RNA Viruses Linked to Eukaryotic Hosts in Thawed Permafrost

Wu, Ruonan; Bottos, Eric; Danna, Vincent; Stegen, James C.; Jansson, Janet; Davison, Michelle

doi:10.1128/msystems.00582-22

Cited by 15 publications

(10 citation statements)

References 77 publications

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“…Interestingly, we also found evidence for pathogen resistance within the tundra genomic signature (PF11203, PF05045), lending credence to a small number of recent studies suggesting permafrost environments as one of the largest reservoirs of soil viruses (139)(140)(141)(142) and a possible linkage between soil methane and viral infection (143).…”

Section: Soil Genomic Potential Corresponds To Ph Bulk Density and Bi...supporting

confidence: 80%

Genomic fingerprints of the world’s soil ecosystems

Graham,

Garayburu-Caruso,

et al. 2023

Preprint

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Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assayed 1512 manually-curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. We reveal novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. Specifically, we demonstrate shifts in the potential for microbial nutrient acquisition across pH gradients; for stress, transport, and redox-based processes across changes in soil bulk density; and for greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes –– more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.ImportanceWe address a critical gap in our understanding of soil microorganisms and their functions, which have a profound impact on our environment. We analyzed 1512 global soils with advanced analytics to create detailed genetic profiles (fingerprints) of soil microbiomes. This reveals novel patterns in how these microorganisms are distributed across different soil environments. For instance, we discovered shifts in their potential to acquire nutrients in relation to soil acidity, as well as changes in stress responses and potential greenhouse gas emissions linked to soil density. We also identified soils with putative high activity that had unique genomic characteristics surrounding resource acquisition, plant-microbe interactions, and fungal activity. Finally, we observed that closely related microorganisms tend to respond in similar ways to changes in their surroundings. Our work is a significant step towards comprehending the intricate world of soil microorganisms and its role in the global climate.

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Section: Soil Genomic Potential Corresponds To Ph Bulk Density and Bi...supporting

confidence: 80%

Genomic fingerprints of the world’s soil ecosystems

Graham,

Garayburu-Caruso,

et al. 2023

Preprint

Self Cite

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“…We need an improved understanding of what controls that balance, and how can that be used in biogeochemical modelling. Other work has demonstrated the activity of viruses in cold to sub-freezing temperature soils (Trubl et al, 2021;Wu et al, 2022) and illustrates the potential for viruses in biogeochemical processes of cold terrestrial worlds, such as Mars.…”

Section: Biogeochemical Cycling and Biosignature Detectionmentioning

confidence: 97%

Astrovirology: how viruses enhance our understanding of life in the Universe

Trubl

Stedman

Bywaters

et al. 2023

International Journal of Astrobiology

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Viruses are the most numerically abundant biological entities on Earth. As ubiquitous replicators of molecular information and agents of community change, viruses have potent effects on the life on Earth, and may play a critical role in human spaceflight, for life-detection missions to other planetary bodies and planetary protection. However, major knowledge gaps constrain our understanding of the Earth's virosphere: (1) the role viruses play in biogeochemical cycles, (2) the origin(s) of viruses and (3) the involvement of viruses in the evolution, distribution and persistence of life. As viruses are the only replicators that span all known types of nucleic acids, an expanded experimental and theoretical toolbox built for Earth's viruses will be pivotal for detecting and understanding life on Earth and beyond. Only by filling in these knowledge and technical gaps we will obtain an inclusive assessment of how to distinguish and detect life on other planetary surfaces. Meanwhile, space exploration requires life-support systems for the needs of humans, plants and their microbial inhabitants. Viral effects on microbes and plants are essential for Earth's biosphere and human health, but virus–host interactions in spaceflight are poorly understood. Viral relationships with their hosts respond to environmental changes in complex ways which are difficult to predict by extrapolating from Earth-based proxies. These relationships should be studied in space to fully understand how spaceflight will modulate viral impacts on human health and life-support systems, including microbiomes. In this review, we address key questions that must be examined to incorporate viruses into Earth system models, life-support systems and life detection. Tackling these questions will benefit our efforts to develop planetary protection protocols and further our understanding of viruses in astrobiology.

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“…This is supported by the detection of site‐specific viral AMGs in desert, grassland, and contaminated soils. These specific AMGs, such as microbial extremotolerance related genes in the Atacama Desert hyperarid soil (Hwang et al, 2021), pesticide degradation‐associated gene L‐DEX exclusively detected in organochlorine pesticide‐contaminated soils (Zheng et al, 2022), and sporulation/organic matter decomposition genes in grassland soils (Wu et al, 2022) provide evidence on the ecological roles of viral AMGs in reprogramming hosts' metabolisms in soils. The presence of these AMGs is most likely designed to maintain, facilitate, or short‐circuit key steps of a metabolic pathway, which provide substantial fitness advantages for the host cell and virus in terms of niche extension under specific conditions (Kieft et al, 2021) (Figure 4).…”

Section: Eco‐evolutionary Significance Of Viral Amgs In Soilmentioning

confidence: 99%

Underexplored viral auxiliary metabolic genes in soil: Diversity and eco‐evolutionary significance

Sun

Yuan

Xia

et al. 2023

Environmental Microbiology

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Bacterial viruses are the most abundant biological entities in soil ecosystems. Owing to the advent of metagenomics and viromics approaches, an ever‐increasing diversity of virus‐encoded auxiliary metabolic genes (AMGs) have been identified in soils, including those involved in the transformation of carbon, phosphorus, and sulfur, degradation of organic pollutants, and antibiotic resistance, among other processes. These viral AMGs can alter soil biogeochemical processes and metabolic activities by interfering with bacterial host metabolism. It is recognized that viral AMGs compensate for host bacterial metabolism outputs by encoding accessory functional genes and are favourable for the hosts' adaptation to stressed soil environments. The eco‐evolutionary mechanisms behind this fascinating diversity of viral AMGs in soil microbiomes have begun to emerge, such as horizontal gene transfer, lytic‐lysogenic conversion, and single‐nucleotide polymorphisms. In this mini‐review, we summarize recent advances in the diversity and function of virus‐encoded AMGs in the soil environment, especially focusing on the evolutionary significance of AMGs involved in virus‐host interactions. This mini‐review also sheds light on the existing gaps and future perspectives that could have major significance for viral AMGs research in soils.

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RNA Viruses Linked to Eukaryotic Hosts in Thawed Permafrost

Abstract: Permafrost is thawing at a rapid pace in the Arctic with largely unknown consequences on ecological processes that are fundamental to Arctic ecosystems. This is the first study to determine the composition of RNA viruses in thawed permafrost.

Cited by 15 publications

References 77 publications

Genomic fingerprints of the world’s soil ecosystems

Genomic fingerprints of the world’s soil ecosystems

Astrovirology: how viruses enhance our understanding of life in the Universe

Underexplored viral auxiliary metabolic genes in soil: Diversity and eco‐evolutionary significance

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