Biodegradation of phenol by cold-adapted bacteria from Antarctic soils

Bioremediation for the recovery of oil polluted marine environment, opportunities and challenges approaching the Blue Growth

The Blue Growth strategy promises a sustainable use of marine resources for the benefit of the society. However, oil pollution in the marine environment is still a serious issue for human, animal, and environmental health; in addition, it deprives citizens of the potential economic and recreational advantages in the affected areas. Bioremediation, that is the use of bio-resources for the degradation of pollutants, is one of the focal themes on which the Blue Growth aims to. A repertoire of marine-derived bio-products, biomaterials, processes, and services useful for efficient, economic, low impact, treatments for the recovery of oil-polluted areas has been demonstrated in many years of research around the world. Nonetheless, although bioremediation technology is routinely applied in soil, this is not still standardized in the marine environment and the potential market is almost underexploited. This review provides a summary of opportunities for the exploiting and addition of value to research products already validated. Moreover, the review discusses challenges that limit bioremediation in marine environment and actions that can facilitate the conveying of valuable products/processes towards the market.

Effects of heavy metals on bacterial growth parameters in degradation of phenol by an Antarctic bacterial consortium

Antarctica has often been perceived as a pristine continent until the recent few decades as pollutants have been observed accruing in the Antarctic environment. Irresponsible human activities such as accidental oil spills, waste incineration and sewage disposal are among the primary anthropogenic sources of heavy metal contaminants in Antarctica. Natural sources including animal excrement, volcanism and geological weathering also contribute to the increase of heavy metals in the ecosystem. A microbial growth model is presented for the growth of a bacterial cell consortium used in the biodegradation of phenol in media containing different metal ions, namely arsenic (As), cadmium (Cd), aluminium (Al), nickel (Ni), silver (Ag), lead (Pb) and cobalt (Co). Bacterial growth was inhibited by these ions in the rank order of Al < As < Co < Pb < Ni < Cd < Ag. Greatest bacterial growth occurred in 1 ppm Al achieving an OD600 of 0.985 and lowest in 1 ppm Ag with an OD600 of 0.090. At a concentration of 1.0 ppm, Ag had a considerable effect on the bacterial consortium, inhibiting the degradation of phenol, whereas this concentration of the other metal ions tested had no effect on degradation. The biokinetic growth model developed supports the suitability of the bacterial consortium for use in phenol degradation.

Autochthonous psychrophilic hydrocarbonoclastic bacteria and its ecological function in contaminated cold environments

Petroleum hydrocarbon (PH) pollution has mostly been caused by oil exploration, extraction, and transportation activities in colder regions, particularly in the Arctic and Antarctic regions, where it serves as a primary source of energy. Due to the resilience feature of nature, such polluted environments become the realized ecological niches for a wide community of psychrophilic hydrocarbonoclastic bacteria (PHcB). In contrast, to other psychrophilic species, PHcB is extremely cold-adapted and has unique characteristics that allow them to thrive in greater parts of the cold environment burdened with PHs. The stated group of bacteria in its ecological niche aids in the breakdown of litter, turnover of nutrients, cycling of carbon and nutrients, and bioremediation. Although such bacteria are the pioneers of harsh colder environments, their growth and distribution remain under the influence of various biotic and abiotic factors of the environment. The review discusses the prevalence of PHcB community in colder habitats, the metabolic processes involved in the biodegradation of PH, and the influence of biotic and abiotic stress factors. The existing understanding of the PH metabolism by PHcB offers confirmation of excellent enzymatic proficiency with high cold stability. The discovery of more flexible PH degrading strategies used by PHcB in colder environments could have a significant beneficial outcome on existing bioremediation technologies. Still, PHcB is least explored for other industrial and biotechnological applications as compared to non-PHcB psychrophiles. The present review highlights the pros and cons of the existing bioremediation technologies as well as the potential of different bioaugmentation processes for the effective removal of PH from the contaminated cold environment. Such research will not only serve to investigate the effects of pollution on the basic functional relationships that form the cold ecosystem but also to assess the efficacy of various remediation solutions for diverse settings and climatic conditions.

Antarctic heavy metal pollution and remediation efforts: state of the art of research and scientific publications

In Antarctica, human activities have been reported to be the major cause of the accumulation of heavy metal contaminants. A comprehensive bibliometric analysis of publications on heavy metal contamination in Antarctica from year 2000 to 2020 was performed to obtain an overview of the current landscape in this line of research. A total of 106 documents were obtained from Scopus, the largest citation database. Extracted data were analysed, and VOSviewer software was used to visualise trends. The result showed an increase in publications and citations in the past 20 years indicating the rising interest on heavy metal contamination in the Antarctic region. Based on the analysis of keywords, the publications largely discuss various types of heavy metals found in the Antarctic water and sediment. The analysis on subject areas detects multiple disciplines involved, wherein the environmental science was well-represented. The top countries and authors producing the most publication in this field were from Australia, China, Brazil and Chile. Numerous efforts have been exercised to investigate heavy metal pollution and its mitigation approaches in the region in the past decades. This paper not only is relevant for scholars to understand the development status and trends in this field but also offers clear insights on the future direction of Antarctic heavy metal contamination and remediation research.

Biodegradation of Petroleum Sludge by Methylobacterium sp. Strain ZASH

A bacterium was isolated from sludge-contaminated soil in a petroleum refinery and tested for its ability to degrade aliphatic hydrocarbon compounds present in petroleum sludge. The isolate was grown on minimal salt media agar supplemented with 1% (w/v) petroleum sludge. The isolate was tentatively identified as Methylobacterium s p. s t rain ZASH based on the partial 16s rDNA molecular phylogeny. The bacterium grew optimally between the temperatures of 30°C and 35°C, pH 7 and 7.5, 0.5% and 1.5% (v/v) Tween 80 as the surfactant, and between 1% and 2% (w/v) peptone as the nitrogen source. The constants derived from the Haldane equation were μmax = 0.039 hr-1, Ks = 0.385% (w/v) total petroleum hydrocarbons (TPH) or 3,850 mg/L TPH, and Ki =1.12% (w/v) TPH or 11,200 mg/L. The maximum biodegradation rate exhibited by this strain was 19 mg/L/hr at an initial TPH concentration of 10,000 mg/L. Gas chromatography analysis revealed that after 15 days the strain was able to degrade all aliphatic n-alkanes investigated with different efficiencies. Shorter n-alkanes were generally degraded more rapidly than longer n-alkanes with 90% removal for C-12 compared to only 30% removal for C-36. The addition of sawdust did not improve bacterial degradation of petroleum hydrocarbons, but it assisted in the removal of remaining undegraded hydrocarbons through adsorption.

Synergistic PAH biodegradation by a mixed bacterial consortium: based on a multi-substrate enrichment approach

Polycyclic aromatic hydrocarbon (PAH) contamination in the environment involves multiple PAHs and various intermediates produced during the microbial metabolic process. A multi-substrate enrichment approach was proposed to develop a mixed bacterial community (MBC) from the activated sludge of a coking wastewater plant. The degradation performance of MBC was evaluated under different initial concentrations of PAHs (25-200 mg/L), temperature (20-35 °C), pH (5.0-9.0), salinity (0-10 g/L NaCl), and coexisting substrates (catechol, salicylic acid, and phthalic acid). The results showed that the degradation rates of phenanthrene and pyrene in all treatments were up to (99 ± 0.71)% and (99 ± 0.90)% after incubation of 5 days, respectively, indicating excellent biodegradation ability of PAHs by MBC. Furthermore, 16S rRNA gene amplicon sequencing analysis revealed that Pseudomonas was dominant, while Burkholderia had the largest proportion in acidic (pH = 5.0) and saline (10 g/L NaCl) environments. However, the proportion of dominant bacteria in MBC was markedly affected by intermediate metabolites. It was shown that MBC had a higher degradation rate of PAHs in the coexisting matrix due to the timely clearance of intermediates reducing the metabolic burden. Overall, our study provided valuable information to help design an effective strategy for the bioremediation of PAHs in complex environments.

Metabolic Pathway of Phenol Degradation of a Cold-Adapted Antarctic Bacteria, Arthrobacter sp

Phenol is an important pollutant widely discharged as a component of hydrocarbon fuels, but its degradation in cold regions is challenging due to the harsh environmental conditions. To date, there is little information available concerning the capability for phenol biodegradation by indigenous Antarctic bacteria. In this study, enzyme activities and genes encoding phenol degradative enzymes identified using whole genome sequencing (WGS) were investigated to determine the pathway(s) of phenol degradation of Arthrobacter sp. strains AQ5-05 and AQ5-06, originally isolated from Antarctica. Complete phenol degradative genes involved only in the ortho-cleavage were detected in both strains. This was validated using assays of the enzymes catechol 1,2-dioxygenase and catechol 2,3-dioxygenase, which indicated the activity of only catechol 1,2-dioxygenase in both strains, in agreement with the results from the WGS. Both strains were psychrotolerant with the optimum temperature for phenol degradation, being between 10 and 15 °C. This study suggests the potential use of cold-adapted bacteria in the bioremediation of phenol pollution in cold environments.

Microbiome structure in biofilms from a volcanic island in Maritime Antarctica investigated by genome-centric metagenomics and metatranscriptomics

Antarctica is the coldest and driest continent on Earth, characterized by polyextreme environmental conditions, where species adapted form complex networks of interactions. Microbial communities growing in these harsh environments can form biofilms that help the associated species to survive and thrive. A rich body of knowledge describes environmental biofilm communities; however, most studies have focused on dominant community members rather than functional complexity and metabolic potential. To overcome these limitations, the present study used genome-centric metagenomics to describe two biofilm samples subjected to different temperature collected in Deception Island, Maritime Antarctica. The results unraveled a complex biofilm microbiome represented by 180 metagenome-assembled genomes. The potential metabolic interactions were investigated using metabolic flux balance analysis and revealed that purple bacteria are the community members with the highest correlations with other bacteria. Due to their predicted mixotrophic behavior, they may play a crucial role in the microbiome, likely supporting the heterotrophic species in biofilms. Metatranscriptomics results revealed that the chaperone system and proteins counteracting ROS and toxic compounds have a major role in maintaining bacterial cell homeostasis in sediments of volcanic origin.

Genotype to ecotype in niche environments: adaptation of Arthrobacter to carbon availability and environmental conditions

Niche environmental conditions influence both the structure and function of microbial communities and the cellular function of individual strains. The terrestrial subsurface is a dynamic and diverse environment that exhibits specific biogeochemical conditions associated with depth, resulting in distinct environmental niches. Here, we present the characterization of seven distinct strains belonging to the genus Arthrobacter isolated from varying depths of a single sediment core and associated groundwater from an adjacent well. We characterized genotype and phenotype of each isolate to connect specific cellular functions and metabolisms to ecotype. Arthrobacter isolates from each ecotype demonstrated functional and genomic capacities specific to their biogeochemical conditions of origin, including laboratory-demonstrated characterization of salinity tolerance and optimal pH, and genes for utilization of carbohydrates and other carbon substrates. Analysis of the Arthrobacter pangenome revealed that it is notably open with a volatile accessory genome compared to previous pangenome studies on other genera, suggesting a high potential for adaptability to environmental niches.

Optimisation of Various Physicochemical Variables Affecting Molybdenum Bioremediation Using Antarctic Bacterium, Arthrobacter sp. Strain AQ5-05

The versatility of a rare metal, molybdenum (Mo) in many industrial applications is one of the reasons why Mo is currently one of the growing environmental pollutants worldwide. Traces of inorganic contaminants, including Mo, have been discovered in Antarctica and are compromising the ecosystem. Bioremediation utilising bacteria to transform pollutants into a less toxic form is one of the approaches for solving Mo pollution. Mo reduction is a process of transforming sodium molybdate with an oxidation state of 6+ to Mo-blue, an inert version of the compound. Although there are a few Mo-reducing microbes that have been identified worldwide, only two studies were reported on the microbial reduction of Mo in Antarctica. Therefore, this study was done to assess the ability of Antarctic bacterium, Arthrobacter sp. strain AQ5-05, in reducing Mo. Optimisation of Mo reduction in Mo-supplemented media was carried out using one-factor-at-a-time (OFAT) and response surface methodology (RSM) approaches. Through OFAT, Mo was reduced optimally with substrate concentration of sucrose, ammonium sulphate, and molybdate at 1 g/L, 0.2 g/L, and 10 mM, respectively. The pH and salinity of the media were the best at 7.0 and 0.5 g/L, respectively, while the optimal temperature was at 10 °C. Further optimisation using RSM showed greater Mo-blue production in comparison to OFAT. The strain was able to stand high concentration of Mo and low temperature conditions, thus showing its potential in reducing Mo in Antarctica by employing conditions optimised by RSM.

Recent advances in the biodegradation of azo dyes

As dye demand continues to rapidly increase in the food, pharmaceutical, cosmetic, paper, textile, and leather industries, an industrialization increase is occurring. Meanwhile, the degradation and removal of azo dyes have raised broad concern regarding the hazards posed by these dyes to the ecological environment and human health. Physicochemical treatments have been applied but are hindered by high energy and economic costs, high sludge production, and chemicals handling. Comparatively, the bioremediation technique is an eco-friendly, removal-efficient, and cost-competitive method to resolve the problem. This paper provides scientific and technical information about recent advances in the biodegradation of azo dyes. It expands the biodegradation efficiency, characteristics, and mechanisms of various microorganisms containing bacteria, fungi, microalgae, and microbial consortia, which have been reported to biodegrade azo dyes. In addition, information about physicochemical factors affecting dye biodegradation has been compiled. Furthermore, this paper also sketches the recent development and characteristics of advanced bioreactors.

Statistical Optimisation and Kinetic Studies of Molybdenum Reduction Using a Psychrotolerant Marine Bacteria Isolated from Antarctica

The extensive industrial use of the heavy metal molybdenum (Mo) has led to an emerging global pollution with its traces that can even be found in Antarctica. In response, a reduction process that transforms hexamolybdate (Mo6+) to a less toxic compound, Mo-blue, using microorganisms provides a sustainable remediation approach. The aim of this study was to investigate the reduction of Mo by a psychrotolerant Antarctic marine bacterium, Marinomonas sp. strain AQ5-A9. Mo reduction was optimised using One-Factor-At-a-Time (OFAT) and Response Surface Methodology (RSM). Subsequently, Mo reduction kinetics were further studied. OFAT results showed that maximum Mo reduction occurred in culture media conditions of pH 6.0 and 50 ppt salinity at 15 °C, with initial sucrose, nitrogen and molybdate concentrations of 2.0%, 3.0 g/L and 10 mM, respectively. Further optimization using RSM identified improved optimum conditions of pH 6.0 and 47 ppt salinity at 16 °C, with initial sucrose, nitrogen and molybdate concentrations of 1.8%, 2.25 g/L and 16 mM, respectively. Investigation of the kinetics of Mo reduction revealed Aiba as the best-fitting model. The calculated Aiba coefficient of maximum Mo reduction rate (µmax) was 0.067 h−1. The data obtained support the potential use of marine bacteria in the bioremediation of Mo.

Growth Optimisation and Kinetic Profiling of Diesel Biodegradation by a Cold-Adapted Microbial Consortium Isolated from Trinity Peninsula, Antarctica

Simple Summary

Diesel fuel is very crucial for anthropogenic activities in Antarctica and the surges in annual demand mean higher likelihood of spillages from improper handling during transportation, storage and disposal processes. The impacts can be very extensive or well-contained depending on the scale of the spills as well as the terrain involved. Nevertheless, the freezing temperature and prolonged solar irradiance in the south pole greatly hampered the natural attenuation and photovolatilisation of petrogenic hydrocarbons, contributing to their persistency. The most susceptible groups are the soil microorganisms, mosses, seabirds and pinnipeds as they are easily found near the shore where hydrocarbons spillage is very common. Microbial bioremediation is a well-established approach in restoring many hydrocarbons-polluted areas, thus the current study focused on the optimisation and application of locally isolated microbial consortium to simulate the in situ diesel clean-up process in aqueous medium. This study highlights the ability of the selected consortium to degrade diesel almost completely at moderately low temperature, suggesting its potential application in Antarctic settings.

Abstract

Pollution associated with petrogenic hydrocarbons is increasing in Antarctica due to a combination of increasing human activity and the continent’s unforgiving environmental conditions. The current study focuses on the ability of a cold-adapted crude microbial consortium (BS24), isolated from soil on the north-west Antarctic Peninsula, to metabolise diesel fuel as the sole carbon source in a shake-flask setting. Factors expected to influence the efficiency of diesel biodegradation, namely temperature, initial diesel concentration, nitrogen source type and concentration, salinity and pH were studied. Consortium BS24 displayed optimal cell growth and diesel degradation activity at 1.0% NaCl, pH 7.5, 0.5 g/L NH₄Cl and 2.0% v/v initial diesel concentration during one-factor-at-a-time (OFAT) analyses. The consortium was psychrotolerant based on the optimum growth temperature of 10‒15 °C. In conventionally optimised media, the highest total petroleum hydrocarbons (TPH) mineralisation was 85% over a 7-day incubation. Further optimisation of conditions predicted through statistical response-surface methodology (RSM) (1.0% NaCl, pH 7.25, 0.75 g/L NH₄Cl, 12.5 °C and 1.75% v/v initial diesel concentration) boosted mineralisation to 95% over a 7-day incubation. A Tessier secondary model best described the growth pattern of BS24 in diesel-enriched medium, with maximum specific growth rate, μ_max, substrate inhibition constant, K_i and half saturation constant, K_s, being 0.9996 h⁻¹, 1.356% v/v and 1.238% v/v, respectively. The data obtained suggest the potential of microbial consortia such as BS24 in bioremediation applications in low-temperature diesel-polluted soils.

Genome sequencing of cold-adapted Planococcus bacterium isolated from traditional shrimp paste and protease identification

BACKGROUND

Psychrophiles have evolved to adapt to freezing environments, and cold-adapted enzymes from these organisms can maintain high catalytic activity at low temperature. The use of cold-adapted enzymes has great potential for the revolution of food and molecular biology industries.

RESULTS

In this study, four different strains producing protease were isolated from traditional fermented shrimp paste, one of which, named Planococcus maritimus XJ11 by 16S rRNA nucleotide sequence analysis, exhibited the largest protein hydrolysis clear zone surrounding the colonies. Meanwhile, the strain P. maritimus XJ11 was selected for further investigation because of its great adaptation to low temperature, low salinity and alkaline environment. The enzyme activity assay of P. maritimus XJ11 indicated that the optimum conditions for catalytic activity were pH 10.0 and 40 °C. Moreover, the enzyme also showed an increasing activity with temperatures from 10 to 40 °C and retained more than 67% activity of the maximum over a broad range of salinity (50-150 g L^-1 ). Genome sequencing analysis revealed that strain XJ11 possessed one circular chromosome of 3 282 604 bp and one circular plasmid of 67 339 bp, with a total number of 3293 open reading frames (ORFs). Besides, 21 genes encoding protease, including three serine proteases, were identified through the NR database.

CONCLUSION

Cold-adapted bacterium P. maritimus XJ11 was capable of producing alkaline proteases with high catalytic efficiency at low or moderate temperatures. Furthermore, the favorable psychrophilic and enzymatic characters of strain P. maritimus XJ11 seem to have a promising potential for industrial application. © 2020 Society of Chemical Industry.

The Use of Response Surface Methodology as a Statistical Tool for the Optimisation of Waste and Pure Canola Oil Biodegradation by Antarctic Soil Bacteria

Hydrocarbons can cause pollution to Antarctic terrestrial and aquatic ecosystems, both through accidental release and the discharge of waste cooking oil in grey water. Such pollutants can persist for long periods in cold environments. The native microbial community may play a role in their biodegradation. In this study, using mixed native Antarctic bacterial communities, several environmental factors influencing biodegradation of waste canola oil (WCO) and pure canola oil (PCO) were optimised using established one-factor-at-a-time (OFAT) and response surface methodology (RSM) approaches. The factors include salinity, pH, type of nitrogen and concentration, temperature, yeast extract and initial substrate concentration in OFAT and only the significant factors proceeded for the statistical optimisation through RSM. High concentration of substrate targeted for degradation activity through RSM compared to OFAT method. As for the result, all factors were significant in PBD, while only 4 factors were significant in biodegradation of PCO (pH, nitrogen concentration, yeast extract and initial substrate concentration). Using OFAT, the most effective microbial community examined was able to degrade 94.42% and 86.83% (from an initial concentration of 0.5% (v/v)) of WCO and PCO, respectively, within 7 days. Using RSM, 94.99% and 79.77% degradation of WCO and PCO was achieved in 6 days. The significant interaction for the RSM in biodegradation activity between temperature and WCO concentration in WCO media were exhibited. Meanwhile, in biodegradation of PCO the significant factors were between (1) pH and PCO concentration, (2) nitrogen concentration and yeast extract, (3) nitrogen concentration and PCO concentration. The models for the RSM were validated for both WCO and PCO media and it showed no significant difference between experimental and predicted values. The efficiency of canola oil biodegradation achieved in this study provides support for the development of practical strategies for efficient bioremediation in the Antarctic environment.

Bibliometric Analysis of Hydrocarbon Bioremediation in Cold Regions and a Review on Enhanced Soil Bioremediation

Simple Summary

Anthropogenic activities in cold regions require petroleum oils to support various purposes. With the increased demand of petroleum, accidental oil spills are generated during transportation or refuelling processes. Soil is one of the major victims in petroleum pollution, hence studies have been devoted to find solutions to remove these petroleum hydrocarbons. However, the remote and low-temperature conditions in cold regions hindered the implementation of physical and chemical removal treatments. On the other hand, biological treatments in general have been proposed as an innovative approach to attenuate these hydrocarbon pollutants in soils. To understand the relevancy of biological treatments for cold regions specifically, bibliometric analysis has been applied to systematically analyse studies focused on hydrocarbon removal treatment in a biological way. To expedite the understanding of this analysis, we have summarised these biological treatments and suggested other biological applications in the context of cold conditions.

Abstract

The increased usage of petroleum oils in cold regions has led to widespread oil pollutants in soils. The harsh environmental conditions in cold environments allow the persistence of these oil pollutants in soils for more than 20 years, raising adverse threats to the ecosystem. Microbial bioremediation was proposed and employed as a cost-effective tool to remediate petroleum hydrocarbons present in soils without significantly posing harmful side effects. However, the conventional hydrocarbon bioremediation requires a longer time to achieve the clean-up standard due to various environmental factors in cold regions. Recent biotechnological improvements using biostimulation and/or bioaugmentation strategies are reported and implemented to enhance the hydrocarbon removal efficiency under cold conditions. Thus, this review focuses on the enhanced bioremediation for hydrocarbon-polluted soils in cold regions, highlighting in situ and ex situ approaches and few potential enhancements via the exploitation of molecular and microbial technology in response to the cold condition. The bibliometric analysis of the hydrocarbon bioremediation research in cold regions is also presented.

Five-Year Enhanced Natural Attenuation of Historically Coal-Tar-Contaminated Soil: Analysis of Polycyclic Aromatic Hydrocarbon and Phenol Contents

The objective of this study was to assess the soil pollution on an industrial wasteland, where coal-tar was processed in the period between 1880 and 1997, and subsequent to assess the decline in the content of phenols and polycyclic aromatic hydrocarbons (PAHs) during enhanced natural attenuation. The soil of the investigated area was formed from a layer of uncompacted fill. Twelve sampling points were established in the investigated area for collecting soil samples. A study conducted in 2015 did not reveal any increase in the content of heavy metals, monoaromatic hydrocarbons (BTEX), and cyanides. However, the content of PAHs and phenols was higher than the content permitted by Polish norms in force until 2016. In the case of PAHs, it was observed for individual compounds and their total contents. Among the various methods, enhanced natural attenuation was chosen for the remediation of investigated area. Repeated analyses of the contents of phenols and PAHs were conducted in 2020. The results of the analyses showed that enhanced natural attenuation has led to efficient degradation of the simplest substances—phenol and naphthalene. The content of these compounds in 2020 was not elevated compared to the standards for industrial wastelands. The three- and four-ring hydrocarbons were degraded at a lower intensity. Based on the mean decrease in content after 5-year enhanced natural attenuation, the compounds can be arranged in the following order: phenols > naphthalene > phenanthrene > fluoranthene > benzo(a)anthracene > chrysene > anthracene.

Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07

Study of the potential of Antarctic microorganisms for use in bioremediation is of increasing interest due to their adaptations to harsh environmental conditions and their metabolic potential in removing a wide variety of organic pollutants at low temperature. In this study, the psychrotolerant bacterium Rhodococcus sp. strain AQ5-07, originally isolated from soil from King George Island (South Shetland Islands, maritime Antarctic), was found to be capable of utilizing phenol as sole carbon and energy source. The bacterium achieved 92.91% degradation of 0.5 g/L phenol under conditions predicted by response surface methodology (RSM) within 84 h at 14.8 °C, pH 7.05, and 0.41 g/L ammonium sulphate. The assembled draft genome sequence (6.75 Mbp) of strain AQ5-07 was obtained through whole genome sequencing (WGS) using the Illumina Hiseq platform. The genome analysis identified a complete gene cluster containing catA, catB, catC, catR, pheR, pheA2, and pheA1. The genome harbours the complete enzyme systems required for phenol and catechol degradation while suggesting phenol degradation occurs via the β-ketoadipate pathway. Enzymatic assay using cell-free crude extract revealed catechol 1,2-dioxygenase activity while no catechol 2,3-dioxygenase activity was detected, supporting this suggestion. The genomic sequence data provide information on gene candidates responsible for phenol and catechol degradation by indigenous Antarctic bacteria and contribute to knowledge of microbial aromatic metabolism and genetic biodiversity in Antarctica.

Enhancement of phenol biodegradation: Metabolic division of labor in co-culture of Stenotrophomonas sp. N5 and Advenella sp. B9

The aim of this work is to study the synergistic effect of Stenotrophomonas sp. N5 and Advenella sp. B9 co-culture (COC) on enhancement of phenol biodegradation. These two strains utilizing phenol as sole carbon and energy source were isolated from phenol-containing coking wastewater. The results of biodegradation experiment showed the COC of N5 and B9 has stronger capability to degrade phenol than either of mono-culture (MOC). Growth kinetics studies indicated inhibitory effect of phenol on COC was reduced by the interaction of N5 and B9 in COC. The RNA-Seq results demonstrated that phenol biodegradation was enhanced by metabolic division of labor (DOL) in COC based on the expression of key genes for phenol degradation. GO enrichment analysis of differentially expressed genes (DEGs) indicated DEGs between COC and MOC degradation systems are mainly concentrated in the synthesis of cell components, microbial growth and metabolism, and catalytic activity. The expression of 3 transcriptional factors (LysR, Two-component system response regulator, and TetR families) which can regulate degradation of aromatic compounds, was identified beneficial to phenol degradation.

Response Surface Methodology Optimization and Kinetics of Diesel Degradation by a Cold-Adapted Antarctic Bacterium, Arthrobacter sp. Strain AQ5-05

Petroleum hydrocarbons, notably diesel oil, are the main energy source for running amenities in the Antarctic region and are the major cause of pollution in this area. Diesel oil spills are one of the major challenges facing management of the Antarctic environment. Bioremediation using bacteria can be an effective and eco-friendly approach for their remediation. However, since the introduction of non-native organisms, including microorganisms, into the Antarctic or between the distinct biogeographical regions within the continent is not permitted under the Antarctic Treaty, it is crucial to discover native oil-degrading, psychrotolerant microorganisms that can be used in diesel bioremediation. The primary aim of the current study is to optimize the conditions for growth and diesel degradation activity of an Antarctic local bacterium, Arthrobacter sp. strain AQ5-05, using the Plackett-Burman approach and response surface method (RSM) via a central composite design (CCD) approach. Based on this approach, temperature, pH, and salinity were calculated to be optimum at 16.30 °C, pH 7.67 and 1.12% (w/v), respectively. A second order polynomial regression model very accurately represented the experimental figures’ interpretation. These optimized environmental conditions increased diesel degradation from 34.5% (at 10 °C, pH 7.00 and 1.00% (w/v) salinity) to 56.4%. Further investigation of the kinetics of diesel reduction by strain AQ5-05 revealed that the Teissier model had the lowest RMSE and AICC values. The calculated values for the Teissier constants of maximal growth rate, half-saturation rate constant for the maximal growth, and half inhibition constants (μmax, Ks, and Ki), were 0.999 h−1, 1.971% (v/v) and 1.764% (v/v), respectively. The data obtained therefore confirmed the potential application of this cold-tolerant strain in the bioremediation of diesel-contaminated Antarctic soils at low temperature.

Biosurfactant Production and Growth Kinetics Studies of the Waste Canola Oil-Degrading Bacterium Rhodococcus erythropolis AQ5-07 from Antarctica

With the progressive increase in human activities in the Antarctic region, the possibility of domestic oil spillage also increases. Developing means for the removal of oils, such as canola oil, from the environment and waste "grey" water using biological approaches is therefore desirable, since the thermal process of oil degradation is expensive and ineffective. Thus, in this study an indigenous cold-adapted Antarctic soil bacterium, Rhodococcus erythropolis strain AQ5-07, was screened for biosurfactant production ability using the multiple approaches of blood haemolysis, surface tension, emulsification index, oil spreading, drop collapse and "MATH" assay for cellular hydrophobicity. The growth kinetics of the bacterium containing different canola oil concentration was studied. The strain showed β-haemolysis on blood agar with a high emulsification index and low surface tension value of 91.5% and 25.14 mN/m, respectively. Of the models tested, the Haldane model provided the best description of the growth kinetics, although several models were similar in performance. Parameters obtained from the modelling were the maximum specific growth rate (qmax), concentration of substrate at the half maximum specific growth rate, Ks% (v/v) and the inhibition constant Ki% (v/v), with values of 0.142 h-1, 7.743% (v/v) and 0.399% (v/v), respectively. These biological coefficients are useful in predicting growth conditions for batch studies, and also relevant to "in field" bioremediation strategies where the concentration of oil might need to be diluted to non-toxic levels prior to remediation. Biosurfactants can also have application in enhanced oil recovery (EOR) under different environmental conditions.

Biodegradation of Phenol by Rhodococcus sp. Strain SKC: Characterization and Kinetics Study

This study focuses on the kinetics of a pure strain of bacterium Rhodococcus sp. SKC, isolated from phenol-contaminated soil, for the biodegradation of phenol as its sole carbon and energy source in aqueous medium. The kinetics of phenol biodegradation including the lag phase, the maximum phenol degradation rate, maximum growth rate (R_m) and maximum yield coefficient (Y) for each S_i (initial phenol concentration, mg/L) were fitted using the Gompertz and Haldane models of substrate inhibition (R² > 0.9904, RMSE < 0.00925). The values of these parameters at optimum conditions were μ_max = 0.30 h⁻¹, K_s = 36.40 mg/L, and K_i = 418.79 mg/L, and that means the inhibition concentration of phenol was 418.79 mg/L. By comparing with other strains of bacteria, Rhodococcus sp. SKC exhibited a high yield factor and tolerance towards phenol. This study demonstrates the potential application of Rhodococcus sp. SKC for the bioremediation of phenol contaminate.

Actinobacteria and Cyanobacteria Diversity in Terrestrial Antarctic Microenvironments Evaluated by Culture-Dependent and Independent Methods

Bacterial diversity from McMurdo Dry Valleys in Antarctica, the coldest desert on earth, has become more easily assessed with the development of High Throughput Sequencing (HTS) techniques. However, some of the diversity remains inaccessible by the power of sequencing. In this study, we combine cultivation and HTS techniques to survey actinobacteria and cyanobacteria diversity along different soil and endolithic micro-environments of Victoria Valley in McMurdo Dry Valleys. Our results demonstrate that the Dry Valleys actinobacteria and cyanobacteria distribution is driven by environmental forces, in particular the effect of water availability and endolithic environments clearly conditioned the distribution of those communities. Data derived from HTS show that the percentage of cyanobacteria decreases from about 20% in the sample closest to the water source to negligible values on the last three samples of the transect with less water availability. Inversely, actinobacteria relative abundance increases from about 20% in wet soils to over 50% in the driest samples. Over 30% of the total HTS data set was composed of actinobacterial strains, mainly distributed by 5 families: Sporichthyaceae, Euzebyaceae, Patulibacteraceae, Nocardioidaceae, and Rubrobacteraceae. However, the 11 actinobacterial strains isolated in this study, belonged to Micrococcaceae and Dermacoccaceae families that were underrepresented in the HTS data set. A total of 10 cyanobacterial strains from the order Synechococcales were also isolated, distributed by 4 different genera (Nodosilinea, Leptolyngbya, Pectolyngbya, and Acaryochloris-like). In agreement with the cultivation results, Leptolyngbya was identified as dominant genus in the HTS data set. Acaryochloris-like cyanobacteria were found exclusively in the endolithic sample and represented 44% of the total 16S rRNA sequences, although despite our efforts we were not able to properly isolate any strain from this Acaryochloris-related group. The importance of combining cultivation and sequencing techniques is highlighted, as we have shown that culture-dependent methods employed in this study were able to retrieve actinobacteria and cyanobacteria taxa that were not detected in HTS data set, suggesting that the combination of both strategies can be usefull to recover both abundant and rare members of the communities.

Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach

Although Antarctica was once believed to be a sterile environment, it is now clear that the microbial communities inhabiting the Antarctic continent are surprisingly diverse. Until the beginning of the new millennium, little was known about the most abundant inhabitants of the continent: prokaryotes. From then on, however, the rising use of deep sequencing techniques has led to a better understanding of the Antarctic prokaryote diversity and provided insights in the composition of prokaryotic communities in different Antarctic environments. Although these cultivation-independent approaches can produce millions of sequences, linking these data to organisms is hindered by several problems. The largest difficulty is the lack of biological information on large parts of the microbial tree of life, arising from the fact that most microbial diversity on Earth has never been characterized in laboratory cultures. These unknown prokaryotes, also known as microbial dark matter, have been dominantly detected in all major environments on our planet. Laboratory cultures provide access to the complete genome and the means to experimentally verify genomic predictions and metabolic functions and to provide evidence of horizontal gene transfer. Without such well-documented reference data, microbial dark matter will remain a major blind spot in deep sequencing studies. Here, we review our current understanding of prokaryotic communities in Antarctic ice-free soils based on cultivation-dependent and cultivation-independent approaches. We discuss advantages and disadvantages of both approaches and how these strategies may be combined synergistically to strengthen each other and allow a more profound understanding of prokaryotic life on the frozen continent.

Biodegradation of phenol by cold-tolerant bacteria isolated from alpine soils of Binaloud Mountains in Iran

Degradation of phenol is considered to be a challenge because of harsh environments in cold regions and ground waters. Molecular characterization of phenol degrading bacteria was investigated to gain an insight into the biodegradation in cold areas. The psychrotolerant and psychrophiles bacteria were isolated from alpine soils in the northeast of Iran. These strains belonged to Pseudomonas sp., Stenotrophomonas spp. and Shinella spp. based on analysis of the 16S rRNA gene. These strains were capable of the complete phenol degradation at a concentration of 200 mg L^-1 at 20 °C. Moreover, the strains could degrade phenol at a concentration of 400 and 600 mg L^-1 at a higher time. Effects of environmental factors were studied using one factor at a time (OFAT) approach for Pseudomonas sp.ATR208. When the bacterium was grown in a liquid medium with 600 mg L^-1 of concentration supplemented with optimum carbon and nitrogen sources, more than 99% of phenol removal was obtained at 20 °C and 24 h. Therefore, the present study indicated the potential of the local cold tolerant bacteria in the phenol bioremediation.