Genome analysis provides insights into crude oil degradation and biosurfactant production by extremely halotolerant Halomonas desertis G11 isolated from Chott El-Djerid salt-lake in Tunisian desert

Functional and structural responses of a halophilic consortium to oily sludge during biodegradation

Biotreatment of oily sludge and the involved microbial communities, particularly in saline environments, have been rarely investigated. We enriched a halophilic bacterial consortium (OS-100) from petroleum refining oily sludge, which degraded almost 86% of the aliphatic hydrocarbon (C10-C30) fraction of the oily sludge within 7 days in the presence of 100 g/L NaCl. Two halophilic hydrocarbon-degrading bacteria related to the genera Chromohalobacter and Halomonas were isolated from the OS-100 consortium. Hydrocarbon degradation by the OS-100 consortium was relatively higher compared to the isolated bacteria, indicating potential synergistic interactions among the OS-100 community members. Exclusion of FeCl2, MgCl2, CaCl2, trace elements, and vitamins from the culture medium did not significantly affect the hydrocarbon degradation efficiency of the OS-100 consortium. To the contrary, hydrocarbon biodegradation dropped from 94.1 to 54.4% and 5% when the OS-100 consortium was deprived from phosphate and nitrogen sources in the culture medium, respectively. Quantitative PCR revealed that alkB gene expression increased up to the 3rd day of incubation with 11.277-fold, consistent with the observed increments in hydrocarbon degradation. Illumina-MiSeq sequencing of 16 S rRNA gene fragments revealed that the OS-100 consortium was mainly composed of the genera Halomonas, Idiomarina, Alcanivorax and Chromohalobacter. This community structure changed depending on the culturing conditions. However, remarkable changes in the community structure were not always associated with remarkable shifts in the hydrocarbonoclastic activity and vice versa. The results show that probably synergistic interactions between community members and different subpopulations of the OS-100 consortium contributed to salinity tolerance and hydrocarbon degradation.

Extremophiles and their expanding biotechnological applications

Microbial life is not restricted to any particular setting. Over the past several decades, it has been evident that microbial populations can exist in a wide range of environments, including those with extremes in temperature, pressure, salinity, and pH. Bacteria and Archaea are the two most reported types of microbes that can sustain in extreme environments, such as hot springs, ice caves, acid drainage, and salt marshes. Some can even grow in toxic waste, organic solvents, and heavy metals. These microbes are called extremophiles. There exist certain microorganisms that are found capable of thriving in two or more extreme physiological conditions simultaneously, and are regarded as polyextremophiles. Extremophiles possess several physiological and molecular adaptations including production of extremolytes, ice nucleating proteins, pigments, extremozymes and exopolysaccharides. These metabolites are used in many biotechnological industries for making biofuels, developing new medicines, food additives, cryoprotective agents etc. Further, the study of extremophiles holds great significance in astrobiology. The current review summarizes the diversity of microorganisms inhabiting challenging environments and the biotechnological and therapeutic applications of the active metabolites obtained as a response to stress conditions. Bioprospection of extremophiles provides a progressive direction with significant enhancement in economy. Moreover, the introduction to omics approach including whole genome sequencing, single cell genomics, proteomics, metagenomics etc., has made it possible to find many unique microbial communities that could be otherwise difficult to cultivate using traditional methods. These findings might be capable enough to state that discovery of extremophiles can bring evolution to biotechnology.

Microbial diversity in polyextreme salt flats and their potential applications

Recent geological, hydrochemical, and mineralogical studies performed on hypersaline salt flats have given insights into similar geo-morphologic features on Mars. These salt-encrusted depressions are widely spread across the Earth, where they are characterized by high salt concentrations, intense UV radiation, high evaporation, and low precipitation. Their surfaces are completely dry in summer; intermittent flooding occurs in winter turning them into transitory hypersaline lakes. Thanks to new approaches such as culture-dependent, culture-independent, and metagenomic-based methods, it is important to study microbial life under polyextreme conditions and understand what lives in these dynamic ecosystems and how they function. Regarding these particular features, new halophilic microorganisms have been isolated from some salt flats and identified as excellent producers of primary and secondary metabolites and granules such as halocins, enzymes, carotenoids, polyhydroxyalkanoates, and exopolysaccharides. Additionally, halophilic microorganisms are implemented in heavy metal bioremediation and hypersaline wastewater treatment. As a result, there is a growing interest in the distribution of halophilic microorganisms around the world that can be looked upon as good models to develop sustainable biotechnological processes for all fields. This review provides insights into diversity, ecology, metabolism, and genomics of halophiles in hypersaline salt flats worldwide as well as their potential uses in biotechnology.

Halomonas rhizosphaerae sp. nov. and Halomonas kalidii sp. nov., two novel moderate halophilic phenolic acid-degrading species isolated from saline soil

Four vanillic acid-degrading bacterial strains, named LR5S13T, LR5S20, and M4R5S39T and LN1S58, were isolated from Kalidium cuspidatum rhizosphere and bulk soils, respectively. Phylogenetic analysis based on 16S rRNA gene as well as core genome revealed that LR5S13T and LR5S20 clustered closely with each other and with Halomonas ventosae Al12T, and that the two strains shared the highest similarities (both 99.3 %) with H. ventosae Al12T, in contrast, M4R5S39T and LN1S58 clustered together and with Halomonas heilongjiangensis 9-2T, and the two strains shared the highest similarities (99.4 and 99.2 %, respectively) with H. heilongjiangensis 9-2T. The average nucleotides identities based on BLAST (ANIb) and digital DNA-DNA hybridization (dDDH) values of strains LR5S13T to LR5S20, and M4R5S39T to LN1S58, were both higher than the threshold values for delineation of a species. The ANIb and dDDH values of the four strains to their closely relatives were lower than the threshold values. All four strains take phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as the major polar lipids, Summed Feature 8, Summed Feature 3, and C16:0 as the major fatty acids. Based on the phylogenetic and phenotypic results, the four strains should be classified as two novel Halomonas species. Therefore, Halomonas rhizosphaerae sp. nov. (type strain LR5S13T = KCTC 8016T = CGMCC 1.62049T) and Halomonas kalidii (type strain M4R5S39T = KCTC 8015T = CGMCC 1.62047T) are proposed. The geographical distribution analysis based on 16S rRNA gene revealed that the two novel species are widely distributed across the globe, specifically in highly saline habits, especially in Central and Eastern Asia.

Removal of nitrate nitrogen by Pseudomonas JI-2 under strong alkaline conditions: Performance and mechanism

The nitrate nitrogen removal characteristics of Pseudomonas JI-2 under strong alkaline conditions and the composition and functional groups of extracellular polymeric substance were analyzed. Furthermore, nontargeted metabonomics and bioinformatics technology were used to investigate the alkaline tolerance mechanism. JI-2 removed 11.05 mg N/(L·h) of nitrate with the initial pH, carbon to nitrogen ratio and temperature were 11.0, 8 and 25 °C respectively. Even when the pH was maintained at 11.0, JI-2 could still effectively remove nitrate. JI-2 contains a large number of Na+/H+ antiporters, such as Mrp, Mnh (mnhACDEFG) and Pha (phaACDEFG), which can stabilize the intracellular acid-base environment, and SlpA can enable quick adaptation to alkaline conditions. Moreover, JI-2 responds to the strong alkaline environment by secreting more polysaccharides, acidic functional groups and compatible solutes and regulating key metabolic processes such as pantothenate and CoA biosynthesis and carbapenem biosynthesis. Therefore, JI-2 can survive in strong alkaline environments and remove nitrate efficiently.

Isolation, identification, and screening of biosurfactant-producing and hydrocarbon-degrading bacteria from oil and gas industrial waste

Qatar is one of the biggest oil and gas producers in the world, coupled with it is challenging environmental conditions (high average temperature: >40 °C, low annual rainfall: 46.71 mm, and high annual evaporation rate: 2200 mm) harbors diverse microbial communities that are novel and robust, with the potential to biodegrade hydrocarbons. In this study, we collected hydrocarbon contaminated sludge, wastewater and soil samples from oil and gas industries in Qatar. Twenty-six bacterial strains were isolated in the laboratory from these samples using high saline conditions and crude oil as the sole carbon source. A total of 15 different bacterial genera were identified in our study that have not been widely reported in the literature or studied for their usage in the biodegradation of hydrocarbons. Interestingly, some of the bacteria that were identified belonged to the same genus however, demonstrated variable growth rates and biosurfactant production. This indicates the possibility of niche specialization and specific evolution to acquire competitive traits for better survival. The most potent strain EXS14, identified as Marinobacter sp., showed the highest growth rate in the oil-containing medium as well as the highest biosurfactant production. When this strain was further tested for biodegradation of hydrocarbons, the results showed that it was able to degrade 90 to 100% of low and medium molecular weight hydrocarbons and 60 to 80% of high molecular weight (C35 to C50) hydrocarbons. This study offers many promising leads for future studies of microbial species and their application for the treatment of hydrocarbon contaminated wastewater and soil in the region and in other areas with similar environmental conditions.

Physiological and genomic insights into abiotic stress of halophilic archaeon Natrinema altunense 4.1R isolated from a saline ecosystem of Tunisian desert

Halophilic archaea are polyextremophiles with the ability to withstand fluctuations in salinity, high levels of ultraviolet radiation, and oxidative stress, allowing them to survive in a wide range of environments and making them an excellent model for astrobiological research. Natrinema altunense 4.1R is a halophilic archaeon isolated from the endorheic saline lake systems, Sebkhas, located in arid and semi-arid regions of Tunisia. It is an ecosystem characterized by periodic flooding from subsurface groundwater and fluctuating salinities. Here, we assess the physiological responses and genomic characterization of N. altunense 4.1R to UV-C radiation, as well as osmotic and oxidative stresses. Results showed that the 4.1R strain is able to survive up to 36% of salinity, up to 180 J/m² to UV-C radiation, and at 50 mM of H₂O₂, a resistance profile similar to Halobacterium salinarum, a strain often used as UV-C resistant model. In order to understand the genetic determinants of N. altunense 4.1R survival strategy, we sequenced and analyzed its genome. Results showed multiple gene copies of osmotic stress, oxidative stress, and DNA repair response mechanisms supporting its survivability at extreme salinities and radiations. Indeed, the 3D molecular structures of seven proteins related to responses to UV-C radiation (excinucleases UvrA, UvrB, and UvrC, and photolyase), saline stress (trehalose-6-phosphate synthase OtsA and trehalose-phosphatase OtsB), and oxidative stress (superoxide dismutase SOD) were constructed by homology modeling. This study extends the abiotic stress range for the species N. altunense and adds to the repertoire of UV and oxidative stress resistance genes generally known from haloarchaeon.

Petroleum Hydrocarbon Catabolic Pathways as Targets for Metabolic Engineering Strategies for Enhanced Bioremediation of Crude-Oil-Contaminated Environments

Anthropogenic activities and industrial effluents are the major sources of petroleum hydrocarbon contamination in different environments. Microbe-based remediation techniques are known to be effective, inexpensive, and environmentally safe. In this review, the metabolic-target-specific pathway engineering processes used for improving the bioremediation of hydrocarbon-contaminated environments have been described. The microbiomes are characterised using environmental genomics approaches that can provide a means to determine the unique structural, functional, and metabolic pathways used by the microbial community for the degradation of contaminants. The bacterial metabolism of aromatic hydrocarbons has been explained via peripheral pathways by the catabolic actions of enzymes, such as dehydrogenases, hydrolases, oxygenases, and isomerases. We proposed that by using microbiome engineering techniques, specific pathways in an environment can be detected and manipulated as targets. Using the combination of metabolic engineering with synthetic biology, systemic biology, and evolutionary engineering approaches, highly efficient microbial strains may be utilised to facilitate the target-dependent bioprocessing and degradation of petroleum hydrocarbons. Moreover, the use of CRISPR-cas and genetic engineering methods for editing metabolic genes and modifying degradation pathways leads to the selection of recombinants that have improved degradation abilities. The idea of growing metabolically engineered microbial communities, which play a crucial role in breaking down a range of pollutants, has also been explained. However, the limitations of the in-situ implementation of genetically modified organisms pose a challenge that needs to be addressed in future research.

Genome Analysis of Halomonas elongata Strain 153B and Insights Into Polyhydroxyalkanoate Synthesis and Adaptive Mechanisms to High Saline Environments

Species of the Halomonas genus are gram-negative, aerobic, moderately halophilic bacteria that synthesize polyhydroxyalkanoates (PHAs) and other high-value products that have a wide range of potential uses in the food, feed, cosmetics, pharmaceutical, and chemical sectors. Genome sequencing studies allow for the description and comparison of genetic traits with other strains and species, allowing for the exploration of the organism's potential, necessary to further biotechnology applications. Here, the genome of Halomonas elongata strain 153B was sequenced, its features compared to 5 other strains and 7 species, and a description of features for adaptations to hypersaline environments and bioproducts synthesis was done. Whole-genome analysis showed H. elongata 153B has more similar features to the reference strain H. elongata DSM 2581 compared to 4 other reported strains. Comparative genomics showed 2064 core genomic clusters between the strains and 666 singletons for strain 153B. Several genes in transport and signaling, osmoregulation, and oxidative stress that have roles in adaptation to environments with high osmolarity were also revealed. These appear to form an intricate network of overlapping systems carefully coordinated to bring about adaptation. H. elongata 153B genes for the synthesis of PHAs, ectoine, vitamins, and the degradation of drugs and aromatic compounds were described. The results will aid in the study of halophile physiology, provide a mine for valuable enzymes, and help speed up research for other biotechnology applications.

Diversity assessment of photosynthesizers: comparative analysis of pre-cultivated and natural microbiome of sediments from Cerrado biome in Maranhão, Brazil

Photosynthetic microorganisms are important components of most ecosystems and have important roles regarding biogeochemical cycles and the basis of the trophic chain. However, they sometimes are present in low abundance compared to other heterotrophic organisms. The Chapada das Mesas National Park (PNCM) is a Conservation Unit in Brazilian Cerrado biome, which is considered a hotspot for biodiversity conservation and possesses important rivers, waterfalls, and springs with economical and touristic importance. The aim of this study was to perform a comparative analysis of enriched and total microbiome of sediments to understand the impact of pre-cultivation in discovery of underrepresented groups like photosynthesizers. All sediment samples were cultivated in BG-11 medium under illumination to enrich for photosynthetic microorganisms and both the raw samples and the enriched ones were submitted to DNA extraction and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene on the Ion Torrent platform. The reads were analyzed using QIIME2 software and the Phyloseq package. The enrichment allowed detection and identification of many genera of cyanobacteria in the Chapada das Mesas National Park (PNCM), which would probably not be possible without the combination of approaches. A total of 58 groups of photosynthetic microorganisms were classified in the samples from the enrichments and their relative abundance based on amplified 16S rRNA sequences were estimated, highlighting the genus Synechocystis which represented 10.10% of the abundance of the phylum Cyanobacteria and the genus Dunaliella, which represented 45.66% of the abundance of algae as the most abundant groups at the PNCM. In the enrichments, microorganisms from the phyla Proteobacteria (45.2%), Bacteroidetes (18%), and Planctomycetes (3.3%) were also identified, since there are ecological associations between the photosynthetic community and other groups of heterotrophic microorganisms. As for the functional analysis, metabolic functions associated with methanotrophy and methylotrophy, hydrocarbon degradation, phototrophy, and nitrogen fixation were predicted. The results highlight a great diversity of photosynthetic microorganisms in Cerrado and the importance of using a combination of approaches when analyzing target groups which are usually underrepresented such as cyanobacteria and microalgae.

Degradation potential of alkanes by diverse oil-degrading bacteria from deep-sea sediments of Haima cold seep areas, South China Sea

Marine oil spills are a significant concern worldwide, destroying the ecological environment and threatening the survival of marine life. Various oil-degrading bacteria have been widely reported in marine environments in response to marine oil pollution. However, little information is known about culturable oil-degrading bacteria in cold seep of the deep-sea environments, which are rich in hydrocarbons. This study enriched five oil-degrading consortia from sediments collected from the Haima cold seep areas of the South China Sea. Parvibaculum, Erythrobacter, Acinetobacter, Alcanivorax, Pseudomonas, Marinobacter, Halomonas, and Idiomarina were the dominant genera. Further results of bacterial growth and degradation ability tests indicated seven efficient alkane-degrading bacteria belonging to Acinetobacter, Alcanivorax, Kangiella, Limimaricola, Marinobacter, Flavobacterium, and Paracoccus, whose degradation rates were higher in crude oil (70.3–78.0%) than that in diesel oil (62.7–66.3%). From the view of carbon chain length, alkane degradation rates were medium chains > long chains > short chains. In addition, Kangiella aquimarina F7, Acinetobacter venetianus F1, Limimaricola variabilis F8, Marinobacter nauticus J5, Flavobacterium sediminis N3, and Paracoccus sediminilitoris N6 were first identified as oil-degrading bacteria from deep-sea environments. This study will provide insight into the bacterial community structures and oil-degrading bacterial diversity in the Haima cold seep areas, South China Sea, and offer bacterial resources to oil bioremediation applications.

Funneling lignin-derived compounds into polyhydroxyalkanoate by Halomonas sp. Y3

Lignin-derived compounds (LDCs) biological funneling for polyhydroxyalkanoate (PHA) synthesis has been attractive but elusive. Herein, the Halomonas sp. Y3 is isolated and developed for PHA production from LDCs. Of the tested 13 LDCs, 4-hydroxybenzoic acid (4-HBA), protocatechuate (PA), catechol (CAT), and vanillic acid (VA) exhibit a hyper-degradation and production with 87.2 %, 85.8 %, 84.7 %, and 83.4 % TOC removal rate and 535.2 mg/L, 506.5 mg/L, 435.6 mg/L, and 440.8 mg/L PHA concentration, respectively. The Halomonas sp. Y3 genome is sequenced by identifying numerous genes responsible for LDCs funneling, stress response, and PHA biosynthesis. An open unsterilized fermentation with optimal conditions of pH 9.0 and NaCl 60 g/L is investigated, achieving a completely aseptic effect and significantly improved PHA production from LDCs. Overall, the results indicate that the Halomonas sp. Y3 is an ideal candidate for LDC bioconversion and exhibits a great potential to realize black liquor valorization.

Extremophilic Bacterium Halomonas desertis G11 as a Cell Factory for Poly-3-Hydroxybutyrate-co-3-Hydroxyvalerate Copolymer’s Production

Microbial polyhydroxyalkanoates (PHA) are biodegradable and biocompatible bio-based polyesters, which are used in various applications including packaging, medical and coating materials. In this study, an extremophilic hydrocarbonoclastic bacterium, previously isolated from saline sediment in the Tunisian desert, has been investigated for PHA production. The accumulation of intracellular PHA granules in Halomonas desertis G11 was detected by Nile blue A staining of the colonies. To achieve maximum PHA yield by the strain G11, the culture conditions were optimized through response surface methodology (RSM) employing a Box-Behnken Design (BBD) with three independent variables, namely, substrate concentration (1–5%), inoculum size (1–5%) and incubation time (5–15 days). Under optimized conditions, G11 strain produced 1.5 g/L (68% of DCW) of PHA using glycerol as a substrate. Application of NMR (1H and 13C) and FTIR spectroscopies showed that H. desertis accumulated PHA is a poly-3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV). The genome analysis revealed the presence of typical structural genes involved in PHBV metabolism including phaA, phaB, phaC, phaP, phaZ, and phaR, coding for acetyl-CoA acetyltransferase, acetoacetyl-CoA reductase, class I polyhydroxyalkanoates synthases, phasin, polyhydroxyalkanoates depolymerase and polyhydroxyalkanoates synthesis repressor, respectively. Glycerol can be metabolized to 1) acetyl-CoA through the glycolysis pathway and subsequently converted to the 3HB monomer, and 2) to propionyl-CoA via the threonine biosynthetic pathway and subsequently converted to the 3HV monomer. In silico analysis of PhaC1 from H. desertis G11 indicated that this enzyme belongs to Class I PHA synthase family with a “lipase box”-like sequence (SYCVG). All these characteristics make the extremophilic bacterium H. desertis G11 a promising cell factory for the conversion of bio-renewable glycerol to high-value PHBV.

Whole genome sequencing of the halophilic Halomonas qaidamensis XH36, a novel species strain with high ectoine production

Here, we report the whole genome of a novel halophilic Halomonas species strain XH36 with high ectoine production potential. The genome was 3,818,310 bp in size with a GC content of 51.97%, and contained 3533 genes, 61 tRNAs and 18 rRNAs. The phylogenetic analysis using the 16s rRNA genes, the UBCGs and the TYGS database indicated that XH36 belongs to a novel Halomonas species, which we named as Halomonas qaidamensis. Osmoadaptation related genes including Na(+) and K(+) transport and compatible solute accumulation were both present in the XH36 genome, the latter of which mainly contained ectoine, 5-hydroxyectoine and betaine. HPLC validation studies showed that H. qaidamensis XH36 accumulated ectoine to cope with salt stress, and the content of ectoine could be as high as 315 mg/g CDW under 3 mol/l NaCl. Our results show that XH36 is a new promising industrial strain for ectoine production, and the genomic analysis will guide us to better understand its salt-induced osmoadaptation mechanisms, and provide theoretical references for future application research of ectoine.

Nitrate removal by alkali-resistant Pseudomonas sp. XS-18 under aerobic conditions: Performance and mechanism

To improve poor nitrate removal by microorganisms under strong alkaline conditions, a new type of aerobic nitrification-reducing bacteria was isolated in this study. Using nitrogen balance and genome information, the capacity of Pseudomonas XS-18 to remove nitrate and the mechanism of alkali tolerance were analyzed. At pH 11.0, XS-18 could remove 12.17 mg N/(L·h) nitrate. At C/N ratios of 13.0 and 25 °C, nitrite and ammonia nitrogen were barely enriched. XS-18 could reduce nitrate through dissimilation and assimilation, and 21.74% and 77.39% of nitrate was converted into cellular components and organic nitrogen, respectively. Meanwhile, functional genes (nirBD, nasAB, gdhA, glnA, and gltBD) associated with nitrogen metabolism were determined. In addition, Na⁺/H⁺ antiporters (MnhACDEFG, PhaACDEFG, NhaCD and TrkAH) and a cell surface protein (SlpA) from the XS-18 genome, as well as compatible solutes that help stabilize intracellular pH, were also characterized. XS-18 possessed significant potential in alkaline wastewater treatment.

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.

Effect of Gamma Irradiation on Enhanced Biological Activities of Exopolysaccharide from Halomonas desertis G11: Biochemical and Genomic Insights

In this work, a native exopolysaccharide (nEPS) produced by Halomonas desertis G11 isolated from a Tunisian extreme environment was modified by gamma irradiation. Characterization as well as the antioxidant and antitumor activities of nEPS and its gamma-irradiated derivatives (iEPSs) were comparatively evaluated. In vitro and in vivo antioxidant potentials were determined by using different methods and through different antioxidant enzymes. The antitumor activity was checked against a human colon cancer cell line. Analyses of the complete genome sequence were carried out to identify genes implicated in the production of nEPS. Thus, the genomic biosynthesis pathway and the export mechanism of nEPS were proposed. Analyses of irradiation data showed that iEPSs acquired new functional groups, lower molecular weights, and gained significantly (p < 0.05) higher antioxidant and antitumor abilities compared with nEPS. These findings provide a basis for using iEPSs as novel pharmaceutical agents for human therapies.

Overview of Approaches to Improve Rhizoremediation of Petroleum Hydrocarbon-Contaminated Soils

Soil contamination with petroleum hydrocarbons (PHCs) has become a global concern and has resulted from the intensification of industrial activities. This has created a serious environmental issue; therefore, there is a need to find solutions, including application of efficient remediation technologies or improvement of current techniques. Rhizoremediation is a green technology that has received global attention as a cost-effective and possibly efficient remediation technique for PHC-polluted soil. Rhizoremediation refers to the use of plants and their associated microbiota to clean up contaminated soils, where plant roots stimulate soil microbes to mineralize organic contaminants to H2O and CO2. However, this multipartite interaction is complicated because many biotic and abiotic factors can influence microbial processes in the soil, making the efficiency of rhizoremediation unpredictable. This review reports the current knowledge of rhizoremediation approaches that can accelerate the remediation of PHC-contaminated soil. Recent approaches discussed in this review include (1) selecting plants with desired characteristics suitable for rhizoremediation; (2) exploiting and manipulating the plant microbiome by using inoculants containing plant growth-promoting rhizobacteria (PGPR) or hydrocarbon-degrading microbes, or a combination of both types of organisms; (3) enhancing the understanding of how the host–plant assembles a beneficial microbiome, and how it functions, under pollutant stress. A better understanding of plant–microbiome interactions could lead to successful use of rhizoremediation for PHC-contaminated soil in the future.

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

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

Occurrence and biodegradation of hydrocarbons at high salinities

Hypersaline environments are found around the world, above and below ground, and many are exposed to hydrocarbons on a continuous or a frequent basis. Some surface hypersaline environments are exposed to hydrocarbons because they have active petroleum seeps while others are exposed because of oil exploration and production, or nearby human activities. Many oil reservoirs overlie highly saline connate water, and some national oil reserves are stored in salt caverns. Surface hypersaline ecosystems contain consortia of halophilic and halotolerant microorganisms that decompose organic compounds including hydrocarbons, and subterranean ones are likely to contain the same. However, the rates and extents of hydrocarbon biodegradation are poorly understood in such ecosystems. Here we describe hypersaline environments potentially or likely to become contaminated with hydrocarbons, including perennial and transient environments above and below ground, and discuss what is known about the microbes degrading hydrocarbons and the extent of their activities. We also discuss what limits the microbial hydrocarbon degradation in hypersaline environments and whether there are opportunities for inhibiting (oil storage) or stimulating (oil spills) such biodegradation as the situation requires.

Degradation of Hydrocarbons and Heavy Metal Reduction by Marine Bacteria in Highly Contaminated Sediments

Investigations on the ability of bacteria to enhance removal of hydrocarbons and reduce heavy metal toxicity in sediments are necessary to design more effective bioremediation strategies. In this study, five bacterial strains, Halomonas sp. SZN1, Alcanivorax sp. SZN2, Pseudoalteromonas sp. SZN3, Epibacterium sp. SZN4, and Virgibacillus sp. SZN7, were isolated from polluted sediments from an abandoned industrial site in the Gulf of Naples, Mediterranean Sea, and tested for their bioremediation efficiency on sediment samples collected from the same site. These bacteria were added as consortia or as individual cultures into polluted sediments to assess biodegradation efficiency of polycyclic aromatic hydrocarbons and heavy metal immobilisation capacity. Our results indicate that these bacteria were able to remove polycyclic aromatic hydrocarbons, with a removal rate up to ca. 80% for dibenzo-anthracene. In addition, these bacteria reduced arsenic, lead, and cadmium mobility by promoting their partitioning into less mobile and bioavailable fractions. Microbial consortia generally showed higher performance toward pollutants as compared with pure isolates, suggesting potential synergistic interactions able to enhance bioremediation capacity. Overall, our findings suggest that highly polluted sediments select for bacteria efficient at reducing the toxicity of hazardous compounds, paving the way for scaled-up bioremediation trials.

New Plant Growth-Promoting, Chromium-Detoxifying Microbacterium Species Isolated From a Tannery Wastewater: Performance and Genomic Insights

Hexavalent chromium [Cr(VI)], widely generated by tannery activities, is considered among the most toxic substances and causes a serious damage for the environment and for human health. Interestingly, some microorganisms have a potential of bioremediation of chromium-contaminated wastewaters and soils through the reduction of Cr(VI) (soluble and harmful form) into Cr(III) (stable and non-toxic form). Here, we present the full genome sequence of a novel heavy-metal-resistant, plant growth-promoting bacterium (PGPB), Microbacterium metallidurans TL13, which was isolated from a Tunisian leather industry. The strain TL13 was resistant to many heavy metals, such as chromium, copper, nickel, cobalt, and arsenic. The 50% TL13 growth inhibitory concentration (IC₅₀) values of HgCl₂, CoCl₂, K₂Cr₂O₇, CuSO₄, NiCl₂, FeSO₄, and Na₂HAsO₄ are 368, 445, 676, 1,590, 1,680, 4,403, and 7,007 mg/L, respectively, with the following toxicity order: HgCl₂ > CoCl₂ > K₂Cr₂O₇ > CuSO₄ > NiCl₂ > FeSO₄ > Na₂HAsO₄. This new strain was also able to promote the growth of the hybrid tomato (Elika F1) under chromium metal stress. Its whole genome sequence length was estimated to be 3,587,460 bp (3,393 coding sequences) with a G + C content of 70.7%. Functional annotation of the genome of TL13 revealed the presence of open reading frames (ORFs) involved in adaptation to metal stress, such as the chromate transport protein, cobalt–zinc–cadmium resistance protein, copper resistance protein, copper responsive transcriptional regulator, multidrug resistance transporters, arsenical resistance operon repressor, arsenate reductase, arsenic resistance protein, mercuric resistance operon regulatory protein, mercuric ion reductase, and organomercurial lyase. Moreover, genes for the production of glutathione peroxidase, catalase, superoxide dismutase, and thioredoxin reductase, which confer a higher tolerance to oxidative/metal stresses, were identified in TL13 genome. In addition, genes for heat shock tolerance, cold shock tolerance, glycine-betaine production, mineral phosphate solubilization, ammonia assimilation, siderophores, exopolysaccharides, polyketides, and lytic enzymes (cellulase, chitinase, and proteases) production that enable bacteria to survive biotic/abiotic stress and to promote plant growth and health were also revealed. Based on genome analysis and experimental approaches, strain TL13 appears to have evolved from various metabolic strategies and could play a role in ensuring sustainable environmental and agricultural systems.