What microbes mean for agriculture

How do microbes help the environment? How can they revolutionize agriculture to help feed a growing world? We ask Jonathan Eisen, a leading researcher in the evolution and diversity of microbes and the role they play in the health of ecosystems.


Microbes are tiny organisms such as bacteria, fungi and algae that interact with plants, animals and soil. They’re so widespread that a single gram of soil contains around 10 billion bacteria, 10 million fungi and one billion viruses. Yet we’re only just beginning to understand what microbes do, how they impact the environment, and how they can be developed as biobased solutions for agriculture. Jonathan Eisen of the University of California, Davis, tells us more.

Novozymes: How do microbes help ecosystems?

Jonathan Eisen: A really important caveat is that microbes are not there to help, but they do play an important role in the health of ecosystems. In the past, we haven’t really understood their contributions to ecosystems. Now we know a lot more about the individual contributions of microbes but we don’t know how whole communities work and how they interact. 

For instance, in any ocean system the primary productivity – unless you’re near the coast – is mostly from microbes floating in the water. If you go to the bottom of the ocean, productivity is from chemosynthesis (the process by which organisms produce food by using chemical energy).

We know about the potential of microbes to revolutionize bioagriculture. Is it difficult to bring microbial-based solutions to farmers?

Eisen: The complexity of these systems is overwhelming. I don’t want to overplay the comparison to the tropical rainforest but there are probably thousands of different species of microbes on different parts of a single rice plant. There are different microbes in the leaves, stem, roots and the different parts of the roots. It’s amazing, but it’s a mess.

The microbes that are in a particular field site, that’s basically their planet. One little change in the pH (how acidic or alkaline a substance is), or the angle of the plant toward the sun, or the average temperature, or the predators, or the things pooping on the field, can change everything. I don’t find it surprising that we’re having a hard time manipulating those communities to have an effect. It’s unquestionably possible, but it’s going to be hard.

Is the agricultural community ready to embrace microbes?

Eisen: I think it is ready because farmers have appreciated for a long time that you can impact the diversity in your soil. Whether that’s by avoiding a monoculture, or whether that’s organic material added on to the field, many farmers have known for a long time that many of these things may have positive impacts. Those impacts may be coming from the microbiome.

Where do you see bioagriculture going in the years ahead?

Eisen: We know so little. I think that the big thing is going to be developing model systems, or large enough data sets, that we can actually infer the functional contributions of microbes to particular systems as opposed to retrospective analyses of hosts.

What a lot of people are doing now is observational correlation of microbial communities and particular traits in hosts. But how can we test the contribution of one microbe when there are ten thousand microbes in the system? What we’re moving toward is resonance experiments where we can actually test contributions of particular microbes.

What I think is coming next is combining studies of microbes and a study of hosts, with things like elemental tracking in a system. If we think that microbes in the soil around rice are affecting nitrogen, you should be able to track that. So, the future is field studies of functional properties in the environment in real time.

* Follow Jonathan Eisen on Twitter at @phylogenomics and at http://phylogenomics.wordpress.com

*Novozymes' microbial-based biocontrol and bioyield enhancer products work to naturally produce healthier crops and improve yields.

*Novozymes formed The BioAg Alliance with Monsanto in December 2013 to research, develop and commercialize sustainable biological solutions that use naturally derived microbial technology to significantly increase the productivity of the world’s crops.