Infauna selectively enhance DNA virus diversity and activity in marine sediments

This study demonstrates that sediment-dwelling infauna selectively enhance the abundance, diversity, and transcriptional activity of DNA viruses through bacterial-mediated mechanisms, thereby establishing infauna as a critical regulator of viral dynamics and biogeochemical cycling in marine benthic ecosystems.

The Gist

Imagine the ocean floor not as a quiet, empty desert, but as a bustling, chaotic city built inside the mud. In this city, the bacteria are the millions of tiny workers, the viruses are the invisible viruses that infect them, and the infauna (tiny worms, clams, and crustaceans living in the mud) are the construction crews and traffic controllers.

For a long time, scientists thought the viruses in the mud were just passive passengers, waiting for bacteria to show up so they could infect them. But this new study reveals that the construction crew (the infauna) is actually the architect of the viral world, and they have a very specific taste in tenants.

Here is the story of what happens when the worms get busy, explained simply:

1. The Construction Crew (Infauna)

Think of the infauna as a team of tiny bulldozers and gardeners living in the sediment. They burrow, eat, and pump water through the mud. This activity is called bioturbation.

• What they do: They mix the soil, bring fresh oxygen down, and stir up nutrients.
• The result: They turn a stagnant, muddy pile into a dynamic, high-energy neighborhood.

2. The Two Types of Tenants: DNA vs. RNA Viruses

The study looked at two very different types of viruses living in this mud city:

• DNA Viruses: These are mostly bacteriophages (viruses that only infect bacteria). They are like the "local delivery drivers" who only work with the tiny bacterial workers.
• RNA Viruses: These mostly infect larger creatures like fungi, protists, or small animals. They are like the "long-distance couriers" who deal with bigger, slower-moving targets.

3. The Big Discovery: The "DNA" Boom

When the researchers increased the number of worms (the construction crew) in their experiment, something fascinating happened:

• The DNA Virus Party: The number of DNA viruses exploded (tripling in some cases!). Their diversity went up, and they became much more active.

  • Why? The worms stirred the mud, creating currents that forced the viruses and bacteria to bump into each other more often. It's like a crowded dance floor where the music is turned up; the viruses (dancers) and bacteria (partners) are forced to meet and interact.
  • The Shift: The viruses didn't just sit around; they switched from "sleep mode" (hiding inside bacteria) to "attack mode" (lytic cycle), actively replicating and bursting out of their hosts.

• The RNA Virus Silence: Meanwhile, the RNA viruses didn't care at all. Their numbers and activity stayed exactly the same.

  • Why? Their hosts (fungi and larger animals) are too big to be tossed around by the tiny worm currents. They aren't as sensitive to the "stirring" of the mud. The worms are busy shaking the small bacteria, but the larger animals are just sitting there, unaffected.

4. The "Engine" Analogy

The study found that it wasn't just about how many bacteria were there (the population size), but how active they were.

• The Old View: Viruses are like moths to a flame; if there are more bacteria (flames), there are more viruses (moths).
• The New View: The worms are the wind. They don't just create more flames; they fan the embers, making the bacteria work harder and move faster. This "wind" blows the viruses right into the bacteria's faces, triggering a viral explosion.

5. Why Does This Matter?

This is a game-changer for how we understand the ocean:

• The Carbon Cycle: When viruses burst bacteria, they release carbon and nutrients back into the water. By making the worms stir the mud, we are indirectly turning on the "virus switch," which speeds up how fast the ocean recycles nutrients.
• The Hidden Connection: We used to think of worms, bacteria, and viruses as separate groups. This study shows they are a three-way team. The worms change the environment, which wakes up the bacteria, which in turn wakes up the viruses.

The Bottom Line

The ocean floor is a complex machine. This study shows that the tiny worms living in the mud are the master switches. When they get busy digging and breathing, they selectively supercharge the DNA viruses that infect bacteria, turning a quiet mudflat into a viral factory. Meanwhile, the RNA viruses just watch from the sidelines, unaffected by the chaos.

It turns out that in the deep, dark mud, the worms are the ones calling the shots on who gets to party and who stays home.

Technical Summary

1. Problem Statement

Viruses are the most abundant biological entities in marine sediments, playing critical roles in microbial mortality, organic matter turnover, and biogeochemical cycling. While it is well-established that viral abundance is driven by "bottom-up" controls (host availability and productivity) and physicochemical factors (oxygen, organic matter), the influence of infauna (sediment-dwelling meiofauna and macrofauna) on viral communities remains largely unexplored.

Infauna are known "ecosystem engineers" that reshape sediment structure through bioturbation (burrowing, feeding, ventilation), altering microscale heterogeneity and microbial processes. However, it is unknown whether these physical disturbances selectively impact different viral groups. Specifically, the study addresses the gap in understanding how infaunal gradients affect DNA viruses (predominantly bacteriophages) versus RNA viruses (predominantly eukaryotic-infecting), given their distinct host associations and life-history traits.

2. Methodology

The study employed a combination of controlled infaunal gradient incubations and multi-omics approaches (metagenomics and metatranscriptomics).

• Experimental Design:
  • Location: Storfjärden Bay, Finland (brackish coastal sediment).
  • Treatments: Sediment cores were manipulated to create four distinct infaunal conditions (plus a baseline):
    1. LM: Low meiofauna abundance.
    2. HM: High meiofauna abundance.
    3. HMM: High meiofauna + Macrofauna (Macoma balthica).
    4. Baseline: Unmanipulated natural sediment.
  • Duration: 10-day incubation under controlled in-situ conditions (6.5°C, dark).
• Sampling & Sequencing:
  • Surface sediment (0–1 cm) was sampled for DNA and RNA extraction.
  • Metagenomics (DNA): Used to assess viral and bacterial abundance, diversity, and genomic potential.
  • Metatranscriptomics (RNA): Used to assess viral transcriptional activity (infection cycles) and bacterial metabolic activity.
• Bioinformatic Analysis:
  • Viral Identification: DNA viruses were identified via de novo assembly, binning (SemiBin2), and viral classification (PHAMB, CheckV). RNA viruses were identified via de novo assembly of metatranscriptomes, RdRp detection, and DeepVirFinder.
  • Quantification: Viral abundance was calculated using adjusted coverage depth (CoverM).
  • Activity Profiling: Genomes were classified as Lytic-active, Active unknown, or Inactive based on the expression of structural/lytic genes (e.g., holin, endolysin, capsid).
  • Statistical Modeling: Generalized Linear Models (GLMs) and PERMANOVA were used to determine drivers of viral community composition, comparing bacterial abundance (DNA) vs. bacterial activity (RNA) as predictors. Co-occurrence networks (SparCC) linked viruses to potential hosts.

3. Key Contributions

• Selective Viral Response: The study provides the first evidence that infauna selectively drive the dynamics of DNA viruses while leaving RNA viruses largely unaffected in terms of abundance and diversity.
• Mechanism of Action: It elucidates that infauna influence DNA viruses not just by increasing host numbers, but by enhancing virus-host encounter rates through physical mixing and pore-water flow, thereby shifting the balance toward lytic infection strategies.
• Integration of Viral Ecology: The work integrates viruses into the "faunal-microbial" framework, demonstrating that bioturbation is a critical, previously overlooked regulator of sedimentary viral ecosystems.

4. Key Results

A. DNA Viruses: Enhanced Abundance, Diversity, and Activity

• Abundance & Diversity: Under high infauna conditions (HM and HMM), DNA virus abundance increased 3-fold compared to low infauna (LM). Shannon diversity, Simpson diversity, and richness were also significantly higher.
• Community Composition: DNA viral communities clustered distinctly by infauna treatment (explaining 37% of variance). The dominant family, Peduoviridae (lysogenic dsDNA phages), increased significantly in abundance.
• Drivers: When using bacterial activity (metatranscriptomic proxy) as a predictor, infauna emerged as a significant driver of DNA virus abundance and composition. In contrast, bacterial abundance (metagenomic proxy) alone did not explain the variance as well as the combination of infauna and activity.
• Infection Cycle: High infauna conditions (HMM) correlated with a higher proportion of lytic-active viruses. Transcriptional profiling showed increased expression of viral replication and structural genes (head, tail, packaging) in high-infauna treatments, indicating active virion production.

B. RNA Viruses: No Quantitative Response

• Stability: Total RNA virus abundance, diversity, and richness showed no significant differences across infauna treatments.
• Composition: While minor compositional shifts occurred, no specific RNA viral taxa showed differential abundance.
• Drivers: RNA viruses correlated with abiotic factors (CH₄, DIC flux, O₂ consumption) and bacterial activity but were decoupled from the mechanical effects of infauna. This is attributed to their hosts (eukaryotes like protists/fungi) being larger, less mobile, and having slower population turnover rates compared to bacteria, making them less susceptible to short-term bioturbation-induced mixing.

C. Host Interactions and Mechanisms

• Co-occurrence: Network analysis linked DNA viruses (Peduoviridae, Zobellviridae) to specific bacterial genera (e.g., Gallionella, Desulfobulbus, Methylomonas).
• Bioturbation Effect: The study proposes that infauna create microscale heterogeneity (oxic-anoxic interfaces) and generate pore-water flows. This physical mixing increases the encounter rate between non-motile viruses and motile/small bacterial hosts, accelerating infection cycles and promoting the coexistence of lytic and temperate strategies.

5. Significance and Implications

• Ecological Framework: This study redefines sedimentary viral ecology by positioning infauna as a primary driver of DNA viral dynamics. It suggests that viral communities are not just passive responders to microbial density but are actively shaped by the physical engineering of the habitat.
• Biogeochemical Cycling: By promoting lytic cycles and increasing viral turnover of bacteria, infauna-mediated viral activity likely accelerates the release of dissolved organic matter (the "viral shunt") and influences nutrient cycling (C, N, P) in coastal sediments.
• Evolutionary Pressure: The increased encounter rates driven by bioturbation may intensify virus-host coevolution and horizontal gene transfer (via AMGs), further shaping microbial community resilience and function.
• Future Directions: The findings suggest that models of benthic biogeochemistry must account for the "fauna-virus-microbe" triad, particularly in how physical disturbance regulates the speed and intensity of microbial mortality.

In conclusion, the paper demonstrates that infauna act as a selective filter and amplifier for DNA viruses in marine sediments, driving a shift toward higher diversity and lytic activity through physical mixing, while RNA viruses remain decoupled from these specific bioturbation effects due to host size and temporal dynamics.