Aerobic Hydrocarbon-Degrading Alphaproteobacteria: Rhodobacteraceae (Roseobacter)

Buchan, Alison; González, José M.; Chua, Michelle J.

doi:10.1007/978-3-030-14796-9_8

Cited by 10 publications

(3 citation statements)

References 59 publications

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“…Following the initial screen, efforts were focused on members of the marine Roseobacteraceae family, an abundant and active group of heterotrophic bacteria with known abilities to degrade lignin-derived aromatic compounds ( 27 ) (Fig. S2).…”

Section: Resultsmentioning

confidence: 99%

Evidence for novel polycyclic aromatic hydrocarbon degradation pathways in culturable marine isolates

Walton,

Buchan

2024

Microbiol Spectr

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Polycyclic aromatic hydrocarbons (PAHs) are common toxic and carcinogenic pollutants in marine ecosystems. Despite their prevalence in these habitats, relatively little is known about the natural microflora and biochemical pathways that contribute to their degradation. Approaches to investigate marine microbial PAH degraders often heavily rely on genetic biomarkers, which requires prior knowledge of specific degradative enzymes and genes encoding them. As such, these biomarker-reliant approaches cannot efficiently identify novel degradation pathways or degraders. Here, we screen 18 marine bacterial strains representing the Pseudomonadota, Bacillota, and Bacteroidota phyla for degradation of two model PAHs, pyrene (high molecular weight) and phenanthrene (low molecular weight). Using a qualitative PAH plate screening assay, we determined that 16 of 18 strains show some ability to degrade either or both compounds. Degradative ability was subsequently confirmed with a quantitative high-performance liquid chromatography approach, where an additional strain showed some degradation in liquid culture. Several members of the prominent marine Roseobacteraceae family degraded pyrene and phenanthrene with varying efficiency (1.2%–29.6% and 5.2%–52.2%, respectively) over 26 days. Described PAH genetic biomarkers were absent in all PAH degrading strains for which genome sequences are available, suggesting that these strains harbor novel transformation pathways. These results demonstrate the utility of culture-based approaches in expanding the knowledge landscape concerning PAH degradation in marine systems. IMPORTANCE Polycyclic aromatic hydrocarbon (PAH) pollution is widespread throughout marine environments and significantly affects native flora and fauna. Investigating microbes responsible for degrading PAHs in these environments provides a greater understanding of natural attenuation in these systems. In addition, the use of culture-based approaches to inform bioinformatic and omics-based approaches is useful in identifying novel mechanisms of PAH degradation that elude genetic biomarker-based investigations. Furthermore, culture-based approaches allow for the study of PAH co-metabolism, which increasingly appears to be a prominent mechanism for PAH degradation in marine microbes.

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Section: Resultsmentioning

confidence: 99%

Evidence for novel polycyclic aromatic hydrocarbon degradation pathways in culturable marine isolates

Walton,

Buchan

2024

Microbiol Spectr

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“…In the absence of other more bioavailable additives, we hypothesize that this lean composition may lead to a community supported by hydrocarbon metabolism, utilizing hydrocarbons from the formation itself, instead of being heavily influenced by additive chemistry in input fluids. The taxonomic analysis identified several lineages that have previously been implicated with hydrocarbon degradation, such as Alcanivorax , Marinobacter , Halomonas , Thalassolituus , Flavobacterium and Idiomarina [ 50 – 52 ]. Significantly, isolates of the genus Marinobacter recovered from the Utica Point Pleasant formation have the potential to use aliphatic and aromatic hydrocarbons [ 45 ].…”

Section: Resultsmentioning

confidence: 99%

New microbiological insights from the Bowland shale highlight heterogeneity of the hydraulically fractured shale microbiome

Hernandez-Becerra

Cliffe

Xiu

et al. 2023

Environmental Microbiome

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Background Hydraulically fractured shales offer a window into the deep biosphere, where hydraulic fracturing creates new microbial ecosystems kilometers beneath the surface of the Earth. Studying the microbial communities from flowback fluids that are assumed to inhabit these environments provides insights into their ecophysiology, and in particular their ability to survive in these extreme environments as well as their influence on site operation e.g. via problematic biofouling processes and/or biocorrosion. Over the past decade, research on fractured shale microbiology has focused on wells in North America, with a few additional reported studies conducted in China. To extend the knowledge in this area, we characterized the geochemistry and microbial ecology of two exploratory shale gas wells in the Bowland Shale, UK. We then employed a meta-analysis approach to compare geochemical and 16S rRNA gene sequencing data from our study site with previously published research from geographically distinct formations spanning China, Canada and the USA. Results Our findings revealed that fluids recovered from exploratory wells in the Bowland are characterized by moderate salinity and high microbial diversity. The microbial community was dominated by lineages known to degrade hydrocarbons, including members of Shewanellaceae, Marinobacteraceae, Halomonadaceae and Pseudomonadaceae. Moreover, UK fractured shale communities lacked the usually dominant Halanaerobium lineages. From our meta-analysis, we infer that chloride concentrations play a dominant role in controlling microbial community composition. Spatio-temporal trends were also apparent, with different shale formations giving rise to communities of distinct diversity and composition. Conclusions These findings highlight an unexpected level of compositional heterogeneity across fractured shale formations, which is not only relevant to inform management practices but also provides insight into the ability of diverse microbial consortia to tolerate the extreme conditions characteristic of the engineered deep subsurface.

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“…Uncultivated representatives of the Rhodobacteraceae family were identified in most of the samples studied. This family includes bacteria inhabiting marine ecosystems, for example, bacteria of the genus Roseobacter , which have been repeatedly isolated from polar microbial communities and for which the ability to use aromatic hydrocarbons and alkanes has been shown [ 64 ].…”

Section: Resultsmentioning

confidence: 99%

Microbial Communities of Seawater and Coastal Soil of Russian Arctic Region and Their Potential for Bioremediation from Hydrocarbon Pollutants

et al. 2022

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The development of Arctic regions leads to pollution of marine and coastal environments with oil and petroleum products. The purpose of this work was to determine the diversity of microbial communities in seawater, as well as in littoral and coastal soil, and the potential ability of their members to degrade hydrocarbons degradation and to isolate oil-degrading bacteria. Using high-throughput sequencing of the V4 region of the 16S rRNA gene, the dominance of bacteria in polar communities was shown, the proportion of archaea did not exceed 2% (of the total number of sequences in the libraries). Archaea inhabiting the seawater belonged to the genera Nitrosopumilus and Nitrosoarchaeum and to the Nitrososphaeraceae family. In the polluted samples, members of the Gammaproteobacteria, Alphaproteobacteria, and Actinomycetes classes predominated; bacteria of the classes Bacteroidia, Clostridia, Acidimicrobiia, Planctomycetia, and Deltaproteobacteria were less represented. Using the iVikodak program and KEGG database, the potential functional characteristics of the studied prokaryotic communities were predicted. Bacteria were potentially involved in nitrogen and sulfur cycles, in degradation of benzoate, terephthalate, fatty acids, and alkanes. A total of 19 strains of bacteria of the genera Pseudomonas, Aeromonas, Oceanisphaera, Shewanella, Paeniglutamicibacter, and Rhodococcus were isolated from the studied samples. Among them were psychrotolerant and psychrophilic bacteria growing in seawater and utilizing crude oil, diesel fuel, and motor oils. The data obtained suggest that the studied microbial communities could participate in the removal of hydrocarbons from arctic seawater and coastal soils and suggested the possibility of the application of the isolates for the bioaugmentation of oil-contaminated polar environments.

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Aerobic Hydrocarbon-Degrading Alphaproteobacteria: Rhodobacteraceae (Roseobacter)

Cited by 10 publications

References 59 publications

Evidence for novel polycyclic aromatic hydrocarbon degradation pathways in culturable marine isolates

Evidence for novel polycyclic aromatic hydrocarbon degradation pathways in culturable marine isolates

New microbiological insights from the Bowland shale highlight heterogeneity of the hydraulically fractured shale microbiome

Microbial Communities of Seawater and Coastal Soil of Russian Arctic Region and Their Potential for Bioremediation from Hydrocarbon Pollutants

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