesis that specialized anaerobic hydrocarbon-degrading bacteria have been selected by hydrocarbon concentrations present in King George Island soils.