Enrichment of antibiotic resistant genes and pathogens in face masks from coastal environments

Face masks (FMs) are essential to limit the spread of the coronavirus during pandemic, a considerable of which are accumulated on the coast. However, limited is known about the microbial profile in the biofilm of the face masks (so-called plastisphere) and the impacts of face masks on the surrounding environments. We herein performed face mask exposures to coastal sediments and characterized the microbial community and the antibiotic resistome. We detected 64 antibiotic-resistance genes (ARGs) and 12 mobile gene elements (MGEs) in the plastisphere. Significant enrichments were found in the relative abundance of total ARGs in the plastisphere compared to the sediments. In detail, the relative abundance of tetracycline, multidrug, macrolide-lincosamide-streptogramin B (MLSB), and phenicol-resistant genes had increased by 5-10 times. Moreover, the relative abundance of specific hydrocarbonoclastic bacteria (e.g., Polycyclovorans sp.), pathogens (e.g., Pseudomonas oleovorans), and total MGEs significantly increased in the sediments after face mask exposure, which was congruent with the alteration of pH value and metal concentrations in the microcosms. Our study demonstrated the negative impacts of FMs on coastal environments regardless of the profiles of ARGs or pathogens. These findings improved the understanding of the ecological risks of face masks and underlined the importance of beach cleaning.

Alcanivorax quisquiliarum sp. nov., isolated from anaerobic fermentation liquid of food waste by high-throughput cultivation

Strain CY1518^T was isolated from an anaerobic fermentation liquid of food waste treatment plant in Beijing, PR China, and characterized to assess its taxonomy. Cells of CY1518^T were Gram-stain-negative, oxidase-negative, catalase-positive and ellipsoidal. Growth occurred at 20-42 °C (optimum, 37 °C), pH 6.0-10.0 (optimum, pH 8) and with 0-6.0 % (w/v) NaCl (optimum, 1.5%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CY1518^T belongs to the genus Alcanivorax, with the highest sequence similarity to Alcanivorax pacificus W11-5^T (95.97 %), followed by Alcanivorax indicus SW127^T (95.08%). The similarity between strain CY1518^T and other strains of Alcanivorax was less than 95 %. The genomic DNA G+C content of strain CY1518^T was 60.88 mol%. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain CY1518^T and the closely related taxa A. pacificus W11-5^T and A. indicus SW127^T were 77.61, 78.03 and 21.2 % and 74.15, 70.02 and 19.3%, respectively. The strain was able to use d-serine, Tween 40 and some organic acid compounds for growth. The polar lipids comprised aminophospholipid, diphosphatidylglycerol, glycolipid, an unknown polar lipid, phosphatidylethanolamine, phosphatidylglycerol and phospholipid. The principal fatty acids (>5 %) were C_19 : 0 cyclo ω8c (36.3%), C_16 : 0 (32.3%), C_12 : 0 3-OH (8.3%) and C_12 : 0 (7.6%). Based on its phenotypic, genotypic and genomic characteristics, strain CY1518^T represents a novel species in the genus Alcanivorax, for which the name Alcanivorax quisquiliarum sp. nov. is proposed. The type strain is CY1518^T (=GDMCC 1.2918^T=JCM 35120^T).

High abundance of hydrocarbon-degrading Alcanivorax in plumes of hydrothermally active volcanoes in the South Pacific Ocean

Species within the genus Alcanivorax are well known hydrocarbon-degraders that propagate quickly in oil spills and natural oil seepage. They are also inhabitants of the deep-sea and have been found in several hydrothermal plumes. However, an in-depth analysis of deep-sea Alcanivorax is currently lacking. In this study, we used multiple culture-independent techniques to analyze the microbial community composition of hydrothermal plumes in the Northern Tonga arc and Northeastern Lau Basin focusing on the autecology of Alcanivorax. The hydrothermal vents feeding the plumes are hosted in an arc volcano (Niua), a rear-arc caldera (Niuatahi) and the Northeast Lau Spreading Centre (Maka). Fluorescence in situ hybridization revealed that Alcanivorax dominated the community at two sites (1210-1565 mbsl), reaching up to 48% relative abundance (3.5 × 104 cells/ml). Through 16S rRNA gene and metagenome analyses, we identified that this pattern was driven by two Alcanivorax species in the plumes of Niuatahi and Maka. Despite no indication for hydrocarbon presence in the plumes of these areas, a high expression of genes involved in hydrocarbon-degradation was observed. We hypothesize that the high abundance and gene expression of Alcanivorax is likely due to yet undiscovered hydrocarbon seepage from the seafloor, potentially resulting from recent volcanic activity in the area. Chain-length and complexity of hydrocarbons, and water depth could be driving niche partitioning in Alcanivorax.

Phylogenomic analysis of the genus Alcanivorax: proposal for division of this genus into the emended genus Alcanivorax and two novel genera Alloalcanivorax gen. nov. and Isoalcanivorax gen. nov

The members of the genus Alcanivorax are key players in the removal of petroleum hydrocarbons from polluted marine environments. More than half of the species were described in the last decade using 16S rRNA gene phylogeny and genomic-based metrics. However, the 16S rRNA gene identity (<94 %) between some members of the genus Alcanivorax suggested their imprecise taxonomic status. In this study, we examined the taxonomic positions of Alcanivorax species using 16S rRNA phylogeny and further validated them using phylogenomic-related indexes such as digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI), percentage of conserved proteins (POCP) and comparative genomic studies. ANI and dDDH values confirmed that all the Alcanivorax species were well described at the species level. The phylotaxogenomic analysis showed that Alcanivorax species formed three clades. The inter-clade values of AAI and POCP were less than 70 %. The pan-genome evaluation depicted that the members shared 1223 core genes and its number increased drastically when analysed clade-wise. Therefore, these results necessitate the transfer of clade II and clade III members into Isoalcanivorax gen. nov. and Alloalcanivorax gen. nov., respectively, along with the emended description of the genus Alcanivorax sensu stricto.

Alcanivorax limicola sp. nov., isolated from a soda alkali-saline soil

An alkaliphilic and aerobic bacterium, designated as strain JB21^T, was isolated from a soda alkali-saline soil sample in Heilongjiang, Northeast China. Strain JB21^T is a Gram-stain-negative, rod-shaped, non-motile and amylase-positive bacterium. Growth occurred at 15-45 °C (optimum, 35-37 °C), in the presence of 0-15.0% (w/v) NaCl (optimum, 1.0%) and at pH 6.5-10.5 (optimum, pH 8.5-9.5). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JB21^T was most closely related to type strains of the genus Alcanivorax, with the highest sequence similarity to Alcanivorax indicus SW127^T (96.3%), and shared 95.4-93.1% sequence identity with other valid type strains of this genus. The major cellular fatty acids identified were C_16:0 and summed feature 8 (C_18:1ω6c and/or C_18:1ω7c). The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. The genomic G + C content of strain JB21^T was 61.3 mol%. The digital DNA-DNA hybridization (dDDH) estimation and average nucleotide identity (ANI) between strain JB21^T and type strains of the genus Alcanivorax were 18.3-23.2% and 69.2-79.0%, respectively. On the basis of its phenotypic and phylogenetic characteristics, we suggest the creation of a new species within the Alcanivorax genus, named Alcanivorax limicola sp. nov., type strain JB21^T (= CGMCC 1.16632^T = JCM 33717^T).

Alcanivorax profundimaris sp. nov., a Novel Marine Hydrocarbonoclastic Bacterium Isolated from Seawater and Deep-Sea Sediment

Two novel Alcanivorax-related strains, designated ST75FaO-1^T and 521-1, were isolated from the seawater of the South China Sea and the deep-sea sediment of the West Pacific Ocean, respectively. Both strains are Gram-stain-negative, rod-shaped, and non-motile, and grow at 10-40 °C, pH 5.0-10.0, in the presence of 1.0-15.0% (w/v) NaCl. Their 16S rRNA gene sequences showed 99.9% similarity. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that both strains belong to the genus Alcanivorax, and share 92.9-98.1% sequence similarity with all valid type strains of this genus, with the highest similarity being to type strain Alcanivorax venustensis DSM 13974^T (98.0-98.1%). Digital DNA-DNA hybridization (dDDH) and average nucleotide identity values between strains ST75FaO-1^T and 521-1 were 75.7% and 97.1%, respectively, while the corresponding values with A. venustensis DSM 13974^T were only 25.4-25.6% and 82.4-82.7%, respectively. The two strains contained similar major cellular fatty acids including C_16:0, C_18:1 ω7c/ω6c, C_19:0 cyclo ω8c, C_16:1 ω7c/ω6c, C_12:0 3-OH, and C_12:0. The genomic G + C content of strains ST75FaO-1^T and 521-1 were 66.3% and 66.1%, respectively. Phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, and one unidentified polar lipid were present in both strains. On the basis of phenotypic and genotypic characteristics, the two strains represent a novel species within the genus Alcanivorax, for which the name Alcanivorax profundimaris sp. nov. is proposed. The type strain is ST75FaO-1^T (= MCCC 1A17714^T = KCTC 82142^T).

Effects of Elevated pCO2 on the Survival and Growth of Portunus trituberculatus

Identifying the response of Portunus trituberculatus to ocean acidification (OA) is critical to understanding the future development of this commercially important Chinese crab species. Recent studies have reported negative effects of OA on crustaceans. Here, we subjected swimming crabs to projected oceanic CO₂ levels (current: 380 μatm; 2100: 750 μatm; 2200: 1500 μatm) for 4 weeks and analyzed the effects on survival, growth, digestion, antioxidant capacity, immune function, tissue metabolites, and gut bacteria of the crabs and on seawater bacteria. We integrated these findings to construct a structural equation model to evaluate the contribution of these variables to the survival and growth of swimming crabs. Reduced crab growth shown under OA is significantly correlated with changes in gut, muscle, and hepatopancreas metabolites whereas enhanced crab survival is significantly associated with changes in the carbonate system, seawater and gut bacteria, and activities of antioxidative and digestive enzymes. In addition, seawater bacteria appear to play a central role in the digestion, stress response, immune response, and metabolism of swimming crabs and their gut bacteria. We predict that if anthropogenic CO₂ emissions continue to rise, future OA could lead to severe alterations in antioxidative, immune, and metabolic functions and gut bacterial community composition in the swimming crabs through direct oxidative stress and/or indirect seawater bacterial roles. These effects appear to mediate improved survival, but at the cost of growth of the swimming crabs.

Alcanivorax sediminis sp. nov., isolated from deep-sea sediment of the Pacific Ocean

A taxonomic study was carried out on strain PA15-N-34^T, which was isolated from deep-sea sediment of Pacific Ocean. The bacterium was Gram-stain-positive, oxidase- and catalase-positive and rod-shaped. Growth was observed at salinity of 0-15.0% NaCl and at temperatures of 10-45 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PA15-N-34^T belonged to the genus Alcanivorax, with the highest sequence similarity to Alcanivorax profundi MTEO17^T (97.7 %), followed by Alcanivorax nanhaiticus 19 m-6^T (97.3 %) and 12 other species of the genus Alcanivorax (93.4 %-97.0 %). The average nucleotide identity and DNA-DNA hybridization values between strain PA15-N-34^T and type strains of the genus Alcanivorax were 71.46-81.78% and 18.7-25.2 %, respectively. The principal fatty acids (>10 %) were summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c; 31.2 %), C_16 : 0 (25.0 %) and summed feature 3 (14.6 %). The DNA G+C content was 57.15 mol%. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, four unidentified aminolipids and three unidentified lipids. The novel strain can be differentiated from its closest type strain by a negative test for urease and the presence of diphosphatidylglycerol and aminolipid. The combined genotypic and phenotypic data show that strain PA15-N-34^T represents a novel species within the genus Alcanivorax, for which the name Alcanivorax sediminis sp. nov. is proposed, with the type strain PA15-N-34^T (=MCCC 1A14738^T=KCTC 72163^T).

Marine Biosurfactants: Biosynthesis, Structural Diversity and Biotechnological Applications

Biosurfactants are amphiphilic secondary metabolites produced by microorganisms. Marine bacteria have recently emerged as a rich source for these natural products which exhibit surface-active properties, making them useful for diverse applications such as detergents, wetting and foaming agents, solubilisers, emulsifiers and dispersants. Although precise structural data are often lacking, the already available information deduced from biochemical analyses and genome sequences of marine microbes indicates a high structural diversity including a broad spectrum of fatty acid derivatives, lipoamino acids, lipopeptides and glycolipids. This review aims to summarise biosyntheses and structures with an emphasis on low molecular weight biosurfactants produced by marine microorganisms and describes various biotechnological applications with special emphasis on their role in the bioremediation of oil-contaminated environments. Furthermore, novel exploitation strategies are suggested in an attempt to extend the existing biosurfactant portfolio.

Biodegradation of long chain alkanes in halophilic conditions by Alcanivorax sp. strain Est-02 isolated from saline soil

In this study, through a multistep enrichment and isolation procedure, a halophilic bacterial strain was isolated from unpolluted saline soil, which was able to effectively and preferentially degrade long chain alkanes (especially tetracosane and octacosane). The strain was identified by 16S rRNA gene sequence as an Alcanivorax sp. The growth of strain Est-02 was optimized at the presence of tetracosane in different NaCl concentrations, temperatures, and pH. The consumption of different heavy alkanes was also investigated. Optimal culture conditions of the strain were determined to be as follows: 10% NaCl, temperature 25-35 °C and pH 7. Alcanivorax sp. strain Est-02 was able to use a wide range of aliphatic substrates ranging from C₁₄ to C₂₈ with clear tendency to utilize heavy chain hydrocarbons of C₂₄ and C₂₈. During growth on a mixture of alkanes (C₁₄-C₂₈), the strain consumed 60% and 65% of tetracosane and octacosane, respectively, while only about 40% of the lower chain alkanes were degraded. This unique ability of the strain Est-02 in efficient and selective biodegradation of long chain hydrocarbons could be further exploited for remediation of wax and heavy oil contaminated soils or upgrading of heavy crude oils. Comparison of the sequence of alkane hydroxylase gene (alkB) of strain Est-02 with previously reported sequences for Alcanivorax spp. and other hydrocarbon degraders, showed a remarkable phylogenetic distance between the sequence alkB of Est-02 and other alkane-degrading bacteria.

Alcanivorax profundi sp. nov., isolated from deep seawater of the Mariana Trench

A Gram-stain-negative, rod-shaped, non-motile, strictly aerobic strain, designated as MTEO17^T, was isolated from a 1000 m deep seawater sample of the Mariana Trench. Growth was observed at 10-45 °C (optimum, 37 °C), in the presence of 0.0-12.0 % NaCl (w/v; optimum, 3.0 %) and at pH 6.0-10.0 (optimum, pH 7.0-8.0). Phylogenetic analysis, based on the 16S rRNA gene sequence, revealed that strain MTEO17^T belonged to the genus Alcanivorax and showed the highest sequence similarity of 97.9 % to Alcanivorax nanhaiticus MCCC 1A05629^T. The estimated average nucleotide identity and DNA-DNA hybridization values between strain MTEO17^T and A. nanhaiticus MCCC 1A05629^T were 78.98 and 23.80 %, respectively. The significant dominant fatty acids were C16 : 0, summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The polar lipids comprised two phosphatidylethanolamines, one phosphatidylglycerol, one unidentified phospholipid and four unidentified polar lipids. The DNA G+C content of strain MTEO17^T was 57.5 %. On the basis of the polyphasic evidence, strain MTEO17^T is proposed to represent a novel species of the genus Alcanivorax, for which the name Alcanivorax profundi sp. nov. is proposed. The type strain is MTEO17^T (=KCTC 52694^T=MCCC 1K03252^T).

Alcanivorax mobilis sp. nov., a new hydrocarbon-degrading bacterium isolated from deep-sea sediment

A taxonomic study was carried out on strain MT13131^T, which was isolated from deep-sea sediment of the Indian Ocean during the screening of oil-degrading bacteria. The chain length range of n-alkanes (C8 to C32) oxidized by strain MT13131^T was determined in this study. The bacterium was Gram-negative, oxidase- and catalase-positive, single rod shaped, and motile by peritrichous flagella. Growth was observed at salinities of 1-12 % and at temperatures of 10-42 °C. The isolate was capable of Tween 20, 40 and 80 hydrolysis, but incapable of gelatin, cellulose or starch hydrolysis. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MT13131^T belonged to the genus Alcanivorax, with highest sequence similarity to Alcanivorax marinus R8-12^T (96.92 %), other species of genus Alcanivorax shared 92.96-96.69 % sequence similarity. The principal fatty acids were summed feature 3 (C16 : 1ω6c/ω7c), summed feature 8 (C18 : 1ω7c/ω6c), C16 : 0 and C12 : 0 3OH. The G+C content of the chromosomal DNA was 64.2 mol%. Phosphatidylglycerol, phosphatidylethanolamine, three aminolipids and three phospholipids were present. The combined genotypic and phenotypic data showed that strain MT13131^T represents a novel species within the genus Alcanivorax, for which the name Alcanivorax mobilis sp. nov. is proposed, with the type strain MT13131^T (=MCCC 1A11581^T=KCTC 52985^T).

Differential expression of the three Alcanivorax borkumensis SK2 genes coding for the P450 cytochromes involved in the assimilation of hydrocarbons

Alcanivorax borkumensis, a marine bacterium highly specialized in degrading linear and branched alkanes, plays a key ecological role in the removal of marine oil spills. It contains several alternative enzyme systems for terminal hydroxylation of alkanes, including three P450 cytochromes (P450-1, P450-2 and P450-3). The present work shows cytochrome P450-1 to be expressed from the promoter of the upstream gene fdx. Promoter P_fdx was more active when C₈ -C₁₈ n-alkanes or pristane were assimilated than when pyruvate was available. The product of ABO_0199 (named CypR) was identified as a transcriptional activator of P_fdx . The inactivation of cypR impaired growth on tetradecane, showing the importance of the fdx-P450-1 and/or cypR genes. P450-2 expression was low-level and constitutive under all conditions tested, while that of P450-3 from promoter P_450-3 was much higher when cells assimilated pristane than when n-alkanes or pyruvate were available. However, the inactivation of P450-3 had no visible impact on pristane assimilation. Cyo terminal oxidase, a component of the electron transport chain, was found to stimulate promoter P_P450-3 activity, but it did not affect promoters P_fdx or P_P450-2 . A. borkumensis, therefore, appears to carefully coordinate the expression of its multiple hydrocarbon degradation genes using both specific and global regulatory systems.

Comparative metabolomic studies of Alkanivorax xenomutans showing differential power output in a three chambered microbial fuel cell

Metabolomic study of electrogenic bacteria is a necessity to understand the extent of complex organic matter degradation and to invent new co-culture techniques to achieve complete degradation. In this study, we have subjected Alkanivorax xenomutans (KCTC 23751^T; NBRC 108843^T), a bacterium capable for biodegradation of complex hydrocarbons, to oxic and anoxic conditions in a three chambered microbial fuel cell. In an attempt to understand the molecular mechanisms during the electrogenic processes of A. xenomutans, intra cellular (endo metabolome or the fingerprint) and exo metabolome (extracellular metabolome or the foot print) were analyzed under oxic and anoxic conditions, using FTIR and GC-MS. Interpretation of the data revealed higher number of metabolites in the anoxic fraction as compared to oxic fraction. In addition, expression of putative metabolites that influence electron transfer like flavins, fumarate and quinones were found to be predominant in the organisms when grown in anoxic conditions. Hence, the presence of anoxic conditions governed the electrogenic bacteria to produce enhanced power output by modulating differential metabolomic profiling, compared to the culture grown in oxic conditions.

Alcanivorax nanhaiticus sp. nov., isolated from deep sea sediment

A taxonomic study was carried out on strain 19-m-6T, which was isolated from deep sea sediment of the South China Sea during the screening of alkane-degrading bacteria. The isolate was Gram-reaction-negative, and oxidase- and catalase- positive. On the basis of 16S rRNA gene sequence similarity, strain 19-m-6T was shown to belong to the genus Alcanivorax, related to Alcanivorax jadensis T9T (97.5 %), Alcanivorax hongdengensis A-11-3T (97.3  %), A. lcanivorax borkumensis SK2T (96.6 %) and seven other species of the genus Alcanivorax(93.9-95.4 %). Average nucleotide identity values between strain 19-m-6T and A. jadensis T9T, A. hongdengensis A-11-3T and A. borkumensis SK2T were 85.12, 85.87 and 84.35 %, respectively. The estimated DNA-DNA hybridization values between strain 19-m-6T and these three type strains were 22.0, 22.6 and 21.2 %, respectively. Four alkane hydroxylase (alkB) genes were obtained from the draft genome sequence. The G+C content of the chromosomal DNA was 56.44 mol%. The major fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, one aminolipid, three phospholipids, two glycolipids and two aminophospholipids. According to its phenotypic features, fatty acid composition and 16S rRNA gene sequence, the novel strain fitted well into the genus Alcanivorax, but could be clearly distinguished from all other known Alcanivorax species described to date. The nameAlcanivorax nanhaiticus sp. nov. is thus proposed, with 19-m-6T (=MCCC 1A05629T=KCTC 52137T) as the type strain.

Alcanivorax dieselolei, an alkane-degrading bacterium associated with the mucus of the zoanthid Palythoa caribaeorum (Cnidaria, Anthozoa)

Analyses of 16S rDNA genes were used to identify the microbiota isolated from the mucus of the zoanthid Palythoa caribaeorum at Porto de Galinhas on the coast of Pernambuco State, Brazil. This study is important as the first report of this association, because of the potential biotechnological applications of the bacterium Alcanivorax dieselolei, and as evidence for the presence of a hydrocarbon degrading bacterium in a reef ecosystem such as Porto de Galinhas.

Aliikangiella marina gen. nov., sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122, and proposal of Kangiellaceae fam. nov. in the order Oceanospirillales

A Gram-stain-negative, non-motile, non-spore-forming, long rod-shaped bacterium, designated strain GYP-15T, was isolated from the culture broth of a marine microalga, Picochloruma sp. 122. Phylogenetic analyses revealed that strain GYP-15T shared 90.6 % 16S rRNA gene sequence similarity with its closest relative, Kangiella aquimarina KCTC 12183T, and represents a distinct phylogenetic lineage in a robust clade consisting of GYP-15T and members of the genera Kangiella and Pleionea in the order Oceanospirillales. Chemotaxonomic and physiological characteristics, including major cellular fatty acids, NaCl tolerance and pattern of carbon source utilization, could also readily distinguish strain GYP-15T from all established genera and species. Thus, it is concluded that strain GYP-15T represents a novel species of a new genus, for which the name Aliikangiella marina gen. nov., sp. nov. is proposed. The type strain of Aliikangiella marina is GYP-15T ( = MCCC 1K01163T = KCTC 42667T). Based on phylogenetic results, 16S rRNA gene signature nucleotide pattern and some physiological characteristics, the three genera Kangiella, Pleionea and Aliikangiella are proposed to make up a novel family, Kangiellaceae fam. nov., in the order Oceanospirillales.

Screening of biosurfactant-producing bacteria from offshore oil and gas platforms in North Atlantic Canada

From offshore oil and gas platforms in North Atlantic Canada, crude oil, formation water, drilling mud, treated produced water and seawater samples were collected for screening potential biosurfactant producers. In total, 59 biosurfactant producers belong to 4 genera, namely, Bacillus, Rhodococcus, Halomonas, and Pseudomonas were identified and characterized. Phytogenetic trees based on 16S ribosomal deoxyribonucleic acid (16S rDNA) were constructed with isolated strains plus their closely related strains and isolated strains with biosurfactant producers in the literature, respectively. The distributions of the isolates were site and medium specific. The richness, diversity, and evenness of biosurfactant producer communities in oil and gas platform samples have been analyzed. Diverse isolates were found with featured properties such as effective reduction of surface tension, producing biosurfactants at high rate and stabilization of water-in-oil or oil-in-water emulsion. The producers and their corresponding biosurfactants had promising potential in applications such as offshore oil spill control, enhancing oil recovery and soil washing treatment of petroleum hydrocarbon-contaminated sites.

Alcanivorax xenomutans sp. nov., a hydrocarbonoclastic bacterium isolated from a shrimp cultivation pond

Two bacterial strains (JC109T and JC261) were isolated from a sediment sample collected from a shrimp cultivation pond in Tamil Nadu (India). Cells were Gram-stain-negative, motile rods. Both strains were positive for catalase and oxidase, hydrolysed Tween 80, and grew chemo-organoheterotrophically with an optimal pH of 6 (range pH 4–9) and at 30 °C (range 25–40 °C). Based on 16S rRNA gene sequence analysis, strains JC109T and JC261 were identified as belonging to the genus Alcanivorax with Alcanivorax dieselolei B-5T (sequence similarity values of 99.3 and 99.7 %, respectively) and Alcanivorax balearicus MACL04T (sequence similarity values of 98.8 and 99.2 %, respectively) as their closest phylogenetic neighbours. The 16S rRNA gene sequence similarity between strains JC109T and JC261 was 99.6 %. The level of DNA–DNA relatedness between the two strains was 88 %. Strain JC109T showed 31±1 and 26±2 % DNA–DNA relatedness with A. dieselolei DSM 16502T and A. balearicus DSM 23776T, respectively. The DNA G+C content of strains JC109T and JC261 was 54.5 and 53.4 mol%, respectively. Polar lipids of strain JC109T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids and two unidentified lipids. The major fatty acids were C10 : 0, C12 : 0, C16 : 0, C12 : 0 3-OH, C16 : 1ω7c, C18 : 1ω7c and C19 : 0 cyclo ω8c. Both strains could utilize diesel oil and a variety of xenobiotics as carbon and energy sources. The results of physiological, biochemical, chemotaxonomic and molecular analyses allowed the clear differentiation of strains JC109T and JC261 from all other members of the genus Alcanivorax . Strains JC109T and JC261 are thus considered to represent a novel species, for which the name Alcanivorax xenomutans sp. nov. is proposed. The type strain is JC109T ( = KCTC 23751T = NBRC 108843T).

Alcanivorax marinus sp. nov., isolated from deep-sea water

A taxonomic study was carried out on strain R8-12(T), which was isolated from deep-sea water of the Indian Ocean during the screening of oil-degrading bacteria. The isolate was Gram-stain-negative, oxidase and catalase-positive. Growth was observed at salinities from 0.5 to 15 % (optimum 3 %), at pH from 6-10 (optimum 7-8) and at temperatures from 10 to 42 °C (optimum 28 °C). On the basis of 16S rRNA gene sequence similarity, strain R8-12(T) was shown to belong to the genus Alcanivorax and to be related to Alcanivorax venustensis DSM 13974(T) (97.2 %), A. dieselolei B-5(T) (95.0 %), A. balearicus MACL04(T) (94.6 %), A. hongdengensis A-11-3(T) (94.3 %), A. jadensis T9(T) (93.8 %), A. borkumensis SK2(T) (93.7 %) and A. pacificus W11-5(T) (93.7 %). The gyrB sequence similarities between R8-12(T) and other species of the genus Alcanivorax ranged from 77.9 % to 86.9 %. The major fatty acids were C16 : 0 (31.8 %), C18 : 1ω7c (20.3 %), C19 : 0ω8c cyclo (15.8 %) and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) (8.9 %). The polar lipids were phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two aminolipids (AL1-AL2) and two phospholipids (PL1-PL2). Three alkane hydroxylase (alkB) genes were identified in the genome. The G+C content of the chromosomal DNA was 66.1 mol%. DNA-DNA hybridization showed that strain R8-12(T) and A. venustensis DSM 13974(T) had a DNA-DNA relatedness of 63±3 %. According to its phenotypic features and fatty acid composition as well as the 16S rRNA and gyrB gene sequences, the novel strain represents a member of the genus Alcanivorax, but could be easily distinguished from all other known species of the genus Alcanivorax described to date. The name Alcanivorax marinus sp. nov. is proposed, with the type strain R8-12(T) ( = MCCC 1A00382(T) = LMG 24621(T) = CCTCC AB 208234(T)).

Pleionea mediterranea gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater

A Gram-negative, aerobic, cream-pigmented, non-motile, non-spore-forming straight rod, strain MOLA115T, was isolated from a coastal water sample from the Mediterranean Sea. On the basis of phylogenetic analysis of the 16S rRNA gene sequences, strain MOLA115T was shown to belong to the Gammaproteobacteria , adjacent to members of the genera Marinicella , Arenicella and Kangiella , sharing less than 89 % 16S rRNA gene sequence similarity with strains of all recognized species within the Gammaproteobacteria . The only isoprenoid quinone was ubiquinone-8. Polar lipids in strain MOLA115T included phosphatidylethanolamine, an aminolipid, phosphatidylglycerol and an aminophospholipid. Fatty acid analysis revealed iso-C15 : 0 and iso-C17 : 1ω9c to be the dominant components. The DNA G+C content was 44.5 mol%. Based upon the phenotypic and phylogenetic data, we propose that strain MOLA115T should be considered to represent a novel species in a new genus, for which the name Pleionea mediterranea gen. nov., sp. nov. is proposed. The type strain of Pleionea mediterranea is MOLA115T ( = CIP 110343T = DSM 25350T).

Enzymes and genes involved in aerobic alkane degradation

Alkanes are major constituents of crude oil. They are also present at low concentrations in diverse non-contaminated because many living organisms produce them as chemo-attractants or as protecting agents against water loss. Alkane degradation is a widespread phenomenon in nature. The numerous microorganisms, both prokaryotic and eukaryotic, capable of utilizing alkanes as a carbon and energy source, have been isolated and characterized. This review summarizes the current knowledge of how bacteria metabolize alkanes aerobically, with a particular emphasis on the oxidation of long-chain alkanes, including factors that are responsible for chemotaxis to alkanes, transport across cell membrane of alkanes, the regulation of alkane degradation gene and initial oxidation.

Genome sequence of the alkane-degrading bacterium Alcanivorax hongdengensis type strain A-11-3

Alcanivorax hongdengensis A-11-3(T) was isolated from an oil-enriched consortium enriched from the surface seawater of Hong-Deng dock in the Straits of Malacca and Singapore. Strain A-11-3(T) can degrade n-alkane and produce a lipopeptide biosurfactant. Here we report the genome of A-11-3(T) and the genes associated with alkane degradation.

Diversity of flavin-binding monooxygenase genes (almA) in marine bacteria capable of degradation long-chain alkanes

Many bacteria have been reported as degraders of long-chain (LC) n-alkanes, but the mechanism is poorly understood. Flavin-binding monooxygenase (AlmA) was recently found to be involved in LC-alkane degradation in bacteria of the Acinetobacter and Alcanivorax genera. However, the diversity of this gene and the role it plays in other bacteria remains unclear. In this study, we surveyed the diversity of almA in marine bacteria and in bacteria found in oil-enrichment communities. To identify the presence of this gene, a pair of degenerate PCR primers were was designed based on conserved motifs of the almA gene sequences in public databases. Using this approach, we identified diverse almA genes in the hydrocarbon-degrading bacteria and in bacterial communities from the surface seawater of the Xiamen coastal area, the South China Sea, the Indian Ocean, and the Atlantic Ocean. As a result, almA was positively detected in 35 isolates belonging to four genera, and a total of 39 different almA sequences were obtained. Five isolates were confirmed to harbor two to three almA genes. From the Xiamen coastal area and the Atlantic Ocean oil-enrichment communities, a total of 60 different almA sequences were obtained. These sequences mainly formed two clusters in the phylogenetic tree, named Class I and Class II, and these shared 45-56% identity at the amino acid level. Class I contained 11 sequences from bacteria represented by the Salinisphaera and Parvibaculum genera. Class II was larger and more diverse, and it was composed of 88 sequences from Proteobacteria, Gram-negative bacteria, and the enriched bacterial communities. These communities were represented by the Alcanivorax and Marinobacter genera, which are the two most popular genera hosting the almA gene. AlmA was also detected across a wide geographical range, as determined by the origin of the bacterial host. Our results demonstrate the diversity of almA and confirm its high rate of occurrence in hydrocarbon-degrading bacteria, indicating that this gene plays an important role in the degradation of LC alkanes in marine environments.

Bioreactor-based bioremediation of hydrocarbon-polluted Niger Delta marine sediment, Nigeria

Crude oil-polluted marine sediment from Bonny River loading jetty Port Harcourt, Nigeria was treated in seven 2.5 l stirred-tank bioreactors designated BNPK, BNK5, BPD, BNO₃, BUNa, BAUT, and BUK over a 56-day period. Five bioreactors were biostimulated with either K₂HPO₄, NH₄NO₃, (NH₄)₂SO₄, NPK, urea or poultry droppings while unamended (BUNa) and heat-killed (BAUT) treatments were controls. For each bioreactor, 1 kg (wet weight) sediment amended with 1 l seawater were spiked with 20 ml and 20 mg of crude oil and anthracene which gave a total petroleum hydrocarbons (TPH) range of 106.4–116 ppm on day 0. Polycyclic aromatic hydrocarbons (PAH) in all spiked sediment slurry ranged from 96.6 to 104.4 ppm. TPH in each treatment was ≤14.9 ppm while PAH was ≤6.8 ppm by day 56. Treatment BNO₃ recorded highest heterotrophic bacterial count (9.8 × 10⁸ cfu/g) and hydrocarbon utilizers (1.15 × 10⁸ cfu/g). By day 56, the percentages of biodegradation of PAHs, as measured with GC–FID were BNK5 (97.93%), BNPK (98.38%), BUK (98.82%), BUNa (98.13%), BAUT (93.08%), BPD (98.92%), and BNO₃ (98.02%). BPD gave the highest degradation rate for PAH. TPH degradation rates were as follows: BNK5 (94.50%), BNPK (94.77%), BUK (94.10%), BUNa (94.77%), BAUT (75.04%), BPD (95.35%), BNO₃ (95.54%). Fifty-six hydrocarbon utilizing bacterial isolates obtained were Micrococcus spp. 5 (9.62%), Staphylococcus spp. 3 (5.78%), Pseudomonas spp. 7 (13.46%), Citrobacter sp. 1 (1.92%), Klebsiella sp. 1 (1.92%), Corynebacterium spp. 5 (9.62%), Bacillus spp. 5 (9.62%), Rhodococcus spp. 7 (13.46%), Alcanivorax spp. 7 (13.46%), Alcaligenes sp. 1 (1.92%), Serratia spp. 2 (3.85%), Arthrobacter spp. 7 (13.46%), Nocardia spp. 2 (3.85%), Flavobacterium sp. 1 (1.92%), Escherichia sp. 1 (1.92%), Acinetobacter sp. 1 (1.92%), Proteus sp. 1 (1.92%) and unidentified bacteria 10 (17%). These results indicate that the marine sediment investigated is amenable to bioreactor-based bioremediation and that abiotic factors also could contribute to hydrocarbon attenuation as recorded in the heat-killed (BAUT) control.

Genes involved in alkane degradation in the Alcanivorax hongdengensis strain A-11-3

Alcanivorax hongdengensis A-11-3 is a newly identified type strain isolated from the surface water of the Malacca and Singapore Straits that can degrade a wide range of alkanes. To understand the degradation mechanism of this strain, the genes encoding alkane hydroxylases were obtained by PCR screening and shotgun sequencing of a genomic fosmid library. Six genes involved in alkane degradation were found, including alkB1, alkB2, p450-1, p450-2, p450-3 and almA. Heterogeneous expression analysis confirmed their functions as alkane oxidases in Pseudomonas putida GPo12 (pGEc47ΔB) or Pseudomonas fluorescens KOB2Δ1. Q-PCR revealed that the transcription of alkB1 and alkB2 was enhanced in the presence of n-alkanes C(12) to C(24); three p450 genes were up-regulated by C(8)-C(16) n-alkanes at different levels, whereas enhanced expression of almA was observed when strain A-11-3 grew with long-chain alkanes (C(24) to C(36)). In the case of branched alkanes, pristane significantly enhanced the expression of alkB1, p450-3 and almA. The six genes enable strain A-11-3 to degrade short (C(8)) to long (C(36)) alkanes that are straight or branched. The ability of A. hongdengensis A-11-3 to thrive in oil-polluted marine environments may be due to this strain's multiple systems for alkane degradation and its range of substrates.

Alcanivorax pacificus sp. nov., isolated from a deep-sea pyrene-degrading consortium

A taxonomic study was carried out on a novel bacterial strain, designated W11-5T, which was isolated from a pyrene-degrading consortium enriched from deep-sea sediment of the Pacific Ocean. The isolate was Gram-reaction-negative and oxidase- and catalase-positive. Growth was observed in 0.5–12 % (w/v) NaCl and at 10–42 °C. On the basis of 16S rRNA gene sequence analysis, strain W11-5T was shown to belong to the genus Alcanivorax with a close relation to A. dieselolei B-5T (93.9 % 16S rRNA sequence similarity), A. balearicus MACL04T (93.1 %), A. hongdengensis A-11-3T (93.1 %), A. borkumensis SK2T (93.0 %), A. venustensis ISO4T (93.0 %) and A. jadensis T9T (92.9 %). Similarities between the gyrB gene sequences of W11-5T and other species of the genus Alcanivorax were between 76.8 and 80.8 %. The principal fatty acids were C12 : 0 3-OH (8.0 %), C16 : 0 (29.1 %) and C18 : 1ω7c (27.4 %). The G+C content of the chromosomal DNA was 60.8 mol%. Based on its morphology, physiology and fatty acid composition as well as the results of 16S rRNA and gyrB gene sequence analyses, strain W11-5T ( = MCCC 1A00474T  = CCTCC AB 208236T  = LMG 25514T) represents a novel species of the genus Alcanivorax, for which the name Alcanivorax pacificus sp. nov. is proposed.

Gene diversity of CYP153A and AlkB alkane hydroxylases in oil-degrading bacteria isolated from the Atlantic Ocean

Alkane hydroxylases, including the integral-membrane non-haem iron monooxygenase (AlkB) and cytochrome P450 CYP153 family, are key enzymes in bacterial alkane oxidation. Although both genes have been detected in a number of bacteria and environments, knowledge about the diversity of these genes in marine alkane-degrading bacteria is still limited, especially in pelagic areas. In this report, 177 bacterial isolates, comprising 43 genera, were obtained from 18 oil-degrading consortia enriched from surface seawater samples collected from the Atlantic Ocean. Many isolates were confirmed to be the first oil-degraders in their affiliated genera including Brachybacterium, Idiomarina, Leifsonia, Martelella, Kordiimonas, Parvibaculum and Tistrella. Using degenerate PCR primers, alkB and CYP153A P450 genes were surveyed in these bacteria. In total, 82 P450 and 52 alkB gene fragments were obtained from 80 of the isolates. These isolates mainly belonged to Alcanivorax, Bacillus, Erythrobacter, Martelella, Parvibaculum and Salinisphaera, some of which were reported, for the first time, to encode alkane hydroxylases. Phylogenetic analysis showed that both genes were quite diverse and formed several clusters, most of which were generated from various Alcanivorax bacteria. Noticeably, some sequences, such as those from the Salinisphaera genus, were grouped into a distantly related novel cluster. Inspection of the linkage between gene and host revealed that alkB and P450 tend to coexist in Alcanivorax and Salinisphaera, while in all isolates of Parvibaculum, only P450 genes were found, but of multiple homologues. Multiple homologues of alkB mostly cooccurred in Alcanivorax isolates. Conversely, distantly related isolates contained similar or even identical sequences. In summary, various oil-degrading bacteria, which harboured diverse P450 and alkB genes, were found in the surface water of Atlantic Ocean. Our results help to show the diversity of P450 and alkB genes in prokaryotes, and to portray the geographic distribution of oil-degrading bacteria in marine environments.