A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts

Graham, Emily B.; Camargo, Antonio Pedro; Wu, Ruonan; Neches, Russell Y.; Nolan, Matt; Paez-Espino, David; Kyrpides, Nikos C.; Jansson, Janet K.; McDermott, Jason E.; Hofmockel, Kirsten S.; ,

doi:10.1101/2023.11.02.565391

Cited by 3 publications

(1 citation statement)

References 165 publications

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“…Finally, we also highlight the high abundance of soil DNA viruses which are increasingly thought to influence soil biogeochemistry, relative to other microorganisms (Neri et al . 2022; Roux and Emerson 2022; Graham et al . 2023; Jansson and Wu 2023).…”

Section: Discussionmentioning

confidence: 99%

Revealing the taxonomy and functional potential of urban soil microbiomes

Stohel,

Song,

Turetcaia

et al. 2024

Preprint

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Urbanization is a leading cause of global biodiversity loss, but its impact on soil microorganisms and biogeochemistry remains uncertain. To address this gap, we investigate urban soil microbiome composition using metagenomic sequences from the Global Urban Soil Environment Ecology Network (GLUSEEN). We seek to reveal (1) changes in taxonomic composition and functional potential and (2) ubiquitous (core) taxa and metabolisms across the urban soil microbiome. We hypothesize that soil taxonomic and functional diversity are correlated due to the unique selective pressures of the urban ecosystem, and that the potential for carbon, nutrient, and pollutant cycling is a key feature of the urban soil microbiome. We find that Baltimore soil microbiomes are distinct from all other cities, displaying the highest taxonomic and lowest functional diversity. Only 66.3% of taxonomic and functional composition is correlated across all cities, highlighting differing functional potential within similar soil microbial taxa. Metabolic processes involving carbon and nitrogen cycling are abundant, as well as xenobiotic degradation. Core urban microbiota include many common soil bacteria and methane- and nitrogen-cycling archaea. Understanding the predominant characteristics of microbial taxonomy and functional potential in urban soils will aid in understanding feedback between growing metropolitan areas and processes driving climate change.

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Section: Discussionmentioning

confidence: 99%

Revealing the taxonomy and functional potential of urban soil microbiomes

Stohel,

Song,

Turetcaia

et al. 2024

Preprint

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Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils

Barnett,

Shade

2024

Preprint

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Viruses are important components of the soil microbiome, influencing microbial population dynamics and the functions of their hosts. However, the relationships and feedbacks between virus dynamics, microbial host dynamics, and environmental disturbance is not understood. Centralia, PA, USA, is the site of an underground coal seam fire that has been burning for over 60 years. As the fire moves along the coal seam, previously heated soils cool to ambient temperature, creating a gradient of heat disturbance intensity and recovery. We examined annual soil viral population dynamics over seven consecutive years in Centralia using untargeted metagenome sequencing. Viral communities changed over time and were distinct between fire-affected and reference sites. Dissimilarity in viral communities was greater across sites (space) than within a site across years (time), and cumulative viral diversity more rapidly stabilized within a site across years than within a year across sites. There also were changes in CRISPR investment as soils cooled, corresponding to shifts in viral diversity. Finally, there were also differences in viral-encoded auxiliary metabolic genes between fire-affected and reference sites. These results indicate that despite high site-to-site soil viral diversity, there was surprising viral community consistency within a site over the years and shifting host-viral interactions in soils recovering from disturbance. Together, these results provide insights into how viral and host communities collectively respond to unpredicted environmental disturbance.

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Exploring the Multifaceted Role of Viruses in Sustaining Biodiversity: Mechanisms, Implications, and Contributions to Ecosystems Stability

Hejran,

Alimyar,

Afghan

et al. 2024

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Viruses, traditionally recognized as pathogenic agents, are increasingly acknowledged for their indispensable roles in sustaining biodiversity and fostering ecosystem stability. This review examines the multifaceted contributions of viruses, exploring their influence on nutrient cycling, genetic diversification, and regulation of microbial populations. By mediating microbial interactions, facilitating horizontal gene transfer, and driving co-evolutionary processes, viruses shape the intricate tapestry of life across diverse ecosystems. The primary aim of this study is to synthesize contemporary findings in virology to highlight the universal ecological importance of viruses. Drawing upon research conducted in marine, terrestrial, and extreme habitats, the review delineates the mechanisms through which viruses mediate ecological balance. Utilizing meta-analyses of global virome datasets, coupled with advanced metagenomics and bioinformatics methodologies, this investigation unveils the nuanced interplay between viral activity and ecosystem functionality. The results illuminate the significant role of viruses in regulating population dynamics, promoting evolutionary innovation, and maintaining genetic reservoirs critical for ecological resilience. This research enriches our understanding of viral influence on biogeochemical cycles and biodiversity, establishing viruses as integral components of global ecosystems. Furthermore, it contributes a paradigm shift in virology, advocating for a broader perspective that transcends the traditional view of viruses as mere pathogens. The practical implications are profound, providing insights for conservation biology and climate resilience strategies. By reimagining viruses as keystones of ecological health, this work underscores the necessity of integrating viral ecology into holistic environmental and evolutionary research frameworks, advancing scientific and practical knowledge of ecosystem sustainability.

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A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts

Cited by 3 publications

References 165 publications

Revealing the taxonomy and functional potential of urban soil microbiomes

Revealing the taxonomy and functional potential of urban soil microbiomes

Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils

Exploring the Multifaceted Role of Viruses in Sustaining Biodiversity: Mechanisms, Implications, and Contributions to Ecosystems Stability

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