The reign of viruses in acid mine drainage


Breaking down the microbiology world one bite at a time

The reign of viruses in acid mine drainage

Did you know that mining contributes to at least 40% of water pollution? In 2013, Earthworks published “Polluting the Future” highlighting the staggeringly high amount of water (e.g., 16.7-16.9 billion gallons a year in the US) polluted by mining only. A considerably huge source of water pollution, isn’t it? Now imagine the cost needed to treat it, if it is even considered in the first place…. It is indeed a heavy-handed task. This is why this article involving mine drainage is important to us. But let’s start with: what is it?

Such water pollution is attributed to mining activity as mine drainage, and it is of essentially three types

  1. Acidic: water is highly acidic (pH 3) and rich in heavy metals.
  2. Alkaline: occurs when calcite or dolomite is majorly present.
  3. Metal: when high levels of lead or other metals drain from these abandoned mines into the water source.

Considering the huge environmental and economic impact among other factors, this article focuses on acidic mine drainage (AMD) and its dynamic microbial ecosystem; and more particularly, how viruses with environmental factors regulate the assembly of microbial communities in AMD. 

Image 1: Acid mine drainage (AMD) at Ohio Valley Mushroom Farm Site in North Lima, USA. Image source:

Why Viruses in Acid Mine Drainage systems?

Though less studied than other forms of life in AMD, viruses are instrumental in influencing the dynamics of this ecosystem that sustains life despite inhospitable high acidic conditions.

In a recent study by Zhenghua Liu and team (2023), 96% of the viruses were unable to be classified thus staying ambiguous. And yet, these unknown viruses were equally affected by pH and microbial richness as they intimately interacted with the microbes found within the AMD.

The prominence of viruses in host genomic evolution have also been emphasised from previous studies isolating microbes from AMD. For example, viral genes responsible for energy supply in low-nutrient environments were found in the  heterotrophic bacteria, Alicyclobacillus.

Image 2: The virus-host-environment interaction triangle. Image source: Shao-Ming Gao (2022)

Reigning under the influence of environmental factors

Viruses stabilise the ecosystem in many ways. At times they prey on microbial cells, especially the fast growers, and other times they sync with the host “heartily” helping the latter thrive. But they always ensure that they dwell in the system, no matter what.

Regulating microbial abundance can occur in two ways.

First, an increase in viruses in AMD does not always correspond to changes in microbial abundance; sometimes, though still ample, microbial load still remains stagnant despite an increase in viral content. This is seen in Acidiphilium.

However, in chemoautotrophs like Thermoplasmatota, there is a shift. The viral load increases with host abundance. Since viruses usually opt for a lysogenic cycle instead of lytic (more details on the cycles here), they are found in increasing density as the host cells become plentiful. At this point, viruses provide a competitive edge to dominant host species through viral genes and increased host abundance. This induced competition leads to selection of the fittest.

Moreover, viruses are cunning with the ultimate motto of “survival and multiplication only”. It is thus no wonder that they manipulate their hosts to control them; this is by inducing host competitiveness (extra food privilege to Sulfobacillus by sharing their secret gene), or aid them in environmental adaptation (generously donating a survival kit (gene) for the cell wall-less Cuniculiplasma to adapt to the acidic AMD) by reprogramming host metabolism through auxiliary metabolic genes (AMGs). 

In this barter system, hosts emerge as the best adaptable survivors in AMD while phages, for their part, prompt the hosts for extra energy consumption and a touch of additional metabolic burden on the microbial host cells to establish their sway.

Viruses shape the microbial community

Changes in species behaviour thanks to viral interference, can further reshape the community structure. While viruses influence the evolutionary trajectory and phylogeny of microbes, they at times even override environmental selection to stabilise the system.

This happens in AMD in copper mines, where viruses are on par with the environment in influencing the microbial community. But in AMD, with multiple metals (polymetallic), viruses overshadow even the environment when it comes to influencing microbial community assembly.

Image 3: Mechanisms through which viruses affect microbes in Acid Mine Drainage much more than environmental stressors. Image source: Original image by Tejaswini Petkar. Information source: Zhenghua Liu et al (2023). 

For the viruses to work their charm, the microbes must fall into the viruses’ host range and be susceptible to them. This is why viral predation on microbes is rather heterogeneous in nature and not homogenous (similar) within the AMD.

Hence, they can shape the community more prominently. Were viruses non-specific and encompassed a wide host range, viral predation would be considered homogenous, and then they would be governed by environmental factors as well. What a fine balance between being played and playing the game, right?

On an endnote…

Viruses in AMD are considerably still unknown, diverse, and even differ depending on the AMD, as seen in the case of copper and polymetallic mines. Despite this, they are quite clever little folks that exert immense power to shape the microbial circle — at times influenced by nature, or other times, even shadowing the environmental influence!
As for the scientists involved in the research, they did it! They completed the quest and found answers that unravelled the power dynamics among the players occurring in the inhospitable AMD, and it is obvious who the head honcho of this system clearly is:  the viruses!

Link to the original post:  Liu, Z., Huang, Y., Zhang, T., Meng, D., Jiang, Z., Yang, Z., … & Yin, H. (2023). Viruses Regulate Microbial Community Assembly Together with Environmental Factors in Acid Mine Drainage. Applied and Environmental Microbiology, e01973-22.

Featured image: Original image created by Tejaswini Petkar using  and