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There is emerging concern regarding the unintentional and often unrecognized antimicrobial properties of “non-antimicrobial” pesticides. This includes insecticides, herbicides, and fungicides commonly used in agriculture that are known to produce broad ranging, off-target effects on beneficial wildlife, even at seemingly non-toxic low dose exposures. Notably, these obscure adverse interactions may be related to host-associated microbiome damage occurring from antimicrobial effects, rather than the presumed toxic effects of pesticides on host tissue. Here, we critically review the literature on this topic as it pertains to the rhizosphere microbiome of crop plants and gut microbiome of pollinator insects (namely managed populations of the western honey bee, Apis mellifera), since both are frequent recipients of chronic pesticide exposure. Clear linkages between pesticide mode of action and host-specific microbiome functionalities are identified in relation to potential antimicrobial risks. For example, inherent differences in nitrogen metabolism of plant- and insect-associated microbiomes may dictate whether neonicotinoid-based insecticides ultimately exert antimicrobial activities or not. Several other context-dependent scenarios are discussed. In addition to direct effects (e.g., microbicidal action of the parent compound or breakdown metabolites), pesticides may indirectly alter the trajectory of host-microbiome coevolution in honey bees via modulation of social behaviours and the insect gut-brain axis - conceivably with consequences on plant-pollinator symbiosis as well. In summary, current evidence suggests: (1) immediate action is needed by regulatory authorities in amending safety assessments for “non-antimicrobial” pesticides; and (2) that the development of host-free microbiome model systems could be useful for rapidly screening pesticides against functionally distinct microbial catalogues of interest.
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Daisley et al. Microbiome Res Rep 2022;1:6
DOI: 10.20517/mrr.2021.08 Microbiome Research
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Open AccessReview
Deteriorating microbiomes in agriculture - the
unintended effects of pesticides on microbial life
Brendan A. Daisley1,2, Anna M. Chernyshova1, Graham J. Thompson1, Emma Allen-Vercoe2
1Department of Biology, Western University, London, ON N6A 5C1, Canada.
2Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
Correspondence to: Dr. Emma Allen-Vercoe, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road
East, Guelph, ON N1G 2W1, Canada. E-mail:
How to cite this article: Daisley BA, Chernyshova AM, Thompson GJ, Allen-Vercoe E. Deteriorating microbiomes in agriculture -
the unintended effects of pesticides on microbial life. Microbiome Res Rep 2022;1:6.
Received: 1 Dec 2021 First Decision: 10 Jan 2022 Revised: 12 Jan 2022 Accepted: 21 Jan 2022 Published: 25 Jan 2022
Academic Editor: Marco Ventura Copy Editor: Xi-Jun Chen Production Editor: Xi-Jun Chen
There is emerging concern regarding the unintentional and often unrecognized antimicrobial properties of “non-
antimicrobial” pesticides. This includes insecticides, herbicides, and fungicides commonly used in agriculture that
are known to produce broad ranging, off-target effects on beneficial wildlife, even at seemingly non-toxic low dose
exposures. Notably, these obscure adverse interactions may be related to host-associated microbiome damage
occurring from antimicrobial effects, rather than the presumed toxic effects of pesticides on host tissue. Here, we
critically review the literature on this topic as it pertains to the rhizosphere microbiome of crop plants and gut
microbiome of pollinator insects (namely managed populations of the western honey bee, Apis mellifera), since
both are frequent recipients of chronic pesticide exposure. Clear linkages between pesticide mode of action and
host-specific microbiome functionalities are identified in relation to potential antimicrobial risks. For example,
inherent differences in nitrogen metabolism of plant- and insect-associated microbiomes may dictate whether
neonicotinoid-based insecticides ultimately exert antimicrobial activities or not. Several other context-dependent
scenarios are discussed. In addition to direct effects (e.g., microbicidal action of the parent compound or
breakdown metabolites), pesticides may indirectly alter the trajectory of host-microbiome coevolution in honey
bees via modulation of social behaviours and the insect gut-brain axis - conceivably with consequences on plant-
pollinator symbiosis as well. In summary, current evidence suggests: (1) immediate action is needed by regulatory
authorities in amending safety assessments for “non-antimicrobial” pesticides; and (2) that the development of
host-free microbiome model systems could be useful for rapidly screening pesticides against functionally distinct
microbial catalogues of interest.
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Keywords: Microbiome, host-microbe interactions, agriculture, pesticides, microbial evolution, microbe-xenobiotic
interactions, bioremediation, environmental sustainability
Arguably, there is a microbial component inherent to all known systems on Earth with cumulative evidence
supporting that niche-adapted microbial communities play unequivocally important roles in total
ecosystem functioning[1]. This includes, but is not limited to, the facilitation of marine and atmospheric
biogeochemical processes, regulation of soil-plant nutrient cycling, and maintenance of healthy animal
communities. Emerging ideologies such as “Planetary Health” and “OneHealth” emphasize these
fundamental roles of microbial metabolic processes in supporting macroscopic reality at the systems-level,
and further suggest that microorganisms should be viewed as unified constituents rather than as separate
entities, as they have been historically regarded[2,3].
Consistent with these schemas is the holobiont (or hologenome) theory of evolution[4] which posits that
host-microbe co-adaptation has driven functional interdependence between many animal species and their
gut microbiomes (i.e., referring to the community of microorganisms residing in the intestinal tract as well
as their collective metabolic potential). Exemplifying this interdependence, animal species frequently rely on
their gut microbiomes for nutrition, pathogen exclusion, and immunomodulatory functions[5]. The human
gut microbiome has been well characterized in this regard, although there is substantial evidence from
insect species too - including the western honey bee (Apis mellifera). In particular, this eusocial insect
species relies heavily on the bacterial members of its gut microbiota as a result of depauperate immune and
detoxification gene repertoires[6]. Similar relationships exist between plant hosts and the microbe-dense soil
zone surrounding plant roots, known as the rhizosphere (or “microbe storehouse”), that plays a
multifunctional role in supporting plant growth and is a critical factor influencing crop yields in
agriculture[7]. The functional similarities between the gut microbiome of animals and the rhizosphere
microbiome of plants have been discussed previously[8], as has the related theory of “the host microbiome as
an ecosystem on a leash”[9].
Here, we draw attention to the neglected fact that anthropogenic activities (primarily those over the past
century relating to farming practices) have introduced an astonishing number of pesticides and other
agrochemical xenobiotics into the environment (~90,000 active products registered in the NPIRS database
alone[10]), and that many can exert unintentional antimicrobial activities that disrupt host-microbiome
homeostasis[11]. These activities include the microbicidal or microbiostatic properties exhibited by various
herbicides, insecticides, and fungicides, which together constitute over 95% of all pesticides used
worldwide[12]. To note, these effects are often unforeseen (e.g., insecticides - by design - target insects, not
microbes) and are not adequately monitored by regulatory agencies since most pesticides are classified as
“non-antimicrobial” chemicals. It is thus conceivable that widespread extinction of plant and animal host-
adapted microbes may already be occurring, undetected, as a result of chronic sub-lethal pesticide exposures
(i.e., through the use of compounds deemed non-toxic to the physiology of off-target host species, but not
necessarily their microbiomes). Nonetheless, it is difficult to ascertain the extent of damage, since baseline
host-associated microbiome data is often lacking.
We can gain some insight into the long-term consequences of microbiome damage from industrialized
human societies that have undergone a systematic depletion in host-adapted microbes due to
transgenerational antibiotic exposure (i.e., missing microbe hypothesis[13]) and excessive use of disinfectants
(i.e., hygiene hypothesis of disease[14]). Importantly, these reductions in microbial diversity are directly
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associated with altered functionality of the gut microbiome, and are thought to represent a major instigating
factor behind the growing global epidemic of chronic, non-communicable, metabolic disease[15]. Such
metabolic disorders include irritable bowel syndrome[16], type-2 diabetes[17], obesity[18], atherosclerosis[19], and
several types of cancer[20]. Thus, while the use of antibiotics and disinfectants have undoubtedly
revolutionized clinical healthcare and tremendously reduced the spread and lethality of infectious diseases,
persistent exposure to antimicrobial agents may pose significant long-term health complications.
An analogous scenario could be the case for the effects of pesticides, which have revolutionized the
agricultural industry (e.g., through minimizing crop loss to pest species) but may pose serious risks to
wildlife metabolic health and long-term environmental sustainability. Previous reports have exhaustively
described the consequential physiological effects of pesticides on off-target plant and animal tissue[21-24]. In
this review, we detail the current knowledge relating to the important non-canonical mechanisms by which
certain pesticides can obstruct plant and pollinator health via off-target interactions with the host
microbiome [Figure 1]. Specific attention will be given to managed western honey bees (A. mellifera) on the
basis of their proclivity to encounter pesticides, their unsustainable colony loss over the past decade, and
their importance to agriculture and global food security.
The Environmental Protection Agency (EPA) of the United States broadly classifies pesticides to be any
chemical compound utilized for the purpose of killing crop pests that interfere with agricultural production
- most commonly referring to that of herbicides, insecticides, and fungicides. A longstanding issue
surrounding the use of pesticides, however, is the off-target deleterious effects they can have on a broad
range of species found in terrestrial and aquatic ecosystems. In efforts to make sound regulatory judgements
about these risks, authoritative bodies worldwide have attempted to implement minimum data and safety
information requirements in relation to a given pesticide product’s potential for causing unreasonable
adverse effects. For example, the EPA’s regulation “Data Requirements for Registration” (issued in 1984
under title 40, part 158 of the Code of Federal Regulations) specifies that risk assessments for the
registration of new pesticides must evaluate the Ecological Risks, Human Health Risks, and Environmental
Accumulation Risks[25]. It is important to note, however, that compliance with regard to ecological
assessments extends only to “non-target plants, fish, and wildlife species” without any legislative guidance
provided for microorganisms.
Only recently in 2013 did the EPA promulgate the final rules on data requirements (revised part 158 W) to
provide distinct jurisdiction for “antimicrobial” and “non-antimicrobial” pesticides under the Federal
Insecticide, Fungicide, and Rodenticide Act (FIFRA). Many pesticides with potential antimicrobial
properties are nonetheless still registered as “non-antimicrobial” products (and are thus regulated under
conventional mandates) as the result of mutually exclusive categorization schemas and a long list of
exemptions. For example, an “antimicrobial pesticide” is defined under section 2 (mm) of FIFRA as any
pesticide designed to disinfect, sanitize, reduce, or mitigate the growth of bacteria, viruses, fungi, protozoa,
algae, or slime mold[26]. In nearly all cases, though, these criteria are nullified by the presence of additional
claims (e.g., herbicidal or insecticidal properties), which result in the product (e.g., herbicides and
insecticides) being classified as a “non-antimicrobial pesticide”. Perplexingly, agricultural fungicides are also
considered a type of “non-antimicrobial pesticide” despite their registered intent as antimicrobial chemicals
targeting fungal species. Legislative loopholes in classification such as these present a major concern as they
obscure scientific communication and largely ignore the potential health hazards that common
agrochemicals pose on plants and animals through interactions with their host-associated microbial
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Figure 1. Schematic diagram illustrating pesticide-mediated microbiome effects on plants and insect pollinators. Insecticides,
herbicides, and fungicides are commonly used to prevent crop diseases and minimize interference of crop pests in agriculture. These
chemicals are widely popular for their perceptible benefits to crop health and yields over the short term. However, their unintentional
antimicrobial effects can deteriorate the health-promoting microbial communities associated with plants and pollinators via chronic
exposure through plant root exudate and pollen consumption, respectively. Ultimately, the feedback effects on host species have the
potential to reduce long-term crop yields (via depletion of plant-growth promoting symbionts) and bee populations (via depletion of
immune-regulating and pathogen excluding symbionts).
It is foreseeable that any chemical, in great enough quantity, could impede cellular biological function.
Thus, the peak concentration and type of exposure (e.g., acute or chronic), as well as dose-dependent
effects, are important considerations when evaluating the off-target antimicrobial effects of pesticides.
Discussion in this review will accordingly focus on the antimicrobial mechanisms of insecticides, herbicides,
and fungicides at environmentally realistic exposures. A brief in-text summary is provided for each of the
relevant mechanisms shown in Figure 2, whereas a list of known interactions is reported in Table 1.
Direct antimicrobial effects and lessons learned from legacy insecticides
The bulk of pesticide applications almost invariably reaches the soil, facilitating direct interaction with soil
microbes [Figure 2A]. As a result of this intuitive linkage, some of the earliest evidence of pesticides
exhibiting antimicrobial properties comes from studies on the soil microbiome and legacy organochlorine
(OCL) insecticides. By design, OCLs target the nervous system of insects by binding to the GABAA site of
the gamma-aminobutyric acid (GABA) chloride ionophore complex, which ultimately causes paralysis
and/or death via dysregulation of nerve cell membrane polarization. GABA is notably the most common
inhibitory neurotransmitter in both vertebrate and invertebrate systems, and is especially crucial to honey
bee foraging and grooming[45]. In situ investigations on OCLs demonstrate they can also have strong
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Table 1. Antimicrobial effects of common pesticides on plant- and pollinator-associated microbiomes
class Pesticide name Host Effect on host-associated microbiome Ref
Heptachlor Plants Growth inhibition for ~92% of Gram-positive strains tested with no effect on
any Gram-negative strains tested
DDT Plants Decrease in active soil bacterial biomass by ~60% and an increase in fungal
biomass by ~93%
Carbaryl Bees Decreased total gut bacterial loads by ~90% (enumerated via qPCR)
alongside a compositional depletion of Orbales at the order level
Clothianidin Bees Gut region-specific signatures of dysbiosis in bacterial communities after 28-
day exposure
Bees No effect on honey bee gut microbiota after 5-day of exposure and no effect
on the growth of 16 honey bee-derived bacterial strains in pure culture
Plants Species-specific inhibition of ammonia-oxidizing archaea and ammonia-
oxidizing bacteria
Plants Dose- and duration-dependent effects on diversity metrics of rice crop
rhizosphere microbiome
Plants Reduction in culturable fungi by ~37%, coupled with the decrease in β-
glycosidase, fluorescein diacetate hydrolase, acid phosphatase and urease
enzymatic activities
Imidacloprid and thiacloprid Bees Time-dependent effects on bacterial and fungal alpha diversity in honey bees
during 35-day exposure
Thiacloprid Plants Thiacloprid degradation by N2-fixing bacterium Microvirga flocculans produces
breakdown metabolites that feedback to inhibit the growth
Nitenpyram Bees Near-complete clearance of the symbiont Gillimella spp. in honey bees after
14-day exposure
2,4-Dichlorophenoxyacetic acid Plants Reduction of nod gene expression by ~32% in Sinorhizobium meliloti, ultimately
affecting nitrogen fixation and plant hormone signaling
Atrazine Plants Inhibited germination and ~80% reduction in radial growth of fungal
symbiont Trichoderma atroviride
Glyphosate Bees Reduction of symbiotic Snodgrassella alvi alongside the concurrent rise of
entomopathogenic Serratia marcescens in honey bees
Glyphosate Plants Increased prevalence of root-rot inducing Fusarium spp. [40]
Carbendazim and
Plants Dose-dependent inhibition of plant-growth promoting Pseudomonas spp. [41]
Azoxystrobin and
Plants Inhibited radial growth on agar by ~50% for the biocontrol fungus, Fusarium
oxysporum CS-20
Chlorothalonil Bees Altered structure of gut bacterial communities alongside predicted functional
changes to carbohydrate metabolism after 6-week exposure
Pristine (boscalid and
pyraclostrobin mixture)
Bees Dose-dependent compositional changes in the relative abundance of
Gilliamella spp. and Lactobacillus Firm-4/Firm-5 members after 21-day
DDT: Dichlorodiphenyltrichloroethane.
inhibitory effects on microbial growth and overall metabolic activities at the community level in soil[28,46].
Data from in vitro culture-based studies on hundreds of soil bacterial isolates confirm these effects, showing
inhibition of ~74%-100% of the tested Gram-positive strains when exposed to field-realistic concentrations
of γ-hexachlorocyclohexane, bandane, chlordane, heptachlor, and other OCLs[27,47].
Dichlorodiphenyltrichloroethane (DDT) is another well-known OCL with potent antibacterial properties,
and under field conditions causes a ~60% decrease in active soil bacterial biomass and a ~93% increase in
fungal biomass[28] - the latter of which likely represents an indirect response to the former via reduced
competition, rather than a stimulatory response to DDT since OCLs are notoriously recalcitrant to
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Figure 2. Direct and indirect mechanisms through which “non-antimicrobial” pesticides deteriorate bee-associated microbial
communities. The panels on the left (A, B) highlight how both the parent compound and breakdown metabolites of pesticides can cause
direct harm to microbial cells. The panels on the right (C, D) highlight how pesticides can alter microbial homeostasis through
modulating host immune gene expression and behaviour in honey bees.
Importantly, the mechanism by which OCLs exert their differential antimicrobial effects has long been
assumed to be through non-specific physicochemical disruption of (primarily Gram-positive) membrane-
associated processes (e.g., ionic transport, electron transport, cell wall biosynthesis), ultimately leading to
cell lysis and loss of viability[48]. That is, the antimicrobial effects of OCLs were thought to be random and
independent from their designed functions of inhibiting insect GABAergic signalling. Recent evidence,
however, suggests that GABA signalling (beyond its recognized role of neurotransmission in animals) plays
a major role in cross-kingdom chemical communication and quorum sensing events that actively regulate
bacterial-archaeal-fungal community structure[49]. GABA has also been found to represent an essential
bacterial nutrient in certain Gram-positive bacteria, such as the recently identified human gut isolate,
Candidatus “Evtepia gabavorous”[50]. Taken together, this suggests that the antimicrobial effects of OCLs are
not random and may in fact be related to their inhibitory effects on GABAergic signalling. While OCLs are
now banned in most countries due to their environmental persistence (facilitated at least in part by
inhibition of their own bioremediation[48]) and association with a broad range of other wildlife health
concerns[51], they provide an exemplary account of host-microbiome interconnectedness and how
intentional insecticidal properties can directly translate into unintentional microbicidal properties
[Figure 1].
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Other, perhaps more obvious examples of pesticides with antimicrobial properties are those of fungicides
(or simply antifungals when considered beyond their agricultural usage). Pollinating insects are exposed to
especially high levels of fungicides since they are considered “bee-safe” (in terms of acute toxicity) and are
typically applied during periods of peak pollen bloom to prevent the growth of crop disease-causing fungal
pathogens[52]. Perhaps unsurprisingly, a two-year study in managed honey bees showed that in-hive
fungicide contamination was strongly associated with reduced overall fungal concentration and genus-level
fungal diversity in beebread[53] - the main dietary staple of honey bees which consists mostly of collected
pollen. This is important since mounting evidence suggests that fungicides are negatively associated with
pollinator health despite lacking signs of acute toxicity[53-55], and that reductions in beneficial fungi are
associated with poorer pollinator nutrition and increased susceptibility to fungal disease (e.g., Chalkbrood
caused by Ascosphaera apis)[56]. Moreover, certain fungal steroids (produced by Zygosaccharomyces spp.)
have recently been identified as essential to the development of stingless bees, which otherwise fail to pupate
in their absence[57]. These findings potentially explain why group G fungicides (targeting sterol-biosynthesis)
were disproportionately associated with colony loss in a large-scale study on migratory honey bee
operations in the United States[58].
Less intuitively, a broad range of fungicides (e.g., azoxystrobin, chlorothalonil, propamocarb, and
propiconazole) can also negatively influence bacterial communities found in association with bees[43,59,60]. It
is, however, difficult to ascertain the mode of action since the findings are correlative in nature. Based on
the fact that supplementation of beneficial fungi in bees (e.g., Aureobasidium melanogenum) can increase
bacterial community abundance[61], it could be reasoned that a reduction in beneficial fungi (e.g., in
response to fungicide exposure) may also have a negative effect on bacterial loads. Evidence from plants and
rodent models supports the notion that fungi can play a major role in mediating community assembly
within the rhizosphere microbiome[62] and animal gut microbiome[63], respectively. Fungicide-induced
changes in bacterial communities could thus simply be the result of destabilized fungal-bacterial metabolic
networks. Nonetheless, azole-based fungicides possess well established antibacterial properties[64] and
Khan et al.[41] recently demonstrated in vitro that the two disjunct fungicides, hexaconazole and
carbendazim (targeting sterol biosynthesis and microtubule assembly processes, respectively), could both
exert direct bactericidal effects against plant growth-promoting Pseudomonas spp. in a dose-dependent
manner - the mechanisms, however, have not yet been elucidated. Altogether, the current literature suggests
that fungicides can directly disrupt host-associated microbiomes in multifaceted ways and that these off-
target effects (which functionally diminish plant and animal health) are vastly understudied.
Lastly, glyphosate (commonly known as “RoundUp”) is the most popular herbicide used worldwide for
weed control but has been associated with extensive disruption to plant and animal microbiomes[65]. These
effects are explained by the fact that glyphosate targets the 5-enolpyruvyl-shikimate-3-phosphate synthase
(EPSPS) enzyme used in the shikimate pathway (a central metabolic route affecting many adaptive
processes[15]) of plants, bacteria, archaea, fungi, and some protozoa. Animals notably do not possess this
pathway and thus glyphosate should theoretically demonstrate low toxicity towards them. In honey bees,
however, Motta et al.[66] demonstrated that glyphosate exposure results in dose-dependent, microbiome-
mediated toxicity and reduced survival during infection with the Gram-negative opportunistic
entomopathogen, Serratia marcescens. Data from in vitro studies support that glyphosate [rather than its
breakdown metabolite aminomethylphosphonic acid (AMPA)] is the responsible factor involved and can
exert differential antimicrobial properties on the basis of EPSPS class I (sensitive) and II (resistant) binding
affinities[67]. The honey bee symbiont, Snodgrassella alvi, encoding a class I-type EPSPS has been reported to
be consistently lower in abundance during exposure to glyphosate[39]. Together with evidence of S. alvi-
mediated immunoregulatory roles[68], this could potentially strengthen the otherwise somewhat obscure
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linkages between field-realistic glyphosate exposure and apparent susceptibility of honey bees to viral
(Deformed wing virus) and fungal (Nosema ceranae) pathogens[69].
Glyphosate can similarly increase the prevalence of root rot-inducing Fusarium spp. in the plant
rhizosphere microbiome by inhibiting plant symbionts which otherwise antagonize the growth of the
pathogen[40]. Moreover, the directly antifungal effects of glyphosate can impair mycorrhizal colonization and
alter plant-soil nutrient cycling dynamics[70] - an effect that can lead to long-term stunting of plant growth
and a gradual reduction of crop yields[71]. While some studies contest the microbiome-mediated stunting
effects of glyphosate[72,73], a meta-analysis on the topic suggests that the phenomenon is dependent on soil
pH differences[74], which may govern the microbial degradation rates of glyphosate to its inactivate
metabolite, AMPA. Collectively, the current literature indicates that glyphosate (and many other types of
herbicides[75]) can directly exert unintentional antimicrobial effects on plant- and animal-associated
microbial communities, and that these changes can consequently impair host developmental processes and
disease resistance.
Indirect antimicrobial effects via host-mediated immune dysregulation
Neonicotinoid-based insecticides, which induce neurotoxic effects via selective inhibition of insect nicotinic
acetylcholine receptors, are widely popular as a result of their very low toxicity towards humans, but have
faced much scrutiny with regard to their controversial association with declining pollinator populations[76].
One such topic of controversy is the administration of neonicotinoids, which are designed as “systemic
pesticides” intended for uptake and distribution within plant tissue - the goal being to maximize target pest
exposure while minimizing environmental contamination. However, neonicotinoids also accumulate in the
plant root exudate and pollen (in the case of angiosperm plants)[77], meaning that the rhizosphere
microbiome and the gut microbiome of pollinating insects (via oral consumption of pollen) are the primary
recipients of chronic off-target exposure. Nonetheless, studies on the antimicrobial effects of neonicotinoids
have been inconsistent across the literature.
In considering the effects of imidacloprid (a common neonicotinoid) on the honey bee microbiome,
Raymann et al.[31] elegantly demonstrated that there were no obvious impacts on genus-level bacterial
diversity metrics (measured via 16S rRNA gene sequencing) after five days of in-hive exposure. In the same
study, in vitro exposure of 16 honey bee gut-derived bacterial isolates showed essentially no sensitivity (nor
degradation ability) of the strains towards imidacloprid in mono- or mixed-culture experiments. Despite
these seemingly conclusive findings, a follow-up study testing longer exposure durations (as would be
expected from chronic hive contamination under realistic situations[78]) found that imidacloprid (and
thiacloprid) exerted a time-dependent decrease in both bacterial and fungal community alpha diversity,
with the most significant changes occurring after five weeks[34]. Empirical evidence also suggests that
clothianidin[30], nitenpyram[36], thiamethoxam[79], and other types of neonicotinoids[80] can exert bee
microbiome-disrupting side effects during longer periods of chronic exposure, although the responsible
mechanism remains unclear.
One explanation could be that the immunosuppressive effects of neonicotinoids (thought to be at the root
of globally declining populations of bees, fish, amphibians, bats, and birds[81]) act to reduce host-mediated
selective pressures on microbial communities. This notion is supported by the fact that antimicrobial
peptides (AMPs) and other effector molecules produced by the insect innate immune system (e.g., Imd,
Toll, and DUOX pathways[82,83]) possess crucial microbiome-shaping properties via their differential
activities against phylogenetically distinct microbial lineages. For example, the honey bee AMP, apidaecin,
demonstrates magnitudes lower activity against Gram-negative symbionts (e.g., G. apicola and Snodgrassella
Page 9 of Daisley et al. Microbiome Res Rep 2022;1:6
alvi found abundantly in healthy bees) compared with Gram-negative opportunistic pathogens (e.g.,
Escherichia coli)[84]. A noteworthy point to highlight is that host-adapted symbionts possess unique
functions, that in return, help shape innate immune signaling[68]. That is, the persistence of host-adapted
microbial communities is a bidirectional process, and thus this may functionally explain how immune
dysregulation by neonicotinoids could (indirectly) result in a loss of microbial diversity over time under
realistic scenarios of chronic exposure. It is also foreseeable how these effects could exacerbate the loss of
microbial diversity during concurrent exposure to chemicals that do possess antimicrobial capacities, such
is the case for antibiotics[85] and fungicides[86] - the latter of which is consistent with results showing a near
doubling of the apparent honey bee mortality risk over a four-month period during neonicotinoid co-
exposure[78]. Collectively, the current literature suggests that the microbiome-disrupting effects of pesticides
are not always as clear as direct inhibition, and in the case of neonicotinoids in bees, appear to be mediated
indirectly via host immune dysregulation [Figure 2C], and at concentrations not otherwise directly toxic to
bee physiology.
Biotransformation-dependent antimicrobial effects
The potential direct antimicrobial effects of neonicotinoids cannot be ruled out based on bee microbiome
studies alone. Nicotine represents a plant-produced signaling molecule known to interact with soil bacteria
and fungi[87], and thus neonicotinoids (i.e., structurally derived from nicotine) could foreseeably have a
higher probability of interacting with plant-associated microbial communities. In the case of rice (Oryza
sativa) crops, imidacloprid has been found to decrease diversity metrics in the rhizosphere microbiome,
with impact severity shown to be both dose- and duration-dependent[33]. Thus, this could potentially imply
an indirect plant-defense mediated response (i.e., similar to bees) given that imidacloprid (and
thiamethoxam) can significantly reduce plant immune-related gene expression[88]. Nonetheless, laboratory
studies on sandy soils (which deconvolute the potentially confounding variables of plant host-mediated
responses on the rhizosphere microbiome) instead suggest that neonicotinoids can have a direct inhibitory
effect on nitrifying organisms[89], specifically reducing that of ammonia-oxidizing archaea and bacteria in a
species-specific manner[32]. These findings are supported by other soil experiments also showing a dose-
dependent decrease in important soil enzymatic activities (e.g., β-glycosidase, fluorescein diacetate
hydrolase, acid phosphatase and urease) alongside a ~37% reduction in culturable fungi after 30 days of
imidacloprid exposure[33]. Given that neonicotinoids can persist in soil for > 1000 days in some cases[90],
these effects could foreseeably disrupt long-term microbial homeostasis.
Overall, very little mechanistic work has been done to understand the antimicrobial effects of
neonicotinoids, with the bulk of literature focusing on in vitro studies of soil isolates with neonicotinoid-
degrading properties. Interestingly, many of these isolates are nitrifying or N2-fixing bacteria such as
thiacloprid-degrading Microvirga flocculans[35], thiamethoxam-degrading Ensifer adhaerens[91], imidacloprid-
degrading Pseudomonas putida[92]. Moreover, in each of these cases, as well in fungal degradation of
imidacloprid by Aspergillus terreus[93], the breakdown is directly coupled with growth impairment of the
metabolizing strain - suggesting that neonicotinoid metabolites (e.g., nitroso-, guanidine-, and urea[92]) are
the responsible antimicrobial factors involved, rather than the parent compounds. Other examples exist
with at least 40 neonicotinoid-degrading isolates identified so far, mostly from soil or water environments
(see review[94]). Notably, the preferential impact of neonicotinoids on plant growth-promoting N2-fixing
bacteria appears to have long-term adverse outcomes in chickpea and soybean crop yields[95,96], although
data from corn crops show inconsistencies[97]. While these differences could potentially be attributable to
variation in soil parameters (e.g., organic matter, pH, temperature, etc.) known to influence the behaviour of
neonicotinoids[98,99], there is, overall, a lack of literature on the topic and further studies are needed before
any solid conclusions can be drawn.
Page 10 of Daisley et al. Microbiome Res Rep 2022;1:6
Unlike animals, which rely on their diet for nitrogen via protein consumption, plants absorb nitrogen
through their roots, often with the help of their associated microbiomes. This might explain why honey bee-
associated microbial communities cannot degrade neonicotinoids and appear to be largely unaffected by
their presence in culture[31]. It is nonetheless interesting to consider how insect-mediated detoxification of
neonicotinoids (which also produces neonicotinoid metabolites, prior to excretion via the fecal-route[100])
could have insidious effects on the gut microbiome through activating the antimicrobial effects of these
compounds. This has yet to be tested and would be a worthy direction for future studies. To note as well,
microbial biotransformation-dependent toxicity of pesticides is not a unique process to neonicotinoids (see
Table 1). Symbiont-mediated degradation of chlorpyrifos (a common organophosphate insecticide) in
Drosophila melanogaster, for example, exerts pleiotropic effects by producing two metabolites -
chlorpyrifos-oxon (with 10- to 100-fold higher insecticidal activity towards the host) and 3,5,6-trichloro-2-
pyridinol (with potent antimicrobial effects on the gut microbiome)[101] [Figure 2B]. Further, in pest insects
such as the diamondback moth, alydid stinkbug, and crucifer root maggot, the degradation of various
pesticides by microbial symbionts can infer insecticide resistance[102-105]. Together, these findings provide a
basis to speculate on how “biopesticides” (i.e., microorganisms used for pest control) could be favorably
utilized in tandem with pesticides to increase their insecticidal properties by in vivo biotransformation to
more toxic metabolites - an approach that has been proposed in several emerging microbiome management
strategies for agroecosystems[106].
Overall, the discussed material cumulatively highlights three major points: (1) plant- and animal-associated
microbiomes intrinsically differ in their sensitivity towards certain pesticides; (2) microbiome-mediated
biotransformation of pesticides can produce antimicrobial metabolites from otherwise non-antimicrobial
parent compounds; and (3) strategic modulation of host-associated microbiomes in agricultural systems has
potential to offset adverse pesticide interactions.
Behaviour-mediated antimicrobial effects
The antimicrobial effect of pesticides on pollinating insects can be amplified to a systems level through
indirect effects on foraging and other social behaviours [Figure 2D]. Using the honey bee (A. mellifera) as
an example, individual worker bees, which number in the tens of thousands per colony, forage separately
for pollen and nectar. However, their industry is not selfish - instead, they return their foraged goods to the
hive where it is concentrated into honey and pollen stores and ultimately fed to developing larvae[107]. The
social foraging and otherwise colony-oriented behaviour of worker bees thus naturally concentrates any
trace environmental contaminants from afar into higher, localized concentrations that can then accumulate
and in some cases reach toxic levels[108]. Honey bees and other eusocial insects with this type of centralized
foraging are thus vulnerable to bioaccumulation of neonicotinoids and other applied contaminants. The
direct effects of pesticides on honey bee physiology have been intensely investigated[109] but less is known
about the indirect effects that likely arise from pesticide-mediated microbiome disruption and the
downstream effects that this dysbiosis can have on individual and social behaviour.
Unique among insects, honey bees (as well as bumble bees) possess a “core” gut microbiome structure[110]
consisting of 8-10 species clusters within the genera Gilliamella, Snodgrassella, Bombella, Lactobacillus,
Apilactobacillus, and Bombilactobacillus[111]. This community is remarkably consistent across
environments[112], suggesting a strongly co-adapted symbiosis is crucial to the maintenance of bee health and
immunity[113]. For honey bees and other social insects in which individual behaviour has become integrated
into a whole, the composition of symbiotic gut microbes can influence not only the behaviour of individual
insects but also the collective behaviour of entire societies in which they live[114]. The brain-gut-microbiome
axis is one mechanism by which gut microbiomes can influence the individual performance and social
behaviour of workers within the hive[115]. Perturbation of this axis via pesticide-mediated depletion of core
Page 11 of Daisley et al. Microbiome Res Rep 2022;1:6
microbiome members should therefore affect bee behaviour in predictable and potentially manageable
ways. For example, antimicrobial effects on bee gut microbiomes may alter foraging behaviour via
individual performance or dietary preference[116], which when amplified across all individuals and colonies,
can impact pollination services.
Interestingly, the learning performances of honey bees are differentially affected by imidacloprid according
to the season[117]. Underpinning this phenomenon could be the substantial fluctuation in gut microbiome
structure known to occur between winter and summer seasons[118]. There is ample opportunity for feedback
between host and microbiome if, for example, initial changes to microbial communities then bias foraging
preference to influence the plant-associated microbes the bees are exposed to. Subtle behavioural changes
(i.e., otherwise not impacting host survival by itself) could thus hinder natural plant-pollinator microbial
exchange processes and influence the long-term maintenance of co-adapted symbionts. Some remediation
may be possible through the application of beneficial bacteria that off-set the dysbiosis inadvertently caused
by the well-intended application of commercial antibiotics[85] or pesticides[119] to hives.
Given that bee social behaviour is highly coordinated, where the worker caste can specialize into
behavioural subcastes that, besides foragers, include nurses, guards, hygienists, undertakers and scouts[120],
we expect any significant variation in the gut microbiome to affect the bee’s most fundamental behaviours,
including recruitment, hygienic, defensive and appetitive behaviours - all of which are essential to colony’s
eusocial structure[121]. For humans, communication along the brain-gut axis is mediated through immune
mechanisms, elements of the nervous system and microbial metabolites that relay nutrition and health
status from the gut to the brain[122]. For insects and bees in particular, the mechanics of this axis are less well
defined, however, because social insects have evolved a particularly strong dependence upon gut
symbionts[6], there is a strong rationale for investigation of this topic in future studies.
Pesticides, like antibiotics, represent chemical stressors that can exert selective pressures on microbial
communities. Mounting evidence suggests that the evolution of tolerance, resistance, and persistence[123]
towards pesticides may consequently impact microbial response to antibiotics through both generalizable
and specific mechanisms[124]. This represents a major human health concern in relation to the rise of
multidrug-resistant pathogens (or “superbugs”) and hospital-acquired infections that are increasingly
difficult to treat.
One mechanism of overlapping resistance is through efflux pumps (e.g., SMR and MATE families in
particular[125]), which are membrane-bound transporters that can export multiple toxic substrates out of the
cell. For example, Kurenbach et al.[126] found that pre-exposure of E. coli to two herbicides (glyphosate and
dicamba) could significantly increase subsequent tolerance against two broad-spectrum antibiotics
(chloramphenicol and kanamycin) via overexpression of the AcrAB efflux pump - an effect that failed to
occur in the presence of efflux pump inhibitor Phe-Arg β-naphtylamide. Others have also reported that
biocide usage selects for overexpression of efflux pumps[127]. Alternatively, a study on realistic co-exposure of
23 pesticides in E. coli demonstrated that streptomycin-resistance emerged rapidly via selected for
mutations in acrR (encoding a transcriptional repressor that regulates acrAB expression) as well as biofilm,
heat shock, oxidative stress defense, and carbon starvation genes[128].
In the case that pesticides cannot be pumped out of the cell, intrinsic or acquired enzymatic functions can
facilitate overlapping resistance to antibiotics. For example, the plasmid-encoded organophosphorus
hydrolase (OPH) of insecticide-degrading Bacillus isolates (e.g., B. cereus, B. firmus, and B. thuringiensis
Page 12 of Daisley et al. Microbiome Res Rep 2022;1:6
strains from contaminated agricultural sites) can confer multidrug resistance by inactivating
chloramphenical, monochrotophos, ampicillin, cefotaxime, streptomycin and tetracycline antibiotics[129].
The noteworthy point is that similar or identical OPHs have been found in Pseudomonas, Flavobacterium,
Sphingobium, and Agrobacterium spp.[130-132], with molecular evidence suggesting the response genes have
probably evolved within the past 70 years[133]. This coincides directly with the introduction of
organophosphate insecticides and the global rise of antibiotic resistance, and thus it is interesting to
speculate how these processes have co-impacted the evolutionary trajectory of microbial life. Similar
comparisons can be made for several oxidoreductases, transferases, and lyases in terms of conferring
overlapping pesticide and antibiotic resistance properties[124].
Several important areas have been highlighted in this review that deserve future scrutiny. These are
summarized below:
(1) Currently, regulatory oversight of agrochemical usage is inadequate and fails to address potential effects
on ecosystem microbiomes which are in turn critical to environmental health. A reassessment of the
legislative framework that governs the use of agrochemicals is urgently warranted.
(2) Agrochemical toxicity is generally defined as a construct of their direct and acute harmfulness towards
plant and animal species, whereas their detrimental effects on plant- and animal-associated microbiomes
are likely to have more subtle, accumulative consequences. Long-term studies of plant and animal health
(including measurements of microbiome diversity, composition and activity) following exposure to
agricultural compounds are required to allow balanced calculation of risk vs. benefit of agrochemical use.
(3) Microbial biotransformation of agrochemicals is understudied and requires urgent evaluation if we are
to fully understand the impact of a given compound on the environment. Relatedly, bioremediation efforts
need to account for potential adverse effects of breakdown metabolites on not only plant and animal
physiology, but also their host-associated microbial communities.
(4) Antimicrobial resistance is a current global threat to health, and it is imperative that the role of
agrochemical use in the development of antimicrobial resistance is fully studied and appreciated.
(5) The gut-microbiome-brain axis is an emerging field of interest with relevance to pesticide-
neuroimmune interactions and merits particular attention in eusocial bee species, such as honey bees, which
exhibit strong interdependencies on their gut microbiomes.
In addressing these issues as they relate to microbiome-mediated pesticide toxicity, proof of causality is an
important factor to consider. Multi-omics technologies have massively improved our ability to identify
taxonomic- and functional-based correlations of host-associated microbial communities in response to
agrochemical exposures. However, demonstrating an association between pesticide exposure and
microbiome change is not enough to authenticate an antimicrobial effect. As discussed in this review, it
remains challenging (due to confounding host variables) to delineate between direct antimicrobial
properties and indirect microbiome disrupting activities based on in vivo observation alone [Figure 2].
Indeed, culture-based interrogation of host-derived isolates in vitro can be extremely informative, although
not all microbes are culturable and pesticide co-culture experiments with single strains are not adequately
representative of the highly complex polymicrobial interactions that may occur under natural conditions
(see Ref.[134] for review on methodological challenges of pesticide risk assessment).
Page 13 of Daisley et al. Microbiome Res Rep 2022;1:6
Collectively, this indicates a substantial need for model development of host-free rhizosphere and insect gut
microbiome systems. Bioreactor models for the human gut microbiome already exist (e.g., benchtop
“Robogut”[135] and SHIME systems[136]) and are actively being used to decipher microbe-drug interactions
relevant to human disease treatments[137]. Notably, these systems may be easily adapted for agricultural
purposes as well, specifically allowing for high-throughput evaluation of microbe-pesticide interactions
pertaining to honey bee health, commercial crop yield, and environmental health as a whole. Future
development and testing of such models should be an immediate priority based on the fact that current
pesticide risk assessment strategies could also benefit from their use by improving the veracity of new
product safety claims prior to their release.
We have outlined the multifaceted ways in which agricultural chemicals can disrupt microbial ecosystem
function using examples from honey bees and crop plants. Perhaps one of the more alarming aspects of the
current situation is the apparent weakness of regulatory policies, which are riddled with loopholes and
largely ignore contemporary research findings on host microbiome-pesticide interactions.
There is a pressing need to reassess the use of agrochemical xenobiotics through the lens of microbial
ecology and the concurrent or subsequent effects on host (animal and plant) physiology. This is not easy to
do, since most microbial ecosystems are highly complex, and so much of the microbial world remains
unstudied. However, tools to study microbiomes and their functions are now increasingly accessible, and
should be exploited to study microbial ecosystem modulation by herbicides, insecticides and fungicides
across all agricultural sectors as a matter of great urgency.
Authors’ contributions
Contributed to the conceptualization of ideas presented in the manuscript: Daisley BA, Chernyshova AM,
Thompson GJ, Allen-Vercoe E
Drafted the manuscript and generated the figures: Daisley BA
All authors helped in revising the manuscript and agree to be accountable for the content of the work.
Availability of data and materials
Not applicable.
Financial support and sponsorship
This work was supported a Natural Sciences and Engineering Research Council of Canada (NSERC)
Discovery Grant (RGPIN-2020-05647) and an NSERC Postdoctoral Fellowship Award (PDF-558010-2021).
Conflicts of interest
All authors declared that there are no conflicts of interest.
Ethical approval and consent to participate
Not applicable.
Consent for publication
Not applicable.
Page 14 of Daisley et al. Microbiome Res Rep 2022;1:6
© The Author(s) 2022.
Banerjee S, Schlaeppi K, van der Heijden MGA. Keystone taxa as drivers of microbiome structure and functioning. Nat Rev
Microbiol 2018;16:567-76. DOI PubMed
Wabnitz K, Gabrysch S, Guinto R, et al. A pledge for planetary health to unite health professionals in the Anthropocene. Lancet
2020;396:1471-3. DOI PubMed PMC
Trinh P, Zaneveld JR, Safranek S, Rabinowitz PM. One health relationships between human, animal, and environmental
microbiomes: a mini-review. Front Public Health 2018;6:235. DOI PubMed PMC
Guerrero R, Margulis L, Berlanga M. Symbiogenesis: the holobiont as a unit of evolution. Int Microbiol 2013;16:133-43. DOI
Moran NA, Ochman H, Hammer TJ. Evolutionary and ecological consequences of gut microbial communities. Annu Rev Ecol Evol
Syst 2019;50:451-75. DOI PubMed PMC
Barribeau SM, Sadd BM, du Plessis L, et al. A depauperate immune repertoire precedes evolution of sociality in bees. Genome Biol
2015;16:83. DOI PubMed PMC
Busby PE, Soman C, Wagner MR, et al. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol
2017;15:e2001793. DOI PubMed PMC
Ramírez-Puebla ST, Servín-Garcidueñas LE, Jiménez-Marín B, et al. Gut and root microbiota commonalities. Appl Environ
Microbiol 2013;79:2-9. DOI PubMed PMC
Foster KR, Schluter J, Coyte KZ, Rakoff-Nahoum S. The evolution of the host microbiome as an ecosystem on a leash. Nature
2017;548:43-51. DOI PubMed PMC
CERIS. National Pesticide Information Retrieval System. Available from: [Last accessed on
25 Jan 2022].
Prescott SL, Wegienka G, Logan AC, Katz DL. Dysbiotic drift and biopsychosocial medicine: how the microbiome links personal,
public and planetary health. Biopsychosoc Med 2018;12:7. DOI PubMed PMC
FAO. Pesticide use. Global, regional and country trends 1990-2018. Available from:
[Last accessed on 25 Jan 2022].
Blaser MJ. The theory of disappearing microbiota and the epidemics of chronic diseases. Nat Rev Immunol 2017;17:461-3. DOI
Musso G, Gambino R, Cassader M. Obesity, diabetes, and gut microbiota: the hygiene hypothesis expanded? Diabetes Care
2010;33:2277-84. DOI PubMed PMC
Daisley BA, Koenig D, Engelbrecht K, et al. Emerging connections between gut microbiome bioenergetics and chronic metabolic
diseases. Cell Rep 2021;37:110087. DOI PubMed
Franzosa EA, Sirota-Madi A, Avila-Pacheco J, et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease.
Nat Microbiol 2019;4:293-305. DOI PubMed PMC
Qin J, Li Y, Cai Z, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 2012;490:55-60. DOI
Liu R, Hong J, Xu X, et al. Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention. Nat Med
2017;23:859-68. DOI PubMed
Jie Z, Xia H, Zhong SL, et al. The gut microbiome in atherosclerotic cardiovascular disease. Nat Commun 2017;8:845. DOI PubMed
Helmink BA, Khan MAW, Hermann A, Gopalakrishnan V, Wargo JA. The microbiome, cancer, and cancer therapy. Nat Med
2019;25:377-88. DOI PubMed
Johnson RM, Ellis MD, Mullin CA, Frazier M. Pesticides and honey bee toxicity - USA. Apidologie 2010;41:312-31. DOI21.
Rani L, Thapa K, Kanojia N, et al. An extensive review on the consequences of chemical pesticides on human health and
environment. J Clean Prod 2021;283:124657. DOI
Köhler HR, Triebskorn R. Wildlife ecotoxicology of pesticides: can we track effects to the population level and beyond? Science
2013;341:759-65. DOI PubMed
Sharma A, Kumar V, Shahzad B, et al. Worldwide pesticide usage and its impacts on ecosystem. SN Appl Sci 2019;1:1446. DOI24.
EPA. Pesticide Registration Process. Environ Prot Agency 2021. Available from:
pesticide-risks/overview-risk-assessment-pesticide-program [Last accessed on 25 Jan 2022].
eCFR. Protection of Environment. Code Fed Regul 2013. Available from: [Last accessed on 29
November 2021].
Trudgill PW, Widdus R, Rees JS. Effects of organochlorine insecticides on bacterial growth, respiration and viability. J Gen
Microbiol 1971;69:1-13. DOI PubMed
Bollen WB, Morrison HE, Crowell HH. Effect of field and laboratory treatments with BHC and DDT on nitrogen transformations and
soil respiration1. J Econ Entomol 1954;47:307-12. DOI
Nogrado K, Lee S, Chon K, Lee J. Effect of transient exposure to carbaryl wettable powder on the gut microbial community of honey
bees. Appl Biol Chem 2019;62:6. DOI
Page 15 of Daisley et al. Microbiome Res Rep 2022;1:6
Khoury S, Gauthier J, Bouslama S, Cheaib B, Giovenazzo P, Derome N. Dietary contamination with a neonicotinoid (Clothianidin)
gradient triggers specific dysbiosis signatures of microbiota activity along the honeybee (Apis mellifera) digestive tract.
Microorganisms 2021;9:2283. DOI PubMed PMC
Raymann K, Motta EVS, Girard C, Riddington IM, Dinser JA, Moran NA. Imidacloprid decreases honey bee survival rates but does
not affect the gut microbiome. Appl Environ Microbiol 2018;84:e00545-18. DOI
Cycoń M, Piotrowska-Seget Z. Community structure of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in soil treated
with the insecticide imidacloprid. Biomed Res Int 2015;2015:582938. DOI PubMed PMC
Mahapatra B, Adak T, Patil NKB, et al. Imidacloprid application changes microbial dynamics and enzymes in rice soil. Ecotoxicol
Environ Saf 2017;144:123-30. DOI PubMed
Alberoni D, Favaro R, Baffoni L, Angeli S, Di Gioia D. Neonicotinoids in the agroecosystem: In-field long-term assessment on
honeybee colony strength and microbiome. Sci Total Environ 2021;762:144116. DOI PubMed
Zhao Y, Jiang H, Cheng X, et al. Neonicotinoid thiacloprid transformation by the N2-fixing bacterium Microvirga flocculans
CGMCC 1.16731 and toxicity of the amide metabolite. Int Biodeterior Biodegrad 2019;145:104806. DOI
Zhu L, Qi S, Xue X, Niu X, Wu L. Nitenpyram disturbs gut microbiota and influences metabolic homeostasis and immunity in honey
bee (Apis mellifera L.). Environ Pollut 2020;258:113671. DOI PubMed
Fox JE, Starcevic M, Kow KY, Burow ME, McLachlan JA. Nitrogen fixation. Endocrine disrupters and flavonoid signalling. Nature
2001;413:128-9. DOI PubMed
Santoro PH, Cavaguchi SA, Alexandre TM, Zorzetti J, Neves PMOJ. In vitro sensitivity of antagonistic Trichoderma atroviride to
herbicides. Braz arch biol technol 2014;57:238-43. DOI
Motta EVS, Raymann K, Moran NA. Glyphosate perturbs the gut microbiota of honey bees. Proc Natl Acad Sci U S A
2018;115:10305-10. DOI PubMed PMC
Fernandez M, Zentner R, Basnyat P, Gehl D, Selles F, Huber D. Glyphosate associations with cereal diseases caused by Fusarium
spp. in the Canadian Prairies. Eur J Agron 2009;31:133-43. DOI
Khan S, Shahid M, Khan MS, et al. Fungicide-tolerant plant growth-promoting rhizobacteria mitigate physiological disruption of
white radish caused by fungicides used in the field cultivation. Int J Environ Res Public Health 2020;17:7251. DOI PubMed PMC
Fravel D, Deahl K, Stommel J. Compatibility of the biocontrol fungus Fusarium oxysporum strain CS-20 with selected fungicides.
Biological Control 2005;34:165-9. DOI
Kakumanu ML, Reeves AM, Anderson TD, Rodrigues RR, Williams MA. Honey bee gut microbiome is altered by in-hive pesticide
exposures. Front Microbiol 2016;7:1255. DOI PubMed PMC
Degrandi-hoffman G, Corby-harris V, Dejong EW, Chambers M, Hidalgo G. Honey bee gut microbial communities are robust to the
fungicide Pristine® consumed in pollen. Apidologie 2017;48:340-52. DOI
Mustard JA, Jones L, Wright GA. GABA signaling affects motor function in the honey bee. J Insect Physiol 2020;120:103989. DOI
MacRae IC, Raghu K, Castro TF. Persistence and biodegradation of four common isomers of benzene hexachloride in submerged
soils. J Agric Food Chem 1967;15:911-4. DOI
Gray PHH. Effects of benzene hexachloride on soil micro-organisms. Can J Bot 1954;32:1-9. DOI47.
Shahid M, Manoharadas S, Altaf M, Alrefaei AF. Organochlorine pesticides negatively influenced the cellular growth,
morphostructure, cell viability, and biofilm-formation and phosphate-solubilization activities of Enterobacter cloacae strain EAM 35.
ACS Omega 2021;6:5548-59. DOI PubMed PMC
Quillin SJ, Tran P, Prindle A. Potential roles for gamma-aminobutyric acid signaling in bacterial communities. Bioelectricity
2021;3:120-5. DOI PubMed PMC
Strandwitz P, Kim KH, Terekhova D, et al. GABA-modulating bacteria of the human gut microbiota. Nat Microbiol 2019;4:396-403.
Zadoks J, Waibel H. From pesticides to genetically modified plants: history, economics and politics. NJAS - Wagening J Life Sci
2000;48:125-49. DOI
Mullin CA, Frazier M, Frazier JL, et al. High levels of miticides and agrochemicals in North American apiaries: implications for
honey bee health. PLoS One 2010;5:e9754. DOI PubMed PMC
Yoder JA, Jajack AJ, Rosselot AE, Smith TJ, Yerke MC, Sammataro D. Fungicide contamination reduces beneficial fungi in bee
bread based on an area-wide field study in honey bee, Apis mellifera, colonies. J Toxicol Environ Health A 2013;76:587-600. DOI
Park MG, Blitzer EJ, Gibbs J, Losey JE, Danforth BN. Negative effects of pesticides on wild bee communities can be buffered by
landscape context. Proc Biol Sci 2015;282:20150299. DOI PubMed PMC
Bernauer OM, Gaines-Day HR, Steffan SA. Colonies of bumble bees (Bombus impatiens) produce fewer workers, less bee biomass,
and have smaller mother queens following fungicide exposure. Insects 2015;6:478-88. DOI PubMed PMC
Evison SE, Jensen AB. The biology and prevalence of fungal diseases in managed and wild bees. Curr Opin Insect Sci 2018;26:105-
13. DOI PubMed
Paludo CR, Menezes C, Silva-Junior EA, et al. Stingless bee larvae require fungal steroid to pupate. Sci Rep 2018;8:1122. DOI
PubMed PMC
Traynor KS, Pettis JS, Tarpy DR, et al. In-hive Pesticide Exposome: Assessing risks to migratory honey bees from in-hive pesticide
contamination in the Eastern United States. Sci Rep 2016;6:33207. DOI PubMed PMC
Steffan SA, Dharampal PS, Diaz-Garcia L, Currie CR, Zalapa J, Hittinger CT. Empirical, metagenomic, and computational 59.
Page 16 of Daisley et al. Microbiome Res Rep 2022;1:6
techniques illuminate the mechanisms by which fungicides compromise bee health. J Vis Exp 2017. DOI PubMed PMC
Paris L, Peghaire E, Moné A, et al. Honeybee gut microbiota dysbiosis in pesticide/parasite co-exposures is mainly induced by
Nosema ceranae. J Invertebr Pathol 2020;172:107348. DOI PubMed
Hsu CK, Wang DY, Wu MC. A potential fungal probiotic Aureobasidium melanogenum CK-CsC for the Western honey bee, Apis
mellifera. J Fungi (Basel) 2021;7:508. DOI PubMed PMC
Trivedi P, Leach JE, Tringe SG, Sa T, Singh BK. Plant-microbiome interactions: from community assembly to plant health. Nat Rev
Microbiol 2020;18:607-21. DOI PubMed
van Tilburg Bernardes E, Pettersen VK, Gutierrez MW, et al. Intestinal fungi are causally implicated in microbiome assembly and
immune development in mice. Nat Commun 2020;11:2577. DOI PubMed PMC
Jackson CJ, Lamb DC, Kelly DE, Kelly SL. Bactericidal and inhibitory effects of azole antifungal compounds on Mycobacterium
smegmatis. FEMS Microbiol Lett 2000;192:159-62. DOI PubMed
Syromyatnikov MY, Isuwa MM, Savinkova OV, Derevshchikova MI, Popov VN. The effect of pesticides on the microbiome of
animals. Agriculture 2020;10:79. DOI
Motta EVS, Mak M, De Jong TK, et al. Oral or topical exposure to glyphosate in herbicide formulation impacts the gut microbiota
and survival rates of honey bees. Appl Environ Microbiol 2020;86:e01150-20. DOI PubMed PMC
Blot N, Veillat L, Rouzé R, Delatte H. Glyphosate, but not its metabolite AMPA, alters the honeybee gut microbiota. PLoS One
2019;14:e0215466. DOI PubMed PMC
Horak RD, Leonard SP, Moran NA. Symbionts shape host innate immunity in honeybees. Proc Biol Sci 2020;287:20201184. DOI
PubMed PMC
Castelli L, Balbuena S, Branchiccela B, et al. Impact of chronic exposure to sublethal doses of glyphosate on honey bee immunity,
gut microbiota and infection by pathogens. Microorganisms 2021;9:845. DOI PubMed PMC
Helander M, Saloniemi I, Omacini M, Druille M, Salminen JP, Saikkonen K. Glyphosate decreases mycorrhizal colonization and
affects plant-soil feedback. Sci Total Environ 2018;642:285-91. DOI PubMed
Van Bruggen AHC, He MM, Shin K, et al. Environmental and health effects of the herbicide glyphosate. Sci Total Environ 2018;616-
617:255-68. DOI PubMed
Schlatter DC, Yin C, Hulbert S, Burke I, Paulitz T. Impacts of repeated glyphosate use on wheat-associated bacteria are small and
depend on glyphosate use history. Appl Environ Microbiol 2017;83:e01354-17. DOI PubMed PMC
Ramirez-Villacis DX, Finkel OM, Salas-González I, et al. Root microbiome modulates plant growth promotion induced by low doses
of glyphosate. mSphere 2020;5:e00484-20. DOI PubMed PMC
Nguyen DB, Rose MT, Rose TJ, Morris SG, van Zwieten L. Impact of glyphosate on soil microbial biomass and respiration: a meta-
analysis. Soil Biol Biochem 2016;92:50-7. DOI
Ramakrishnan B, Maddela NR, Venkateswarlu K, Megharaj M. Linkages between plant rhizosphere and animal gut environments:
interaction effects of pesticides with their microbiomes. Environ Adv 2021;5:100091. DOI
Goulson D. The insect apocalypse, and why it matters. Curr Biol 2019;29:R967-71. DOI PubMed76.
Sánchez-Bayo F. Environmental science. The trouble with neonicotinoids. Science 2014;346:806-7. DOI PubMed77.
Tsvetkov N, Samson-Robert O, Sood K, et al. Chronic exposure to neonicotinoids reduces honey bee health near corn crops. Science
2017;356:1395-7. DOI PubMed
Macías-Macías JO, Tapia-Rivera JC, De la Mora A, et al. Nosema ceranae causes cellular immunosuppression and interacts with
thiamethoxam to increase mortality in the stingless bee Melipona colimana. Sci Rep 2020;10:17021. DOI PubMed PMC
Jones JC, Fruciano C, Hildebrand F, et al. Gut microbiota composition is associated with environmental landscape in honey bees.
Ecol Evol 2018;8:441-51. DOI PubMed PMC
Mason R, Tennekes H, Sánchez-Bayo F, Jepsen P. Immune suppression by neonicotinoid insecticides at the root of global wildlife
declines. J Environ Immunol Toxicol 2013;1:3-12. DOI
Chmiel JA, Daisley BA, Burton JP, Reid G. Deleterious effects of neonicotinoid pesticides on drosophila melanogaster immune
pathways. mBio 2019;10:e01395-19. DOI PubMed PMC
Daisley BA, Trinder M, McDowell TW, et al. Neonicotinoid-induced pathogen susceptibility is mitigated by Lactobacillus plantarum
immune stimulation in a Drosophila melanogaster model. Sci Rep 2017;7:2703. DOI PubMed PMC
Kwong WK, Mancenido AL, Moran NA. Immune system stimulation by the native gut microbiota of honey bees. R Soc Open Sci
2017;4:170003. DOI PubMed PMC
Daisley BA, Pitek AP, Chmiel JA, et al. Lactobacillus spp. attenuate antibiotic-induced immune and microbiota dysregulation in
honey bees. Commun Biol 2020;3:534. DOI PubMed PMC
Woodcock BA, Bullock JM, Shore RF, et al. Country-specific effects of neonicotinoid pesticides on honey bees and wild bees.
Science 2017;356:1393-5. DOI PubMed
Lisuma JB, Mbega ER, Ndakidemi PA. Influence of nicotine released in soils to the growth of subsequent maize crop, soil bacteria
and fungi. Int J Agric Biol 2019;22:1-12. DOI
Wulff JA, Kiani M, Regan K, Eubanks MD, Szczepaniec A. Neonicotinoid insecticides alter the transcriptome of soybean and
decrease plant resistance. Int J Mol Sci 2019;20:783. DOI PubMed PMC
Cycoń M, Piotrowska-Seget Z. Biochemical and microbial soil functioning after application of the insecticide imidacloprid. J Environ
Sci (China) 2015;27:147-58. DOI PubMed
Bonmatin JM, Giorio C, Girolami V, et al. Environmental fate and exposure; neonicotinoids and fipronil. Environ Sci Pollut Res Int
2015;22:35-67. DOI PubMed PMC
Page 17 of Daisley et al. Microbiome Res Rep 2022;1:6
Zhou GC, Wang Y, Zhai S, et al. Biodegradation of the neonicotinoid insecticide thiamethoxam by the nitrogen-fixing and plant-
growth-promoting rhizobacterium Ensifer adhaerens strain TMX-23. Appl Microbiol Biotechnol 2013;97:4065-74. DOI PubMed
Lu TQ, Mao SY, Sun SL, Yang WL, Ge F, Dai YJ. Regulation of hydroxylation and nitroreduction pathways during metabolism of
the neonicotinoid insecticide imidacloprid by pseudomonas putida. J Agric Food Chem 2016;64:4866-75. DOI PubMed
Mohammed YMM, Badawy MEI. Biodegradation of imidacloprid in liquid media by an isolated wastewater fungus Aspergillus
terreus YESM3. J Environ Sci Health B 2017;52:752-61. DOI PubMed
Pang S, Lin Z, Zhang W, Mishra S, Bhatt P, Chen S. Insights into the microbial degradation and biochemical mechanisms of
neonicotinoids. Front Microbiol 2020;11:868. DOI PubMed PMC
Shahid M, Khan MS, Ahmed B, Syed A, Bahkali AH. Physiological disruption, structural deformation and low grain yield induced
by neonicotinoid insecticides in chickpea: A long term phytotoxicity investigation. Chemosphere 2021;262:128388. DOI PubMed
Douglas MR, Rohr JR, Tooker JF, Kaplan I. EDITOR’S CHOICE: Neonicotinoid insecticide travels through a soil food chain,
disrupting biological control of non-target pests and decreasing soya bean yield. J Appl Ecol 2015;52:250-60. DOI
Myresiotis CK, Vryzas Z, Papadopoulou-Mourkidou E. Effect of specific plant-growth-promoting rhizobacteria (PGPR) on growth
and uptake of neonicotinoid insecticide thiamethoxam in corn (Zea mays L.) seedlings. Pest Manag Sci 2015;71:1258-66. DOI
Flores-Céspedes F, González-Pradas E, Fernández-Pérez M, Villafranca-Sánchez M, Socías-Viciana M, Ureña-Amate MD. Effects of
dissolved organic carbon on sorption and mobility of imidacloprid in soil. J Environ Qual 2002;31:880-8. DOI PubMed
Oi M. Time-dependent sorption of imidacloprid in two different soils. J Agric Food Chem 1999;47:327-32. DOI PubMed99.
Suchail S, Guez D, Belzunces LP. Discrepancy between acute and chronic toxicity induced by imidacloprid and its metabolites in.
Apis mellifera ;20:2482-6. DOI PubMed
Daisley BA, Trinder M, McDowell TW, Collins SL, Sumarah MW, Reid G. Microbiota-mediated modulation of organophosphate
insecticide toxicity by species-dependent interactions with lactobacilli in a drosophila melanogaster insect model. Appl Environ
Microbiol 2018;84:e02820-17. DOI PubMed PMC
Xia X, Zheng D, Zhong H, et al. DNA sequencing reveals the midgut microbiota of diamondback moth, Plutella xylostella (L.) and a
possible relationship with insecticide resistance. PLoS One 2013;8:e68852. DOI PubMed PMC
Lukwinski AT, Hill JE, Khachatourians GG, Hemmingsen SM, Hegedus DD. Biochemical and taxonomic characterization of bacteria
associated with the crucifer root maggot (Delia radicum). Can J Microbiol 2006;52:197-208. DOI PubMed
Engel P, Moran NA. The gut microbiota of insects - diversity in structure and function. FEMS Microbiol Rev 2013;37:699-735. DOI
Almeida LG, Moraes LA, Trigo JR, Omoto C, Cônsoli FL. The gut microbiota of insecticide-resistant insects houses insecticide-
degrading bacteria: a potential source for biotechnological exploitation. PLoS One 2017;12:e0174754. DOI PubMed PMC
French E, Kaplan I, Iyer-Pascuzzi A, Nakatsu CH, Enders L. Emerging strategies for precision microbiome management in diverse
agroecosystems. Nat Plants 2021;7:256-67. DOI PubMed
Erler S, Denner A, Bobiş O, Forsgren E, Moritz RF. Diversity of honey stores and their impact on pathogenic bacteria of the
honeybee, Apis mellifera. Ecol Evol 2014;4:3960-7. DOI PubMed PMC
Blacquière T, Smagghe G, van Gestel CA, Mommaerts V. Neonicotinoids in bees: a review on concentrations, side-effects and risk
assessment. Ecotoxicology 2012;21:973-92. DOI PubMed PMC
Cullen MG, Thompson LJ, Carolan JC, Stout JC, Stanley DA. Fungicides, herbicides and bees: a systematic review of existing
research and methods. PLoS One 2019;14:e0225743. DOI PubMed PMC
Martinson VG, Danforth BN, Minckley RL, Rueppell O, Tingek S, Moran NA. A simple and distinctive microbiota associated with
honey bees and bumble bees. Mol Ecol 2011;20:619-28. DOI PubMed
Daisley BA, Reid G. BEExact: a metataxonomic database tool for high-resolution inference of bee-associated microbial communities.
mSystems 2021;6:e00082-21. DOI PubMed PMC
Kwong WK, Medina LA, Koch H, et al. Dynamic microbiome evolution in social bees. Sci Adv 2017;3:e1600513. DOI PubMed
Kwong WK, Moran NA. Gut microbial communities of social bees. Nat Rev Microbiol 2016;14:374-84. DOI PubMed PMC113.
Jones JC, Fruciano C, Marchant J, et al. The gut microbiome is associated with behavioural task in honey bees. Insectes Soc
2018;65:419-29. DOI PubMed PMC
Liberti J, Engel P. The gut microbiota - brain axis of insects. Curr Opin Insect Sci 2020;39:6-13. DOI PubMed115.
Koch H, Brown MJ, Stevenson PC. The role of disease in bee foraging ecology. Curr Opin Insect Sci 2017;21:60-7. DOI PubMed116.
Decourtye A, Lacassie E, Pham-Delègue MH. Learning performances of honeybees (Apis mellifera L) are differentially affected by
imidacloprid according to the season. Pest Manag Sci 2003;59:269-78. DOI PubMed
Kešnerová L, Emery O, Troilo M, Liberti J, Erkosar B, Engel P. Gut microbiota structure differs between honeybees in winter and
summer. ISME J 2020;14:801-14. DOI PubMed PMC
Chmiel JA, Daisley BA, Pitek AP, Thompson GJ, Reid G. Understanding the effects of sublethal pesticide exposure on honey bees: a
role for probiotics as mediators of environmental stress. Front Ecol Evol 2020;8:22. DOI
Robinson GE. Regulation of division of labor in insect societies. Annu Rev Entomol 1992;37:637-65. DOI PubMed120.
Nouvian M, Reinhard J, Giurfa M. The defensive response of the honeybee Apis mellifera. J Exp Biol 2016;219:3505-17. DOI
Martin CR, Osadchiy V, Kalani A, Mayer EA. The brain-gut-microbiome axis. Cell Mol Gastroenterol Hepatol 2018;6:133-48. DOI
PubMed PMC
Page 18 of Daisley et al. Microbiome Res Rep 2022;1:6
Brauner A, Fridman O, Gefen O, Balaban NQ. Distinguishing between resistance, tolerance and persistence to antibiotic treatment.
Nat Rev Microbiol 2016;14:320-30. DOI PubMed
Ramakrishnan B, Venkateswarlu K, Sethunathan N, Megharaj M. Local applications but global implications: can pesticides drive
microorganisms to develop antimicrobial resistance? Sci Total Environ 2019;654:177-89. DOI PubMed
Blanco P, Hernando-Amado S, Reales-Calderon JA, et al. Bacterial multidrug efflux pumps: much more than antibiotic resistance
determinants. Microorganisms 2016;4:14. DOI PubMed PMC
Kurenbach B, Marjoshi D, Amábile-Cuevas CF, et al. Sublethal exposure to commercial formulations of the herbicides dicamba, 2,4-
dichlorophenoxyacetic acid, and glyphosate cause changes in antibiotic susceptibility in Escherichia coli and Salmonella enterica
serovar Typhimurium. mBio 2015;6:e00009-15. DOI PubMed PMC
Fraise AP. Biocide abuse and antimicrobial resistance--a cause for concern? J Antimicrob Chemother 2002;49:11-2. DOI PubMed127.
Xing Y, Wu S, Men Y. Exposure to environmental levels of pesticides stimulates and diversifies evolution in Escherichia coli toward
higher antibiotic resistance. Environ Sci Technol 2020;54:8770-8. DOI PubMed
Rangasamy K, Athiappan M, Devarajan N, Parray JA. Emergence of multi drug resistance among soil bacteria exposing to
insecticides. Microb Pathog 2017;105:153-65. DOI PubMed
Harper LL, McDaniel CS, Miller CE, Wild JR. Dissimilar plasmids isolated from Pseudomonas diminuta MG and a Flavobacterium
sp. (ATCC 27551) contain identical opd genes. Appl Environ Microbiol 1988;54:2586-9. DOI PubMed PMC
Horne I, Sutherland TD, Harcourt RL, Russell RJ, Oakeshott JG. Identification of an opd (organophosphate degradation) gene in an
Agrobacterium isolate. Appl Environ Microbiol 2002;68:3371-6. DOI PubMed PMC
Mulbry WW, Karns JS. Parathion hydrolase specified by the Flavobacterium opd gene: relationship between the gene and protein. J
Bacteriol 1989;171:6740-6. DOI PubMed PMC
Singh BK. Organophosphorus-degrading bacteria: ecology and industrial applications. Nat Rev Microbiol 2009;7:156-64. DOI
Utembe W, Kamng’ona AW. Gut microbiota-mediated pesticide toxicity in humans: Methodological issues and challenges in the risk
assessment of pesticides. Chemosphere 2021;271:129817. DOI PubMed
McDonald JA, Schroeter K, Fuentes S, et al. Evaluation of microbial community reproducibility, stability and composition in a
human distal gut chemostat model. J Microbiol Methods 2013;95:167-74. DOI PubMed
. Van de Wiele T, Van den Abbeele P, Ossieur W, Possemiers S, Marzorati M. The Simulator of the Human Intestinal Microbial
Ecosystem (SHIME®). In: Verhoeckx K, Cotter P, López-expósito I, Kleiveland C, Lea T, Mackie A, Requena T, Swiatecka D,
Wichers H, editors. The Impact of Food Bioactives on Health. Cham: Springer International Publishing; 2015. p. 305-17. DOI
Daisley BA, Chanyi RM, Abdur-Rashid K, et al. Abiraterone acetate preferentially enriches for the gut commensal Akkermansia
muciniphila in castrate-resistant prostate cancer patients. Nat Commun 2020;11:4822. DOI PubMed PMC
... Once they are released into the environment, xenobiotics can bioaccumulate within the food chain due to their affinity for organic substances, causing toxic adverse effects on natural ecosystems, humans, animals, and economic insects [6]. Furthermore, unintended effects have been reported on the host-associated microbiome [7]. ...
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Background Because of its social nature, the honeybee is regularly exposed to environmental toxicants such as heavy metals and xenobiotics. These toxicants are known to exert strong selective pressure on the gut microbiome’s structure and diversity. For example, resistant microbial members are more likely to dominate in maintaining a stable microbiome, which is critical for bee health. Therefore, the aim of this study was to examine the Enterococcus faecium strains isolated from bee guts for their in vitro growth and tolerability to diverse heavy metals and xenobiotics. An additional aim was to analyze the genomes of E. faecium isolates to assess the molecular bases of resistance and compare them with E. faecium species isolated from other environmental sources. Results The E. faecium bee isolates were able to tolerate high levels (up to 200 mg/L) of toxicants, including cadmium, zinc, benzoate, phenol and hexane. Moreover, the isolates could tolerate toluene and copper at up to 100 mg/L. The genome of E. faecium Am5, isolated from the larval stage of Apis mellifera gut, was about 2.7 Mb in size, had a GC content of 37.9% and 2,827 predicted coding sequences. Overall, the Am5 genome features were comparable with previously sequenced bee-gut isolates, E. faecium Am1, Bee9, SM21, and H7. The genomes of the bee isolates provided insight into the observed heavy metal tolerance. For example, heavy metal tolerance and/or regulation genes were present, including czcD (cobalt/zinc/cadmium resistance), cadA (exporting ATPase), cutC (cytoplasmic copper homeostasis) and zur (zinc uptake regulation). Additionally, genes associated with nine KEGG xenobiotic biodegradation pathways were detected, including γ-hexachlorocyclohexane, benzoate, biphenyl, bisphenol A, tetrachloroethene, 1,4-dichlorobenzene, ethylbenzene, trinitrotoluene and caprolactam. Interestingly, a comparative genomics study demonstrated the conservation of toxicant resistance genes across a variety of E. faecium counterparts isolated from other environmental sources such as non-human mammals, humans, avians, and marine animals. Conclusions Honeybee gut-derived E. faecium strains can tolerate a variety of heavy metals. Moreover, their genomes encode many xenobiotic biodegradation pathways. Further research is required to examine E. faecium strains potential to boost host resistance to environmental toxins.
... Herbicides break down in soil in several ways, releasing carbon in a simpler form that could be used as a source of nutrients (Pileggi et al., 2020), leading MBC to increase. Herbicides also have a significant impact on microbial molecular factories (MMFs) by disrupting critical functions like respiration, photosynthesis, and biosynthetic reactions, as well as cell development and division and molecular composition (Daisley et al., 2022). When compared to natural, geographical, and temporal fluctuation in soil microbial biomass, herbicide effects are usually short term and minimal. ...
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The present investigation determines the persistence of herbicides like butachlor and pretilachlor in Indian soil, and their impact on soil biological properties including microbial biomass carbon (MBC), total microbial population numbers, and enzyme activities. Butachlor was degraded faster in autumn rice soil (t1/2 of 10–13 days) than in winter rice soil (half-life of 16–18 days). The t1/2 of pretilachlor in winter rice was 12–16 days. Regardless of the seasons under cultivation, no pesticide residue was detected in rice at harvest. Herbicides induced an initial decline (0–14th days after application) in MBC (averages of 332.7–478.4 g g⁻¹ dry soil in autumn rice and 299.6–444.3 g g⁻¹ dry soil in winter rice), microbial populations (averages of 6.4 cfu g⁻¹ in autumn rice and 4.6 cfu g⁻¹ in winter rice), and phosphatase (averages of 242.6–269.3 μg p-nitrophenol g⁻¹ dry soil h⁻¹ in autumn rice and 188.2–212.2 μg p-nitrophenol g⁻¹ dry soil h⁻¹ in winter rice). The application of herbicides favored dehydrogenase (averages of 123.1–156.7 g TPF g⁻¹ dry soil in autumn and 126.7–151.1 g TPF g⁻¹ dry soil in winter) and urease activities (averages of 279.0–340.4 g NH4 g⁻¹ soil 2 h⁻¹ in autumn and 226.7–296.5 g NH4 g⁻¹ soil 2 h⁻¹ in winter) in rice soil at 0–14th DAA. The study suggests that applications of butachlor and pretilachlor at the rates of 1000 g ha⁻¹ and 750 g ha⁻¹, respectively, to control the weeds in the transplanted rice fields do not have any negative impact on the harvested rice and associated soil environment.
... microbiota shifts, and that LX3 treatment can modulate immunemicrobiota dynamics in a way that supports further enrichment of the aforementioned symbionts (Figs. 4 and 5). While the underlying drivers of this biological phenomenon remain unclear, cumulative cross-continental evidence indicates a mechanism distinct from spatially-dependent environmental factors (at least within temperate climates [70,71]) known to impact honey bee microbiota composition, such as differences in forage type [72] and pesticide exposure [73]. ...
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Managed honey bee ( Apis mellifera ) populations play a crucial role in supporting pollination of food crops but are facing unsustainable colony losses, largely due to rampant disease spread within agricultural environments. While mounting evidence suggests that select lactobacilli strains (some being natural symbionts of honey bees) can protect against multiple infections, there has been limited validation at the field-level and few methods exist for applying viable microorganisms to the hive. Here, we compare how two different delivery systems—standard pollen patty infusion and a novel spray-based formulation—affect supplementation of a three-strain lactobacilli consortium (LX3). Hives in a pathogen-dense region of California are supplemented for 4 weeks and then monitored over a 20-week period for health outcomes. Results show both delivery methods facilitate viable uptake of LX3 in adult bees, although the strains do not colonize long-term. Despite this, LX3 treatments induce transcriptional immune responses leading to sustained decreases in many opportunistic bacterial and fungal pathogens, as well as selective enrichment of core symbionts including Bombilactobacillus , Bifidobacterium , Lactobacillus , and Bartonella spp. These changes are ultimately associated with greater brood production and colony growth relative to vehicle controls, and with no apparent trade-offs in ectoparasitic Varroa mite burdens. Furthermore, spray-LX3 exerts potent activities against Ascosphaera apis (a deadly brood pathogen) likely stemming from in-hive dispersal differences, whereas patty-LX3 promotes synergistic brood development via unique nutritional benefits. These findings provide a foundational basis for spray-based probiotic application in apiculture and collectively highlight the importance of considering delivery method in disease management strategies.
... Frequent pesticide usage might hamper the world's ecosystem and increase various diseases. Due to antimicrobial effects, strong relations between pesticides and microbiome decline were sued (Chukwuka et al. 2022, Daisley et al. 2022, Ayari et al. 2023. The prevalence of respiratory diseases (tuberculosis, Johne's disease, etc.) is increasing with time in various resource-limited regions (Rehman et al. 2022). ...
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Cite as: Latif Ahmad, Shafia Tahseen Gul, Xiaoxia Du, Riaz Hussain, Muhammad Rafiq Khanani, Shajeela Iram, Aziz Ur Rehman & Ahrar Khan (2023): Dose- and dosage-dependent spectrum of respiratory toxicity of cypermethrin in rabbits, Toxin Reviews, 42(3):573-582. DOI:10.1080/15569543.2023.2204334: Pyrethroids are popular insecticides. Shortness of breath and dyspnea are key signs of exposure;however, their respiratory effects are rarely studied. This study investigated the combination andratios of specific blood tests and lung lesions as respiratory effects of cypermethrin (CY) in rabbits.The effects of CY at various doses and times are the novelty of this study. Doses (50, 100, weight) of CY were injected intraperitoneally every week for up to 9 weeks inrabbits assigned into four equal groups. Data analysis revealed various respiratory signs, signifi-cantly (p�0.05) lower fibrinogen, higher neutrophils-lymphocytes (NL), LDH-lymphocytes (LL),and De-Ritis ratios (DR), and lesions in the lungs. The frequency and incidence of these effectswere dose and dosage dependent. The CY leads to pulmonary signs and allergic effects. Lunginjury increases cell-free heme in plasma, causing pulmonary edema with hemolysis. Emphysemaand fibrosis followed the migration of basophils and mononuclear cells to the lungs. This studyinferred that CY exposure caused lower fibrinogen, higher NL, LL, and DR ratios, and pulmonarylesions, which forecast poor immunity, especially increased risk for cardiac and lung diseases.
... Similarly, although several types of microorganisms have been proven to be effective for plant stress alleviation and growth promotion (Nephali et al., 2020), only a few formulations have reached the market, mainly due to the lack of reproducibility in the field of the results observed in laboratory and greenhouse conditions. This failure could be related to: i) loss of microorganism viability during the shelf storage or even during the treatment; ii) poor stability in the formulation or scarcity of methods to store the microorganisms without disrupting their microbial interactions; iii) incomplete or poor-quality formulation; iv) management practices (such as chemical inputs, fertilizers, tillage, etc.) that affect agricultural microbiomes through modifications of microbe-microbe and plant-microbe interactions; and v) competitivity of the microorganism inoculated (Daisley et al., 2022;French et al., 2021;Vassilev et al., 2020). ...
Over the past decades, the atmospheric CO2 concentration and global average temperature have been increasing, and this trend is projected to soon become more severe. This scenario of climate change intensifies abiotic stress factors (such as drought, flooding, salinity, and ultraviolet radiation) that threaten forest and associated ecosystems as well as crop production. These factors can negatively affect plant growth and development with a consequent reduction in plant biomass accumulation and yield, in addition to increasing plant susceptibility to biotic stresses. Recently, biostimulants have become a hotspot as an effective and sustainable alternative to alleviate the negative effects of stresses on plants. However, the majority of biostimulants have poor stability under environmental conditions, which leads to premature degradation, shortening their biological activity. To solve these bottlenecks, micro- and nano-based formulations containing biostimulant molecules and/or microorganisms are gaining attention, as they demonstrate several advantages over their conventional formulations. In this review, we focus on the encapsulation of plant growth regulators and plant associative microorganisms as a strategy to boost their application for plant protection against abiotic stresses. We also address the potential limitations and challenges faced for the implementation of this technology, as well as possibilities regarding future research.
... Some pesticides contain anti-microbial compounds, which may harm the environmental microbiome. Pesticides may indirectly change the trajectory of host-microbiome coevolution in honey bees and alter their social behaviours, with potential implications for plant-pollinator symbioses [49]. Herbicides such as glyphosate have been shown to affect neuronal communication, resulting in altered behaviours and gut microbiota in rodent models [50]. ...
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Early childhood is a time of rapid physiological, cognitive, and social development, affected by various environmental factors. The physical environment, including the environmental microbiome (the entire consortium of microorganisms and their theatre of activity in a given environment), plays an essential role in childhood development and can be shaped in ways to support health and wellbeing. In this Perspective article, we present considerations for early childhood education settings that wish to shape their outdoor and indoor environments to optimise human and ecosystem health. This is done in line with the latest evidence base on optimising health-supporting interactions between humans and environmental microbiota, but also in pedagogically and developmentally appropriate ways. Based on the Microbiome-Inspired Green Infrastructure (MIGI) principles, the considerations presented here not only support health through human–nature interactions and a healthier natural environment, but also promote a closer, reciprocal relationship between children and their natural environments.
... These non-target organisms can be economically important like pollinators or some insects beneficial to the farmers and disruption of food chain and biogeochemical cycles [1,2,3]. Recently, the ill effects of antimicrobial activity of pesticides on the non-target microorganisms like rhizosphere microflora is reported [4]. It should be ensured that the used pesticide is biodegradable after its action is exerted and it does not affect the non-target plants and animals [5]. ...
... Altered transgenerational immune priming could be one factor involved in the case of AFB [34,35], although findings have been inconsistent or context-dependent for other infectious bacterial diseases [36] as well as viral diseases [37]. Determining how repeat exposure to antibiotics (as well as pesticides with antimicrobial properties [1]) affects immune function and long-term health trajectory of honey bees under controlled conditions is a topic worthy of future investigation. ...
Paenibacillus larvae is a spore-forming bacterial entomopathogen and causal agent of the important honey bee larval disease, American foulbrood (AFB). Active infections by vegetative P. larvae are often deadly, highly transmissible, and incurable for colonies but, when dormant, the spore form of this pathogen can persist asymptomatically for years. Despite intensive investigation over the past century, this process has remained enigmatic. Here, we provide an up-to-date synthesis on the often overlooked microbiota factors involved in the spore-to-vegetative growth transition (corresponding with the onset of AFB disease symptoms) and offer a novel outlook on AFB pathogenesis by focusing on the 'collaborative' and 'competitive' interactions between P. larvae and other honey bee-adapted microorganisms. Furthermore, we discuss the health trade-offs associated with chronic antibiotic exposure and propose new avenues for the sustainable control of AFB via probiotic and microbiota management strategies.
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The rising use of pesticides in modern agriculture has led to a shift in disease burden in which exposure to these chemicals plays an increasingly important role. The human gut microbiome, which is partially responsible for the biotransformation of xenobiotics, is also known to promote biotransformation of environmental pollutants. Understanding the effects of occupational pesticide exposure on the gut microbiome can thus provide valuable insights into the mechanisms underlying the impact of pesticide exposure on health. Here we investigate the impact of occupational pesticide exposure on human gut microbiome composition in 7198 participants from the Dutch Microbiome Project of the Lifelines Study. We used job-exposure matrices in combination with occupational codes to retrieve categorical and cumulative estimates of occupational exposures to general pesticides, herbicides, insecticides and fungicides. Approximately 4% of our cohort was occupationally exposed to at least one class of pesticides, with predominant exposure to multiple pesticide classes. Most participants reported long-term employment, suggesting a cumulative profile of exposure. We demonstrate that contact with insecticides, fungicides and a general “all pesticides” class was consistently associated with changes in the gut microbiome, showing significant associations with decreased alpha diversity and a differing beta diversity. We also report changes in the abundance of 39 different bacterial taxa upon exposure to the different pesticide classes included in this study. Together, the extent of statistically relevant associations between gut microbial changes and pesticide exposure in our findings highlights the impact of these compounds on the human gut microbiome.
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The conventional viewpoint of single-celled microbial metabolism fails to adequately depict energy flow at the systems level in host-adapted microbial communities. Emerging paradigms instead support that distinct microbiomes develop interconnected and interdependent electron transport chains that rely on cooperative production and sharing of bioenergetic machinery (i.e., directly involved in generating ATP) in the extracel-lular space. These communal resources represent an important subset of the microbial metabolome, designated here as the ''pantryome'' (i.e., pantry or external storage compartment), that critically supports micro-biome function and can exert multifunctional effects on host physiology. We review these interactions as they relate to human health by detailing the genomic-based sharing potential of gut-derived bacterial and archaeal reference strains. Aromatic amino acids, metabolic cofactors (B vitamins), menaquinones (vitamin K2), hemes, and short-chain fatty acids (with specific emphasis on acetate as a central regulator of symbiosis) are discussed in depth regarding their role in microbiome-related metabolic diseases.
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Pesticides are increasing honeybee (Apis mellifera) death rates globally. Clothianidin neonicotinoid appears to impair the microbe-immunity axis. We conducted cage experiments on newly emerged bees that were 4-6 days old and used a 16S rRNA metataxonomic approach to measure the impact of three sublethal clothianidin concentrations (0.1, 1 and 10 ppb) on survival, sucrose syrup consumption and gut microbiota community structure. Exposure to clothianidin significantly increased mortality in the three concentrations compared to controls. Interestingly, the lowest clothianidin concentration was associated with the highest mortality, and the medium concentration with the highest food intake. Exposure to clothianidin induced significant variation in the taxonomic distribution of gut microbiota activity. Co-abundance network analysis revealed local dysbiosis signatures specific to each gut section (midgut, ileum and rectum) were driven by specific taxa. Our findings confirm that exposure to clothianidin triggers a reshuffling of beneficial strains and/or potentially pathogenic taxa within the gut, suggesting a honeybee's symbiotic defense systems' disruption, such as resistance to microbial colonization. This study highlights the role of weak transcriptional activity taxa in maintaining a stable honeybee gut microbiota. Finally, the early detection of gut dysbiosis in honeybees is a promising biomarker in hive management for assessing the impact exposure to sublethal xenobiotics.
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Aureobasidium melanogenum has been used as an animal feed additive for improving the health of pets, however, it has not yet been applied in honey bees. Here, a fungal strain CK-CsC isolated from bee bread pollen, was identified as A. melanogenum. Following characterizing CK-CsC fermentation broth, the 4-days fermentation broth (SYM medium or bee pollen) of the CK-CsC was used to feed newly emerged adult honey bees in cages under laboratory-controlled conditions for analysis of survival, gene expression of nutrient and antibacterial peptide, and gut microbiota of honey bees. It was found that the CK–CsC fermentation broth (SYM medium or bee pollen) is nontoxic to honey bees, and can regularly increase nutrient gene expression of honey bees. However, significant mortality of bees was observed after bees were fed on the supernatant liquid of the fermentation broth. Notably, this mortality can be lowered by the simultaneous consumption of bee pollen. The honey bees that were fed bee pollen exhibited more γ-Proteobacteria, Bacteriodetes, and Actinobacteria in their gut flora than did the honey bees fed only crude supernatant liquid extract. These findings indicate that A. melanogenum CK–CsC has high potential as a bee probiotic when it was fermented with bee pollen.
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Glyphosate is the most used pesticide around the world. Although different studies have evidenced its negative effect on honey bees, including detrimental impacts on behavior, cognitive, sensory and developmental abilities, its use continues to grow. Recent studies have shown that it also alters the composition of the honey bee gut microbiota. In this study we explored the impact of chronic exposure to sublethal doses of glyphosate on the honey bee gut microbiota and its effects on the immune response, infection by Nosema ceranae and Deformed wing virus (DWV) and honey bee survival. Glyphosate combined with N. ceranae infection altered the structure and composition of the honey bee gut microbiota, for example by decreasing the relative abundance of the core members Snodgrassella alvi and Lactobacillus apis. Glyphosate increased the expression of some immune genes, possibly representing a physiological response to mitigate its negative effects. However, this response was not sufficient to maintain honey bee health, as glyphosate promoted the replication of DWV and decreased the expression of vitellogenin, which were accompanied by a reduced life span. Infection by N. ceranae also alters honey bee immunity although no synergistic effect with glyphosate was observed. These results corroborate previous findings suggesting deleterious effects of widespread use of glyphosate on honey bee health, and they contribute to elucidate the physiological mechanisms underlying a global decline of pollination services.
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The failure of current universal taxonomic databases to support the rapidly expanding field of bee microbiota research has led to many investigators relying on “in-house” reference sets or manual classification of sequence reads (usually based on BLAST searches), often with vague identity thresholds and subjective taxonomy choices. This time expensive, error- and bias-prone process lacks standardization, cripples the potential for comparative cross-study analysis, and in many cases is likely to sway study conclusions.
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An in vitro study was conducted to assess the impact of organochlorine pesticides (OCPs) on cellular growth, morphology, cell viability, biofilm-formation activity, and growth-regulating substances of a soil bacterium. Phosphate-solubilizing EAM 35 isolated from rhizosphere soil was molecularly identified as Enterobacter cloacae (accession number MT672578.1). Strain EAM 35 tolerated varying levels of OCPs, viz., benzene hexachloride (BHC), chlorpyrifos (CP), dieldrin (DE), and endosulfan (ES). The toxicity of OCPs to strain EAM 35 was displayed in a concentration-dependent manner. Among the OCPs, ES at a concentration of 200 μM showed a higher toxicity, where it maximally reduced the bacterial synthesis of indole-3-acetic acid (IAA), salicylic acid (SA), and 2,3-dihydroxy-benzoic acid (DHBA) by 73% (p ≤ 0.001), 85% (p ≤ 0.005), and 83% (p ≤ 0.001), respectively, over the control. While comparing the toxicity of OCPs to P-solubilizing activity of E. cloacae after 10 days of growth, the toxicity pattern followed the order ES (mean value = 82.6 μg mL–1) > CP (mean value = 93.2 μg mL–1) > DE (mean value = 113.6 μg mL–1) > BHC (mean value = 127 μg mL–1). Furthermore, OCP-induced surface morphological distortion in E. cloacae EAM 35 was observed as gaps, pits on both cellular facets, and fragmented and disorganized cell structure under a scanning electron microscope (SEM). The membrane-compromised cells increased as the concentrations of OC pesticides increased from 25 to 200 μM. Additionally, microbial counts (log10 CFU/mL) were also affected after pesticide exposure and decreased with increasing concentrations. While assessing the impact of OCPs on inhibition (%) of log10 CFU/mL, 150, 175, and 200 μM concentrations of ES completely reduced the growth of E. cloacae. Similarly, while comparing the toxicity of higher concentrations of OCPs to bacterial growth, sensitivity followed the order ES > DE > CP > BHC. In addition, the biofilm-formation ability of strain EAM 35 was inhibited in a pesticide-dose-dependent manner, and it was statistically (p ≤ 0.05, p ≤ 0.005, and p ≤ 0.001) significant. Conclusively, the present study clearly suggests that before applying pesticides to soil, their recommended dose should carefully be monitored.
Pesticides are becoming a significant transnational pollutant in agricultural production environments. This review presents the interconnectedness and interaction effects of pesticides with the microbiomes in the environments of plant rhizosphere and animal (limited to insect and human) guts. The metabolic growth and functions of rhizosphere microbiomes are altered by complex mechanisms involving redox reactions and preferential substrate utilization. The rhizospheres of crop plants with the assemblies of microbiota and other biotic components are sensitive to the deliberate introduction of pesticides. Pesticides become one of the major drivers for the metabolic processes, which rely on the evolutionary mechanisms, including the genetic exchange events within the rhizosphere microbiomes. Pesticides, even at the below detection levels, in the rhizosphere enable the plant uptake which can be up to 1% of the dose applied and trophic transfers involving the animal gut environments. To overcome the metabolic constraints due to the nutrient-poor plant diets contaminated with pesticides, insects gain the resistance traits, mainly due to the pesticide-degrading members of the gut microbiomes. Such evolved microbiome members and their genes can increase their spread of resistance in the environment. Like the insect gut microbiomes, the human gut microbiomes get modulated by the pesticide-laden plant foods, leading to dysbiosis. The confounding effects of pesticides on the gut microbiomes which include mutational and genetic exchange events can upsurge many health disorders. The evolutionary and microbiome perspectives on the rhizosphere and animal guts as the hotspots of metabolic and horizontal gene transfer (HGT) events need careful considerations to mitigate the risks and health hazards due to extensive and intensive application of synthetic chemical pesticides in the modern agriculture.
It is now established that the gut microbiome influences human neurology and behavior, and vice versa. Distinct mechanisms underlying this bidirectional communication pathway, termed the gut-brain axis, are becoming increasingly uncovered. This review summarizes recent interkingdom signaling research focused on gamma-aminobutyric acid (GABA), a human neurotransmitter and ubiquitous signaling molecule found in bacteria, fungi, plants, invertebrates, and mammals. We detail how GABAergic signaling has been shown to be a crucial component of the gut-brain axis. We further describe how GABA is also being found to mediate interkingdom signaling between algae and invertebrates, plants and invertebrates, and plants and bacteria. Based on these emerging results, we argue that obtaining a complete understanding of GABA-mediated communication in the gut-brain axis will involve deciphering the role of GABA signaling and metabolism within bacterial communities themselves.
Substantial efforts to characterize the structural and functional diversity of soil, plant and insect-associated microbial communities have illuminated the complex interacting domains of crop-associated microbiomes that contribute to agroecosystem health. As a result, plant-associated microorganisms have emerged as an untapped resource for combating challenges to agricultural sustainability. However, despite growing interest in maximizing microbial functions for crop production, resource efficiency and stress resistance, research has struggled to harness the beneficial properties of agricultural microbiomes to improve crop performance. Here, we introduce the historical arc of agricultural microbiome research, highlighting current progress and emerging strategies for intentional microbiome manipulation to enhance crop performance and sustainability. We synthesize current practices and limitations to managing agricultural microbiomes and identify key knowledge gaps in our understanding of microbe-assisted crop production. Finally, we propose research priorities that embrace a holistic view of crop microbiomes for achieving precision microbiome management that is tailored, predictive and integrative in diverse agricultural systems. Managing agricultural microbiomes is an efficient approach to improve crop performance in agroecosystems. This Review summarizes the current state of knowledge from less to more targeted approaches to manage soil, plant and pest-associated microbiomes. The authors also identify the knowledge gaps in relation to current agricultural practices in microbiome management.
Many in vivo and in vitro studies have shown that pesticides can disrupt the functioning of gut microbiota (GM), which can lead to many diseases in humans. While the tests developed by the Organization of Economic Cooperation and Development (OECD) are expected to capture most apical effects resulting from GM disruptions, exclusion of GM in the risk assessment might mischaracterize hazards or overestimate/underestimate risks, especially when extrapolating results from one species to another species or population with a substantially different GM. On the other hand, direct assessment of GM-mediated effects may face challenges in identifying hazards, since not all GM perturbations will lead to human adverse effects. In this regard, reliable and validated biomarkers for common GM-mediated adverse effects may be very useful in the identification of GM-mediated pesticide toxicity. Nevertheless, proving causality of GM-mediated effects will need modifications of Bradford Hill criteria as well as Koch's postulates, which are more suitable for the “one-pathogen” paradigm. Furthermore, risk assessment of GM-mediated effects may require pesticide toxicokinetics along the gut, possibly through modelling, and the establishment of the involvement of GM in the mechanism of action (MOA) of the pesticide. Risk assessment of GM mediated effects also requires the standardization of experimental approaches as well as the establishment of microbial reference communities, since variations exist among GM in human populations.