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.     

Growth and polyhydroxybutyrate production by Ralstonia eutropha in emulsified plant oil medium

Polyhydroxyalkanoates (PHAs) are natural polyesters synthesized by bacteria for carbon and energy storage that also have commercial potential as bioplastics. One promising class of carbon feedstocks for industrial PHA production is plant oils, due to the high carbon content of these compounds. The bacterium Ralstonia eutropha accumulates high levels of PHA and can effectively utilize plant oil. Growth experiments that include plant oil, however, are difficult to conduct in a quantitative and reproducible manner due to the heterogeneity of the two-phase medium. In order to overcome this obstacle, a new culture method was developed in which palm oil was emulsified in growth medium using the glycoprotein gum arabic as the emulsifying agent. Gum arabic did not influence R. eutropha growth and could not be used as a nutrient source by the bacteria. R. eutropha was grown in the emulsified oil medium and PHA production was measured over time. Additionally, an extraction method was developed to monitor oil consumption. The new method described in this study allows quantitative, reproducible R. eutropha experiments to be performed with plant oils. The method may also prove useful for studying growth of different bacteria on plant oils and other hydrophobic carbon sources.     

Isolation of alkane‐degrading bacteria from deep‐sea Mediterranean sediments

Aims: To isolate and identify alkane‐degrading bacteria from deep‐sea superficial sediments sampled at a north‐western Mediterranean station. Methods and Results: Sediments from the water/sediment interface at a 2400 m depth were sampled with a multicorer at the ANTARES site off the French Mediterranean coast and were promptly enriched with Maya crude oil as the sole source of carbon and energy. Alkane‐degrading bacteria belonging to the genera Alcanivorax, Pseudomonas, Marinobacter, Rhodococcus and Clavibacter‐like were isolated, indicating that the same groups were potentially involved in hydrocarbon biodegradation in deep sea as in coastal waters. Conclusions: These results confirm that members of Alcanivorax are important obligate alkane degraders in deep‐sea environments and coexist with other degrading bacteria inhabiting the deep‐subsurface sediment of the Mediterranean. Significance and Impact of the Study: The results suggest that the isolates obtained have potential applications in bioremediation strategies in deep‐sea environments and highlight the need to identify specific piezophilic hydrocarbon‐degrading bacteria (HCB) from these environments.     

Occurrence, production, and export of lipophilic compounds by hydrocarbonoclastic marine bacteria and their potential use to produce bulk chemicals from hydrocarbons

Petroleum (or crude oil) is a complex mixture of hydrocarbons. Annually, millions of tons of crude petroleum oil enter the marine environment from either natural or anthropogenic sources. Hydrocarbon-degrading bacteria (HDB) are able to assimilate and metabolize hydrocarbons present in petroleum. Crude oil pollution constitutes a temporary condition of carbon excess coupled to a limited availability of nitrogen that prompts marine oil-degrading bacteria to accumulate storage compounds. Storage lipid compounds such as polyhydroxyalkanoates (PHAs), triacylglycerols (TAGs), or wax esters (WEs) constitute the main accumulated lipophilic substances by bacteria under such unbalanced growth conditions. The importance of these compounds as end-products or precursors to produce interesting biotechnologically relevant chemicals has already been recognized. In this review, we analyze the occurrence and accumulation of lipid storage in marine hydrocarbonoclastic bacteria. We further discuss briefly the production and export of lipophilic compounds by bacteria belonging to the Alcanivorax genus, which became a model strain of an unusual group of obligate hydrocarbonoclastic bacteria (OHCB) and discuss the possibility to produce neutral lipids using A. borkumensis SK2.     

Petroleum Bioremediation in Seawater Using Guano as the Fertilizer

The biodegradation of hydrocarbon pollutants in open systems, such as oceans, is generally limited by the availability of utilizable nitrogen and phosphorus sources. Here the authors demonstrate the potential of overcoming this problem with guano as the fertilizer. In the first set of experiments, the principle and conditions for growing bacteria on a water insoluble fertilizer was established, using uric acid as the nitrogen source and a pure culture of an isolated hydrocarbon-degrading bacterium, Alcanivorax sp. OK2. Using a simulated open system, it was demonstrated that uric acid (the major nitrogen component of guano) binds to crude oil and is available for the growth of strain OK2 and petroleum degradation. In the second set of experiments, using a simulated open system, it was demonstrated that commercial guano was an effective source of nitrogen and phosphorus for the growth of marine bacteria on crude oil. Bacterial cultures reached over 10⁸ cells per ml and 70% of the crude oil was degraded. Controls using ammonium sulfate and phosphate in place of guano in the simulated open system reached only 10⁶ cells per ml and showed no detectable hydrocarbon degradation. Isolation and characterization of the bacteria in the crude oil/guano cultures indicated that they were primarily strains of Alcanivorax and Alteromonas.     

Saccharopolyspora: an underexplored source for bioactive natural products

Actinomycetes are a rich source for secondary metabolites with a diverse array of biological activities. Among the various genera of actinomycetes, the genus Saccharopolyspora has long been recognized as a potential source for antibiotics and other therapeutic leads that belong to diverse classes of natural products. Members of the genus Saccharopolyspora have been widely reported from several natural sources including both terrestrial and marine environments. A plethora of this genus has been chemically investigated for the production of novel natural products with interesting pharmacological effects. Therefore, Saccharopolyspora is considered one of the pharmaceutical important genera that could provide further chemical diversity with potential lead compounds. In this review, the literature from 1976 until December 2018 was covered, providing a comprehensive survey of all natural products derived from this genus and their semi-synthetic derivatives along with their biological activities, whenever applicable. Moreover, the biological diversity of Saccharopolyspora species and their habitats were also discussed.     

Bacterial Diversity of Lonar Soda Lake of India

Total seventy four bacteria were isolated from Lonar soda lake of Maharashtra state, India. Eleven isolates were identified using morphological, biochemical and molecular analysis. The bacteria isolated belonged to phylum firmicutes and proteobacteria. Majorities (eight) were firmicutes and three were proteobacteria. For the first time we are reporting Alcanivorax spp. which is a genus well known for its oil degradation capacity, indicate the probable existence of oil reservoir in vicinity of Lonar lake. In addition all the eleven bacteria are potential producers of industrially important enzymes, pigments, antibiotics as well.     

Shifts in alkane-degrading bacteria genotypes during bioremediation of a vegetated coastal soil

The effect of plants (milo, oleander and buffelgrass) and hexadecane (1 g/kg of soil) on the diversity of hexadecane-degraders in a coastal soil was investigated. Hexadecane was rapidly degraded during the first 56 days. Its depletion was not plant-enhanced but was slightly retarded by milo and buffelgrass. The diversity of the dominant cultured hexadecane-degrading bacteria was based on sequencing of the V6-8 region of 16S rDNA. On day 0, Alphaproteobacteria prevailed. By day 56, Gammaproteobacteria dominated the contaminated samples whereas similar numbers of Alphaproteobacteria and Gammaproteobacteria genotypes occurred in the uncontaminated samples. Bacteria related to Alcanivorax, a specialized alkane-degrading marine bacterium, were found in all contaminated samples except for buffelgrass rhizospheres, which solely harbored Pseudomonas indica. On day 114, when hexadecane was highly depleted in the contaminated treatments, similar numbers of Alpha- and Gammaproteobacteria genotypes occurred in contaminated and uncontaminated samples. At this stage Alcanivorax had virtually disappeared. Thus in this coastal soil the prevalence of the alkane-dependent Alcanivorax may be a useful indicator of bioremediation progress provided the plant cover favors the dominance of Alcanivorax.     

Über das ätherische Öl von Grünalgen

Zusammenfassung Einzellige Grünalgen der Gattung Chlorella bilden ätherische Öle. Die in einem Teil dieser Öle vorkommenden Guajanolide (Proazulene) haben sich als brauchbares taxonomisches Merkmal erwiesen. Einzelne Arten bilden größenordnungsmäßig ebenso viel ätherisches Öl wie höhere Pflanzen.

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On the essential oil of green algaeI. The oils of the genus Chlorella

Unicellular green algae of the genus Chlorella are able to synthesize essential oils. Some guajanolides (i.e., proazulenes) were shown to be its main components. Certain species produce as much oil as do higher plants. Formation of essential oils can serve as a taxonomic character in the genus Chlorella.

     

Media Formulation using Complex Organic Nutrients for Improved Activity,Productivity, and Yield of Candida rugosa Lipase and Esterase Enzymes

Abstract

Candida rugosa is an excellent source of multiple lipase and esterase enzymes; therefore, it is of technological importance to formulate the medium that provides high activity for each enzyme. In this work, the cultivation medium comprising complex nutrients that provided the highest activity, productivity, and yield of C. rugosa enzymes individually was formulated. Time courses of the extracellular and intracellular lipase and esterase activities of C. rugosa were represented and the role of protease in the cultivation progress was discussed. Urea, soy-peptone, yeast extract, a mixture of soy-peptone and yeast extract, cheese whey, and wheat mill bran were tested for their lipolytic and esterasic activities. Urea provided considerably higher extracellular lipase activity when compared to other nitrogen sources; however, soy-peptone provided the highest extracellular esterase activity. Hazelnut, olive, sesame, soybean, and flax seed oils affected the enzyme activities to different extents related to their fatty acid compositions. Hazelnut oil and olive oil provided the highest extracellular lipase and esterase activities, respectively, whereas sesame oil produced the highest biomass. High C₁₈ and C₁₆ ester contents of vegetable oils promoted high lipase and esterase productions, respectively. A temperature of 30°C yielded the highest extracellular and intracellular lipase and esterase activities; however, 35°C produced the highest biomass.     

Screening and its potential application of lipolytic activity from a marine environment: characterization of a novel esterase from <Emphasis Type="Italic">Yarrowia lipolytica</Emphasis> CL180

To develop an enantioselective lipase/esterase hydrolyzing racemic ofloxacin ester to levofloxacin, samples were collected from a variety of marine environments such as cold sea, hydrothermal vent area, sediment, tidal flat area, arctic sea, marine organisms, and so on. Microorganisms were isolated by plating on an enrichment medium with simultaneous detection of lipolytic activities and screened for the hydrolysis of ofloxacin ester. Three candidates among isolates were selected, and one of them, identified as Yarrowia lipolytica CL180, hydrolyzed preferentially S-enantiomer of racemic ofloxacin ester. The lipase/esterase gene (yli180) was cloned by screening a genomic library. The sequence analysis revealed an open reading frame consisting of 1,431 bp that encoded a protein of 476 amino acids with a molecular mass of 53 kDa. The yli180 gene was expressed in Escherichia coli and purified to homogeneity. The optimum activity of the recombinant protein (rYli180) occurred at pH 7.5 and 35°C, respectively. rYli180 preferentially hydrolyzed p-nitrophenyl esters of fatty acids with short chain lengths of ≤10 carbon atoms. This study represents a novel esterase of type B1 carboxylesterase/lipase family from a marine isolate, showing a potential usage as a biocatalyst because of enantioselectivity toward racemic ofloxacin ester.     

Polyphasic approach for assessing changes in an autochthonous marine bacterial community in the presence of Prestige fuel oil and its biodegradation potential

A laboratory experiment was conducted to identify key hydrocarbon degraders from a marine oil spill sample (Prestige fuel oil), to ascertain their role in the degradation of different hydrocarbons, and to assess their biodegradation potential for this complex heavy oil. After a 17-month enrichment in weathered fuel, the bacterial community, initially consisting mainly of Methylophaga species, underwent a major selective pressure in favor of obligate hydrocarbonoclastic microorganisms, such as Alcanivorax and Marinobacter spp. and other hydrocarbon-degrading taxa (Thalassospira and Alcaligenes), and showed strong biodegradation potential. This ranged from >99% for all low- and medium-molecular-weight alkanes (C₁₅–C₂₇) and polycyclic aromatic hydrocarbons (C₀- to C₂- naphthalene, anthracene, phenanthrene, dibenzothiophene, and carbazole), to 75–98% for higher molecular-weight alkanes (C₂₈–C₄₀) and to 55–80% for the C₃ derivatives of tricyclic and tetracyclic polycyclic aromatic hydrocarbons (PAHs) (e.g., C₃-chrysenes), in 60 days. The numbers of total heterotrophs and of n-alkane-, aliphatic-, and PAH degraders, as well as the structures of these populations, were monitored throughout the biodegradation process. The salinity of the counting medium affects the counts of PAH degraders, while the carbon source (n-hexadecane vs. a mixture of aliphatic hydrocarbons) is a key factor when counting aliphatic degraders. These limitations notwithstanding, some bacterial genera associated with hydrocarbon degradation (mainly belonging to α- and γ-Proteobacteria, including the hydrocarbonoclastic Alcanivorax and Marinobacter) were identified. We conclude that Thalassospira and Roseobacter contribute to the degradation of aliphatic hydrocarbons, whereas Mesorhizobium and Muricauda participate in the degradation of PAHs.     

Microbial Community Composition in Crude Oils and Asphalts from the Kurdistan Region of Iraq

Abstract

To identify hydrocarbon-degrading microorganisms contributing to the formation of heavy oil we investigated the microbial community composition in different types of crude oils from oil-production facilities and in crude oil and asphalt from different natural seeps from the Kurdistan Region of Iraq (KRI). Crude oils from five out of six production facilities did not contain microorganisms detectable by 16S rRNA gene PCR amplicon sequencing likely reflecting a low microbial abundance in these samples. Crude oil and asphalt from the natural seeps hosted diverse microbial communities. The same phylotypes of uncultivated Deferribacteres and Thermodesulfobacteraceae were predominant community members across crude oils and asphalts from separate geographical locations. Soils surrounding seeps did not contain these phylotypes suggesting that they originate from the subsurface and although they seem commonly detected in hydrocarbon-rich environments their role in hydrocarbon-degradation is unknown. GC-MS analyses showed that mainly aromatic hydrocarbons were present in the crude oil and asphalt and that they were undergoing biodegradation - likely with sulfate and nitrate as terminal oxidants. In agreement, only bssA gene, but not assA gene-carrying microorganisms were detectable in the analyzed sampled. Overall our study identified several abundant uncultivated taxa with likely roles in transformation of nitrate, sulfate and hydrocarbons.     

Detection of Hyperthermophilic Archaea of the Genus Desulfurococcus by Hybridization with Oligonucleotide Probes

Based on the analysis of nucleotide sequences of 16S rRNA, oligonucleotide probes were designed for the detection and identification of representatives of the genus Desulfurococcus (kingdom Crenarchaeota of the domain Archaea). The detection procedure included obtaining PCR products on DNA isolated from pure cultures, enrichments, or natural samples with a designed Crenarchaeota-specific primer pair: Cren 7F (5"-TTCCGGTTGATCCYGCCGGACC-3") and Cren 518R (5"-GCTGGTWTTACCGCGGCGGCTGA-3"). The PCR products were hybridized with Dig-11-dUTP–labeled oligonucleotide probes targeting the genus Desulfurococcus (Dco 198, 5"-CGTTAACYCCYGCCACACC-3") and its species D. mobilis (Dco_mob 198, 5"-CGTTAACCCCTGCCACACC-3") and D. amylolyticus (Dco_amy 198, 5"-CGTTAACCCCCGCCACACC-3"). With the use of these primers and probes, four new strains isolated from hydrotherms of Kamchatka and Kunashir Island were identified as members of the speciesDesulfurococcus amylolyticus. Desulfurococcus representatives were detected in several natural samples, including a sample taken from a marine hydrotherm at Kunashir Island; this demonstrates that representatives of this genus occur not only in terrestrial but also in marine environments.     

Novel diversity within Roseofilum (Desertifilaceae,Cyanobacteria) from marine benthic mats with description of four new species

Benthic cyanobacterial mats (BCMs) are natural phenomena in marine environments. Reports of BCMs occurring across coastal marine environments have increased, partly driven by nutrient loading and climate change; thus, there is a need to understand the diversity involved in the proliferations and potential toxicity of the BCMs. Furthermore, marine cyanobacterial mats are observed growing on and affecting the health of corals with one specific cyanobacterial genus, Roseofilum, dominating the microbial mats associated with black band disease (BBD), a destructive polymicrobial disease that affects corals. To explore the diversity of Roseofilum, cyanobacterial mats from various marine habitats were sampled, and individual isolates were identified based on morphology, 16S rRNA gene phylogenies, 16S–23S ITS rRNA region sequence dissimilarities, and phylogenomics. Four novel species of Roseofilum were isolated from benthic marine mats, three from the coasts of Florida, United States (R. capinflatum sp. nov., R. casamattae sp. nov., and R. acuticapitatum sp. nov.) and one from the coast of France (R. halophilum sp. nov.). Our analyses revealed that Roseofilum associated with coral BBD and those not associated with corals but rather from coastal benthic mats are systematically distinct based on both phylogenetic and phylogenomic analyses. Enzyme-linked immunosorbent assay (ELISA) and LC–MS data indicated that microcystin production was found in one of the four species.     

Efficient production of polyhydroxyalkanoates from plant oils by Alcaligenes eutrophus and its recombinant strain

The ability of Alcaligenes eutrophus to grow and produce polyhydroxyalkanoates (PHA) on plant oils was evaluated. When olive oil, corn oil, or palm oil was fed as a sole carbon source, the wild-type strain of A. eutrophus grew well and accumulated poly(3-hydroxybutyrate) homopolymer up to approximately 80% (w/w) of the cell dry weight during its stationary growth phase. In addition, a recombinant strain of A. eutrophus PHB⁻4 (a PHA-negative mutant), harboring a PHA synthase gene from Aeromonas caviae, was revealed to produce a random copolyester of 3-hydroxybutyrate and 3-hydroxyhexanoate from these plant oils with a high cellular content (approximately 80% w/w). The mole fraction of 3-hydroxyhexanoate units was 4–5 mol% whatever the structure of the triglycerides fed. The polyesters produced by the A. eutrophus strains from olive oil were 200–400 kDa (the number-average molecular mass). The results demonstrate that renewable and inexpensive plant oils are excellent carbon sources for efficient production of PHA using A. eutrophus strains. Received: 3 September 1997 / Received revision: 10 November 1997 / Accepted: 16 November 1997     

STUDY OF THE ESSENTIAL LEAF OILS OF THE GENUS MONARDA (LABIATAE)

Vapor-phase chromatographic patterns obtained from the distilled essential oils of 20 taxa in the genus Monarda (Labiatae) are discussed. The influence of leaf tissue maturity, plant habitat, and oil storage upon the composition of the essential oils was investigated, as well as similarities of leaf and flower oils in the same plant. The taxa of the subgenus Cheilyctis have very similar chromatographic “fingerprints” which confirm their homogeneity. On the other hand, the polyploid subgenus Monarda has heterogeneous patterns of essential oil composition among its species. A population of M. fistulosa gave evidence of being a chemical race.     

NEW WORLD JUGLANDACEAE. II. HICKORY NUT OILS,PHENETIC SIMILARITIES,AND EVOLUTIONARY IMPLICATIONS IN THE GENUS CARYA

Gas chromatographic analyses of the nut oils of 155 samples, representing 15 taxa of Carya, confirm the basic uniformity of fatty-acid composition within the walnut family. All taxa contain small amounts of the saturated fatty acids—palmitic and stearic—and variable amounts of the unsaturated oleic and linoleic acids, and at least trace amounts of linolenic. Quantitative differences in the relative amounts of the five fatty acids support the morphologic recognition of two sections within the genus. Members of the section Carya are characterized by higher linoleic and lower oleic acid percentages than are those of section Apocarya. It is also true, however, that tetraploids of section Carya tend to have higher linoleic and lower oleic acid percentages than diploids within the same section. Numerical analyses of the oil data reveal close similarities between certain members of the more “primitive” section Apocarya and the diploid members of section Carya. The highly heterogeneous assemblage within section Apocarya could be split into three groups on the basis of oil data. It is equally obvious, however, that the American taxa of the genus Carya have had a long and reticulate phylogeny and that recognition of additional categories above the species level would not result in natural assemblages.