Metavirome mining from fjord sediments of Svalbard Archipelago

IF 2.8 3区 农林科学 Q3 ENVIRONMENTAL SCIENCES
Bhavya Kachiprath, Jayanath Gopi, Manomi Sarasan, Jayesh Puthumana, E. R. Chaithanya, Rosamma Philip
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引用次数: 0

Abstract

Purpose

Viruses are the largest genetic repository and most diverse host-associated replicating organisms in a wide range of ecosystems in the entire biosphere. Although playing crucial roles in numerous processes such as nutrient cycles, viral shunt, and population control within marine ecosystems, viral communities continue to be the least explored biological entities, particularly in extreme marine habitats. Therefore, details about the viral diversity and their metabolic potential from Arctic sediments has great importance.

Methods

Sediment samples were collected from two Arctic fjords, Kongsfjorden and Krossfjorden, in Svalbard. Viral nucleic acids were extracted from both fjord sediments after a pre-processing step. Illumina Novaseq based shotgun sequencing was performed and bioinformatic analysis was done to explore viral communities and their functional potential.

Results

An array of DNA and RNA viruses especially bacteriophages along with viruses infecting algae, plants, molluscs, shrimps, fishes, amphibians, reptiles, birds, humans, and other mammals were detected from both fjords. The double-stranded DNA viruses were the most abundant (Siphoviridae, Podoviridae, Myoviridae, and Phycodnaviridae), followed by single-stranded DNA (Inoviridae) and RNA (Retroviridae and Betaflexiviridae) viruses from both metavirome. Functional analysis explored genes encoding virus structures, enzymes for phage replication, integration and excision and proteins related to phage regulation of gene expression.

Conclusions

Fjord metavirome analysis revealed the occurrence of virus groups endemic to Arctic freshwater and marine habitats along with an extra pool of unclassified or unassigned virus reads. Viruses infecting a variety of bacterial groups, and other higher trophic levels in fjord environments were explored. Functional annotation revealed the abundance of phage-related structural genes and metabolic genes. Comparative analysis revealed the abundance of dsDNA viruses from Caudovirales (Myoviridae, Podoviridae and Siphoviridae) in all the analysed Arctic samples in different proportions. The present study enhances our understanding of viral diversity and their metabolic potential in Arctic fjord sediments.

Abstract Image

从斯瓦尔巴群岛的峡湾沉积物中挖掘元病毒体
目的病毒是整个生物圈广泛生态系统中最大的基因库和最多样化的宿主相关复制生物。虽然病毒群落在海洋生态系统的营养循环、病毒分流和种群控制等众多过程中发挥着至关重要的作用,但它仍然是探索最少的生物实体,尤其是在极端的海洋生境中。因此,详细了解北极沉积物中的病毒多样性及其新陈代谢潜力具有重要意义。经过预处理步骤后,从这两个峡湾的沉积物中提取了病毒核酸。结果 在两个峡湾中都检测到了一系列 DNA 和 RNA 病毒,尤其是噬菌体病毒,以及感染藻类、植物、软体动物、虾、鱼类、两栖动物、爬行动物、鸟类、人类和其他哺乳动物的病毒。双链 DNA 病毒数量最多(Siphoviridae、Podoviridae、Myoviridae 和 Phycodnaviridae),其次是单链 DNA 病毒(Inoviridae)和 RNA 病毒(Retroviridae 和 Betaflexiviridae)。功能分析探讨了编码病毒结构的基因、噬菌体复制、整合和切除的酶以及与噬菌体调控基因表达有关的蛋白质。研究还探讨了峡湾环境中感染各种细菌群和其他较高营养级的病毒。功能注释显示了噬菌体相关结构基因和代谢基因的丰富程度。比较分析表明,在所有分析的北极样本中,dsDNA 病毒(Caudovirales)(Myoviridae、Podoviridae 和 Siphoviridae)的数量和比例各不相同。本研究加深了我们对北极峡湾沉积物中病毒多样性及其代谢潜力的了解。
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来源期刊
Journal of Soils and Sediments
Journal of Soils and Sediments 环境科学-土壤科学
CiteScore
7.00
自引率
5.60%
发文量
256
审稿时长
3.5 months
期刊介绍: The Journal of Soils and Sediments (JSS) is devoted to soils and sediments; it deals with contaminated, intact and disturbed soils and sediments. JSS explores both the common aspects and the differences between these two environmental compartments. Inter-linkages at the catchment scale and with the Earth’s system (inter-compartment) are an important topic in JSS. The range of research coverage includes the effects of disturbances and contamination; research, strategies and technologies for prediction, prevention, and protection; identification and characterization; treatment, remediation and reuse; risk assessment and management; creation and implementation of quality standards; international regulation and legislation.
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