Cultivation of deep-sea bacteria from the Northwest Pacific Ocean and characterization of Limnobacter profundi sp. nov., a phenol-degrading bacterium

IF 2.8 2区 生物学 Q1 MARINE & FRESHWATER BIOLOGY
Mirae Kim, Jaeho Song, Seung Yeol Shin, Kazuhiro Kogure, Ilnam Kang, Jang-Cheon Cho
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引用次数: 0

Abstract

Despite previous culture-independent studies highlighting the prevalence of the order Burkholderiales in deep-sea environments, the cultivation and characterization of deep-sea Burkholderiales have been infrequent. A total of 243 deep-sea bacterial strains were isolated from various depths in the Northwest Pacific Ocean, with 33 isolates (13.6%) from a depth of 4000 m classified into Burkholderiales. Herein, we report the isolation and genome characteristics of strain SAORIC-580T, from a depth of 4000 m in the Northwest Pacific Ocean. The strain showed a close phylogenetic relationship with Limnobacter thiooxidans CS-K2T, sharing 99.9% 16S rRNA gene sequence identity. The complete whole-genome sequence of strain SAORIC-580T comprised 3.3 Mbp with a DNA G+C content of 52.5%. Comparative genomic analysis revealed average nucleotide identities between 79.4–85.7% and digital DNA-DNA hybridization values of 19.9–29.5% when compared to other Limnobacter genomes, indicating that the strain represents a novel species within the genus. Genomic analysis revealed unique adaptations to deep-sea conditions, including genes associated with phenol degradation, stress responses, cold adaptation, heavy metal resistance, signal transduction, and carbohydrate metabolism. The SAORIC-580T genome was found to be more abundant in the deep sea than at the surface in the trenches of the Northwest Pacific Ocean, suggesting adaptations to the deep-sea environment. Phenotypic characterization highlighted distinct differences from other Limnobacter species, including variations in growth conditions, enzyme activities, and phenol degradation capabilities. Chemotaxonomic markers of the strain included ubiquinone-10, major fatty acids such as C16:0, C16:1, and C18:1, and major polar lipids including phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. Based on the polyphasic taxonomic data, it is concluded that strain SAORIC-580T (= KACC 21440T = NBRC 114111T) represents a novel species, for which the name Limnobacter profundi sp. nov. is proposed.
西北太平洋深海细菌的培养和一种苯酚降解细菌 Limnobacter profundi sp.
尽管之前的独立培养研究强调深海环境中普遍存在伯克霍尔德氏菌,但深海伯克霍尔德氏菌的培养和特征描述并不常见。我们从西北太平洋不同深度共分离出 243 株深海细菌,其中 33 株(13.6%)来自 4000 米深处,被归类为 Burkholderiales。在此,我们报告了从西北太平洋 4000 米深处分离到的 SAORIC-580T 菌株及其基因组特征。该菌株与Limnobacter thiooxidans CS-K2T具有密切的系统发育关系,16S rRNA基因序列相同度高达99.9%。菌株 SAORIC-580T 的完整全基因组序列为 3.3 Mbp,DNA G+C 含量为 52.5%。基因组比较分析显示,与其他林杆菌基因组相比,该菌株的平均核苷酸相同度为 79.4%-85.7%,数字 DNA-DNA 杂交值为 19.9%-29.5%,表明该菌株代表了林杆菌属中的一个新物种。基因组分析揭示了对深海条件的独特适应,包括与苯酚降解、应激反应、冷适应、重金属抗性、信号转导和碳水化合物代谢相关的基因。在西北太平洋的海沟中发现,SAORIC-580T 基因组在深海中的含量高于在海面上的含量,这表明它适应了深海环境。表型特征突显了与其他林杆菌物种的明显差异,包括生长条件、酶活性和苯酚降解能力的变化。该菌株的化学分类标记包括泛醌-10、主要脂肪酸(如 C16:0、C16:1 和 C18:1)以及主要极性脂质(包括磷脂酰乙醇胺、磷脂酰甘油和二磷脂酰甘油)。根据多相分类学数据,得出结论:SAORIC-580T(= KACC 21440T = NBRC 114111T)菌株代表了一个新物种,建议将其命名为 Profundi 利姆诺杆菌新种(Limnobacter profundi sp.nov.)。
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来源期刊
Frontiers in Marine Science
Frontiers in Marine Science Agricultural and Biological Sciences-Aquatic Science
CiteScore
5.10
自引率
16.20%
发文量
2443
审稿时长
14 weeks
期刊介绍: Frontiers in Marine Science publishes rigorously peer-reviewed research that advances our understanding of all aspects of the environment, biology, ecosystem functioning and human interactions with the oceans. Field Chief Editor Carlos M. Duarte at King Abdullah University of Science and Technology Thuwal is supported by an outstanding Editorial Board of international researchers. This multidisciplinary open-access journal is at the forefront of disseminating and communicating scientific knowledge and impactful discoveries to researchers, academics, policy makers and the public worldwide. With the human population predicted to reach 9 billion people by 2050, it is clear that traditional land resources will not suffice to meet the demand for food or energy, required to support high-quality livelihoods. As a result, the oceans are emerging as a source of untapped assets, with new innovative industries, such as aquaculture, marine biotechnology, marine energy and deep-sea mining growing rapidly under a new era characterized by rapid growth of a blue, ocean-based economy. The sustainability of the blue economy is closely dependent on our knowledge about how to mitigate the impacts of the multiple pressures on the ocean ecosystem associated with the increased scale and diversification of industry operations in the ocean and global human pressures on the environment. Therefore, Frontiers in Marine Science particularly welcomes the communication of research outcomes addressing ocean-based solutions for the emerging challenges, including improved forecasting and observational capacities, understanding biodiversity and ecosystem problems, locally and globally, effective management strategies to maintain ocean health, and an improved capacity to sustainably derive resources from the oceans.
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