Photo: Some unassuming soil in a forest but the foundation of ecosystems in every possible way. Pinegrove Park, Ottawa, ON, Canada.

This is a follow up to my last post where I wanted to go into more of the environmental microbiology of forest microbial communities and our current understanding of them. And again this seems really relevant to consider the health of our forests and natural spaces to properly manage wildfires as California is right now battling a massive wildfire yet again. This fire in Ventura County has already done extensive damage and claimed one life so far that we know of. It’s been reported that this fire is closing in on the cities of Ventura and Santa Paula now as well. This has me remembering how around a year and a half ago when all of Fort McMurray was evacuated and people of the town suffered severe losses as the fire spread through neighbourhoods.

There is a great importance to manage and be stewards of our wild spaces. The best solutions are fairly straight-forward have controlled burns, managed logging, as well as managed clearance of underbrush that’s done through a combination of government agencies like Canadian Forest Service and the B.C. Ministry of Forests, Lands, Natrual Resource Operations & Rural Development, as well as contracted independent organizations. At the level of individuals we can continue to support budgets approved for these agencies. But probably the theoretically easiest way to help is to be sure to pull our heads out of our asses and not flick butts, be vigilant on open fires, etc.

A way to also help manage is to better be able to assess the long-term health of our environment, our forests and grasslands. I’m stressing the importance of microbial communities here as these really are the foundation of our environments. And specifically, a high amount of biodiversity is key to having healthy environments.

Research into whole microbial communities of anything is still a new area to be investigating – forests, oceans, subterranean caves, our own intestines, it goes on. Advances in technology and only recently made it so scientists can start asking questions like “what’s every single species of microbe there in that soil?”

We were blown away by how much is there. The most prominent technology that we’ve used so far probe microbial diversity of environmental soils has been through sequencing the DNA (deoxyribonucleic acid, the genetic material) present as well as the RNA (ribonucleic acid, the more “business-end” of genetic codes). This brings up an important distinction that is made when studying microbial communities – the microbiota and the microbiome. What we know of our natural world is very much through and limited by our technology.

Through use of technology is how we experimentally investigate questions about the natural world and in a lot of instances there’s certain questions that we just don’t yet have the technology to be able to probe the world about, at best we’re limited in the view we actually get of what’s going on. This is why there’s a very well established distinction between the terms microbiota and the microbiome.

The microbiota refers to all the microbes that exist in a certain environment and make up the whole microbial community, all species populations represent. The microbiome is the entirety of genetic material in the microbial community, it’s the sequence data of the genomes (DNA) and/or transcriptomes (RNA) of all populations present in the microbial community. The use of “-ome” added to the end of a word refers to the whole thing of some species’ or population’s make up whether it be DNA (genome), RNA (transcriptome), protein (proteome), or nutrients/metabolites/organic compounds used and made (metabolome). So, when trying to ask that question, “what’s every single species of microbe there in that soil?” using sequencing technology what we directly learn about is the microbiome which gives us an idea of what the microbiota but we’re only directly looking at sequence data, not growing and looking at the microbes living in the environment.

When microbiomes of forest soils (or any environment for that matter) scientists were floored by the fact that there are massively greater numbers of species or more appropriately, taxa (or even more appropriately technical, operational taxonomic units – OTUs) that can be sequenced than what has ever been observed when growing or culturing forest soil samples in the lab. The discrepancy between sequencing and culturing was huge. Right away it was clear that vast majority of the natural microbial community of forests cannot be grown in the lab. This was then also telling us that we can’t recreate the conditions of the natural environment in forest soil. Attempts have certainly been made and progress achieved to culture more and more of the microbiota but microbiome data consistently shows that we’re not achieving 100%, there’s much more biodiversity present than we can cultivate.

Mimicking exactly the chemical compositions of the soils has provided minimal progress showing us that it’s really something about how microbes interact with each other that is key to creating that foundation of a healthy environment. This is what’s given us our biggest realization of how little we know – microbes interact with each other in ecosystems and we’re pretty clueless as to even how they do it. And that’s largely where we’re at with our understanding with microbial communities of forests, scientists have been working hard to get a view of the diversity of the microbiota through understanding the microbiome. So far it has been difficult to really learn what a healthy forest microbiota looks like, there’s a lot of variety depending on the specific forest that is studied. But through upsets and disasters like fires looking at the microbiome and how it changes has given us insight into how forests will rebound. And looking at regions where severe microbial disruption of a forest has led to a massive decrease of forest rebound and health such as under logging conditions that remove underbrush and top soil can at least start giving us an idea of what emerges in microbial communities when a forest is unhealthy – mostly it appears so far that a depletion and having a sustained lack of diversity that results after a major upset is what leads to long-term reduction in health and instability in a forest environment.

There’s still a lot of work to do still to gain the details of the microbial component of ecosystems to then really be able to understand what makes a healthy, sustainable system that’s not prone to things such as rampant fires, diminishing populations of all forms of life, and at worst collapse. But a definite trend it seems already is that healthy forests have rich microbial diversity that has accumulated over time. It’s also really important to note that these microbial community members have intricate relationships and inter-dependence that we’re just scratching the surface but is essential for a healthy environment. Though, for the immediate future we can keep practicing responsible management and have a heightened awareness of the impacts we have as our foundations for healthy forests in the long-run.

If anyone is curious about how to help victims of the current wildfire in California here’s a couple of links to reputable organizations directly supporting those affected by this wildfire.

The American Red Cross, California Fire Foundation, and keep an eye on GoFundMe as local initiatives for affected communities get started.

Also, here’s a sampling of the research out there investigating forest microbiomes:

DeAngelis KM, et al. 2015. Long-term forest soil warming alters microbial communities in temperate forest soils. Front Microbiol, 6:104.

Tian J, et al. 2015. Linkages between soil organic matter fractions and the microbial metabolic functional diversity within a broad-leaved Korean pine forest. Eur J Soil Biol, 66:57-64.

Wilhelm RC, et al. 2017. Biogeography and organic matter removal shape long-term effects of timber harvesting on forest soil microbial communities. ISME J, 11:2552-68.

Žifčáková L, et al. 2016. Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter. Environ Microbiol, 18:288-301.

Correction: Originally when posting this I stated that environment departments and Parks Canada being the government organizations that manage forests. They are in involved but it was brought to my attention that the Canadian Forest Service and the B.C. Ministry of Forests, Lands, Natrual Resource Operations & Rural Development are really the primary government organizations involved in monitoring and management of forests with regard to wildfires in this case.