Small Won­ders

Mi­cro­bial prod­ucts have the po­ten­tial to help farm­ers bet­ter man­age nu­tri­ents and slay pests. Im­prov­ing prod­uct con­sis­tency, though, is key.

Successful Farming - - CONTENTS - By Gil Gul­lick­son Ex­ec­u­tive Ed­i­tor, Crops Tech­nol­ogy Il­lus­tra­tions By Alex Fine

On the sur­face, a crop field seems as dull as, well, dirt. Un­der­neath it, though, is an in­vis­i­ble war that’s con­stantly be­ing waged. Soil mi­crobes (like bac­te­ria and fungi) con­tin­u­ally slug it out for food and dom­i­nance. Some of these mi­crobes are bad, but many are good since they aid in tasks like the trans­fer of crop nu­tri­ents or pest con­trol.

It’s into this fray that mi­cro­bial and bi­o­log­i­cal prod­ucts en­ter. At best, mi­crobes in­tro­duced to the soil as seed treat­ments or as liq­uid can play well with ex­ist­ing soil or­gan­isms and help crops bet­ter use nu­tri­ents or slay pests. Soy­bean farm­ers have long used in­oc­u­lants to jump-start ni­tro­gen-fix­ing rhi­zo­bia bac­te­ria in the soil.

At worst, these prod­ucts suf­fer from a “bugs in a jug” stigma of the days when sales­men sold them with a shoe shine, a smile, no sci­ence and no ben­e­fit.

“If you look back over the last 15, 20, 25 years at the evo­lu­tion of mi­cro­bial prod­ucts in agri­cul­ture, the road is lit­tered with ones that have come and gone. It’s not be­cause they never worked; it’s be­cause they gave in­con­sis­tent re­sults,” says Michael Mi­ille, CEO of Joyn Bio, a joint ven­ture formed ear­lier this year be­tween Bayer and Ginkgo Bioworks to de­velop prod­ucts to im­prove plant ni­tro­gen ef­fi­ciency.

“We want to get away from the image of the guy brew­ing some­thing in a bath­tub and sell­ing it to his neigh­bor,” says Ernie San­ders, vice pres­i­dent of prod­uct de­vel­op­ment for Pivot Bio. “It’s not how the chem­i­cal in­dus­try grew, it’s not how the biotech in­dus­try grew, and it’s not how the bi­o­log­i­cal in­dus­try will grow.”

step change

Mi­ille says the in­dus­try gained more cred­i­bil­ity ear­lier this decade, when large agri­cul­tural seed and chem­i­cal com­pa­nies bought small mi­cro­bial firms. Bayer bought AgraQuest in 2012. Later that year, BASF ac­quired Becker Un­der­wood and Syn­genta bought Pas­teuria Bio­science. Novozymes and Mon­santo – since pur­chased by Bayer – closed on the BioAg Al­liance in 2013. DuPont – now part of Corteva Agri­science – ac­quired Taxon Bio­sciences in 2015. “In Bayer’s case, I think it was con­cerned about the re­stric­tions on and the (po­ten­tial) loss of its chem­i­cal port­fo­lio,” says Mi­ille. “The com­pany saw bi­o­log­i­cals as an al­ter­na­tive so­lu­tion that could ei­ther com­ple­ment or, in some cases, help bol­ster its chem­i­cal port­fo­lio. I think Mon­santo

got into it with the BioAg Al­liance from a to­tally dif­fer­ent view­point. It had this enor­mous DeKalb fran­chise that be­came de­pen­dent on seed treat­ments. It also started to see some suc­cess with some of these mi­crobes.

“All of a sud­den, you started mov­ing from $3 to $5 mil­lion (an­nual) R&D (re­search and de­vel­op­ment) bud­gets to be­ing part of $400 to $500 mil­lion R&D bud­gets,” says Mi­ille.

Farm­ers don’t have to use mi­cro­bial and bi­o­log­i­cal prod­ucts to their fields to boost mi­crobe num­bers. Cov­er­ing the ground year-round with cash and cover crops can spur mi­cro­bial growth on its own, says Jodi DeJong-Hughes, Univer­sity of Min­nesota Ex­ten­sion soils spe­cial­ist. “Im­prove their food source and sta­bi­lize their en­vi­ron­ment, and the mi­crobe num­bers will grow au­to­mat­i­cally,” she says.

Selec­tively op­ti­miz­ing mi­crobes

In­dus­try of­fi­cials, though, say they are aim­ing mi­cro­bial and bi­o­log­i­cal prod­ucts for cer­tain tasks. “The in­dus­try has evolved from just go­ing out and col­lect­ing mi­crobes and see­ing how they work to now us­ing tech­nolo­gies that ac­tu­ally en­gi­neer or selec­tively op­ti­mize mi­crobes for spe­cific pur­poses,” says Mi­ille.

“As late as the 1970s, sci­en­tists would use mi­cro­scopes to study the shapes of mi­crobes to clas­sify them,” adds Brooke Bissinger, di­rec­tor of en­to­mol­ogy for AgBiome. To­day, sci­en­tists can se­quence mi­crobe genomes at a low cost, just as they have se­quenced hu­man and corn genomes. (A genome is an or­gan­ism’s com­plete set of DNA, in­clud­ing all of its genes. Se­quenc­ing DNA means de­ter­min­ing the or­der of four chem­i­cal build­ing blocks – also called bases – that in­clude ade­nine, thymine, cy­to­sine, and gua­nine.)

AgBiome has iso­lated and se­quenced more than 50,000 mi­crobes that it stores in its genome data­base, says Bissinger.

“From these mi­crobes, we’ve iden­ti­fied more than 12 mil­lion genes, 4,300 of which have the po­ten­tial to con­trol in­sects, and that’s re­ally just the be­gin­ning. We’ve screened these mi­crobes against im­por­tant crop pests and weeds, so we can go back and mine our data­base to find sim­i­lar mi­crobes that rapidly ex­pand our pool of can­di­dates,” Bissinger says.

“You can take genes from one mi­crobe that has a spe­cific ac­tiv­ity and insert them into an­other mi­crobe,” adds Mi­ille. “This is be­ing done in a spe­cific and con­trolled way. It’s evolv­ing even fur­ther with gene-edit­ing tools like CRISPR-Cas9 and oth­ers. Much of this is now au­to­mated, driven by soft­ware and high through-put in­stru­men­ta­tion.”

So far, the reg­u­la­tory ap­proval path is clear for mi­crobes. “Some of it goes through the EPA (En­vi­ron­men­tal Pro­tec­tion Agency), de­pend­ing on the claims made, and some of it goes through the states,” Mi­ille says. “It’s a much less oner­ous and an eas­ier path than the one used for trans­genic crops.”

What’s on Tap

The mi­cro­bial prod­ucts that com­pa­nies sell are mul­ti­ply­ing faster than mi­crobes.

“We can take ad­van­tage of the fact that mi­crobes are al­ways bat­tling it out over re­sources and for sur­vival,” says Bissinger. “These mi­crobes al­ready know how to kill and at­tack pests in crops. By study­ing these mi­crobes, we can fig­ure out how they do it and then put it to good use for agri­cul­ture.” Mi­crobes also have the po­ten­tial to com­ple­ment tools like chem­i­cals, Bissinger adds. BASF’s Pon­cho/ Vo­tivo 2.0 com­bines chem­i­cal in­sect con­trol in the Pon­cho com­po­nent with Vo­tivo’s bi­o­log­i­cal con­trol of ne­ma­todes and a bac­terium that BASF of­fi­cials say en­hances soil mi­cro­bial ac­tiv­ity.

Some aim at dis­eases. AgBiome has a fed­er­ally ap­proved bi­o­log­i­cal fungi­cide that is ef­fec­tive against fun­gal dis­eases like Rhi­zoc­to­nia. AgBiome is team­ing with SePRO to dis­trib­ute the prod­uct in the U.S. turf and or­na­men­tal mar­ket un­der the trade name of Zio. Oth­ers, like Pivot Bio, has a mi­cro­bial prod­uct on tap for 2019 that pull ni­tro­gen from the at­mos­phere for use by corn roots.

“Our mi­crobe ad­heres to the root of the corn plant, takes ni­tro­gen from the air, and con­verts it into a form for plant up­take,” San­ders says. Ni­tro­gen that goes di­rectly to the roots re­duces the po­ten­tial that com­mer­cially ap­plied N has to leach into ground­wa­ter or wa­ter­ways, he adds.

Other prod­ucts prom­ise to boost nu­tri­ent up­take in plants, such as a class of agri­cul­tural bi­o­log­i­cal prod­ucts from NewLeaf Sym­bi­otics called M-trophs, says Sher­man Hollins, busi­ness de­vel­op­ment man­ager with NewLeaf Sym­bi­otics. They can be ap­plied in-fur­row, on seed, or as a fo­liar spray.

the wild west

Mi­cro­bial and bi­o­log­i­cal prod­ucts face sev­eral hur­dles that in­clude the fol­low­ing.

• Lim­ited safety and ef­fi­cacy reg­u­la­tion.

Fer­til­iz­ers and pes­ti­cides all have state and fed­eral reg­u­la­tions to help en­sure safety and ef­fi­cacy.

Mi­cro­bial prod­ucts? Wel­come to the Wild West of agri­cul­tural in­puts.

“There are no reg­u­la­tions,” says Ca­ley Gasch, a North Dakota State Univer­sity soil sci­en­tist. “With these prod­ucts, it’s pretty much a free-for-all. There are no guar­an­tees.”

• Sur­viv­abil­ity un­der ad­verse weather.

Since mi­crobes are liv­ing or­gan­isms, weather im­pacts sur­viv­abil­ity.

“Mi­cro­bial ac­tiv­ity di­min­ishes as soil tem­per­a­tures reach 80°F.,” says DeJongHughes. This can be ac­cen­tu­ated in dry soils.”

• Soil dis­tur­bance.

“Tillage re­sets the clock

on mi­cro­bial suc­ces­sion and de­vel­op­ment,” says Kurt Steineke, Michi­gan State Univer­sity Ex­ten­sion soil spe­cial­ist. “A dif­fer­ent com­mu­nity is present in no-till vs. tilled sys­tems.”

Frosty wel­come

Mi­crobes en­ter­ing the soil also face an up­hill bat­tle due to ex­ist­ing soil mi­crobes.

“The soil is a busy place and a dif­fi­cult com­mu­nity to in­fil­trate,” says Gasch.

She cal­cu­lates that 1 square me­ter of soil 15 cen­time­ters deep con­tains 105 tril­lion colony-form­ing units (CFUs). A CFU is a unit used to es­ti­mate the num­ber of vi­able bac­te­ria or fun­gal cells in a sam­ple.

Mean­while, 10 gal­lons for a bac­te­rial prod­uct con­tain­ing 250 mil­lion CFU per gal­lon adds up to 2.5 bil­lion CFUs.

“Ad­ding 2.5 bil­lion cells to a fiercely com­pet­i­tive com­mu­nity of 105 tril­lion cells would ini­tially in­crease the cell count by 0.0024%,” she says. “These num­bers don’t ac­count for fungi, which can be just as preva­lent in soils as bac­te­ria or other soil or­gan­isms that prey on bac­te­ria. We do not have the tools to mea­sure and track the suc­cess of the mi­crobes that might be added in a com­mer­cial prod­uct.”

Any yield bump that may oc­cur could be due to the death of nu­tri­ent-packed mi­cro­bial cells that act as fer­til­izer, she adds.

Guer­rilla war­fare

Most agri­cul­tural mi­cro­bial prod­ucts aim at the soil sur­round­ing plants, says Ge­of­frey von Maltzahn, co-founder and chief in­no­va­tion of­fi­cer with In­digo Ag.

“You’re at­tempt­ing to add a mi­crobe into a guer­rilla war­fare sit­u­a­tion, where the num­ber of un­friendly mi­crobes vastly out­num­bers the rel­a­tively small amount of mi­crobes that you’re pro­vid­ing to that com­mu­nity,” he says.

That’s why In­digo Ag is tar­get­ing mi­crobes liv­ing in the plant, points out von Maltzahn.

“I still re­mem­ber be­ing stunned by a seem­ingly sim­ple ob­ser­va­tion that per­haps ev­ery plant in the world has mi­crobes that live not only around them in the soil but also in­side their tis­sues,” says von Maltzahn. “You see sit­u­a­tions where, un­der ex­treme drought, there are two plants among thou­sands that thrive. These are sit­u­a­tions where the en­vi­ron­ment is uni­form, and ge­net­ics wouldn’t be the rea­son for such dra­matic dif­fer­ences. We sim­ply ask what role the mi­crobes in­side them play in their sur­vival.”

In­digo Ag started a “sur­vivor plant” sam­pling sys­tem in fields where it col­lects and ge­net­i­cally se­quences sur­vivor plants. The com­pany then cul­tures these mi­crobes and trans­fers them to agri­cul­tural seeds in the form of seed treat­ments.

“We then see if those seeds de­rive a ben­e­fit rel­a­tive to the seeds that don’t re­ceive the mi­crobe,” says von Maltzahn. “We have demon­strated causal re­la­tion­ships be­tween these mi­crobes and stress re­silience in our labs, green­houses, and field tri­als over thou­sands of com­mer­cial acres.”

De­ci­pher­ing claims

Not sur­pris­ingly, claims of yield in­creases, pest con­trol, and in­put sav­ings ac­com­pany all of these prod­ucts. So do they work?

Tim Couser al­ways keeps this quote by John McGil­licuddy (an Iowa City, Iowa, agron­o­mist) handy:

“Ev­ery­thing will work once in agron­omy, and noth­ing works all the time.”

“The farmer’s prob­lem is that we test a prod­uct on a small area one year and it works,” says the Ne­vada, Iowa, farmer. “Then we put it on ev­ery acre the next year, and it doesn’t work.” Couser has worked with sev­eral com­pa­nies and says the prod­ucts have po­ten­tial. Since their cost of­ten ranges be­tween $10 to $15 per acre, though, they need to be on-farm tested to make sure they pro­vide a suf­fi­cient re­turn, he says. “The best way to tell if they work is with a split planter test, with the prod­uct used on one side of the planter and the check on the other,” he says. Gasch ad­vises farm­ers con­sid­er­ing mi­cro­bial and bi­o­log­i­cal prod­ucts to first test them on a few acres of their farm. “Look for val­i­da­tion from un­bi­ased sources, such as from a univer­sity or an in­de­pen­dent agron­o­mist,” she says.

Time will tell

De­vel­op­ing con­sis­tent re­sults takes time, says Mi­ille. “We have some pre­lim­i­nary in­di­ca­tions that we’re on the right track and that it’s achiev­able,” he says. “We know enough about the genes and have the tools to be­lieve that one day, we can ac­tu­ally take a host mi­crobe and re­duce syn­thetic ni­tro­gen ap­pli­ca­tions by hav­ing the mi­crobe de­liver 30%, 40%, and 50% of a plant’s ni­tro­gen needs and still main­tain the same yield.”

Still, Mi­ille es­ti­mates prod­uct com­mer­cial­iza­tion is four to five years away.

“Com­pa­nies have been try­ing to crack this nut for 30 to 40 years,” he says. “It’s not go­ing to hap­pen in one or two years. You don’t get many chances to make a first im­pres­sion. When you launch a prod­uct, it bet­ter work all the time.”

A ton of mi­cro­scopic bac­te­ria may be ac­tive in each acre of soil, ac­cord­ing to NRCS. Fungi and other soil or­gan­isms, in­clud­ing those that prey on bac­te­ria, also add life to soil.

Ernie San­ders

Ca­ley Gasch

Tim Couser

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