Viruses in Nature

Viruses in Nature

Viruses are among the most abundant, diverse, and poorly understood biological entities on Earth. They occur throughout the oceans, lakes, rivers, soils, forests, wetlands, plants, fungi, animals, ice sheets, deep sediments, hot springs, and other environments. Modern metagenomic research has revealed an enormous virosphere containing vast numbers of viral lineages that were previously invisible to science.

Although viruses are often discussed primarily as agents of disease, environmental research presents a much broader picture. Viruses kill some organisms, coexist with others, alter host metabolism, move genes between organisms, influence evolutionary change, and sometimes form relationships that benefit their hosts. At ecosystem scales, these interactions can affect biodiversity, food webs, nutrient cycling, primary production, decomposition, and the movement and storage of carbon.

The Hidden Virosphere

Environmental sequencing has transformed scientific understanding of viral diversity. Large-scale metagenomic studies have uncovered hundreds of thousands of viral genomes and genome fragments from natural environments, while many studies suggest that most viral diversity remains undescribed.

Viruses occur wherever cellular organisms are found. Bacteriophages infect bacteria, archaeal viruses infect archaea, mycoviruses infect fungi, plant viruses circulate through natural vegetation, and diverse viruses inhabit insects, fish, birds, mammals, algae, protists, and other organisms. Giant viruses have further expanded traditional ideas about how large and genetically complex viruses can become.

This enormous collection of viruses and their genetic diversity is sometimes described as the virosphere. Rather than forming an isolated biological world, the virosphere is intertwined with nearly every major ecosystem and with the organisms upon which those ecosystems depend.

Viruses as Ecological Regulators

One of the most important ecological roles of viruses comes from their ability to regulate host populations. Bacteriophages can destroy large numbers of bacteria and archaea, while viruses of algae and other microorganisms can influence the rise and collapse of microbial populations and plankton blooms.

Viral infection can therefore prevent particular microbial populations from becoming overwhelmingly dominant. By selectively infecting successful hosts, viruses may help preserve microbial diversity and reshape competition among species and strains.

Viral relationships are not always destructive. Some viruses persist within hosts without immediately killing them, while others can alter host traits in ways that may occasionally improve survival under particular environmental conditions. Research on plants, fungi, bacteria, and other organisms increasingly shows that virus-host relationships can range from pathogenic to neutral and even mutualistic.

Viruses are therefore better understood as ecological participants whose effects depend upon the virus, host, surrounding community, and environmental conditions.

Oceans, Lakes, Rivers, and the Global Carbon Cycle

Marine environments contain extraordinarily large populations of viruses. Ocean viruses infect cyanobacteria, heterotrophic bacteria, algae, protists, and many other organisms that form the foundation of marine food webs.

When viruses rupture microbial cells through lysis, cellular material is released into the surrounding water. Rather than moving directly into larger organisms, some of this organic matter becomes available again to bacteria and other microorganisms. This process, commonly known as the viral shunt, redirects carbon and nutrients through microbial food webs.

Because marine microorganisms participate heavily in global photosynthesis and carbon cycling, viral infection can influence processes operating far beyond individual cells. Viruses can affect phytoplankton abundance, photosynthetic activity, nutrient availability, carbon export, and the cycling of nitrogen, phosphorus, sulfur, and other elements.

Freshwater environments contain similarly complex viromes. Lakes and rivers support rapidly changing viral populations whose abundance and composition can vary with season, temperature, nutrients, host populations, pollution, and other environmental conditions.

Long-term studies of lakes demonstrate that viral communities can persist, disappear, reappear, and evolve over periods ranging from seasons to decades. These findings make time itself an important component of viral biodiversity.

Soil, Forests, Wetlands, and Permafrost

Soil contains an enormous but historically understudied viral community. Advances in metagenomics are revealing thousands of viral populations associated with bacteria, fungi, plant roots, and other components of terrestrial ecosystems.

Soil viruses may influence decomposition, nutrient availability, microbial competition, plant health, and the cycling of carbon. Bacteriophages surrounding plant roots can modify microbial communities in the rhizosphere, potentially influencing both beneficial microorganisms and plant pathogens.

Viral communities vary considerably among forests, grasslands, agricultural soils, wetlands, peatlands, deserts, and disturbed landscapes. Moisture, soil texture, acidity, vegetation, land use, and hydrology can all influence which viruses occur and how active they become.

Peatlands and permafrost are particularly important because of their enormous stores of organic carbon. Research along thawing permafrost gradients suggests that viruses interact with microorganisms involved in carbon processing and methane production. Environmental warming may therefore alter not only microbial communities but also the viral communities that regulate them.

Ancient permafrost also preserves viruses for exceptionally long periods. Studies of these frozen environments are expanding knowledge of viral persistence and evolution while raising questions about how thawing landscapes may alter previously isolated microbial ecosystems.

Viruses of Plants, Fungi, and Wildlife

Natural plants contain diverse viral communities that have historically received far less attention than viruses affecting agricultural crops. Metagenomic studies increasingly show that apparently healthy wild plants may carry numerous viruses without obvious symptoms.

Plant-virus interactions depend strongly on environmental conditions and host genetics. A virus that harms a plant under one set of circumstances may have little effect under another, and some viral infections may even improve host tolerance to environmental stress.

Fungi also contain their own viruses, known as mycoviruses. These viruses can influence fungal growth, reproduction, pathogenicity, and ecological relationships. In some cases, viral infection reduces the ability of a fungus to cause disease, creating interest in the possible use of mycoviruses for biological control.

Wild animals possess equally complex viromes. Research involving bats, birds, fish, insects, ticks, mosquitoes, pollinators, primates, and other wildlife reveals large numbers of previously unknown viruses.

Wildlife virome research can help explain viral biodiversity and evolution, but it also illustrates an important distinction between discovering viruses and demonstrating disease risk. Most viruses detected in wildlife are not known to cause human disease. Their distribution is shaped by host biology, geography, habitat, migration, diet, climate, and interactions among species.

Phages, Viral Life Strategies, and Coevolution

Viruses employ different ecological strategies. Lytic viruses reproduce within a host and eventually rupture the infected cell. Temperate viruses can instead integrate into or persist alongside host genomes, sometimes remaining dormant for extended periods.

The balance between these strategies can shift with host abundance, environmental conditions, competition, and ecosystem structure. Research into lysis and lysogeny has produced continuing debate over when viruses benefit from rapidly destroying hosts and when persistence within successful host populations provides an evolutionary advantage.

Hosts meanwhile evolve defenses against viruses. Bacteria and archaea possess systems such as CRISPR and restriction-modification mechanisms, while viruses evolve countermeasures. This continuing evolutionary struggle can produce rapid genetic diversification in both viruses and their hosts.

Viruses can also carry auxiliary metabolic genes capable of modifying host metabolism during infection. Such genes have been associated with carbon, nitrogen, sulfur, phosphorus, photosynthesis, and other metabolic pathways. Their discovery suggests that some viruses influence ecosystems not only by killing organisms but also by temporarily reprogramming what infected cells do.

Researchers nevertheless caution that the ecological importance of predicted viral metabolic genes must be demonstrated experimentally rather than inferred solely from sequence data.

Giant Viruses and Extreme Environments

The discovery of giant viruses challenged older assumptions that viruses necessarily possess small genomes and simple biological structures. Giant viruses can contain remarkably large genomes and infect algae, amoebae, protists, and other microbial eukaryotes.

They have now been detected in oceans, sediments, soils, lakes, permafrost, polar environments, and other ecosystems. Their diversity suggests that giant viruses are longstanding components of microbial evolution rather than biological curiosities.

Viruses also occur in some of Earth's most extreme environments. Studies have detected distinctive viral communities in hydrothermal vents, hot springs, deep ocean waters, Antarctic environments, Greenland ice, polar lakes, and ancient permafrost.

These environments demonstrate the extraordinary ecological range of viruses. Viral communities can remain active under conditions of extreme temperature, acidity, darkness, nutrient scarcity, and isolation, often evolving alongside equally specialized microbial hosts.

Environmental Change and Human Influence

Viral ecology is sensitive to environmental change. Warming, altered rainfall, drought, ocean acidification, nutrient pollution, land-use change, agriculture, urbanization, aquaculture, and habitat disturbance can reshape both host communities and the viruses associated with them.

Climate change may alter marine viral infection by changing ocean temperature, circulation, stratification, and primary production. On land, warming and changing moisture can modify virus-host interactions in soils and permafrost. Wetland disturbance, groundwater alteration, pollution, and changes in vegetation can similarly reorganize viral communities.

Human-created environments can also become distinct viral habitats. Constructed wetlands, agricultural soils, urban rivers, drinking-water systems, aquaculture sites, and even microplastic surfaces support virus-host communities whose composition can differ from surrounding natural environments.

Understanding these responses may become increasingly important because viral activity can affect ecosystem resilience, microbial diversity, decomposition, disease dynamics, and carbon and nutrient cycling.

A New View of Viruses in Nature

The growing field of viral ecology is changing the traditional image of viruses as biological entities important mainly because they cause disease. In natural ecosystems, viruses are deeply integrated into ecological processes.

They regulate microorganisms, redirect nutrients, alter metabolism, contribute to evolutionary change, influence plant and fungal relationships, interact with wildlife, and participate in the functioning of oceans, soils, freshwater systems, wetlands, forests, and extreme environments.

Much of this viral world remains unknown. Improvements in metagenomics, long-read sequencing, single-cell methods, environmental monitoring, and virus-host identification continue to reveal previously hidden viral diversity at an extraordinary rate.

Conclusion

Viruses are fundamental components of Earth's ecosystems. Their ecological significance extends from microscopic interactions within individual cells to processes affecting entire food webs and global biogeochemical cycles.

The evidence gathered across marine, freshwater, terrestrial, plant, fungal, wildlife, polar, and extreme environments shows that viruses cannot be understood solely as pathogens. They are predators, genetic agents, metabolic manipulators, evolutionary partners, and sometimes mutualists.

As scientists continue exploring the global virosphere, viral ecology is likely to become increasingly important to understanding biodiversity, ecosystem resilience, climate feedbacks, microbial evolution, and the functioning of the living planet.

General Viral Ecology and the Virosphere

| Kristina D. A. Mojica and Corina P. D. Brussaard | Annual Review of Marine Science | 2026

Marine Viruses and Their Role in Marine Ecosystems and Carbon Cycling — A modern synthesis of how viral infections influence marine microbial communities, nutrient recycling and the ocean carbon cycle.

| Yang Gao et al. | Frontiers in Public Health | 2022-03-29

The "Regulator" Function of Viruses on Ecosystem Carbon Cycling in the Anthropocene — Reviews evidence that viruses influence carbon processing and storage across marine, freshwater and terrestrial ecosystems.

| Anne Chevallereau et al. | Nature Reviews Microbiology | 2021-08-09

Interactions between bacterial and phage communities in natural environments — Reviews how bacteriophages shape bacterial population sizes, diversity, evolution and community structure in natural ecosystems.

| Steven Batinovic et al. | Pathogens | 2019-07-12

Bacteriophages in Natural and Artificial Environments — Surveys the distribution and ecological importance of bacteriophages in soils, aquatic ecosystems and human-modified environments.

| David Paez-Espino et al. | Nature | 2016-08-17

Uncovering Earth's virome — A large-scale metagenomic survey uncovered more than 125,000 partial DNA viral genomes and demonstrated the immense, largely unexplored diversity of viruses across Earth's habitats.

| Télesphore Sime-Ngando | Frontiers in Microbiology | 2014-07-24

Environmental bacteriophages: viruses of microbes in aquatic ecosystems — Explores phage diversity, viral mortality of microbes, lysogeny and the consequences of infection for aquatic food webs and nutrient cycles.

| Marilyn J. Roossinck | Nature Reviews Microbiology | 2011

The good viruses: viral mutualistic symbioses — Examines beneficial viral relationships involving bacteria, plants, fungi, insects and animals, showing that viruses can enhance host survival and adaptation.

| Curtis A. Suttle | Nature Reviews Microbiology | 2007-10

Marine viruses — major players in the global ecosystem — A seminal review explaining how enormous viral populations influence microbial mortality, evolution, genetic diversity and global biogeochemical cycles.

| Markus G. Weinbauer | FEMS Microbiology Reviews | 2004-05

Ecology of prokaryotic viruses — A foundational review of viral abundance, diversity, lysis, lysogeny and ecological effects in marine, freshwater and terrestrial environments.

| K. Eric Wommack and Rita R. Colwell | Microbiology and Molecular Biology Reviews | 2000

Virioplankton: Viruses in Aquatic Ecosystems — A classic synthesis establishing viruses as abundant and ecologically significant components of marine and freshwater microbial communities.

Marine Viruses and Ocean Ecosystems

| Marguerite V. Langwig and Karthik Anantharaman | Annual Review of Marine Science | 2026-08-13

Decoding the Deep: The Ecology, Biogeography, and Evolution of Deep-Sea Viruses — Synthesizes emerging knowledge of viral diversity, evolution, host relationships and ecosystem functions throughout the deep ocean.

| Various authors | Applied and Environmental Microbiology | 2026-03-05

Viruses in marine sediments: a review of their effect on biogeochemistry and microbial interactions — Reviews how viruses affect microbial mortality, carbon processing, gene exchange and nutrient cycling within marine sediments.

| Various authors | Advanced Science | 2026

Diversity and Ecological Potentials of Marine Viruses Inhabiting Continental Shelf Seas — A massive viral survey of China's continental shelf seas expands known marine viral diversity and examines ecological and metabolic functions.

| Chong Wang, Rikuan Zheng and Chaomin Sun | Nature Communications | 2025-11-19

Deep-sea viral diversity and their role in host metabolism of complex organic matter — Investigates how deep-sea viruses alter microbial metabolism associated with the processing of complex organic material.

| Benjamin Minch and Mohammad Moniruzzaman | npj Viruses | 2025-04-21

Expansion of the genomic and functional diversity of global ocean giant viruses — Expands the known genomic diversity of giant viruses and reveals their broad distribution and potential functions in marine ecosystems.

| Various authors | Nature Communications | 2024-05-14

Long-read powered viral metagenomics in the oligotrophic Sargasso Sea — Long-read sequencing recovers previously inaccessible complete viral genomes and exposes major gaps in existing reference collections.

| Meishun Yu et al. | Nature Communications | 2024-04-15

Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments — Finds diverse viruses associated with seamount sediments and links them to microbial hosts involved in carbon, nitrogen and sulfur cycling.

| Various authors | Microbiome | 2024

Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans — Constructs a global catalog of tens of thousands of virus-associated metabolic genes potentially involved in ocean biogeochemical cycling.

| Various authors | Nature Communications | 2024

Globally occurring pelagiphage infections create ribosome-deprived cells — Shows that phages infecting globally dominant SAR11 bacteria can generate metabolically unusual "zombie" cells throughout multiple ocean basins.

| Tianliang He et al. | Journal of Advanced Research | 2023-04-17

Environmental viromes reveal the global distribution signatures of deep-sea DNA viruses — Maps deep-ocean DNA viral diversity and identifies geographic and environmental patterns in deep-sea viral communities.

| Xinyi Zhang et al. | Journal of Advanced Research | 2023-04-11

Environmental viromes reveal global virosphere of deep-sea sediment RNA viruses — Reveals extensive and previously poorly characterized RNA virus diversity in sediments from the deep ocean.

| Various authors | Viruses | 2023-02-20

Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species — Five years of Pacific Ocean sampling reveals persistent, seasonal, occasional and sporadic cyanophage populations.

| Ilia Maidanik et al. | The ISME Journal | 2022-06-20

Cyanophages from a less virulent clade dominate over their sister clade in global oceans — Demonstrates that less aggressive cyanophages can achieve greater environmental abundance and ecological impact than more virulent relatives.

| Michael C. G. Carlson et al. | Nature Microbiology | 2022-04-01

Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean — Links cyanophage infection patterns to the abundance and geographic distribution of important oceanic primary producers.

| Fuh-Kwo Shiah et al. | Science Advances | 2022

Viral shunt in tropical oligotrophic ocean — Investigates how viral destruction of microbes redirects organic matter away from larger organisms and back into microbial cycling.

| Hannah Locke et al. | Advances in Virus Research | 2022

Marine viruses and climate change: Virioplankton, the carbon cycle, and our future ocean — Explores how ocean warming, acidification, stratification and circulation changes may alter virus-mediated carbon recycling and export.

| Tristan E. G. Biggs, Jef Huisman and Corina P. D. Brussaard | The ISME Journal | 2021-06-21

Viral lysis modifies seasonal phytoplankton dynamics and carbon flow in the Southern Ocean — Shows that viruses influence phytoplankton seasonality and redirect organic carbon through Southern Ocean food webs.

| Various authors | mSystems | 2021

Genome and Ecology of a Novel Alteromonas Podovirus, ZP6, Representing a New Viral Genus, Mareflavirus — Characterizes a newly isolated marine phage and maps its ecological distribution across major Global Ocean Virome zones.

| Various authors | The ISME Journal | 2020

Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline — Examines viruses along strong oxygen and chemical gradients and links them with microbial processes in an unusual anoxic marine basin.

| Ann C. Gregory et al. | Cell | 2019-05-16

Marine DNA Viral Macro- and Microdiversity from Pole to Pole — The Global Ocean Viromes 2.0 project identifies nearly 200,000 viral populations and divides ocean viral communities into five major ecological zones.

| Ella T. Sieradzki et al. | Nature Communications | 2019-03-12

Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes — Shows that active viral infections are closely intertwined with photosynthetic microbial activity in the ocean.

| Various authors | Frontiers in Microbiology | 2019

Metagenomic Analysis of the Diversity of DNA Viruses in the Surface and Deep Sea of the South China Sea — Reveals sharp differences between surface and deep-sea viral communities and links viral patterns with nutrients and carbon flux.

| Hagay Enav et al. | Nature Communications | 2018-11-08

Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean — Shows how infection of less-than-optimal microbial hosts can promote evolutionary diversification among marine viruses.

| Mya Breitbart et al. | Nature Microbiology | 2018-06-04

Phage puppet masters of the marine microbial realm — Discusses how bacteriophages manipulate microbial metabolism and reshape microbial populations throughout the world's oceans.

| Rebecca Vega Thurber et al. | Nature Reviews Microbiology | 2017-04-01

Virus-host interactions and their roles in coral reef health and disease — Reviews the complex roles of viruses associated with corals, microbes and reef organisms in both healthy and stressed reef ecosystems.

| Simon Roux et al. | Nature | 2016

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses — Global ocean metagenomes revealed thousands of viral populations and auxiliary metabolic genes with potential roles in sulfur, nitrogen and other elemental cycles.

| Jennifer R. Brum and Matthew B. Sullivan | Nature Reviews Microbiology | 2015-02-02

Rising to the challenge: accelerated pace of discovery transforms marine virology — Reviews technological advances that dramatically expanded knowledge of marine viral diversity, hosts and ecosystem functions.

| Rui Zhang, Wei Wei and Lanlan Cai | Nature Reviews Microbiology | 2014-11-14

The fate and biogeochemical cycling of viral elements — Explores what happens to viral particles and their chemical components after production, degradation and movement through marine food webs.

| Luis F. Jover et al. | Nature Reviews Microbiology | 2014-06-16

The elemental composition of virus particles: implications for marine biogeochemical cycles — Examines how the physical production and destruction of virus particles themselves influence carbon, nitrogen and phosphorus budgets.

| Matthew B. Sullivan, John B. Waterbury and Sallie W. Chisholm | Nature | 2003-08-28

Cyanophages infecting the oceanic cyanobacterium Prochlorococcus — An influential study revealing diverse viruses infecting Prochlorococcus, one of the planet's most important photosynthetic microorganisms.

Freshwater Viruses, Lakes, and Rivers

| Various authors | Nature Communications | 2026-08

Elevation-structured viral ecological strategies along glacier-fed rivers on the Qinghai-Tibet Plateau — A glacier-to-river survey finds viral communities shifting from temperate lifestyles at high elevations toward increasingly lytic strategies downstream.

| Kira Moon, Ilnam Kang and Jang-Cheon Cho | Scientific Data | 2026-05-05

Virome datasets and viral metagenome-assembled genomes from aquaculture-impacted freshwater environments — Provides genome-resolved viral datasets from river sites upstream, downstream and directly exposed to fish-farm effluent.

| Yumary M. Vasquez et al. | Nature Communications | 2026

Vicennial metagenomic time series unveils evolutionary dynamics of giant viruses in a freshwater ecosystem — Twenty years of Lake Mendota data reveal long-term persistence, adaptation and changing host associations among giant viruses.

| Tao Wang et al. | Nature Communications | 2025-08-21

Metagenomic analysis reveals how multiple stressors disrupt virus–host interactions in multi-trophic freshwater mesocosms — Warming, nutrients and pesticides restructure freshwater viral diversity and simplify virus-host ecological networks.

| Zhichao Zhou et al. | Nature Microbiology | 2025

Unravelling viral ecology and evolution over 20 years in a freshwater lake — A two-decade dataset reveals long-term changes, persistence and evolutionary dynamics within a natural freshwater viral community.

| Various authors | Science of the Total Environment | 2024-10-10

Eutrophication impacts the distribution and functional traits of viral communities in lakes — Examines how nutrient enrichment restructures lake viral communities and alters their potential ecological functions.

| Yu Zheng, Zihao Gao, Shuai Wu and Aidong Ruan | Viruses | 2024

Community Structure, Drivers, and Potential Functions of Different Lifestyle Viruses in Chaohu Lake — Compares lytic and temperate viral communities and investigates environmental controls over their distributions and functions.

| Various authors | Viruses | 2023

Genomic Analysis and Taxonomic Characterization of Seven Bacteriophage Genomes Metagenomic-Assembled from the Dishui Lake — Reconstructs novel phages from an artificial freshwater lake and places them within broader freshwater viral diversity.

| Ali H. A. Elbehery and Li Deng | Frontiers in Microbiology | 2022-09-28

Insights into the global freshwater virome — Reviews freshwater viral biodiversity, virus-host relationships, geographic patterns and potential roles in ecosystem processes.

| Various authors | Virologica Sinica | 2022

Metagenomic analysis of viral community in the Yangtze River expands known eukaryotic and prokaryotic virus diversity in freshwater — Provides a broad survey of DNA and RNA viruses inhabiting one of the world's largest river systems.

| Yuri I. Wolf et al. | Nature Microbiology | 2020-07-20

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome — Sequencing near the Yangtze estuary uncovers more than 4,500 RNA viruses and greatly expands the known evolutionary tree of RNA viruses.

| Various authors | The ISME Journal | 2017

Temporal dynamics of uncultured viruses: a new dimension in viral diversity — Demonstrates pronounced temporal turnover among uncultured freshwater viruses and highlights time as a major dimension of viral biodiversity.

| Various authors | Frontiers in Microbiology | 2016

Composition and Interactions among Bacterial, Microeukaryotic, and T4-like Viral Assemblages in Lakes from Both Polar Zones — Compares microbial and viral communities in Arctic and Antarctic lakes and examines relationships among major biological groups.

| Various authors | Applied and Environmental Microbiology | 2012

Temporal Dynamics and Decay of Putatively Allochthonous and Autochthonous Viral Genotypes in Contrasting Freshwater Lakes — Examines the persistence and disappearance of viruses originating inside and outside contrasting lake ecosystems.

| Various authors | PLOS ONE | 2012

Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics — Comparison of two ecologically different lakes reveals strong differences in viral richness and evidence for freshwater-specific viral lineages.

| Rozenn Thomas et al. | Environmental Microbiology | 2011-03

Viral abundance, production, decay rates and life strategies in Lake Bourget, France — Quantifies viral production, destruction, lytic infection and lysogeny to characterize changing viral strategies within a freshwater lake.

| Cindy M. Short, Oksana Rusanova and Steven M. Short | The ISME Journal | 2010-12-02

Quantification of virus genes provides evidence for seed-bank populations of phycodnaviruses in Lake Ontario, Canada — Provides evidence that viral populations can persist at low levels until suitable algal hosts or environmental conditions return.

Soil, Grassland, Forest, and Peatland Viruses

| Gareth Trubl et al. | mSystems | 2026-07-21

Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics — Stable-isotope viromics finds that many grassland virions persist without active replication, supporting the idea of a soil viral seed bank.

| Changhua He et al. | BMC Biology | 2026-07-16

Diversity and potential ecological roles of viruses in Pleistocene permafrost — Characterizes ancient permafrost viral diversity and investigates potential relationships with microbial hosts and ecosystem functions.

| Various authors | Environmental Science & Technology | 2026

Transport and Survival of Marine Tracer Phages in Topsoil at Field Conditions — Field experiments demonstrate long-term phage persistence in soils and event-driven remobilization, emphasizing that retention does not necessarily mean viral inactivation.

| Jia-nan Lu et al. | Nature Communications | 2025-11-13

DNA viral community enhances microbial carbon fixation capacity via auxiliary metabolic genes in contaminated soils — Experimental and metagenomic evidence indicates viruses can stimulate microbial carbon fixation through virus-encoded metabolic functions.

| Ziye Xiong et al. | Environment International | 2025-03

Distance to the water table shapes the diversity and activity of DNA and RNA viruses in a subalpine peatland — Demonstrates strong hydrological control over peatland viral diversity, activity and potential interactions with carbon-cycling microbes.

| Various authors | Publication not listed | 2025

Soil viruses drive carbon turnover during subtropical secondary forest succession — Finds that forest succession alters soil virus richness, community structure and carbohydrate-processing genes with implications for carbon cycling.

| Various authors | Publication not listed | 2025

Ecosystem health shapes viral ecology in peatland soils — Viral diversity and virus-host relationships differ among natural, damaged and restored peatlands, suggesting viruses participate in ecosystem recovery and carbon retention.

| Christine L. Sun et al. | Environmental Microbiology | 2024-07

Virus ecology and 7-year temporal dynamics across a permafrost thaw gradient — Tracks viral communities through seven years of environmental change to examine how thaw reshapes virus-host ecology.

| Xiaolong Liang et al. | Applied Soil Ecology | 2024-05

Studying soil viral ecology under an ecosystem services framework — Connects soil-virus research with ecosystem services such as nutrient cycling, plant productivity, disease regulation and soil health.

| Jason E. McDermott et al. | Nature Microbiology | 2024

A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts — A global synthesis reveals enormous soil viral diversity and identifies viral genes potentially affecting key biogeochemical processes.

| Xiaofang Wang et al. | FEMS Microbiology Ecology | 2024

The role of rhizosphere phages in soil health — Examines bacteriophages surrounding plant roots and their potential effects on beneficial microbes, pathogens, nutrient cycling and plant health.

| Various authors | Nature Ecology & Evolution | 2024

Biogeographic patterns and drivers of soil viromes — Analysis of more than 1,800 soil metagenomes uncovers over 80,000 viral genomes and shows that moisture, soil texture and biome influence global viral biogeography.

| Various authors | Microbiome | 2024

Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China — Surveys forests, grasslands, farms, deserts and mine soils and finds extensive habitat specialization among terrestrial giant viruses.

| Živilė Buivydaitė et al. | Virus Research | 2023-04-30

Meeting report: The first soil viral workshop 2022 — Summarizes major research priorities in soil viral genomics, virus-host interactions, biogeochemistry and the soil food web.

| Andrea Du Toit | Nature Reviews Microbiology | 2023-02-21

Viral regulators of responses to soil warming — Highlights research showing that viral activity can mediate microbial community responses and carbon-processing pathways under warming conditions.

| Janet K. Jansson and Ruonan Wu | Nature Reviews Microbiology | 2022-11-09

Soil viral diversity, ecology and climate change — Reviews rapidly expanding knowledge of soil viromes and their possible roles in microbial ecology, carbon cycling and ecosystem responses to climate change.

| Janet K. Jansson | Environmental Microbiology | 2022-11-05

Soil viruses: Understudied agents of soil ecology — Highlights the growing evidence that viruses regulate soil microorganisms and could affect terrestrial carbon and nutrient transformations.

| Christian Santos-Medellín et al. | Proceedings of the National Academy of Sciences | 2022-11-02

Spatial turnover of soil viral populations and genotypes overlain by cohesive responses to moisture in grasslands — Finds strong geographic turnover in grassland soil viruses while revealing coordinated responses to changing soil moisture.

| Li Bi et al. | Science of the Total Environment | 2022-03-15

Unravelling the ecological complexity of soil viromes: Challenges and opportunities — Reviews methodological obstacles and emerging approaches for studying highly diverse and spatially complex soil viral communities.

| Various authors | Soil Biology and Biochemistry | 2022-03

Soil pH influences the structure of virus communities at local and global scales — Shows that soil acidity is a powerful predictor of viral community composition across both experimentally manipulated and geographically distributed soils.

| Various authors | Nature Communications | 2022

Response of soil viral communities to land use changes — Compares forest, agricultural and urban soils and finds major shifts in viral communities associated with habitat disturbance, pH and moisture.

| Joanne B. Emerson | mSystems | 2019-05-28

Soil Viruses: A New Hope — Outlines why soil viruses represent a major unexplored component of terrestrial biodiversity and could transform understanding of microbial ecology.

| Yakov Kuzyakov and Kyle Mason-Jones | Soil Biology and Biochemistry | 2018-12

Viruses in soil: Nano-scale undead drivers of microbial life, biogeochemical turnover and ecosystem functions — Argues that viral predation and infection may be important but underappreciated drivers of soil nutrient turnover and microbial ecology.

| Joanne B. Emerson et al. | Nature Microbiology | 2018-07-16

Host-linked soil viral ecology along a permafrost thaw gradient — Links viruses to key carbon-cycling microorganisms and suggests viral activity may influence methane production during permafrost thaw.

| Kurt E. Williamson et al. | Annual Review of Virology | 2017-09-29

Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory — Reviews what is known about soil virus abundance, diversity, movement, host interactions and ecological consequences.

| P. Marsh and E. M. H. Wellington | FEMS Microbiology Ecology | 1994-11-01

Phage-host interactions in soil — An early examination of bacteriophage behavior in soils and the environmental factors affecting interactions between phages and bacterial hosts.

Wetlands, Mangroves, Groundwater, and Human-Modified Aquatic Habitats

| Siyuan Fan et al. | Environmental Pollution | 2026-06-15

Experimental evidence for the role of phages in mitigating antibiotic resistance genes in mangrove sediments — Microcosm experiments show that lytic phages can reduce some resistance genes and substantially alter mangrove bacterial communities.

| Yi Sun et al. | Water Research | 2026-04-01

Viral community dynamics and virus–prokaryote interactions in a full-scale constructed wetland — Finds seasonal shifts in phage lifestyles and viral metabolic genes linked to sulfur and other nutrient transformations in wetland biofilms.

| Various authors | Environmental Science & Technology | 2026-03-27

Insights into the Arms Race between Prokaryotic Hosts and Their Viruses in Mangrove Ecosystem — Examines CRISPR, restriction-modification and other antiviral defenses across mangrove sediment communities to reconstruct virus-host coevolution.

| Various authors | Nature Communications | 2026

Diversity and ecological roles of hidden viral players in groundwater microbiomes — Identifies tens of thousands of groundwater viruses and thousands of potential metabolic genes involved in carbon, nitrogen, sulfur and nutrient acquisition.

| Various authors | Publication not listed | 2026

A metagenomic analysis of urban river samples reveals high numbers of sequences related to mycoviruses — Urban river viromes contain an unexpectedly rich collection of RNA viruses related to viruses of fungi and oomycetes.

| Yue Su et al. | Journal of Hazardous Materials | 2024-09-05

Effects of vegetation cover and aquaculture pollution on viral assemblages in mangroves sediments — Shows mangrove viruses respond to vegetation and aquaculture disturbance while carrying genes associated with carbon metabolism and environmental adaptation.

| Various authors | Environmental Research | 2024-07-01

Habitat- and lifestyle-dependent structural and functional characteristics of viruses in mangrove wetlands of different functional zonings — Links viral lifestyles, hosts and environmental conditions with biogeochemical functions across urbanized mangrove habitats.

| Various authors | Nature Water | 2024

Viral metagenome reveals microbial hosts and the associated antibiotic resistome on microplastics — Finds that river microplastics create distinctive viral habitats and new virus-host associations while providing surfaces for genetic exchange.

| Dan Huang et al. | ISME Communications | 2023-05-04

The association of prokaryotic antiviral systems and symbiotic phage communities in drinking water microbiomes — Demonstrates that chlorine exposure restructures both microbial antiviral defenses and relationships with temperate phages.

| Min Jin et al. | Microbiome | 2019

Diversities and potential biogeochemical impacts of mangrove soil viruses — Reveals extensive mangrove viral diversity and virus-encoded carbohydrate-processing genes that may influence decomposition and coastal carbon cycling.

Plant Viruses in Natural Ecosystems

| Andrea M. Fetters and Tia-Lynn Ashman | American Journal of Botany | 2023-03-16

The pollen virome: A review of pollen-associated viruses and consequences for plants and their interactions with pollinators — Reviews how viruses move through pollen and plant-pollinator networks, connecting viral ecology with plant reproduction and insect behavior.

| Andrea M. Fetters et al. | Nature Communications | 2022-01-26

The pollen virome of wild plants and its association with variation in floral traits and land use — Finds diverse viruses associated with wild-plant pollen and examines links among viral communities, flowers, pollination and surrounding land use.

| Beata Hasiów-Jaroszewska, Dieke Boezen and Mark P. Zwart | Viruses | 2021-09-27

Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities — Reviews evidence that wild plants harbor extensive, often asymptomatic viral diversity and can connect natural and agricultural ecosystems.

| Various authors | Plant-Environment Interactions | 2021

Leaf-associated fungal and viral communities of wild plant populations differ between cultivated and natural ecosystems — Shows that land management affects wild-plant fungal and viral communities in different ways.

| Netherlands Institute of Ecology | NIOO-KNAW | 2021

Virus diversity and genome evolution in natural plant ecosystems — Research program investigating viral biodiversity, mixed infections and evolutionary dynamics in wild plants rather than agricultural hosts alone.

| Cristina Rodríguez-Nevado, Rosario G. Gavilán and Israel Pagán | Phytopathology | 2020-01

Host Abundance and Identity Determine the Epidemiology and Evolution of a Generalist Plant Virus in a Wild Ecosystem — Shows that plant abundance and species identity strongly influence virus prevalence and evolution in a natural plant community.

| Pierre Lefeuvre et al. | Nature Reviews Microbiology | 2019-07-16

Evolution and ecology of plant viruses — Reviews how host ecology, transmission, mutation, recombination and environmental change influence the diversification and emergence of plant viruses.

| Hanna Susi et al. | PeerJ | 2019

Diverse and variable virus communities in wild plant populations revealed by metagenomic tools — Metagenomic surveys uncover highly variable and largely unknown viral communities inhabiting naturally occurring plants.

| Various authors | Frontiers in Microbiology | 2018

Addressing Research Needs in the Field of Plant Virus Ecology by Defining Knowledge Gaps and Developing Wild Dicot Study Systems — Proposes natural plant systems for studying virus transmission, host range, community ecology and environmental interactions.

| Various authors | Frontiers in Microbiology | 2018

Addressing Research Needs in the Field of Plant Virus Ecology by Defining Knowledge Gaps and Developing Wild Dicot Study Systems — Develops new wild-plant model systems for studying asymptomatic viral infection outside agriculture.

| Various authors | Springer | 2016

Plant Virus Diversity and Evolution — Reviews the extraordinary diversity and evolutionary mechanisms of plant viruses and the ecological conditions influencing their emergence.

| Jean-Michel Hily et al. | New Phytologist | 2015-09-14

Environment and host genotype determine the outcome of a plant-virus interaction: from antagonism to mutualism — Demonstrates that the same virus can harm or benefit its plant host depending on genotype and environmental conditions.

| Marilyn J. Roossinck | Virology | 2015-05

Plants, viruses and the environment: Ecology and mutualism — Describes plant-virus relationships as a continuum from pathogenic to neutral or beneficial and highlights the importance of environmental context.

| Marilyn J. Roossinck and Fernando García-Arenal | Current Opinion in Virology | 2015-01-29

Ecosystem simplification, biodiversity loss and plant virus emergence — Examines how agricultural expansion, biodiversity loss and ecosystem simplification can influence the movement of viruses between wild and cultivated plants.

| Marilyn J. Roossinck | Annual Review of Genetics | 2012

Plant Virus Metagenomics: Biodiversity and Ecology — Shows how metagenomic methods have revealed extensive plant-virus diversity, particularly among apparently healthy wild plants.

| Cecile M. Malmstrom et al. | Virus Research | 2011-08

The expanding field of plant virus ecology: Historical foundations, knowledge gaps, and research directions — Argues for studying viruses as ecological participants in wild plant communities rather than viewing them solely as agricultural pathogens.

| Wren et al. | PLOS Biology | 2006

Plant Virus Biodiversity and Ecology — Explores the poorly understood diversity of viruses in wild plants and argues for an ecological perspective beyond crop disease.

| Various authors | Advances in Virus Research | 2006

Wild Plants and Viruses: Under-Investigated Ecosystems — Reviews evidence that wild plants support complex viral communities that differ substantially from the crop-centered picture of plant virology.

Mycoviruses and Viruses of Fungi

| Glenda Coromoto Velasquez Serra and Patricia Elizabeth Molleda | Viruses | 2026-02-28

Mycoviruses: Environmental Variables, Vector-Mediated Transmission and Use as a Biocontrol — Examines how environmental conditions and transmission processes shape mycovirus ecology and discusses their potential for biological control.

| Mingde Wu and Guoqing Li | Virology | 2025-05-06

Mycoviruses and their ecological impacts on fungi — Reviews the diversity of viruses infecting fungi and their effects on fungal fitness, pathogenicity, community interactions and ecosystem processes.

| Matteo Galli et al. | Journal of Plant Diseases and Protection | 2024-12-19

A biocontrol perspective on mycoviruses in fungal pathogen management — Reviews how naturally occurring fungal viruses that reduce or alter fungal virulence could be used in environmentally compatible disease management.

| Jiatao Xie and Daohong Jiang | Annual Review of Microbiology | 2024

Understanding the Diversity, Evolution, Ecology, and Applications of Mycoviruses — Synthesizes rapidly expanding knowledge about fungal viruses, their evolutionary origins, ecological effects and potential applications.

| Bianca Hough et al. | Viruses | 2023-05-19

Fungal Viruses Unveiled: A Comprehensive Review of Mycoviruses — Reviews known mycovirus groups, detection methods, interactions with fungi and implications for fungal ecology and disease.

| Lingling Zhou et al. | The ISME Journal | 2021-02-02

A mycovirus modulates the endophytic and pathogenic traits of a plant associated fungus — Shows that viral infection can transform a pathogenic fungus into a nonpathogenic endophyte and indirectly protect its plant host.

| Abu Bakar Siddique | Virus Genes | 2020-05-09

Viruses of endophytic and pathogenic forest fungi — Reviews mycoviruses associated with forest fungi and their possible roles in endophytism, pathogenicity, evolution and forest disease.

| Various authors | FEMS Microbiology Ecology | 2019-07-31

Viruses of fungi and oomycetes in the soil environment — Examines viruses infecting soil fungi and oomycetes and considers their influence on belowground microbial communities and plant-associated disease.

Giant Viruses, Polar Regions, and Permafrost

| Various authors | FEMS Microbiology Ecology | 2026-06-08

Giant viruses of the polar regions: diversity, endemism, adaptation and ecological structuring — Examines how extreme polar conditions structure giant-virus communities and may foster distinctive evolutionary adaptations and endemic lineages.

| Tressy Bosmon, Chantal Abergel and Jean-Michel Claverie | npj Viruses | 2025-02-11

20 years of research on giant viruses — Reviews two decades of discoveries that transformed concepts of viral genome size, complexity, evolution and host interactions.

| Rachel Mackelprang et al. | mSystems | 2025-01-08

Cooling perspectives on the risk of pathogenic viruses from thawing permafrost — Places concerns about ancient permafrost viruses in ecological and epidemiological context while identifying genuine research uncertainties.

| Various authors | Ecological Genetics and Genomics | 2023-12

The Tiny Giants: Overview of Giant Viruses — Provides an overview of giant-virus taxonomy, genome complexity, evolution, host range and ecological significance.

| Jean-Michel Claverie et al. | Viruses | 2023

An Update on Eukaryotic Viruses Revived from Ancient Permafrost — Reports the isolation of infectious viruses from ancient permafrost and discusses what their survival reveals about viral persistence.

| Sofia Rigou et al. | Nature Communications | 2022-10-07

Past and present giant viruses diversity explored through permafrost metagenomics — Uses permafrost DNA to compare ancient and modern giant-virus diversity and investigate long-term evolutionary persistence.

| Frederik Schulz, Chantal Abergel and Tanja Woyke | Nature Reviews Microbiology | 2022-07-28

Giant virus biology and diversity in the era of genome-resolved metagenomics — Reviews how environmental sequencing has radically expanded the known diversity, evolution and ecological distribution of giant viruses.

| Various authors | Viruses | 2019-05

Giant Viruses—Big Surprises — Reviews unexpected aspects of giant-virus genomes, replication systems, evolution and interactions with microbial eukaryotes.

| Philippe Colson et al. | Nature Reviews Microbiology | 2017-04-01

Mimivirus: leading the way in the discovery of giant viruses of amoebae — Reviews the discovery and biology of Mimivirus and the broader revolution it triggered in understanding giant viruses.

| Various authors | Current Opinion in Virology | 2011-07

Giant viruses in the environment: their origins and evolution — Discusses environmental giant-virus diversity and competing ideas about their evolutionary origins and relationships with cellular organisms.

Giant, Algal, and Coral-Associated Viruses

| Mengjie Wu et al. | npj Biofilms and Microbiomes | 2026-02-27

Unveiling the hidden viral biodiversity and potential ecological functions with global coral holobiont virome database — A global coral-virus catalog identifies tens of thousands of viral populations and extensive predicted contributions to nutrient cycling.

| Various authors | The ISME Journal | 2026

Strain-level diversity of giant viruses infecting chlorarachniophyte algae in the subtropical North Pacific — Characterizes closely related giant-virus strains and shows how gene content and DNA methylation differ among natural marine isolates.

| Amir Fromm et al. | Nature Microbiology | 2024-04-11

Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment — Directly links actively infecting giant viruses with individual protist hosts in natural plankton communities.

| Various authors | The ISME Journal | 2024-03-07

Cell-to-cell heterogeneity drives host–virus coexistence in a bloom-forming alga — Shows that variation in susceptibility among individual Emiliania huxleyi cells allows algae and their lytic viruses to coexist.

| Zhenqi Wu et al. | Viruses | 2023-07-20

Diversity, Relationship, and Distribution of Virophages and Large Algal Viruses in Global Ocean Viromes — Finds numerous virophages and giant algal viruses distributed across the oceans and evidence for complex virus–virus–host relationships.

| Various authors | The ISME Journal | 2021

Ecological significance of extracellular vesicles in modulating host-virus interactions during algal blooms — Shows that vesicles released by algae can enhance viral infection and alter broader microbial-food-web dynamics during blooms.

| Mohammad Moniruzzaman et al. | Nature | 2020

Giant virus diversity and host interactions through global metagenomics — Reconstructs more than 2,000 giant-virus genomes and greatly expands their known ecological, genomic and functional diversity across Earth's biomes.

| Various authors | Nature Communications | 2020

Temperate infection in a virus–host system previously known for virulent dynamics — Reveals that the famous Emiliania huxleyi-virus system can exhibit temperate-like behavior rather than being exclusively lytic.

| Various authors | Frontiers in Microbiology | 2020

Coral-Associated Viral Assemblages From the Central Red Sea Align With Host Species and Contribute to Holobiont Genetic Diversity — Finds that coral species and life-history traits strongly structure associated viral communities in the Red Sea.

| Various authors | Frontiers in Microbiology | 2017

Phage and Nucleocytoplasmic Large Viral Sequences Dominate Coral Viromes from the Arabian Gulf — Surveys corals exposed to extreme temperature fluctuations and finds diverse bacteriophages and giant-virus relatives within their viromes.

Viruses in Extreme Environments

| Marguerite V. Langwig et al. | Nature Communications | 2025-05-01

Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems — Nearly 50,000 viruses from hydrothermal vents reveal strong geographic endemism and links between viral communities, vent chemistry and microbial hosts.

| Various authors | mSystems | 2025

Giant viruses specific to deep oceans show persistent presence and activity — Identifies giant-virus lineages repeatedly active in mesopelagic waters and possessing genetic traits associated with survival in dark, nutrient-limited oceans.

| Laura Perini et al. | Microbiome | 2024

Giant viral signatures on the Greenland ice sheet — Detects active giant viruses in snow, ice and algal communities, suggesting viral predation may influence microbial and algal blooms on the ice sheet.

| Various authors | Nature Communications | 2023

Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles — Finds active and locally adapted viruses beneath the Ross Ice Shelf with potential effects on microbial metabolism and nutrient processing.

| Various authors | The ISME Journal | 2020

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat — Single-cell genomics reveals highly localized virus-host relationships and evidence that lysogeny dominates in dense hot-spring microbial mats.

| Various authors | Frontiers in Microbiology | 2018

Bacterial and Archaeal Viruses of Himalayan Hot Springs at Manikaran Modulate Host Genomes — Reconstructs dozens of bacteriophage and archaeal virus genomes from high-temperature Himalayan microbial mats and sediments.

| Various authors | Viruses | 2017-11

Diversity of dsDNA Viruses in a South African Hot Spring Assessed by Metagenomics and Microscopy — Finds a highly novel assemblage of tailed, pleomorphic and archaeal-like viruses in an African thermal spring.

| Various authors | SpringerPlus | 2015

Diversity of putative archaeal RNA viruses in metagenomic datasets of a Yellowstone acidic hot spring — Expands the diversity of putative archaeal RNA viruses and identifies multiple evolutionary lineages within Yellowstone thermal systems.

| Luis E. Servín-Garcidueñas et al. | Genome Announcements | 2013-04-25

Genome Sequence of a Novel Archaeal Fusellovirus Assembled from the Metagenome of a Mexican Hot Spring — Reconstructs a previously unknown archaeal virus directly from a Mexican geothermal microbial community.

| Roberto A. Bolduc et al. | Journal of Virology | 2012

Identification of Novel Positive-Strand RNA Viruses by Metagenomic Analysis of Archaea-Dominated Yellowstone Hot Springs — Reports unusual RNA virus sequences from acidic Yellowstone hot springs dominated by archaeal microorganisms.

Phage Ecology, Viral Life Strategies, and Virus–Host Coevolution

| Cody Martin et al. | Nature Microbiology | 2025-08-27

A call for caution in the biological interpretation of viral auxiliary metabolic genes — Explains why predicted viral metabolic genes require careful validation before conclusions are drawn about their ecological functions.

| Various authors | Science of the Total Environment | 2025-01-10

To kill or to piggyback: Switching of viral lysis-lysogeny strategies depending on host dynamics — Experimental marine communities show viruses shifting between lytic and lysogenic strategies as bacterial abundance and diversity change.

| Kathryn M. Kauffman et al. | Nature Communications | 2022-01-18

Resolving the structure of phage–bacteria interactions in the context of natural diversity — Large-scale sampling of marine Vibrio and their phages reveals highly specific infection networks and strong strain-level structuring in natural communities.

| Shan-Hui Li et al. | Microbiome | 2022

Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts — Finds that lytic and temperate viruses carry systematically different metabolic genes and may alter environmental nutrient cycles in different ways.

| Michael Blazanin and Paul E. Turner | The ISME Journal | 2021-06-14

Community context matters for bacteria-phage ecology and evolution — Reviews how surrounding microbial species alter phage–bacterium interactions, showing that viral ecology cannot always be understood from isolated host-phage pairs.

| Leandro D. Guerrero et al. | The ISME Journal | 2020-10-16

Long-run bacteria-phage coexistence dynamics under natural habitat conditions in an environmental biotechnology system — A three-year metagenomic time series tracks continuous coevolution between Gordonia bacteria and their phages in a complex microbial ecosystem.

| Joshua S. Weitz et al. | Nature | 2017-09-21

Lysis, lysogeny and virus–microbe ratios — Reexamines evidence behind Piggyback-the-Winner and illustrates continuing debate about how viral lifestyles change with microbial abundance.

| Cynthia B. Silveira and Forest L. Rohwer | npj Biofilms and Microbiomes | 2016-07-06

Piggyback-the-Winner in host-associated microbial communities — Develops an ecological model in which temperate phages can benefit abundant bacterial hosts through stable lysogenic relationships.

| Ben Knowles et al. | Nature | 2016-03-24

Lytic to temperate switching of viral communities — Proposes the influential Piggyback-the-Winner model in which lysogeny becomes increasingly important where microbial hosts are abundant.

| Harald Brüssow and Richard W. Hendrix | Journal of Bacteriology | 2004-06

Phage-Host Interaction: an Ecological Perspective — A foundational ecological treatment of phage abundance, host encounter rates, survival strategies and the integration of phages into complex biological communities.

Pollinator, Mosquito, Tick, and Insect Viromes

| Vincent Doublet et al. | Nature Communications | 2025-03-05

Host ecology and phylogeny shape the temporal dynamics of social bee viromes — Shows that bee evolutionary relationships, seasonal timing and shared plant resources all influence viral communities among pollinators.

| Various authors | Science of the Total Environment | 2024-10-10

Landscape structure affects temporal dynamics in the bumble bee virome: Landscape heterogeneity supports colony resilience — Finds that more diverse and connected habitats are associated with reduced viral richness or viral load in field-deployed bumblebee colonies.

| Various authors | Molecular Ecology | 2024

Host species and geography impact bee-associated RNA virus communities with evidence for isolation by distance in viral populations — Wild bee species harbor distinctive viromes structured by host identity and geographic separation.

| Various authors | mSystems | 2024

Discovery and characterization of novel DNA viruses in Apis mellifera: expanding the honey bee virome through metagenomic analysis — Identifies previously unknown large DNA viruses associated with honey bees using genome-binning methods.

| Various authors | Nature Ecology & Evolution | 2024

Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity — Analysis of more than 2,400 mosquitoes finds hundreds of viral species and strong effects of mosquito phylogeny on virome composition.

| Various authors | Virus Evolution | 2023

Composition and global distribution of the mosquito virome — Integrates two decades of research on insect-specific viruses from Aedes, Culex and Anopheles mosquitoes around the world.

| Dominika Kadlečková et al. | mSystems | 2022-05-09

The Virome of Healthy Honey Bee Colonies: Ubiquitous Occurrence of Known and New Viruses in Bee Populations — Demonstrates that apparently healthy colonies carry complex mixtures of bee, plant and bacterial viruses.

| Nannan Li et al. | Viruses | 2022-01-24

Virome Analysis Reveals Diverse and Divergent RNA Viruses in Wild Insect Pollinators in Beijing, China — Sequencing of 50 wild pollinator species discovers dozens of known and novel RNA viruses across multiple insect orders.

| Various authors | Virus Evolution | 2022

Defining virus-carrier networks that shape the composition of the mosquito core virome of a local ecosystem — Maps a complex network linking mosquito species and viruses and demonstrates a relatively stable core virome within a local community.

| Various authors | Virus Evolution | 2021

Tick virome diversity in Hubei Province, China, and the influence of host ecology — Finds that tick species, host animal and feeding status help determine which viruses occur in natural tick populations.

Wildlife and Vertebrate Viromes

| Hao Zhou et al. | npj Biofilms and Microbiomes | 2026-05-09

Virome diversity, evolution, transmission networks, and zoonotic potential of wildlife on the Qinghai-Tibet plateau — Surveys viral diversity across high-altitude wildlife and reconstructs ecological and evolutionary connections among hosts and viruses.

| Various authors | Nature Reviews Microbiology | 2026

Tick-borne viruses: discovery, clinical aspects, influencing factors and control — Reviews the rapidly expanding tick virome and how climate, wildlife hosts, geography and human activity influence viral emergence and distribution.

| Various authors | Viruses | 2025

Characterizing the Bat Virome of Vietnam: A Systematic Review of Viral Diversity and Zoonotic Potential — Synthesizes research on viruses identified in Vietnamese bats while highlighting major geographic and taxonomic sampling gaps.

| Various authors | Publication not listed | 2025

Viral ecology in chiroptera: human-wildlife interactions and pandemic risk — Reviews bat viral ecology with emphasis on how habitat change and human-wildlife contact affect opportunities for viral transmission.

| Various authors | Nature Microbiology | 2024

A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics — Uses thousands of bat metagenomes to examine global RNA-virus diversity and the ecological factors structuring viral circulation.

| Various authors | Viruses | 2024

Unveiling the Virome of Wild Birds: Exploring CRESS-DNA Viral Dark Matter — Sampling thousands of wild birds reveals extensive circular DNA virus diversity, including numerous previously undescribed lineages.

| Various authors | Journal of Virology | 2024

Diversity, evolution, and emergence of fish viruses — Reviews wild fish as powerful systems for understanding ancient virus-host coevolution and the ecological origins of emerging aquatic diseases.

| Various authors | Nature Communications | 2024

Eco-evolutionary dynamics of gut phageome in wild gibbons with seasonal diet variations — Fifteen months of observations show that seasonal feeding changes restructure phage communities and their bacterial hosts in wild primates.

| Various authors | Viruses | 2023

The Virome of Bats Inhabiting Brazilian Biomes: Knowledge Gaps and Biases towards Zoonotic Viruses — Reviews virus research across Brazil's bat-rich ecosystems and argues that pathogen-focused sampling captures only a fraction of natural bat virome diversity.

| Yunyi Kong et al. | Microbiology Spectrum | 2022-10-10

Metatranscriptomics Reveals the Diversity of the Tick Virome in Northwest China — Finds numerous RNA virus lineages within wild ticks and illustrates how metatranscriptomics is transforming knowledge of arthropod viral biodiversity.

| Various authors | Publication not listed | 2022

Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses — Metagenomic sampling reveals diverse viruses in wild and captive birds and illustrates the complexity of avian viral communities.

| Manuel Ruiz-Aravena et al. | Nature Reviews Microbiology | 2021-11-19

Ecology, evolution and spillover of coronaviruses from bats — Connects coronavirus evolution and transmission with bat ecology, geographic distribution, host diversity and human environmental pressures.

| Chee Wah Tan et al. | Current Opinion in Virology | 2021-08

Bat virome research: the past, the present and the future — Surveys advances in bat-virus discovery and discusses how ecological sampling can improve understanding of viral diversity and host relationships.

| Jemma L. Geoghegan et al. | Virus Evolution | 2021

Virome composition in marine fish revealed by meta-transcriptomics — Surveys wild-caught marine fish and finds viral diversity shaped by host evolutionary history, habitat depth, temperature and social behavior.

| Various authors | Microbial Genomics | 2020

Towards an understanding of the avian virome — Reviews viral communities in wild and domestic birds and calls for ecological sampling designs capable of explaining why avian viromes differ among populations.

| Various authors | Nature Reviews Microbiology | 2020

Bat-borne virus diversity, spillover and emergence — Reviews the diversity of viruses associated with bats and the ecological processes that influence cross-species transmission and emergence.

| Kurt J. Vandegrift and Amit Kapoor | Viruses | 2019-06-07

The Ecology of New Constituents of the Tick Virome and Their Relevance to Public Health — Reviews newly discovered tick viruses and emphasizes geography, climate, host movements and ecosystem change as drivers of viral diversity.

| Michelle Wille et al. | Molecular Ecology | 2018-11-22

Virus–virus interactions and host ecology are associated with RNA virome structure in wild birds — Reveals numerous previously unknown avian viruses and shows that geography, host ecology and viral coinfection can structure bird viromes.

| Jemma L. Geoghegan et al. | Journal of Virology | 2018

Hidden diversity and evolution of viruses in market fish — Meta-transcriptomics uncovers a broad range of previously unknown fish viruses and investigates the roles of host density and cross-species transmission.

| David T. S. Hayman | Annual Review of Virology | 2016

Bats as Viral Reservoirs — Reviews the ecology, physiology and population biology underlying the remarkable diversity of viruses detected in bats.