Metagenomic survey reveals hydrocarbon biodegradation potential of Canadian high Arctic beaches

IF 6.2 2区 环境科学与生态学 Q1 GENETICS & HEREDITY
Esteban Góngora, Antoine-O. Lirette, Nastasia J. Freyria, Charles W. Greer, Lyle G. Whyte
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Abstract

Decreasing sea ice coverage across the Arctic Ocean due to climate change is expected to increase shipping activity through previously inaccessible shipping routes, including the Northwest Passage (NWP). Changing weather conditions typically encountered in the Arctic will still pose a risk for ships which could lead to an accident and the uncontrolled release of hydrocarbons onto NWP shorelines. We performed a metagenomic survey to characterize the microbial communities of various NWP shorelines and to determine whether there is a metabolic potential for hydrocarbon degradation in these microbiomes. We observed taxonomic and functional gene evidence supporting the potential of NWP beach microbes to degrade various types of hydrocarbons. The metagenomic and metagenome-assembled genome (MAG) taxonomy showed that known hydrocarbon-degrading taxa are present in these beaches. Additionally, we detected the presence of biomarker genes of aerobic and anaerobic degradation pathways of alkane and aromatic hydrocarbons along with complete degradation pathways for aerobic alkane degradation. Alkane degradation genes were present in all samples and were also more abundant (33.8 ± 34.5 hits per million genes, HPM) than their aromatic hydrocarbon counterparts (11.7 ± 12.3 HPM). Due to the ubiquity of MAGs from the genus Rhodococcus (23.8% of the MAGs), we compared our MAGs with Rhodococcus genomes from NWP isolates obtained using hydrocarbons as the carbon source to corroborate our results and to develop a pangenome of Arctic Rhodococcus. Our analysis revealed that the biodegradation of alkanes is part of the core pangenome of this genus. We also detected nitrogen and sulfur pathways as additional energy sources and electron donors as well as carbon pathways providing alternative carbon sources. These pathways occur in the absence of hydrocarbons allowing microbes to survive in these nutrient-poor beaches. Our metagenomic analyses detected the genetic potential for hydrocarbon biodegradation in these NWP shoreline microbiomes. Alkane metabolism was the most prevalent type of hydrocarbon degradation observed in these tidal beach ecosystems. Our results indicate that bioremediation could be used as a cleanup strategy, but the addition of adequate amounts of N and P fertilizers, should be considered to help bacteria overcome the oligotrophic nature of NWP shorelines.
元基因组调查揭示加拿大北极高纬度地区海滩的碳氢化合物生物降解潜力
由于气候变化,整个北冰洋的海冰覆盖面积不断减少,预计通过包括西北航道 (NWP) 在内的以前无法进入的航道的航运活动将会增加。北极地区通常会遇到的不断变化的天气条件仍将给船舶带来风险,可能导致事故和碳氢化合物不受控制地释放到西北航道海岸线上。我们进行了一项元基因组调查,以确定各种 NWP 海岸线微生物群落的特征,并确定这些微生物群落是否具有降解碳氢化合物的代谢潜力。我们观察到分类学和功能基因证据支持西北太平洋海滨微生物降解各类碳氢化合物的潜力。元基因组和元基因组组装基因组(MAG)分类显示,这些海滩中存在已知的碳氢化合物降解类群。此外,我们还检测到了烷烃和芳香烃好氧和厌氧降解途径的生物标记基因,以及好氧烷烃降解的完整降解途径。烷烃降解基因存在于所有样本中,而且比芳香烃降解基因(11.7 ± 12.3 HPM)更丰富(每百万基因中有 33.8 ± 34.5 个命中,HPM)。由于 MAGs 在 Rhodococcus 属中无处不在(占 MAGs 的 23.8%),我们将 MAGs 与从使用碳氢化合物作为碳源的 NWP 分离物中获得的 Rhodococcus 基因组进行了比较,以证实我们的结果并建立北极 Rhodococcus 的泛基因组。我们的分析表明,烷烃的生物降解是该属核心泛基因组的一部分。我们还发现了作为额外能量来源和电子供体的氮和硫途径,以及提供替代碳源的碳途径。这些途径是在没有碳氢化合物的情况下发生的,使微生物能够在这些营养贫乏的海滩上生存。我们的元基因组分析检测了这些西北太平洋沿岸微生物群中碳氢化合物生物降解的遗传潜力。烷烃代谢是在这些潮汐海滩生态系统中观察到的最普遍的碳氢化合物降解类型。我们的研究结果表明,生物修复可作为一种清洁策略,但应考虑添加适量的氮肥和磷肥,以帮助细菌克服西北太平洋海岸线的寡营养特性。
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来源期刊
Environmental Microbiome
Environmental Microbiome Immunology and Microbiology-Microbiology
CiteScore
7.40
自引率
2.50%
发文量
55
审稿时长
13 weeks
期刊介绍: Microorganisms, omnipresent across Earth's diverse environments, play a crucial role in adapting to external changes, influencing Earth's systems and cycles, and contributing significantly to agricultural practices. Through applied microbiology, they offer solutions to various everyday needs. Environmental Microbiome recognizes the universal presence and significance of microorganisms, inviting submissions that explore the diverse facets of environmental and applied microbiological research.
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