A Researcher's Voyage To A Core Coffee Microbiome

It’s the morning, so go grab yourself some coffee...and make it a double! I’ll take a cappuccino while you're up! Ah, well now that we are thoroughly caffeinated, let’s give those stimulated brain cells something to think about!

Just like you, plants depend on their microbial brethren to flourish and find success in life. Plant microbiomes are beautifully fascinating, and if you missed our last blog post, or prefer wine over coffee, check out that blog post here! It also includes a recipe.

Today, I’ll review the article published by Futhorpe et al. in Phytobiomes at the beginning of 2020. These Canadian researchers set out to determine if coffee plants share a core microbiome.

The microbiome is all the microbes that live on and within a specific thing like a body part or a plant. A core microbiome is looking at the shared microbes across a specific entity. In today’s example, the researchers set out to determine if coffee plants from Costa Rica share the same microbes as ones in Nicaragua. Microbes that exist in coffee in different geographical locations means a couple things: (i) the microbes are able to survive and thrive in the plant, likely this is their preferred place of residence, (ii) the plants are also OK with these neighbors and they may even be working together in a process known as symbiosis, (iii) if we can find microbes that naturally occur in a specific kind of crop across geographical locations and determine that its beneficial to plant health or crop yield, then researchers can develop new natural management strategies for their crop. This all adds up to more coffee!

So please, join me as we journey out of your quarantine houses and into the tropical lands of Costa Rica and Nicaragua. The sites of our Coffee Microbiomes.

The Study

Furhorpe et al. chose 4 different sites in Central America, one that was hot and dry, one that was hot and wet, one that's cool and wet, and one that was cool and dry. Hot meant being hotter than 18-21c (64.4- 69.8 F), which is the preferred temperature for Coffee plants. Likewise, dry meant being less than optimal precipitation, less than 2200mm (86 inches/year) of rain.

They looked at the microbes living inside the roots, which are much like our ‘guts’. In plants, microbes that live inside are called endophytes, endo- meaning internal and -phyte meaning plant. Microbial diversity and concentration are highest in the root tissues, while the above ground parts have lower diversity and fewer endophytes. They provide nutrients to the host in exchange for a nice protected house and some food. These researchers looked at both fungal and bacterial profiles of the microbiome. Bacteria and fungi are both grouped as 'microorganisms'. However, they are genetically very different and so need different methods to analyze.

A Note On Methods

There are many limitations to this and every study. Science is slow, arduous, and messy. It can be very expensive and not all methods are available to all researchers. I’m not saying don’t trust science, but it's not absolute. There’s always more to discover and more elusive endophytes to understand. Studying a microbiome is like studying all the people in NYC at once by a photograph of Times Square. You can see that the general layout consists of many structures, the movement of all the hustle and bustle and that there are a lot of people at any given moment. You get a very surface level image of the kinds of people that live there; you don't see all of the people that live there, and you can’t tell what they are doing or where they are going. This is what microbiome studies are like, a snapshot into a dynamic, ever-changing and diverse world of thousands of microbes.

So what did these researchers find? Is there a core microbiome to coffee?

Researchers found 26 bacterial genera and 11 fungal genera that they denoted as core. There is no universal definition of ‘core microbiome’, but researchers will generally claim a core microbiome based on the microbe's prevalence and abundance. Also note the word ‘genera’ the plural of genus. Genus is a pretty good level of classification rank for microbes; higher levels include species, subspecies and strains. But to give you an idea of the diversity this word covers, every human on earth belongs to the same ‘species’. Across humanity we have differences from the way we look to the way we think to our ambitions and motivations to how we love. This incomprehensible amount of beautiful diversity occurs at the species level even more specific than genus classification!

Fig. 2 from Fulthorpe et al. 2020 Phytobiomes

The core microbiome of coffee is actually quite similar to other plants that have been studied. Fulthorpe et al. found an abundance of arbuscular mycorrhizal fungi (genera: Glomus, Archaespora, Acaulospora). These fungi cozy up to roots of all sorts of plants. They create vast networks extending the reach of the roots, allowing them to access water and nutrients the roots couldn't reach on their own. However, without water, these little helpers will shrivel up and die, cutting off the plant's vast network to water.

As climates become warmer or drier, these beneficial organisms might disappear. Cladosporium was another fungal found abundantly within the coffee root microbiome. This fungus was first described as a pathogen. In more recent years, they have also been found to fight pathogens and promote plant health. See how diverse a genus can be!

On the bacterial side, we can see the same thing. Pantoea and Pseudomonas have been described both as disease-causing and health-promoting microbes. It just depends on the species both of the microbe and the host. Burkholderia and Enterobacter were also found abundantly within the coffee microbiome. They both are well-known plant growth-promoting genera.

So, that coffee you are drinking, no matter where it came from, probably grew with many of these same microbes. By understanding not only who is there, but what they are doing, we can harness this power to create stronger plants. Also, the microbial scale is a great place for understanding climate change. Changes that we perceive as minor, like a slight change in average temperature, could drastically shift the microbial function and composition - maybe even put our beloved coffee bean plants at risk! Microbes may play a role in not only understanding climate shifts, but also in coping with these changes.

Personally, I wonder how the microbial profile of a region influences the flavor of coffee. Coffee from Costa Rica doesn’t taste the same as coffee from Nicaragua, much like a Merlot from California is not that same from a Merlot from France.

Where's your favorite coffee from and how do you think the microbe contribute to the flavor? Tell me in a comment below!