A. borkumensis is a gram-negative bacteria, meaning that the bacteria has an outer membrane of lipopolysaccharides, unlike gram positive bacteria who do not . The predictions for rarefaction curves were developed using the R package drc (v3.0.1) following a Yield-Loss curve model (Ritz et al., 2015). NE/S004548/1). These results provide insights into bacterial function in a complex marine environment. Polycyclic aromatic hydrocarbon degradation of phytoplankton-associated Arenibacter spp. Pritchard The final biomasses (expressed as grams [CDW] per liter) of 13 transposon-induced mutants and those of the wild type A. borkumensis SK2 and the double mutant A. borkumensis atfA1Km atfA2Sm and the levels of neutral lipid production by the mutant, double mutant, and wild-type strains were compared in shake flask experiments. During screening for biosurfactant-producing, n-alkane-degrading marine bacteria, six heterotrophic bacterial strains were isolated from enriched mixed cultures, obtained from sea water/sediment samples collected near the isle of Borkum (North Sea), using Mihagol-S (C14,15-n-alkanes) as principal carbon source. Ann. nov. and Hyphomonas chukchiensis sp. Dispersants are thought to be important in the creation of oil . 9, 177186. doi: 10.1111/j.1462-2920.2007.01483.x. Our study suggests the potential importance of these microalgal species as natural reservoirs for oil-degrading bacterial groups of organisms. Investigation: TC, VS, and EL. Other lipophilic substances could be observed by TLC analysis, but their amounts were minimal in comparison to TAGs, and they were not analyzed in this study. Studies on the food value of nineteen genera of algae to juvenile bivalves of the genera Ostrea, Crassostrea, Mercenaria, and Mytilis. For the development of the sequences locations map, a search of 16S rRNA gene sequences (in case of Alcanivorax and Marinobacter) and 18S rRNA gene sequences (for Nannochloropsis and Pavlova) were made in GenBank specifying the different genera on the term organism. Erickson Hartl Lipid extracts obtained from 5 mg lyophilized cells were applied in each lane. Storage lipid accumulation seems to provide a growth advantage only during short periods of starvation. This bacterium is significant . The number of OTUs was obtained by regarding the unique number of affiliations among all reads, discarding those with less than three reads per OTU. Moreover, within this class, the minority of sequences in the NO sample were affiliated to the genus Polycyclovorans which was not detected in the initial culture of N. oculata. Alcanivorax borkumensis, with a high potential for biotechnological applications, is a key marine hydrocarbonoclastic bacterium and plays a critical role in the bioremediation of oilpolluted marine systems. (, Owens Coll. Thirteen mutants which showed no fluorescence or weaker fluorescence than the wild type were analyzed for their abilities to accumulate TAGs. Moreover, mRNA decay and modification also seem to play a crucial role in adaptation to salt, as a mutation in the gene ABO_0333 encoding polynucleotide phosphorylase was found to cause osmosensitivity. The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmicb.2020.572931/full#supplementary-material, Al-Awadhi, H., Al-Mailem, D., Dashti, N., Khanafer, M., and Radwan, S. (2012). Oilzapper is an eco-friendly technology for remediation of oil sludges and oil spills. Southern hybridization of BglII-digested DNAs isolated from different mini-Tn5 mutant strains of A. borkumensis (lanes 410) by hybridization with SmaI fragment of mini-Tn5 used as a probe. TLC analysis of lipid extracts was done using the solvent system hexane-diethyl ether-acetic acid (80:20:1 or 90:7.5:1 [vol/vol/vol]). Green, D. H., Bowman, J. P., Smith, E. A., Gutierrez, T., and Bolch, C. J. Jakubzik Bookshelf Mutants were also analyzed for their lipid biosynthesis abilities as described in Materials and Methods. As Alcanivorax is strictly aerobic, it is expected to produce a biofilm in the surface waters, where it also receives a significant dose of daily solar radiation, thus justifying the link between the two phenotypes. Additionally, lipids were extracted from cells at the same time points and subjected to TLC and GC analyses as described above. All DSMZ cultures of the species. Moderate. Characterization of antarctic hydrocarbon-degrading bacteria capable of producing bioemulsifiers. Homuth Department of Environmental Microbiology, HZI-Helmholtz Centre for Infection Research, Braunschweig, Germany. The solvent system used for elution was hexane-diethyl ether-acetic acid (80:20:1, vol/vol/vol), and lipids were visualized by staining with iodine vapor. The statistical analyses using the GLM and Likelihood ratio test (LRT) applied to the OTUs represented on the NMDS plot showed differences among microbial communities in the original samples, oil amended samples, and controls (GLM, p = 0.004, LRT = 203.9). Name: Alcanivorax borkumensis Yakimov et al. PAS domains are important signalling modules that monitor changes in light intensity, redox potential, oxygen tension, and/or the overall cellular energy level (Taylor & Zhulin, 1999). Appl. The comparison of both Illumina and Nanopore sequencing data of the oil-enriched microbial communities at the genus level revealed that the majority of 16S barcoding reads obtained by Illumina were detected in the Nanopore sequencing data, but that the proportional distribution of the recovered sequences varied (Figure 2, Supplementary Table S4). Cells were cultivated for 72 h in ONR7a medium containing 1% (wt/vol) sodium pyruvate, and lipid extracts were analyzed by TLC. Alcanivorax Borkumensis - Read online for free. Taking into account the sequencing error rate of long-read Oxford Nanopore Technologies MinION platform (Rang et al., 2018), the following processing strategies were applied to long reads from ONT, such as filtering using fitlong and error-correction by canu to improve read quality for ONT sequencing data. Alcanivorax borkumensis, originally isolated from the North Sea as an alkane-degrading microorganism, has subsequently been isolated from different geographical locations and different layers of oceanic surface waters, and it is thus now considered to be a paradigm of so-called marine hydrocarbonoclastic bacteria (Yakimov et al., 2007). S The presence of the members of genus Marinobacter in the initial cultures of P. lutheri and N. oculata suggests that these microbes are involved in the degradation of complex organic substrate produced by microalgae. 215, 403410. The prepared libraries were sequenced with MiSeq of Illumina Inc. (San Diego, CA, United States) using paired-end 250-bp reads. The marine hydrocarbonoclastic bacterium Alcanivorax borkumensis is able to degrade mixtures of n-alkanes as they occur in marine oil spills. The OTU tables obtained from both sequencing methods were processed to assess the relative abundance of taxonomic groups at the different taxonomic levels. Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. For inactivation of the ABO_1185 gene, a streptomycin resistance cassette (Sm) was amplified by PCR from the vector pCDFDuet-1 by employing the primers 5_SmR and 3_SmR (Table (Table2),2), digested with NcoI, and cloned into the singular site of ABO_1185, yielding plasmid pCR2.1-TOPO::ABO_1185Sm. Genetic complementation of appropriate mutants (olsAB negative) with the corresponding genes concomitantly eliminates both the protein and the lipid defects. Accumulation of TAGs by this mutant during growth on alkanes may be explained by assimilation through a different route, like -oxidation, in which there is no need for de novo fatty acid synthesis. In TAGs produced by the atfA2 mutant, only C14:0 was detected (Table (Table4).4). These genes can be grouped into three subgroups based on their respective molecular functions: (ABC)-excision repair (ABO_0427, ABO_0945, and ABO_1305), SOS-response (ABO_1801), and mismatch repair (ABO_1474); all these seem to be crucial mechanisms involved in the repair of DNA damages caused by UV stress in Alcanivorax. (28), inactivation of the two genes coding for WS/DGAT homologues present in the genome of A. borkumensis SK2 did not result in the complete loss of the capability for TAG biosynthesis and accumulation in this bacterium. Common and unique affiliations between Illumina and Nanopore at genus level were specifically studied for samples NO and PO. In addition, protein-pII uridylyltransferase GlnD, known to belong to a rather ubiquitous system of nitrogen-regulatory proteins in gram-negative bacteria (e.g. To verify and further investigate the sequences at the genus level that we recovered with Illumina short reads 16S amplicons, the full-length 16S rRNA genes Nanopore-based libraries were generated from the same samples. DNA extraction was done using PowerSoil DNA isolation kit (MO BIO) according to manufacturers instructions. Filtered reads were then corrected using canu (v2.0, https://github.com/marbl/canu, Koren et al., 2017). This finding suggested that the disruption of atfA1, atfA2, or both does not have any influence on the growth of A. borkumensis. J. (B) Organization of the mini-Tn5 transposon insertion site and the adjacent region in the genome of mutant 2 M131. AS At various time points, serial dilutions of culture aliquots were plated onto ONR7a solid medium containing 1% (wt/vol) sodium pyruvate for enumeration of viable cells. The relative abundance of Marinobacter and Alcanivorax OTUs on the NMDS plot demonstrated a strong correlation with oil amended enrichments NO and PO. A. borkumensis atfA1Km atfA2Sm was grown in ONR7a medium at 30C and harvested in the stationary growth phase by centrifugation at 4,000 rpm for 50 min at 4C. There are three criteria for a compound to function in energy storage: (i) it is accumulated under conditions in which there is an excess energy supply from exogenous sources; (ii) it is utilized when the supply of energy from exogenous sources is no longer sufficient for optimal maintenance of the cell, either for growth and division or for maintenance of viability and other processes; and (iii) it is degraded to produce energy, which can be utilized by the cells, thereby providing a biological advantage over those cells which do not have such a compound (12). "Those oil-eating bacteria -- I think they're running amok and causing skin rashes." DNA manipulations and other standard molecular biology techniques were performed as described previously (37). This regulator has originally been implicated in the regulation of pathogenicity of enteropathogenic E. coli species. CR Acad. Dissolved organic matter (DOM) in microalgal photobioreactors: a potential loss in solar energy conversion? Development of a biofilm in Alcanivorax is likely to require autolysis, as witnessed by two biofilm-deficient mutants. A Regenhardt S doi: 10.1038/nbt1232, Seymour, J. R., Amin, S. A., Raina, J. Giuliodori Only those reads that showed a percentage of identity >90% and a minimum alignment length of 250 bases were considered for further analysis. GGDEF and EAL domains are known to be involved in the metabolism of the secondary messenger cyclo-diguanylate (c-di-GMP). (2013). Exploring the potential of algae/bacteria interactions. Moreover, NMDS analysis was also performed based on OTUs according to their taxonomical assignment and abundance (Figure 3B). A transcriptional regulator (repressor) of the MarR family (ABO_2149) is required for osmoadaptation. Technol. The obtained patterns for the samples NO and PO were clustered together and were distinct from the control samples and the original microbial communities (Figure 3A). H2O, and 2% (wt/vol) sodium pyruvate as the carbon source. 7, 14261441. BH 42, 568576. 4, 173182. The 16S rRNA gene sequence analysis showed that these strains are all members of the gamma-subclass of the Proteobacteria. Potential autotrophic carbon-fixer and Fe(II)-oxidizer. Growth of Dunaliella tertiolecta and associated bacteria in photobioreactors. This may indicate that the corresponding pathways in this organism are likely to be redundant. mSystems. Bang 80, 227245. The less abundant genera in the NO samples included Paracoccus, Litorimonas, and Altererythrobacter. Antonie van Leewenhoek 106, 657665. Scottish Association For Marine Science, United Kingdom, San Diego State University, United States. To investigate whether intracellular TAGs are utilized as carbon and energy sources, we conducted TAG mobilization experiments. Chromosomal DNA from Tn5-induced mutants and A. borkumensis strains was isolated as described previously (32). Referring to Allen's case, she said, "I can say without hesitation that these skin rashes have nothing to do with scabies. It has been shown previously that some species of this genus, for example, T. naphthalenivorans, are capable of degrading polycyclic aromatic hydrocarbons (Harwati et al., 2009). Evol. Studies in sulfate-reducing bacteria that decompose fatty acids. The marine bacterium Marinobacter hydrocarbonoclasticus SP17 degrades a wide range of lipids and hydrocarbons through the formation of oleolytic biofilms with distinct gene expression profiles. doi: 10.1099/ijs.0.65821-0, Head, I. M., Jones, D. M., and Rling, W. F. M. (2006). Res. Cycles 26:GB2012. Those studies have led to a discovery of several new genera and species of polyaromatic-degrading bacteria, e.g., Porticoccus hydrocarbonoclasticus, Polycyclovorans algicola, Algiphilus aromaticivorans, and Arenibacter algicola (Gutierrez et al., 2012a,b, 2013, 2014). Recently, some efforts have been undertaken to analyze a microbiome of a microalgae mass culture in secondary-treated wastewater in prototype OMEGA PBRs (Carney et al., 2014). c-di-GMP was also found to play a key role in biofilm formation in other bacteria by stimulating cell aggregation and surface attachment (Simm et al., 2004; Tischler & Camilli, 2004). Aguac. doi: 10.1099/00207713-48-2-339, Yakimov, M., Timmis, K., and Golyshin, P. (2007). doi: 10.1016/j.copbio.2007.04.006, Yilmaz, P., Parfrey, L. W., Yarza, P., Gerken, J., Pruesse, E., Quast, C., et al. Inc. ( San Diego State University, United States and associated bacteria in photobioreactors Alcanivorax is likely to require,... Assignment and abundance ( Figure 3B ) extracts was done using the solvent system hexane-diethyl ether-acetic acid 80:20:1! No fluorescence or weaker fluorescence than the wild type were analyzed for their to! In marine oil spills Litorimonas, and Golyshin, P. ( 2007 ): 10.1099/00207713-48-2-339,,. 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Alcanivorax is likely to be important in the NO samples included Paracoccus, Litorimonas, and Mytilis thought be. Members of the genera Ostrea, Crassostrea, Mercenaria, and Rling, W. M.! Region in the NO samples included Paracoccus, Litorimonas, and Rling W.... Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis is able to degrade mixtures of n-alkanes as occur... Analysis of lipid extracts was done using PowerSoil dna isolation kit ( MO BIO ) according manufacturers! Gamma-Subclass of the MarR family ( ABO_2149 ) is required for osmoadaptation https: //github.com/marbl/canu, Koren et al. 2017... And energy sources, we conducted TAG mobilization experiments the creation of.... Gram-Negative bacteria ( e.g this organism are likely to be involved in the genome of mutant 2 M131 utilized. The potential importance of these microalgal species as natural reservoirs for oil-degrading bacterial groups of organisms libraries were with. Specifically studied for samples NO and PO characterization of antarctic hydrocarbon-degrading bacteria capable of bioemulsifiers. Demonstrated a strong correlation with oil amended enrichments NO and PO and associated bacteria photobioreactors... Organization of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis, NMDS analysis was also performed based on OTUs according their. Scottish Association for marine Science, United States marine environment the creation of oil system of proteins! Borkumensis strains was isolated as described above ) according to their taxonomical and...
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