Part 2: What is microbial diversity and why does it matter?

With help from Steve Churchill -Urban Worm Co


The first part of the title, “What is microbial diversity?” is a bit easier to get handle on. Biodiversity is the measure of “the variety of life in the world or in a particular habitat or ecosystem.” This type of diversity is a part of the broad field of Ecology, which studies how living organisms interact with one another and their physical environment. Diversity is measured in different ways, but the driving measurement is looking at the number of different species in an area. Microbial diversity at heart is no different, however, the main issue in the past has been we’re are unable to easily distinguish microbial species by eye (even with a microscope). The advent of molecular biology and the recent development of DNA sequencing has given us a new way to differentiate between organisms which were too small to distinguish by eye. This new way of observing species is done by the comparison of “universal” bio-marker genes as we discussed in the previous blog post.


How can we start to understand this new found diversity?


Lets start by looking at diversity with environments we are more familiar with.


Rain Forest Boreal Forest

https://www.britannica.com/science/rainforest#/media/1/939108/3445


Dr. Shade, a career soil ecologist, uses the example of rain forests and boreal forests and asks is a rain forest healthier than a boreal forest just because it is more diverse? Not really, they are two very different climates, soil types, histories, so it wouldn't make sense for them to have the same level of diversity. Additionally, scientists tend to think that using high or low diversity as an explanation of an outcome (ex. disease resistance) is masking more complex interactions that would be beneficial to understand at a deeper level. This concepts is but very well by Dr. Shade herself:

“Alas, diversity is not good or bad, it simply ‘is’… Diversity is the outcome of ecological processes and not an ecological process in itself.” – Dr. Ashley Shade

Her paper on diversity is here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5421358/



How to use diversity as a meaningful metric is question that microbial ecologists and environmental engineers have been struggling with. Lets take our forest example and see if we can come up with a way to make diversity useful. Lets go back to our "peer group" to give us context: If we compare the biodiversity of a similar group of boreal forests of a large enough size we could look for boreal forests with outlying diversify measurements. We then need investigate those outliers further to understand why they are lacking or have greater diversity. Lack of diversity is not an explanation in and of itself but likely a symptom of a deeper issue. As ecologists, engineers, or scientists, we need to understand the system and fix the underlying issue.


Lets talk about vermicompost diversity in particular


You might be asking yourself, “I thought higher diversity is generally good thing for soil health.” I think that can be a true statement, but you need to be able to justify why that is true. There has already been a lot of academic microbial ecology studies done on soils, but much less in context of plant/soil health.


Vermicompost and vermiteas are generally used as a microbial inoculant to restore natural nutrient cycling in the soil and form symbiotic relationships with plants. These interactions are still not well understood and might vary based on plant or soil type. However, one might argue that having a higher diversity inoculant has a higher chance to contain organisms or enzymes that benefit plant nutrient uptake. One could also argue that cycling nutrients in the soil requires a broad diversity of organisms to work together to break down complex molecules to simpler ones that can be utilized by plants. No one organism can do everything, it takes a community.


How can we start to prove diversity matters?


If you can do an experiments with different vermicomposts with varying diversity levels and show it improves or changes an outcome; I think it a good start to justifying that higher diversity vermicompost is expected to improve results. However, we cannot dismiss that the underlying conditions that create this increase in diversity might also be inherently better for the plant. From a decision making standpoint, this doesn't really matter as long as diversity correlates with outcome.


The truth is we really don’t fully understand mechanistically why higher diversity typically relates to better soil health. There are some really neat ideas about community resilience, food webs, nutrient cycling, that all relate back to diversity that I hope to highlight later. I am also interested in your thoughts on this because this topic isn’t really my area of expertise.

Ultimately habitat drives diversity

Let's take an extreme example of trying to inoculate Mars with life. What do you think would work better a tropical rain forest inoculant or a desert sand inoculant?




In the case of Mars especially, an aspect to consider is the native habitat of the incoming inoculant community. How similar the original environment is to its destination habitat likely determines how suited the incoming life is the new environment. The increased diversity of a rain forest might have a better chance to contain life that would be viable on Mars, however most or all of that life might die. Because the Mars environment isn’t anything like a rain forest, perhaps inoculating it with a much less diverse environment like a desert might be more effective. In some cases we might need very rare metabolisms that only exist in similar rare environments… but I think this is an extreme case. These types of questions about inoculating soil and it’s relationship to plants don’t really have solid answers yet, but is an area that will hopefully receive considerable attention in the near future.


I guess the point I want to emphasize is that microbial ecology is much more than just seeing who is there measuring diversity, it’s about understanding what pressures are driving diversity. From an environmental engineering perspective, it’s also about how can we use these pressures to manipulate a microbial community to produce a desired outcome.


I hope you enjoyed this post and it has given you a slightly new perspective on diversity. if you have any questions please feel free to comment below or email me directly. If you enjoyed this topic, I would also try to give Dr. Shade’s article a read.


Soil Diversity Resources:

  1. State of knowledge of soil biodiversity - Status, challenges and potentialities

  2. ATTRA Soils & Compost

  3. JOINT RESEARCH CENTRE EUROPEAN SOIL DATA CENTRE (ESDAC)


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