Yes, microbes are likely important everywhere, but evidence would be nice (re Atlantic piece on Soil)

Just read this article in the Atlantic: Healthy Soil Bacteria, Healthy People - Mike Amaranthus & Bruce Allyn - The Atlantic.  It is interesting in a few ways.  But what got me a bit up in arms about it is the number of statements and claims that are not backed up by any reference to evidence.  Consider the following:

"Just as we have unwittingly destroyed vital microbes in the human gut through overuse of antibiotics and highly processed foods, we have recklessly devastated soil microbiota essential to plant health through overuse of certain chemical fertilizers, fungicides, herbicides, pesticides, failure to add sufficient organic matter (upon which they feed), and heavy tillage."

OK - sounds serious.  But is it really true?  Have pesticides really devastated soil microbiota?  What about tillage?  Seems possible, but also seems possible that this would not be true.  Would be nice to see the evidence behind this claim.

How about this one:

"Reintroducing the right bacteria and fungi to facilitate the dark fermentation process in depleted and sterile soils is analogous to eating yogurt (or taking those targeted probiotic "drugs of the future") to restore the right microbiota deep in your digestive tract."

Sounds good too.  But way too overly simplistic.  I mean - probiotics for people are a bit of a complicated mess right now.  Some work.  Most probably don't.  Most of the claims are overblown.  So to say we know how to do this well in "soil" definitely seems to be an overstatement.  Again, specific evidence for this would be nice.

And then this:

"Due to new genetic sequencing and production technologies, we have now come to a point where we can effectively and at low cost identify and grow key bacteria and the right species of fungi and apply them in large-scale agriculture."

Soil is a very very complicated place in terms of microbes.  I personally think we are really far away from this utopian view of growing the key species to apply them to large scale ag.  Evidence that this is true?  I don't know of much.  Yes we can sequence things.  We can sequence a lot of things.  But "identify and grow key bacteria and the right species of fungi" - I think we are far from being able to do this robustly.

Another claim in the article has some ring of truth:

We can sow the "seeds" of microorganisms with our crop seeds and, as hundreds of independent studies confirm, increase our crop yields and reduce the need for irrigation and chemical fertilizers.

Yes, this has a ring of truth.  Certainly there are studies - many of them - involving adding microbes to seeds and how that impacts yield and nutrient and water requirements.  And without a doubt in many cases such inoculation can help in many ways.  But the "hundreds of independent studies" claim is a bit misleading as there are also many cases where inoculation does not help.  So we should be cautious before adding microbes to seeds becomes the equivalent of probiotics for people.   Not all probiotics that are claimed to help people actually do anything.  And not all microbes added to seeds will do much of anything useful either.

How about the claim:

Thus the microbial community in the soil, like in the human biome, provides "invasion resistance" services to its symbiotic partner. We disturb this association at our peril

Sounds good.  And has a ring of truth too.  And in general I agree with the sentiment that we should not screw with ecosystems without recognizing that the microbes in those systems may play important and useful roles.  However, just because SOME microbes play important and useful roles in systems does not of course mean that ALL are ones we want to keep.  There will be some in the soil that damage plants and hurt yield and pathogen resistance just as there will be some that are "good" from our point of view.

And then there is this

We are now at a point where microbes that thrive in healthy soil have been largely rendered inactive or eliminated in most commercial agricultural lands; they are unable to do what they have done for hundreds of millions of years, to access, conserve, and cycle nutrients and water for plants and regulate the climate. 

And also

The mass destruction of soil microorganisms began with technological advances in the early twentieth century. 

Sounds nice.  But I don't really know of much evidence that the microbes have been rendered inactive or eliminated in commercial agricultural lands.

I suppose this is all building up to the following

Fortunately, there is now a strong business case for the reintroduction of soil microorganisms in both small farms and large-scale agribusiness. Scientific advances have now allowed us to take soil organisms from an eco-farming niche to mainstream agribusiness. We can replenish the soil and save billions of dollars.

and

For all these reasons, bio fertility products are now a $500 million industry and growing fast. The major agricultural chemical companies, like Bayer, BASF, Novozymes, Pioneer, and Syngenta are now actively selling, acquiring or developing these products.

So --- this is in a way an article promoting the financial benefit of adding microbes to soil.  I think this is reasonable although not completely convincing.  Alas, after reading the article I discovered this about one of the authors

Mike Amaranthus is the chief scientist at Mycorrhizal Applications, Inc., a company working on innovations in soil biology. 

This is not to say that someone with a financial role in convincing the world to add microbes to soil cannot be trusted to provide a good guide about microbes in the soil.  But it would have been nice for this to be mentioned more prominently in the article.  Many of the claims in this article do not pass the smell test to me.  And all of them seem to be pointing towards a solution involving a company that one of the authors is involved in.  If this were about human medical treatments many many people might get bent out of shape by this.  Again, not to say people with financial interests cannot write good articles.  But the potential for conflicts in such cases, as in the case here, is great.  And thus we should view with a tint of extra skepticism some of the claims made by such individuals.  And in this case here I already felt uncomfortable with many of the claims.  I think the Atlantic could do better and could certainly require the author to make more clear in the article itself  what the author's personal interest in the claims are.