An aliquot of each DNA samples was checked for quality and quantity by gel electrophoresis on a 0.8% agarose gel and by measuring the concentration of DNA by Qubit dsDNA HS kit (Life Technology) with Qubit Fluorometer. Therefore, during the next 24 h of incubation, the TAG contents increased from about 2.6 to 11.1% and from 2.2 to 8.7% of the CDW in the wild type SK2 and the atfA2 mutant, respectively. (2014). In contrast, TAGs produced by A. borkumensis SK2 constituted about 13% of the CDW. doi: 10.1016/j.copbio.2007.04.006, Yilmaz, P., Parfrey, L. W., Yarza, P., Gerken, J., Pruesse, E., Quast, C., et al. Biol. The conditions for the PCR were 30 cycles of 94C for 1.5 min, 48C for 1 min, and 72C for 4 min and a final elongation step at 72C for 5 min. The prepared libraries were sequenced with MiSeq of Illumina Inc. (San Diego, CA, United States) using paired-end 250-bp reads. Such lipopolysaccharide-containing capsules might play an important role in bacteria and host cell interactions (Reddy et al., 1993). 1998 Category: Species Proposed as: sp. Biol. Nimtz Evol. Thus, the mini-Tn5 mutation in ABO_2248 encoding a putative ubiquinone biosynthesis protein was found to cause biofilm deficiency. Sequences of isolates obtained from P. lutheri and affiliated with the phylum Bacteroidetes were closely related to the genus Maribacter (99% identity with M. dokdonensis) and Kordia (98% identity with K. algicida). Evol. J. Agric. WR Phycologia 52, 1424. Microbiol. Pronunciation of Alcanivorax borkumensis with 2 audio pronunciations and more for Alcanivorax borkumensis. Cells were cultivated in ONR7a medium containing 1% (wt/vol) sodium pyruvate for 72 h at 30C to promote accumulation of TAGs. Indigenous hydrocarbon-utilizing bacterioflora in oil-polluted habitats in Kuwait, two decades after the greatest man-made oil spill. Microbiol. Appl. RNA decay and maturation during a temperature down-shift seem to represent another phenomenon closely linked to cold adaptation in Alcanivorax: among the cold-sensitive Tn5 mutants, one mutation mapped in gene rnd encoding RNAse D (ABO_1768), which is responsible for maturation of the 3-terminus of tRNA precursors. Sancar Within the Gammaproteobacteria, members of the Alcanivorax and Marinobacter dominated both in enrichments with crude oil and were the two most abundant genera (Figure 1C, Supplementary Table S3). 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. In the clean up of the Deepwater Horizon oil spill, genetically modified microorganisms were used, but some scientists suspect they might have caused health issues for people in the affected areas. (, Owens It's is the bacterium used in the gulf oil spill to degrade the oil. The editor and reviewer's affiliations are the latest provided on their Loop research profiles and may not reflect their situation at the time of review. Thus, one UV-responsive transposon mutation is mapped in ABO_0221 encoding a type II secretion system protein. Oil-eating bacteria produce bio-films. doi: 10.1099/ijs.0.63447-0, Green, D. H., Echavarri-Bravo, V., Brennan, D., and Hart, M. C. (2015). Takano Because mutant A. borkumensis 2 M131 did not show significant differences in the accumulation of TAGs in comparison to the wild type when it was cultivated on alkanes such as hexadecane and octadecane, the results obtained in this study suggest that the transposon insertion in ABO_1185 has an effect on de novo fatty acid biosynthesis. MAR stands for multiple antibiotic resistance and is known to be a repressor of the mar operon (Seoane & Levy, 1995). doi: 10.2216/12-24.1, Gonzalez, J. M., Simo, R., Massana, R., Covert, J. S., Casamayor, E. O., Pedros-Alio, C., et al. and Marinobacter spp. Thus, the sensory box protein encoded by ABO_2691 is involved in biofilm formation. Microbiol. 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. Genome sequence of Porticoccus hydrocarbonoclasticus strain MCTG13d, an obligate polycyclic aromatic hydrocarbon-degrading bacterium associated with marine eukaryotic phytoplankton. Data curation: RB and ST. Writing-original draft preparation: TC. Afterwards, cells were harvested, washed twice, and resuspended in carbon-free ONR7a medium to permit the mobilization of TAGs. Microbiol. 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). S The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. Aquat. IS Park All statistics and visualization of the sequencing were performed using scripts developed under R software (v3.6.3, http://www.R-project.org/) using the core packages. doi: 10.1111/j.1550-7408.1999.tb04612.x, Ueda, H., Otsuka, S., and Senoo, K. (2009). The inoculum and hydrocarbons concentration have a remarkable effect on the biodegradation with the crude enzymes. Environ. Discover the world's research 20 . Inactivation of the cyoB gene has a negative impact on the activity of promoter P P450-3, but does not affect P fdx or . H doi: 10.1111/j.1462-2920.2006.01125.x, Meireles, L. A., Guedes, C., and Malcata, F. X. Environ. Microalgal species, P. lutheri (#931/1, CCAP, Scotland) and N. oculata (#352-567-0226, ZM System, Winchester), were cultured in PBRs for 4 weeks. Look at the map. The hybrid plasmids of the resulting clones harbored a PstI fragment consisting of mini-Tn5 and genomic DNA adjacent to the mini-Tn5 insertion locus. We are very grateful for financial support of this study by the Deutsche Forschungsgemeinschaft (DFG) to A.S. (through grant no. Finally, the library was used to isolate biofilm-deficient mutants as described earlier (O'Toole & Kolter, 1998). They form a diverse group of proteins having only a few features in common (33). Br. The recombinant plasmids from these libraries were sequenced using the oligonucleotides M13-forward and M13-reverse (Table (Table2),2), which hybridize specifically to pBluescript SK(). Dissolved organic matter (DOM) in microalgal photobioreactors: a potential loss in solar energy conversion? We also performed sequencing of the full-length of the 16S rRNA gene using the Oxford Nanopore platform. Propionyl-CoA was apparently not formed in appreciable quantities by A. borkumensis SK2 during growth on pyruvate, since fatty acids with odd-numbered chain lengths were absent. Ecol. ABSTRACTA consortium of the newly isolated bacterial strainsArthrobactersp. Cordone A, D'Errico G, Magliulo M, Bolinesi F, Selci M, Basili M, de Marco R, Saggiomo M, Rivaro P, Giovannelli D, Mangoni O. Biotechnol. Results from TLC analyses of total lipid extracts from these strains after 72 h of cultivation are shown in Fig. J. Exp. FEMS Microbiol. For quantification of intracellular lipids, preparative TLC with subsequent fatty acid analysis by gas chromatography (GC) was performed. 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). Global features of the Alcanivorax borkumensis SK-2 genome. Determining the identity and roles of oil-metabolizing marine bacteria from the Thames estuary, UK. Interaction and signaling between a cosmopolitan phytoplankton and associated bacteria. Pronunciation of Alcanivorax borkumensis with 3 audio pronunciations. This includes children, people with cystic fibrosis or asthma, and African Americans (who are prone to blood disorders), to name a few. A., Coulon, F., Osborn, A. M., Timmis, K. N., and McGenity, T. J. Part of HuffPost Environment. Before Fatty acid contents and compositions of fatty acids of A. borkumensis SK2 and transposon-induced mutantsa. This material is available as part of the online article from: (this link will take you to the article abstract). 8600 Rockville Pike members are ubiquitous in contaminated surface waters and are the first to flourish on a wide range of alkanes after an oil-spill. Careers. BMC Biol. Int. PLoS One 7:41305. doi: 10.1371/journal.pone.0041305, PubMed Abstract | CrossRef Full Text | Google Scholar, Buchan, A., Le Cleir, G. R., Gulvik, C. A., and Gonzalez, J. M. (2014). Nat. doi: 10.1264/jsme2.ME09177, Volkman, J. K., Dunstan, G. A., Jeffrey, S. W., and Kearney, P. S. (1991). Oil pollution is an environmental problem of increasing importance. A Interestingly, the TAGs produced by mutant 2 M191, which showed the smallest octadecenoic acid fraction (12 mol%), also comprised an unusually high percentage of octadecanoic acid (C18:0). B., and Suess, M. J. Fig.4B.4B. The phylum Proteobacteria was the most prominent in all samples. Biotechnol. Regenhardt V4 amplicon sequencing data-based community composition at the phylum- (A), class- (B), and genus-levels (C) of bacterial communities in samples (% of reads). nov. Etymology: bor.kum.en'sis. This finding suggested that the disruption of atfA1, atfA2, or both does not have any influence on the growth of A. borkumensis. UVS, UV sensitive mutants; OS, osmosensitive mutants; TS, low temperature sensitive mutants; BD, biofilm deficient mutants. 12, 686698. This similarity in sequencing data obtained by both methods is based on the proportion of main genera in the bacterial communities. Environ. 124, 387393. The obtained amplicons were pooled and purified using a QIAEX II DNA Extraction kit (Qiagen). Ferrer Microalgae N. oculata (N) hosted the genera Marinobacter, Alcanivorax, Oceanicaulis, Rhodopirellula, Oricola, Roseovarius, Halomonas, Hoefliea, Tropicibacter, Devosia, and Sulfitobacter while the microbial communities of P. lutheri (P) were represented by the genera Marinobacter, Roseovarius, Ulvibacter, Tropicibacter, Thalassospira, and Labrenzia (Supplementary Table S3). Among these were the number of cellular mechanisms that hitherto have not been linked so far to the respective environmental adaptations (UV-induced modulations of c-di-GMP, transport of dicarboxylate, biosynthesis of extracellular polysaccharides, mRNA decay and modification, and a number of novel stress-related regulatory systems). doi: 10.1016/j.pbi.2015.07.003, Coulon, F., McKew, B. Therefore, cell growth and the accumulation and composition of TAGs in cells of A. borkumensis at different cultivation times were analyzed in shake flask experiments. Although the export of TAGs has been reported recently (31), in this study we analyzed only the intracellular accumulation of TAGs in order to establish the function of these compounds in A. borkumensis SK2. Connell One can only wonder about the rest of the ecosystem. Oksanen, J., Blanchet, F. G., Friendly, M., Kindt, R., Legenndre, P., McGlinn, D., et al. (, Mai-Prochnow Description. Exploring mutualistic interactions between microalgae and bacteria in the omics age. official website and that any information you provide is encrypted doi: 10.1093/nar/gkt1209, Keywords: photobioreactor, microalgae-associated bacteria, hydrocarbon-degrading bacteria, 16S rRNA gene amplicon, isolation of oil-degrading bacteria, Citation: Chernikova TN, Bargiela R, Toshchakov SV, Shivaraman V, Lunev EA, Yakimov MM, Thomas DN and Golyshin PN (2020) Hydrocarbon-Degrading Bacteria Alcanivorax and Marinobacter Associated With Microalgae Pavlova lutheri and Nannochloropsis oculata. Technol. Moreover, Alcanivorax seems to use overlapping signal transduction systems linking biofilm formation, UV tolerance, and osmoadaptation. Natural microbial diversity in superficial sediments of Milazzo Harbor (Sicily) and community successions during microcosm enrichment with various hydrocarbons. Scientists anticipated early on that the Gulf leak would cause populations of oil-eating bacteria to soar. Unable to load your collection due to an error, Unable to load your delegates due to an error. BioMed. A transcriptional regulator (repressor) of the MarR family (ABO_2149) is required for osmoadaptation. 634486) and the Supercomputing Wales project (RB) which is part-funded by the European Regional Development Fund (ERDF) via Welsh Government. In this study, we screened a mini-Tn5 transposon library in this double mutant to identify additional enzymes involved in storage lipid accumulation in this hydrocarbonoclastic marine bacterium. Both represented only 0.5% (or less) of total amplicon reads in the original microalgal cultures N. oculata and P. lutheri; however, they increased in their relative abundances and became the predominant genera in crude oil enrichments derived from both microalgae (Supplementary Table S3). Relatively rare in unpolluted seas it quickly comes to dominate the marine microbial ecosystem after . Appl. Abstract. The final files with the reads were aligned against the SILVA 16S rRNA (Yilmaz et al., 2014) database using LAST (v1080, http://last.cbrc.jp/). Polycyclic aromatic hydrocarbon degradation of phytoplankton-associated Arenibacter spp. doi: 10.1038/nmeth.f.303, Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C. A., Turnbaugh, P. J., et al. Metagenome survey of a multispecies and alga-associated biofilm revealed key elements of bacterial-algal interactions in photobioreactors. Environ. The wild type SK2 and the atfA2 mutant exhibited increases in viability within the first 24 h of the experiment; thereafter, the viability decreased rapidly in both cases (Fig. Received: 15 June 2020; Accepted: 01 October 2020; Published: 28 October 2020. nov. Arch. Studies on phylogenetic characterization of microalgae-associated bacterial communities in PBRs undertaken by Lakaniemi et al. Distribution and culturability of the uncultivated AGG58 cluster of the Bacteroidetes phylum in aquatic environments. A total of 3,506 sequences for these two oil-degrading bacterial genera and 88 sequences for microalgae were identified in the GenBank (Supplementary Table S8). Microbial communities co-occurring with P. lutheri and N. oculata in photobioreactors were spiked with crude oil and subjected to 16S rRNA gene amplicon sequencing analysis. 075-15-2019-1659. Evol. Amplification of PCR products was done using the 27F forward primer (5' AGAGTTTGATCMTGGCTCAG-3') and 1492R reverse primer (5'-TACGGYTACCTTGTTACGACTT-3') with barcodes supplied in the kit. For those cases where the retrieved sequences did not show the location coordinates on the GenBank file, the manual check of the articles where they were published (when it was possible) was done. (2010). JS (, Reddy No presence of WEs was observed, suggesting that Alcanivorax is not able to synthesize this class of neutral lipids de novo. As reported by Kalscheuer et al. (2012) were found in samples of coastal waters of Kuwait that were contaminated with oil. nov. and Haloferula sargassicola sp. 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). doi: 10.1016/j.biortech.2012.08.048, Lakaniemi, A. (2017) showed natural phytoplankton-associated bacterial communities exposed to oil changed in community structure toward one with increased numbers of species responsible for the degradation of crude oil. R Espinosa-Urgel Microbiome 2:6. doi: 10.1186/2049-2618, Fellows, I. Gammaproteobacteria was the most abundant class in experiments with crude oil amendment. 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. In order to gain first insights into the molecular mechanisms underlying this organism's remarkable potential for adaptation to different environmental stress factors such as UV radiation, low temperature, osmotic up-shift, and its ability to shift from a planctonic state to sessile growth, a series of randomly induced mini-Tn5 mutants were analyzed with the aim to identify the genes/loci that contribute to this organism's environmental adaptability.
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