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https://www.independentsciencenews.org/health/a-lethal-industrial-farm-fungus-is-spreading-among-us/

(Un)Sustainable Farming
<https://www.independentsciencenews.org/sections/un-sustainable-farming/>,
Commentaries <https://www.independentsciencenews.org/sections/commentaries/>,
Health <https://www.independentsciencenews.org/sections/health/> April 23,
2019
A Lethal Industrial Farm Fungus Is Spreading Among Us

By Alex Liebman and Rob Wallace, PhD

Eighty percent of U.S. antibiotics are used to promote livestock and
poultry growth and protect the animals from the bacterial consequences of
the manure-laden environments in which they are grown. That’s 34 million
pounds a year of antibiotics as of 2015.
<https://nam.edu/antibiotic-resistance-in-humans-and-animals/>
[image: Fungicide and pesticide production at Sapec Crop Protection,
Portugal]Fungicide and pesticide production at Sapec Crop Protection,
Portugal

The agricultural applications help generate drug resistance across multiple
human bacterial infections, killing 23,000-100,000 Americans a year and,
with an increasing amount of antibiotics applied abroad,
<https://www.ncbi.nlm.nih.gov/pubmed/25792457>700,000 people worldwide.
<https://academic.oup.com/trstmh/article/110/7/377/2588524>

Now a fungal <https://en.wikipedia.org/wiki/Fungus>species, *Candida auris*,
has developed
<https://www.nytimes.com/2019/04/06/health/drug-resistant-candida-auris.html>multidrug
resistance
<http://www.frac.info/docs/default-source/publications/monographs/monograph-1.pdf>and
is rapidly spreading across human populations across the globe (see
figure). The CDC reports 90% of *C. auris *infections are clocking in
resistant to one antifungal drug and 30% to two or more.
[image: C.auris cases by country. From CDC (2019)]C.auris cases by country.
From CDC (2019) [image: Clinical cases of Candida auris reported by CDC as
of February 28, 2019: by U.S. state. From CDC (2019).]Clinical cases of
Candida auris reported by CDC as of February 28, 2019: by U.S. state. From
CDC (2019).

*C. auris, *a <https://en.wikipedia.org/wiki/Yeast>yeast,
<https://en.wikipedia.org/wiki/Yeast>is killing immunocompromised patients
in hospitals, clinics, and nursing homes at a prodigious clip, up to 40-60%
of those who suffer bloodstream infections in a month’s time.

In the rooms of the infected and the dead, the fungus appears intransigent
to nearly all attempts at eradication. The fungus can survive
<https://www.nytimes.com/2019/04/06/health/drug-resistant-candida-auris.html>even
a floor-to-ceiling spray of aerosolized hydrogen peroxide.

How have drug-resistant fungi come to haunt the modern hospital and
jeopardize the sterile spaces asepsis addressed 150 years ago?

It is becoming increasingly apparent that *C. auris*’s resistance, and that
of many other fungi species, is traceable to industrial agriculture’s mass
application of fungicides. These chemicals approximate the molecular
structures of antifungal drugs.

Across crops
<http://www.frac.info/expert-fora/benzimidazoles/resistance-risk-and-current-status>—wheat,
banana, barley, apple, among many others—the fungicides select for
resistant strains that find their way into hospitals where they are also
resistant to the drugs administered to patients.
The path of yeast resistance

Matthew Fisher and colleagues recently classified
<https://spiral.imperial.ac.uk:8443/bitstream/10044/1/59856/6/aap7999_CombinedPDF_v3.pdf>six
main classes of fungicides, all rarely used
<https://www.iatp.org/sites/default/files/2014_12_23_Fungicide_LL.pdf> in
the U.S. Midwest before 2007.

The *azoles *and *morpholines *target the ergosterol biosynthetic pathway,
<https://www.wikipathways.org/index.php/Pathway:WP343>which generates the
plasma membrane of fungi cells. The *benzimidazoles *interfere with
fungi cytoskeleton,
<https://en.wikipedia.org/wiki/Cytoskeleton>preventing the assembly of cell
microtubules. <https://en.wikipedia.org/wiki/Microtubule> The *strobilurins
*and *succinate dehydrogenase inhibitors* take more physiological routes,
inhibiting the electron transfer chain
<https://en.wikipedia.org/wiki/Electron_transport_chain> of mitochondrial
respiration. The *anilinopyrimidines *appear to target mitochondrial
signalling pathways.

*Candida auris* has evolved
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5215215/>resistance to a
suite of azole antifungals, including fluconazole,
<https://en.wikipedia.org/wiki/Fluconazole>with variable susceptibilities
to other azoles, amphotericin B, <https://www.drugbank.ca/drugs/DB00681>
and echinocandins. <https://en.wikipedia.org/wiki/Echinocandin> Azoles,
used in both <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1932500/>crop
protection and medical settings,  are broad-spectrum fungicides,
<https://www.ncbi.nlm.nih.gov/pubmed/28485100>annihilating a wide range of
fungi rather than targeting a specific type.
How did fungus and fungicide find each other in the field?

*C. auris, *likely long circulating on its own for thousands of years as
CDC’s Tom Chiller hypothesizes,
<https://www.nytimes.com/2019/04/06/health/drug-resistant-candida-auris.html>
was first isolated in humans from the ear canal of 70-year old Japanese
woman at a Tokyo hospital in 2009 (although a 1996 isolate was subsequently
identified <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3165631/>). Later
isolation found the yeast capable of bloodstream infection.

In an effort to identify the source of the infection, an international
team sequenced
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5215215/>resistant isolates
collected from hospitals across Pakistan, India, South Africa, and
Venezuela, 2012–2015.

Against expectations, the team found divergent amino acid replacements
<https://en.wikipedia.org/wiki/Amino_acid_replacement> associated with
azole resistance among the *ERG11*
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2782262/> single nucleotide
polymorphisms <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2782262/>—one
among several
<https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1007478>such
SNPs—across four geographic regions. They weren’t the same strain,
indicating that each resistant phenotype had emerged independently.

In other words, strains isolated by distance
<https://en.wikipedia.org/wiki/Isolation_by_distance>from each other
evolved unique solutions to the fungicides to which they were exposed.

That might indicate molecular adaptations to different exposures. But it
also might indicate that in response to such wide exposure to fungicides in
the field, each strain evolved
<https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2011.05288.x>its
own unique solution to the problem.

Even though fungi do not horizontally transfer
<https://academic.oup.com/femsle/article/329/1/1/627174> their genes at
rates that virus and bacteria do,  migration of patients and fungi alike,
the latter by way of agricultural trade,
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5095548/> can help increase
diversity in the fungicidal resistance circulating in any one locale.

A second team identified <https://www.ncbi.nlm.nih.gov/pubmed/28204557>multiple
genotypes of different international origins in the relatively bounded
confines of the United Kingdom. A third team, as the nearby map shows,
*identified
*a similar mix in U.S. cases.

But it isn’t clear other than travel-related cases whether all the cases
originated from strains from abroad. Without a baseline of fungal load
among, say, domestic agricultural workers, an endogenous source remains a
possibility.
[image: Distribution of Candida auris clades in the United States.]Distribution
of Candida auris clades in the United States. (A) Maximum parsimony
phylogenetic tree of marker isolates from Colombia, India, Japan, Pakistan,
South Korea, South Africa, Venezuela, and U.S. clinical cases in the USA.
(B) The frequency of U.S. clinical cases by clade. (C) The phylogeography
of introduced clades. Solid lines indicate introductions that are
associated with patients known to have received health care abroad. Adapted
from Chow et al. (2018).

To add to the complexity, there also appear multiple mechanisms by which
resistance emerges.

Dominique Sanglard summarizes
<https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1007478>three:
decreases in drug concentration in fungal cells, alterations of the drug
target, and compensatory mechanisms that depress drug toxicity. Atop these,
the three can be arrived at by a variety of genetic events. Alongside SNPs
are insertions into the fungus genome, deletions, and structural changes,
including gene or chromosome copy events.

One study <https://apsjournals.apsnet.org/doi/10.1094/MPMI-09-15-0218-R>
found *51 genes* related to how sensitive circulating strains of a *Fusarium
* <https://en.wikipedia.org/wiki/Fusarium>blight were to propiconazole,
<https://en.wikipedia.org/wiki/Propiconazole> only a single class of
triazole fungicide.

The road to such resistance can be complex, winding beyond merely evolving
out from underneath an antifungal directly.

In 2015, researchers found
<https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1863-z>that
the *C. auris* genome hosts several genes for the ATP-binding cassette
transporter family,
<https://en.wikipedia.org/wiki/ATP-binding_cassette_transporter> a major
facilitator superfamily (MFS). MFS transports a large variety of substrates
across cell membranes and been shown to effectively dispose
<https://mmbr.asm.org/content/64/4/672>of broad classes of drugs. It
permits *C. auris* to survive an onslaught of antifungal drugs.

The team found that that the *C. auris* genome also encodes a slew of gene
families that facilitate the fungi’s virulence. *C. auris* adaptively forms
biofilms <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5715972/> that
support antifungal resistance by way of a high density of cells, the
presence of sterols <https://en.wikipedia.org/wiki/Sterol> on biofilm
cells, and efficient nutrient use and growth.
Other fungi, other dangers

*Candida auris* is hardly the only deadly fungus converging upon multidrug
resistance. The nearby map shows multiple species overlapping in plant and
human resistance.

One fungus, *Aspergillus fumigatus*, may offer a conditional preview of *C.
auris’s *trajectories present and future.

Azole antifungals itraconazole, voriconazole, and posaconazole have long
been used to treat pulmonary asperillogosis,
<https://err.ersjournals.com/content/20/121/156> the infection caused by *A.
fumigatus. *The fungi causes approximately 200,000 deaths
<http://www.life-worldwide.org/assets/uploads/files/Brown%20fungal%20infections%20killersSciTranslMed%202012.pdf>
per year, in the past decade rapidly developing resistance to antifungal
drugs.
[image: Number of peer-reviewed reports of resistance to azole fungicides
for plants (in blue) and in humans (in red) for pathogens Aspergillus
fumigatus, Candida albicans, C. auris, C. glabrata, Cryptococcus gattii,
and Cryptococcus neoformans. From Fisher (2018).]Number of peer-reviewed
reports of resistance to azole fungicides for plants (in blue) and in
humans (in red) for pathogens Aspergillus fumigatus, Candida albicans, C.
auris, C. glabrata, Cryptococcus gattii, and Cryptococcus neoformans. From
Fisher (2018).

Studies comparing long-term azole users and patients just beginning to take
the drug have shown that drug-resistant *A. fumigatus *was prevalent in
both groups, suggesting that resistance evolved in agricultural
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5461301/> rather than medical
settings.

Researchers have found
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3812019/> biogeographical
evidence that suggests multi-triazole-resistant *A. fumigatus* strains in
clinical and environmental settings share significant overlap. In the
figure nearby, drug resistant *A. fumigatus* found in the field (green) and
in clinical trials (red) map together, demonstrating their coupling in
Europe and Asia.
[image: The global map depicts the geographic distribution of
multi-triazole-resistant Aspergillus fumigatus strains. Two different
mutations are depicted: TR34/L98H (circle) and TR46/Y121F/T289A (square).
The percentages denote the environmental prevalence rates of resistance.
From Chowdhary et al. (2013).]The global map depicts the geographic
distribution of multi-triazole-resistant Aspergillus fumigatus strains. Two
different mutations are depicted: TR34/L98H (circle) and TR46/Y121F/T289A
(square). The percentages denote the environmental prevalence rates of
resistance. From Chowdhary et al. (2013).

Other work recently found <https://www.ncbi.nlm.nih.gov/pubmed/30896313>
azole-resistant *A. fumigatus* related to the use of triazole fungicides in
agricultural fields outside of Bogotá, Colombia. Soils were sampled from an
array of crop fields and *A. fumigatus* was grown on agar treated with
itraconazole or voriconazole fungicides. In more than 25% of cases, *A.
fumigatus* persisted despite the fungicide treatment.

That is, due to agricultural practices, *Aspergillus* is entering hospitals
already adapted to the slew of antifungal cocktails designed to check its
spread. Dumping azoles to control for fungi on grapes, corn, stone fruit,
and a myriad of other crops generated the conditions to accelerate drug
resistance in human patients.

While extensive phylogenetic and biogeographical research remains to be
conducted, a quick perusal of existing distribution maps
<https://sci-hub.tw/10.1016/s1473-3099(17)30316-x>suggests similarities
between *Aspergillus fumigatus* and its younger (and suddenly more
infamous) cohort *Candida auris.* The strains share similar geographical
distributions, occupying many of the same zones described above for *C.
auris*.
Industrial agriculture’s role

With zones of overlapping human and crop resistant cases of *Aspergillus
fumigatus *and the rising specter of a new azole resistant fungus ravaging
clinical settings and evolving at lightning speed, one would hope that
azole fungicide use would be closely monitored
<http://www.frac.info/monitoring-methods> if not just phased out.

The dangers of continuing upon this path of agricultural development are
acute.

Medical and agricultural azole fungicides share similar modes of action, so
when resistance pops up in one arena it is easily transferable to another.
In both agricultural and medical fungicides, the phenyl group of the
chemical forms van der Waals contact
<https://en.wikipedia.org/wiki/Van_der_Waals_force>with the active site of gene
*cyp51A.* <https://www.ncbi.nlm.nih.gov/pubmed/24570417>

Organic chemistry specifics aside, the close similarities that the
Chowdhary group depict in the nearby figure suggest that a mutation in
*Aspergillus
fumigatus *to prevent binding to the *cyp51A* gene in an agricultural
setting—specifically a modification of the 14-α sterol demethylase enzyme
<https://en.wikipedia.org/wiki/Lanosterol_14_alpha-demethylase>—would
likely confer resistance to medical applications of stereochemically
<https://en.wikipedia.org/wiki/Stereochemistry>similar drugs.
[image: Diagram showing similar mode of action in triazoles between medical
(A) and agricultural (B) applications. From Chowdhary et al. (2013).]Diagram
showing similar mode of action in triazoles between medical (A) and
agricultural (B) applications. From Chowdhary et al. (2013).

Agricultural azole fungicides comprise a *third* of the total fungicide
market. Twenty-five different forms of agricultural azole demethylation
inhibitors are in use, compared to just three forms of licensed medical
azoles.

So we shouldn’t be surprised that in applying these fungicides at landscape
scales in the millions of pounds annually, the medical use of triazole
antifungals, using the same mode of action, would rapidly turn ineffective.

Instead of intervening in the interests of global public health to limit
these long-problematic applications, government policy
<https://www.fas.usda.gov/sites/default/files/2015-06/8091411_enclosure.pdf>
in recent years has promoted the lucrative
<https://www.transparencymarketresearch.com/pressrelease/fungicides-market.htm>global
*expansion *of fungicide use, fostering the conditions for virulent
drug-resistant fungi.

In 2009, fungicides were applied on 30% of corn, soybean, and wheat acreage
in the U.S., totaling 80 million acres. Preventative use of fungicides to
control soybean rust quadrupled between 2002 and 2006, despite a dubious
economic rationale.
<https://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-03-11-0091?prevSearch=authorsfield%253A%2528esker%2529&searchHistoryKey=&>
Global sales continue to skyrocket, nearly tripling since 2005, from $8
billion to $21 billion in 2017
<http://www.prweb.com/releases/2012/10/prweb9945474.htm>.

Fungicides expanded not only in sales but also in geographic distribution.

From the maps nearby, we see tetraconazole,
<https://www3.epa.gov/pesticides/chem_search/reg_actions/registration/fs_PC-120603_01-Apr-05.pdf>an
agricultural triazole, moved from isolated usage in the western Plains in
the late 1990s to massive application throughout California’s Central
Valley, the upper Midwest, and the Southeast. Boscalid,
<https://www3.epa.gov/pesticides/chem_search/reg_actions/registration/fs_PC-128008_01-Jul-03.pdf>a
fungicide used in fruit and vegetable crops, has increased from ~ 0.15 to
0.6 million pounds from 2004 to 2016, a 400% increase, and is now widely
applied across the country.
[image: Estimated agricultural use (EPest-high) of fungicides tetraconazole
(left) and boscalid (right) in pounds per U.S. square mile, 1999 and 2014.
State-based and other restrictions on pesticide use were not incorporated
into EPest-high or EPest-low estimates. EPest-low estimates usually reflect
these restrictions because they are based primarily on surveyed data.
EPest-high estimates include more extensive estimates of pesticide use not
reported in surveys, which sometimes include States or areas when use
restrictions have been imposed. Users should consult with State and local
agencies for specific use restrictions. National Water-Quality Assessment
(NAWQA) Project/USGS/ARERC.]Estimated agricultural use (EPest-high) of
fungicides tetraconazole (left) and boscalid (right) in pounds per U.S.
square mile, 1999 and 2014. State-based and other restrictions on pesticide
use were not incorporated into EPest-high or EPest-low estimates. EPest-low
estimates usually reflect these restrictions because they are based
primarily on surveyed data. EPest-high estimates include more extensive
estimates of pesticide use not reported in surveys, which sometimes include
States or areas when use restrictions have been imposed. Users should
consult with State and local agencies for specific use restrictions.
National Water-Quality Assessment (NAWQA) Project/USGS/ARERC.

From within each new locale, the fungicides percolate into the local
environment.

In 2012, USGS scientists studied
<https://www.ncbi.nlm.nih.gov/pubmed/22564453>33 different fungicides used
in potato production and found at least one fungicide in 75% of tested
surface waters and 58% of ground water samples. With half-lives stretching
to several months, azole fungicides are able to easily reach and
persist in aquatic
environments <https://www.ncbi.nlm.nih.gov/pubmed/18939546> by runoff and
spray drift, becoming highly mobile.

As climate change fundamentally reshapes the U.S., bringing higher overall
temperatures and extreme oscillations between drought and heavy rainfall,
fungi are predicted <https://www.ncbi.nlm.nih.gov/pubmed/16701319>to expand
outside of their current ranges while also responding specifically to new
climate regimes. *Aspergillus flavus*, the producer of a cancer-causing
aflatoxin
<https://www.cancer.gov/about-cancer/causes-prevention/risk/substances/aflatoxins>
that reduces corn yields and poisons humans, thrives in drought conditions
and large crop-water deficits.

With the market treated as a force of nature stronger than climate or
public health, under current agricultural production, broad-spectrum
fungicide use is likely only to increase*.*
Farming as its own fungus control

In response to drug-resistant bacteria and fungi, research institutions are
calling for the collection of better data on agricultural antibiotic use
and on the potential economic costs of transitioning away from from high
rates of application.

A 2016 UK report <https://amr-review.org/>, citing the overapplication of
agricultural fungicides, recommended increased surveillance of antibiotic
usage overall and a regulatory apparatus organized by the WHO, FAO, and OIE
that among its duties would list critical antibiotics that should be barred
from agriculture use.

But aside from collecting more information and calling for what appears
minimal regulation, what is to be done?

Given recent travails in antibiotic and herbicide resistance, it seems
likely that chemical companies and their farming clients will pursue
developing new fungicides
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039980/> based on targeted
molecular research, multiple drug cocktails
<https://www.nrdc.org/stories/24-d-most-dangerous-pesticide-youve-never-heard>,
and gene-edited resistance.
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6117396/>

Governmental agencies are likely to impose increased if dubious biosecurity
measures, which also frequently foment xenophobic anxieties
<https://books.google.com/books?hl=en&lr=&id=uZWQBAAAQBAJ&oi=fnd&pg=PA113&dq=biosecurity+xenophobia+labor&ots=D-xOgM0LGF&sig=bVpZREAODkvgcidGUDJquTXzhHA#v=onepage&q&f=false>
and are used to blame workers
<https://farmingpathogens.wordpress.com/2016/11/30/banksgiving/> for
contamination, rather than addressing the systemic failures of industrial
agriculture.

The conjoined motives of powerful medical and agricultural companies are
almost certain to promote ‘solutions’ that exacerbate an arms race between
toxic drug applications and fungal resistance, spew growing permutations of
lethal chemicals into the environment, and further consolidate and privatize
<https://books.google.com/books?id=Z4LfAgAAQBAJ&dq=capitalism+fungicide&lr=&source=gbs_navlinks_s>
the agro-pharmaceutical sector.
<http://www.harvestpublicmedia.org/post/seeds-pesticides-fertilizer-how-big-companies-harnessed-holy-trinity-modern-agriculture>

There is, however, a different, evidence-based paradigm
<https://www.springer.com/us/book/9789811043246> for responding to
fungicidal collapse.

A quick review of agroecological examples suggests that a combination
of disease
modeling <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2610107/> and cultural
practices <https://link.springer.com/article/10.1007/s13593-012-0124-7>such
as crop rotation and cover cropping can greatly reduce the presence of
fungal diseases and thus dependence on fungicides.
[image: Intercropping, here soybean and flax, can increase and diversify
the soil microbiota to exclude pathogenic fungi. Photo: Alexis
Stockford)]Intercropping,
here soybean and flax, can increase and diversify the soil microbiota to
exclude pathogenic fungi. Photo: Alexis Stockford)

In California’s Central Valley, strawberry producers accustomed to
fumigating soils with fungicides to control incidence of *Verticillium *
wilt, <https://en.wikipedia.org/wiki/Verticillium_wilt> a pathogenic soil
fungi, have found that planting broccoli crops in between rotations of
strawberry crops greatly reduced
<https://crec.ifas.ufl.edu/extension/soilipm/1999%20MBAO/Shetty,%20K.G/Shetty,%20K.G.%20(49)%201999%20Presentation.pdf>
levels of *Verticillium. *

Dating back several decades, similar results have been found in the
diversification of potato crop rotations.
<https://link.springer.com/chapter/10.1007/978-94-009-2474-1_15>

Researchers in India—a country where drug-resistant *A. fumigatus* and *C.
auris* have both been found—have studied novel approaches
<http://orgprints.org/32193/1/%2813-24%29%20potato%20disease.pdf> to
controlling late blight in potato.

Potato crops often receive large doses of azole fungicides to control for
fungal pathogens such as late blight. Rather than fungicide treatments,
scientists applied silica to foliar tissue, finding that silica was
absorbed and strengthened the potato’s cell walls against fungal invasion.
Disease infestation rates ranged from 2.8 – 7.9% in the silica-based
integrated management systems and 49.4 – 66.7% in the conventional
fungicide dependent systems.

In general, organic farming
<https://sci-hub.tw/https:/nph.onlinelibrary.wiley.com/doi/abs/10.1111/j.1469-8137.2010.03230.x>
supports mutualistic fungi to a much greater degree than conventional
farming, crowding out pathogenic strains. Crop rotations, the incorporation
of legumes, and the cultivation of soil aggregates support ecological
niches for soil microbiota.

Reducing chemical fertilizers and limiting tillage, two agroecological
practices with major benefits for reduced pollution and enhanced carbon
storage, also select for
<https://onlinelibrary.wiley.com/doi/10.1111/j.1752-4571.2010.00145.x>
beneficial strains of arbuscular mycorrhizal fungi
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4717633/> that form
mutualistic relationships with plant roots and can confer resistance to
soil pathogens.

Integrating agricultural production into a broader matrix of non-crop
vegetation is also important for controlling fungal pathogens. Wild
landscapes <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408149/> reduce
the potential for pathogen populations to adapt to crops and modeling
suggests that contiguous swaths of wild patches reduce the aggressiveness
of pathogens upon agricultural crops.

Ivette Perfecto and John Vandermeer’s labs have done yeoman work, written
up in depth here
<https://www.routledge.com/Coffee-Agroecology-A-New-Approach-to-Understanding-Agricultural-Biodiversity/Perfecto-Vandermeer/p/book/9780415826815>
and summarized here,
<https://farmingpathogens.wordpress.com/2013/02/04/coffee-filter/> tracing
the means by which thatches of ecological relationships—predation,
mutualism, competition, etc.—up and down the food web in which a crop finds
itself can box out pest damage, including, their teams find, from rust
fungi. <https://en.wikipedia.org/wiki/Rust_(fungus)>

The nitty-gritty as it applies to fungi can be found in Vandermeer student
Douglas Jackson’s dissertation
<https://deepblue.lib.umich.edu/handle/2027.42/94026>on agroecological
fungal control in coffee.
[image: Zachary Hajian-Forooshani]Zachary Hajian-Forooshani

Zachary Hajian-Forooshani (pictured), another University of Michigan
student, followed up
<http://eeblog.lsa.umich.edu/2015/08/coffee-in-mexico-larvae-vs-fungi.html>
research from the 1970s and found *Mycodiplosis*
<https://bugguide.net/node/view/750752>fly larvae feed on the coffee rust
the Perfecto-Vandermeer team study in Mexico and Puerto Rico.
More than mining soil

All this work squares well with agroecological theory
<https://www.pnas.org/content/107/13/5786> that under current political
policies and demographic trends, farm fields integrated into a matrix of
nature conservation
<https://onlinelibrary.wiley.com/doi/full/10.1111/j.1523-1739.2006.00582.x>
are more likely than ‘land-sparing’ approaches to conserve natural
resources while simultaneously supporting rural livelihoods and
low-external input food production.

What emerges is a picture of ecological complexity in which fungicidal
warfare is exactly the wrong tool.

Instead, throwing bad money after bad, fungicides today are applied in a
system in which diseases thrive out of simplified landscapes, vast and
uninterrupted genetically identical monocultures, rapidly accelerating
global warming, and an ever quickening pace of global trade.

In a cruel irony, fungicide application places evolutionary pressure on
pathogens to develop resistance *at the same time* that industrial
management provides the near-perfect conditions for fostering and spreading
these virulent mutations.

It all makes sense only when we recognize that the agribusiness sector
views nature as its stiffest competition.
<https://farmingpathogens.wordpress.com/2017/07/11/impermissible-exchange/>

Wiping out local ecologies and the near-free work these offer in helping
farmers enrich their soils, clean their water, pollinate their plants, feed
their livestock, and control pests—pathogenic fungi among them—means the
largest companies can now sell commodified equivalents to a captured market.

The damage done is more than agricultural or economic. It’s a business plan
pursued even at the risk of eroding our capacity to socially reproduce
ourselves as a civilization.

Farmers and food activists have complained industrial agriculture
represents little more than nutrient
<https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/1365-2664.12089>and
carbon mining. <https://freethesoil.org/educate-yourself/> Companies are
compelling farmers to grow so much so fast that production squeezes carbon
out of the soil in the form of food commodities. As a result, land and
water are polluted into such oblivion that food safety
<http://labs.russell.wisc.edu/rissman/files/2012/11/Stuart-and-Gillon-2013-US-Farmland-Conservation-LUP.pdf>cannot
be accounted for.

By that pollution, occupational exposures, outbreaks of increasing
virulence and extent, metabolic diseases such as diabetes, antibiotic
resistance, and now the growing threat of fungicide resistance, carbon
mining now extends to gouging out global public health.

Once the order of the day, alternate agricultures long pursued and updated
by smallholders worldwide, and backed by a growing scientific literature,
offer a way out of that trap.

An earlier version of this article was published as A Factory Farm Fungus
Among Us
<https://arerc.wordpress.com/2019/04/10/a-factory-farm-fungus-among-us/?fbclid=IwAR3zGVpmGffJzodGRbnX7F-Qq51a1JnyqVP-i4znWD3XxOpf_CGPabU1A00>
.

*Alex Liebman is a plant-soil and political ecology researcher with
Lurralde,  <http://lurralde.cl/que-es-lurralde/>a Chilean group supporting
the Atacameña and Ayamara peoples in their struggle for territorial
sovereignty and water rights in the face of multinational copper and
lithium mining interests in the Atacama Desert.*

*Rob Wallace, ,PhD, is an evolutionary biologist and public h*ealth
phylogeographer <https://en.wikipedia.org/wiki/Phylogeography>. He’s the
author of Big Farms Make Big Flu
<https://monthlyreview.org/product/big_farms_make_big_flu/> and, most
recently, co-author of Clear-Cutting Disease Control
<http://wordpress.redirectingat.com/?id=725X1342&xcust=8982&xs=1&isjs=1&url=https%3A%2F%2Fwww.springer.com%2Fus%2Fbook%2F9783319728490&xguid=b550ded2a310ceaa87a334126068ab8a&xuuid=878e69f3567254a1dd6f68cfb4119431&xsessid=&xcreo=0&xed=0&sref=https%3A%2F%2Farerc.wordpress.com%2F2019%2F04%2F10%2Fa-factory-farm-fungus-among-us%2F%3Ffbclid%3DIwAR3zGVpmGffJzodGRbnX7F-Qq51a1JnyqVP-i4znWD3XxOpf_CGPabU1A00&xtz=240&jv=13.15.0-stackpath&bv=2.5.1>
.

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