100 Million Bacteria And Other Apple Microbiome Tales

The best season is upon us. The time of vibrant foliage, pumpkins, apples… and all the microbes that come with that. When it comes to the intersection of food and microbiology, we typically think of fermented foods (ex: sourdough, yogurt, kombucha, etc.). But plants naturally have their own microbes associated with them too. Today, we’ll take a look at apples and their microbial friends.

Here’s 100 Million Bacteria With That Apple

If you enjoy picking apples, what you might not realize is that with every apple you’ve added to your bag, you’ve also harvested 100 million bacteria.

Birgit Wassermann, Henry Müller, and Gabriele Berg from the Graz University of Technology calculated this number in their study of bacteria in different parts of the apple.

They tore apart apples splitting away stems, peels, pump, seeds, and calyx from each other. They then examined microbes present in each of the samples by sequencing the DNA in the samples and visualizing the bacteria by fluorescence microscopy. The fruit pulp and seeds contained the most microbes. The apple peel contained the least. Surprised? 

Microbes in Conventional vs. Organic Apples

Although the number of total bacteria per apple were similar between conventional and organic apples, the types of bacteria from each were different. Escherichia and Shigella were found in most conventional apples, though at low quantities. These microbes weren’t present in organic apples. Lactobacilli, a probiotic, was a dominant type of bacteria found in organic apples tested.

Methylobacterium, which has been reported to enhance the biosynthesis of strawberry flavor compounds, was much more abundant in organic apples, especially in the peel and fruit pulp samples.

The Apple Microbiome Changes After Harvest and Storage

The above study used apples that were stored for a short time at 1-2°C and 1.5-2% carbon dioxide, but apples that make their way into our grocery stores are often stored for months or even a year before they are consumed. These apples sit under a controlled atmosphere, where temperature, humidity, oxygen, and carbon dioxide levels are kept constant.

So what happens to the apple microbiome during this time?

In a research study earlier this year, scientists compared the microbiomes of apples stored under the controlled atmosphere to those stored with ambient gas concentrations. They found that the controlled atmosphere kept opportunistic pathogens, such as Penicillium and Botrytis, from growing on apple skins and also reduced the growth of the pathogenic fungi Neofabraea and Monilinia.

On the other hand, storing the apples under an ambient atmosphere increased the amount of all four pathogens.

The researchers also noticed that the controlled atmosphere also led to an increase in other fungi that could potentially be used to prevent pathogenic organisms from growing after harvest.

The Universal Apple Microbiome

For our last apple story today, we next travel all around the world to examine microbes from apples grown at different geographical locations. Not surprisingly, researchers from this study found that the composition of the apple microbiome depended on the geographical location. They also saw differences in the microbial composition in different parts of the apple and the fungal diversity varied significantly.

Despite these variations, the team was able to define a universal apple microbiome, microbes that are common in most apples from the study. Here are some highlights:

• Sphingomonas and Methylobacterium: These two genuses of bacteria produce the plant growth-promoting hormones gibberellin and indole acetic acid. The species of microbes within these genuses can distinguish between apples from different countries in this study.
• Aureobasidium: Aureobasidium is found on many plants and one species, Aureobasidium pullulans, has been shown to outcompete the fungi Penicillium and Botrytis that cause decay.
• Cladosporium: Cladosporium are commonly found in both living and dead plant material.
• Alternaria: Alternaria is a fungal pathogen that can cause internal rot.
• Vishniacozyma: This genus of yeast seems to be found in a lot of places: corn, glaciers, and soils. Honestly, I could not find much about this genus as it relates to apples.
• Filobasidium and Sporobolomyces: These yeasts have a protective effect on fruits and has been shown to prevent storage decay in apples

Why Study the Apple Microbiome

From the apple stories above, you can now see the importance of microbes when it comes to apples. Understanding the apple microbiome can help us monitor crop health, fight off plant pathogens, improve storage conditions, and optimize flavors of our favorite fall treat. Next time you go apple picking or bake that apple pie, think about all the microbes that your apples have encountered on their journey to you.

Further Reading

An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples? Frontiers in Microbiology. 2021.

Dynamics of the Apple Fruit Microbiome after Harvest and Implications for Fruit Quality. MDPI. 2021

Global Analysis of the Apple Fruit Microbiome: Are All Apples the Same? Environmental Microbiology. 2021.