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Field trialsField trials were conducted in three raised beds (1 × 2 × 0.6 m) on the Penn State University campus from July to August 2020. The raised beds were separated by at least 8 m to avoid treatment cross-contamination. Faba bean (Vicia faba L.) seeds were planted at a density of 20 seeds/ m2 (50 plants per bed), and each bed was caged using a metal-framed tent. “Noseeum” nylon mesh (Outdoor Wilderness Fabric s, Inc., Caldwell, ID) was draped over the frame and the edges buried in the soil of the bed. The sides of the cages were fastened closed with zippers to allow access.InsectsAphid and predator beetle colonies were raised separately on faba bean plants in cages (BugDorm 20 cm × 40 cm × 20 cm, BioQuip Products, Inc., Rancho Dominguez, CA) in the field. Larvae and adults of predator beetles were fed with a combination of A. pisum and Rhopalosiphum padi every other day (Supplementary information Fig. S1). Trials involving plants, insects, and entomopathogenic fungi were conducted according to institutional, national, and international guidelines and legislation.Fungal inoculations (Beavueria bassiana)We released first instar aphid nymphs on each faba bean plant on the raised beds (~ 1100 aphids) by gently shaking plastic containers with groups of 20 nymphs and placing them on the plants using a paintbrush. They were allowed to grow and reproduce for fifteen days. During the night, we sprayed spore suspension of the Beauveria strain GHA (BotaniGard ®, MT, USA) at 1.4 × 106 and 1.4 × 1012 spore ha−1, low and high load respectively. Two days after inoculation, we collected adult aphids (~ 4–5 days old) from the experimental plots and measured physiological parameters (see details below). Next, we released 300 adult beetles inside each aphid–fungal inoculated cage, allowed them to feed for 2–3 days in our experimental cages, and then collected beetles for physiological measurement.Identification of critical thermal limits (CTMax and CTMin) of healthy and infected insectsTo determine critical thermal maximum for locomotion (CTMax) of healthy and infected individuals of each species, we employed a protocol modified from Ribeiro et al.25, using a hotplate with a programmable heating rate controlled by a computer interface (Sable Systems, LV, USA). The temperature was monitored by independent thermocouple channels connected to a Hobo 4-channel data logger. One thermocouple was attached to the surface of the hotplate, and the other sensor was attached inside the glass tube plugged by a cotton ball in which we placed an individual insect. This equipment was located inside an automated thermal chamber (interior dimensions: width 40.5 cm × 35 cm length × 40 cm height). We transferred an adult aphid (4-day-old) into the glass tube and exposed it to increasing temperatures at a rate of 0.3 °C min−1 until its locomotion stopped. CTMax was recorded when the insect turned upside down and could no longer return to the upright position within 5 s. The insect was returned to a faba bean leaf for recovery (n = 10 individuals per treatment).To measure the critical thermal minimum for locomotion (CTMin) of healthy and infected individuals of each species (n = 10 individuals per treatment), we used an insulated incubator where the temperature was monitored by independent thermocouple channels connected to a Hobo 4-channel data logger. The sensors were attached inside three glass tubes, each tube with an adult (3 to 4-day-old), and plugged by a cotton ball. The glass tube was exposed to decreasing temperature at a rate of 0.3 °C min−1 until its locomotion stopped. CTMin was recorded when no movement was recorded within 5 s. The insect was returned to an aphid-infested faba bean leaf for recovery. Data were only considered valid if the insect displayed normal activity 2 h after a CTMax or CTMin test.Impacts of infection on voluntary exposure aphids and predator beetles to extreme thermal zonesTo examine how voluntary exposure to ETZ was affected by fungal infection, we collected aphids and predator beetles (3 to 5 day-old) from our field plots and transferred them to a dark plastic bottle. Next, a bottle containing the insects was attached to a choice test arena following a modified protocol from Navas et al.24. This experimental arena allows insects to freely move across extreme temperatures to access food in containers located at each end of the device. To reach food, individuals had to cross an ETZ, either warm or cold. The location of each insect was recorded after 60 min, and it was classified as: exploration for individuals that left the initial black bottle, warm or cold ETZ crossings. The experiment was replicated ten times for each species and treatment condition [aphid: healthy, infected (low and high spore load); predator beetle: healthy, infected (low and high spore load)].Effects of fungal infection and thermal conditions (critical thermal limits and voluntary exposure to ETZs) on longevity of aphids and predator beetlesTo examine whether fungal infection and thermal conditions alter longevity in aphids and beetles, we isolated three individuals from each factor combination (low, high fungal load, CTMin, CTMax, behavior: crosses to ETZ cold, warm, and no cross) from previous experiments, and counted the number of days the adults survived after the exposure to the thermal condition (n = 3 factor combination).Energetic cost associated with fungal infection of aphid and predator beetles under critical thermal limits and voluntary exposure to ETIntracellular ATP content was determined in neutralized perchloric acid extracts and by a spectrophotometric coupled enzyme assay, based on modified protocol from Churchill and Storey26 content (n = 3 per treatment condition). An insect was ground to powder using a mortar and pestle cooled in liquid nitrogen, and then weighed into 1.5 mL microcentrifuge tubes (Eppendorf). Powder was dissolved with 0.1 mL ice-cold TE buffer (50 mM Tris–HCl, pH 7.5 plus 1 mM EGTA) and homogenized by sonication (15 s, three times), using a Q500 Sonicator system (QSonica, Newtown, CT, USA). An aliquot (10 µL) of the well-mixed homogenate was removed for protein determination. Cells were lysed by adding 6% (v/v) ice-cold perchloric acid, strongly vortexed for 2 min and incubated at 4 °C for 10 min. Next, the cell homogenate was centrifuged at 14,462 rpm and 4 °C for 5 min. The resulting supernatant was neutralized by adding KOH/Tris (3 M/0.1 M) and centrifuged again to discard the perchlorate salts. Extracts were kept at 4 °C for their immediate utilization. ATP content was determined spectrophotometrically by following the production of NADPH at 340 nm (ε = 6.22 mM−1 cm−1) and using CARY WinUV-Vis Spectrophotometer (Agilent, Santa Clara, CA, USA). The following reagents were used for the spectrophotometric coupled enzyme assay: 5 U Hexokinase, 10 U Glucose 6-phosphate dehydrogenase, 1 mM NADP + , 5 mM MgCl2 and 10 mM Glucose in HE buffer (100 mM Hepes-HCl plus 1 mM EGTA, pH 7.0) at 25 °C. Chemicals were purchased from Roche (Manheim, Germany) and Sigma (St Louis, MO, USA).Infection statusWe used two different protocols to confirm fungal infection: (1) placing each individual in wet towel paper inside a Ziploc bag to observe hyphal growth27. (2) For insects used in ATP measurements, we followed a modified protocol from Wraight and Ramos28 and Castrillo et al.29. Insect were washed using a serial dilution technique, vortexed for 10 s, and mounted in a drop of lactophenol blue, diluted with distilled water. We then preserved insect body parts (i.e., legs and abdomen terga) at − 80 °C for 12 months and placed in Petri dishes containing potato dextrose agar (PDA HiMedia-GM096) medium (pH 6.8), and incubated for ten days. To confirm infection by B. bassiana, we observed plates every 3 days, identified fungal growth (dense white mycelia), then randomly chose three samples, collected mycelia, and DNA was extracted using PureLink Genomic DNA Kit (Invitrogen by Thermo Fisher Scientific, Waltham, MA, USA), according to manufacturer’s protocol. Next, we used PCR essays (25 µL) contained 1 × Q5 Hot Start High-Fidelity Master Mix (New England BioLabs), following a protocol modified from Castrillo et al.29 using primers GHTqF1 (5′-TTTTCATCGAAAGGTTGTTTCTCG) and GHTq R1 (5′-CTGTGCTGGGTACTGACGTG) amplified a 96-bp region of the SCAR fragment. The PCR protocol was initial denaturation at 98 °C, followed by 30 cycles at 98 °C for 1 min, annealing at 58 °C for 1 min; and extension at 72 °C for 1 min. PCR products were visualized in a 1.0% (wt/vol) agarose gel stained with ethidium bromide.Data analysisAll data were tested for statistical test assumptions using a qqplot, Levene’s homogeneity test and the Shapiro–Wilk normality test at alpha = 0.05 significance level. For critical thermal limits (CTMax and CTMin) experiments, the data sets were non-normal and transformation did not normalize the residuals, so we used nonparametric ANOVAs (Kruskal–Wallis) followed by post-hoc nonparametric multiple comparisons. For voluntary exposure to ETZs, we used a generalized linear model with treatment (healthy, low and high spore load) with Poisson distribution, followed by comparisons within each treatment group. For healthy insects, we used a t-test to compare crosses between warm or cold ETZs; for infected insects, we conducted ANOVAS for comparisons among 23 °C, warm or cold ETZs.ATP data: Data for CTMax of A. pisum were non-normal, and transformation did not normalize the residuals, nonparametric ANOVAs (Kruskal–Wallis) were then used and followed by post-hoc nonparametric pairwise comparisons with Wilcoxon tests. ATP data sets from voluntary exposure to ETZs were analyzed following the same protocol as described previously for in crosses analysis of ETZ experiment. Longevity was analyzed using a two-way ANOVA with fungal load and thermal condition (critical temperature and behavior) as factors. Analyses were performed in the R programming environment (v. 3.4.3., CRAN project)30 and JMP-Pro version 15 (SAS Institute 2020). More

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Here we show, for the first time, that the toxicity of a pesticide formulation to bees is caused exclusively by a co-formulant (alcohol ethoxylates), rather than the active ingredient. A 0.8 µL acute oral dose of the agricultural fungicide formulation Amistar® caused a range of damage to bees: both lethal, with 23% mortality, and sublethal, with 45% reduced sucrose consumption, 3.8% drop in body weight (whereas the negative control gained 4.8%), and a 302% increase in gut melanisation. For all metrics tested, the Amistar® and alcohol ethoxylates treatments were not statistically different, demonstrating conclusively that the toxicity of the formulation, Amistar®, to bumble bees is driven by the alcohol ethoxylates. These results demonstrate gaps in the regulatory system and highlight the need for a greater research focus on co-formulants.The mortality in the Amistar® treatment, and treatments containing alcohol ethoxylates reached 32% at its highest, which is substantial given that bees are likely to have a high level of exposure to Amistar® and alcohol ethoxylates. The mechanism by which the alcohol ethoxylates cause mortality has not been explicitly isolated, but our results suggest two potential, possibly related, causes. We recorded a 302% increase in the melanised area of bee midguts in the alcohol ethoxylates treatment. A similar effect was observed in Melipona scutellaris exposed to the pure fungicide active ingredient pyraclostrobin alongside a similar reduction in survival37. We suggest that the alcohol ethoxylates are disrupting the structure of the midgut, which the bee immune system is reacting to with melanisation44 (see Fig. 5). In parallel with this gut damage, alcohol ethoxylate treatment drove a 54% reduction in sugar consumption, which persisted throughout the experiment. Supplementary Fig. S3 shows a plot comparing sugar consumption against gut melanisation, with increasing gut melanisation correlated to reduced sugar consumption in the Amistar®, co-formulant mixture and alcohol ethoxylates treatments. Consequently, we propose that mortality was driven by energy depletion due to reduced consumption, which in turn may have been driven by damage to the gut.Figure 5(Left) Bumble bee midgut in the negative control treatment. (Right) Bumble bee midgut in the co-formulant mixture treatment, which contains alcohol ethoxylates. The dark brown patches are areas of melanisation, indicative of damage to the gut. Both bees survived the full 120 h.Full size imageLikely as a consequence of the reduced consumption of sucrose, bumble bees in the alcohol ethoxylates treatment lost 8.4% of their original weight, in stark contrast to the negative control where bees gained 4.8% over the five-day period. This indicates the alcohol ethoxylate treated bees were expending more energy than they were consuming, and thus exhibiting a negative energy balance. This weight loss, while considerable as a percentage of the bee’s total body mass, is also similar in scale to the weight of the sucrose bees consume in one sitting (EA Straw pers. obs.), for which rigorous data do not exist. As such it is possible that a portion of the weight loss is attributable to the reduced sucrose consumption of the bees, meaning they would have less sucrose in their guts at the time of weighing. Sucrose consumption does not, however, explain the failure of alcohol ethoxylate treated bees to gain weight, which was observed in the control treatment. The weight loss, and lack of weight gain, are concerning because they are likely to indicate a reduction in fat reserves, although this has not been experimentally confirmed. Bee fat reserves are important physiologically, in particular in responding to immune threats45,46. Fat reserves allow bees the energetic resources to buffer against challenges, and thus their depletion could expose bees to greater risk from future threats47.The reduced appetite and negative energy balance in alcohol ethoxylates treated bees could have broader effects in the natural environment. Bees pollinate flowers as they forage for nectar and pollen, so a reduction in their appetite could subsequently have effects on ecosystem services. In our experiment, bumble bee appetite was reduced immediately after ingesting a single dose of alcohol ethoxylates or Amistar®. This effect persisted for five days after exposure, indicating a persistent change in consumption behaviour. While nectar-foraging in bumble bees is driven by the needs of the colony48, a reduction in appetite would reduce overall colony nectar consumption, and thus the number of foraging trips made for nectar. Fewer visits to flowers for nectar may lead to reduced pollination, which would be detrimental to crop yields and farm profits. Further studies of how the impacts we have found map onto foraging and pollination are clearly needed. Importantly, the reduction in appetite recorded in our experiment is a sublethal effect, which standard lower tier testing would not detect. When Amistar® is tested on bumble bees for the 2025 renewal of azoxystrobin, this sublethal effect will be missed by regulatory testing, despite the impact it may have on the pollination services such testing is designed to protect. We suggest that a simple modification to the regulatory protocol OECD 247 would be to weigh the sucrose syringes at the start and end of the trials to calculate sucrose consumption, which would allow measurement of this sublethal effect with minimal additional workload.Our results show a slightly, but not significantly, higher level of mortality in the alcohol ethoxylates treatment (30%) than the Amistar® treatment (23%). If this is a real biological difference, one explanation might be that the concentration of alcohol ethoxylates in the Amistar® formulation was lower than that used in the alcohol ethoxylates treatment solution. This is possible because the Amistar® material safety data sheet lists concentrations as a range (10–20% for alcohol ethoxylates), and here we used the upper end of the range. The co-formulant mixture treatment in all metrics was statistically indistinguishable from the alcohol ethoxylates treatment, showing that the toxicity of alcohol ethoxylates is not a result of synergism with other co-formulants.We believe that the implications of our results are not limited to a laboratory setting and a single species, as other published and unpublished research supports our findings. Semi-field flight cage experiments, where Amistar® was applied to a crop, found effects on full bumble bee colonies (Bombus terrestris). Amistar® caused a reduction in average bee weight and a reduction in foraging activity, as our results predict49. This demonstrates that the effects observed in our laboratory testing scale up to effects at a field realistic level. Additionally, in honeybees (Apis mellifera) Amistar® has been found to cause mortality in laboratory experiments at a range of doses50,51, demonstrating the mortality effect found in our experiment is not species specific. However, no mortality was seen in trials on the red mason bee Osmia bicornis (Hellström and Paxton, unpublished data). Additionally, a similar compound, C11 and lower alcohol ethoxylates, has been found in small scale laboratory testing to cause 100% mortality after contact exposure in honeybees31.To measure the exposure of bees to PPP’s, the EU mandates trials that measure chemical residues in pollen and nectar after crops have been sprayed with either active ingredients or formulations34. However, these residue analysis studies only measure active ingredient concentrations, not the co-formulants. As such, we have no systematic data on the exposure of bees to co-formulants7,8,9. This dearth of data means that the exposure of bees to co-formulants is very poorly characterised. To estimate exposure to alcohol ethoxylates, residue data for Amistar®’s active ingredient azoxystrobin could be used as a proxy18,52. However, the chemical properties of alcohol ethoxylates, specifically their surfactant action, make it unlikely that they have an equivalent environmental fate to azoxystrobin, so this would not be appropriate.While we have very little data to quantify bee exposure to alcohol ethoxylates, we know Amistar® can be applied to crops, such as strawberries, during flowering while bees are foraging on them. The Environmental Information Sheet for Amistar® states “[For bees] no risk management is necessary. Amistar® is of low risk to honey bees”53,54,55. In addition, we would note that exposure of bees to alcohol ethoxylates, and related substances, is not exclusively from Amistar®. For example, a cursory search of the Syngenta website56 immediately identified alcohol ethoxylates in five other Syngenta products. Worryingly, the chemical group alcohol ethoxylates sit in, alkoxylated alcohols, are also widely used in adjuvants, which are products which can be added to tank mixtures to modify the action of the agrichemical6. 89 adjuvant products licenced in the UK contain alkoxylated alcohols as the primary ingredient15. To our knowledge, these adjuvants have never been toxicity tested on bees and have no bee exposure mitigation measures in place whatsoever.To complement measures to promote academic research, moving regulatory research beyond its mortality and active ingredient-centric approach to toxicity testing would better reflect the risks pesticides, as used in the field, pose. For regulatory systems to accurately characterise risk they need to estimate the scale of sublethal effects, regardless of initial mortality results33. The results presented here demonstrate that even substances assessed by regulators as ‘bee safe’ can pose a serious hazard to bee health. To reflect potential sublethal differences caused by co-formulation composition, all formulations could undergo a much more rigorous set of lower tier testing or be automatically entered for higher tier testing.In the face of declining bee populations we advocate that a precautionary approach minimising the exposure of bees to potential stressors, where possible, would be prudent. The current legislation allowing application of PPPs directly onto bees and flowering plants does not align with the emerging evidence that co-formulants, adjuvants, herbicides and fungicides can be hazardous to bees8,57. The wealth of untested and undisclosed co-formulants used abundantly in agriculture is a serious and pressing concern for the health of pollinators worldwide. More

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Insects and bacteriaBean bugs were reared in petri dishes (90 mm in diameter and 20-mm high) at 25 °C under a long-day regimen (16-h light, 8-h dark) and fed with soybean seeds and distilled water containing 0.05% ascorbic acid (DWA). Burkholderia symbiont strain SFA119, a MEP-degrading strain conferring MEP resistant in the bean bug, and its GFP-(green fluorescent protein) labeled derivative, strain SJ586, were used in this study. The symbiont was cultured at 30 °C on YG medium (0.5% yeast extract, 0.4% glucose, and 0.1% NaCl). The GFP-labeled strain was constructed by the Tn7 mini-transposon system, as previously described31.Genome sequencingDNA was extracted from cultured cells of strain SFA1 by the phenol–chloroform extraction as previously described32. The DNA library for Illumina short reads (the mean insert size: 500 bp) was constructed by using the Covaris S2 ultrasonicator (Covaris) and the KAPA HyperPrep Kit (Kapa Biosystems). For the library construction for Nanopore long reads, Native Barcoding Expansion (EXP-NBD104, Oxford Nanopore Technologies) and the Ligation Sequencing Kit (SQK-LSK109, Oxford Nanopore Technologies) were used. The genome sequencing was performed with NextSeq using the 2 × 151-bp protocol (Illumina) and GridION using an R9.4.1 flow cell (Oxford Nanopore Technologies). The Illumina short reads were processed by using Sickle Ver 1.33 (available at https://github.com/najoshi/sickle) for removing the low-quality and shorter reads. After processing the Nanopore long-reads with Porechop Ver 0.2.3 (available at https://github.com/rrwick/Porechop) and Filtlong Ver 0.2.0 (available at https://github.com/rrwick/Filtlong), error correction was performed by using Canu Ver 1.833. These processed short- and long reads were assembled by using Unicycler Ver 0.4.734, resulting in the eight circular replicons (Supplementary Fig. 1). The assembled genome was annotated by DFAST Ver 1.1.035. After the homology searches of the protein sequences by blastp 2.5.0 + 36 against the COG database (PMID: 25428365), circular replicons were visualized with circos v 0.69-837. The chromosomes and plasmids were assigned according to the genome of Caballeronia (Burkholderia) cordobensis strain YI2338.Phylogenetic analysisNucleotide sequences of 16 S rRNA gene of representative Burkholderia spp. and outgroup species were aligned by using SINA v1.2.1139. Protein sequences of MEP-degrading genes (mpd, pnpB, and mhqA) and a plasmid-transfer gene (traH) on plasmid 2 were subjected to the blastp search against the nr database (downloaded in Jul. 2019) and top ~30 hit sequences were retrieved for each gene. Multiple sequencing alignments of each gene were constructed with L-INS-I of mafft v7.40740. Gap-including and ambiguous sites in the alignments were then removed. Unrooted maximum-likelihood (ML) phylogenetic trees were reconstructed with RAxML v8.2.341 using the GTR + Γ model (for 16 S rRNA gene) or the LG + Γ model42 (for other genes). The bootstrap values of 1000 replicates for all internal branches were calculated with a rapid bootstrapping algorithm43.Preparation of SFA1 cultures for RNA-seqBurkholderia symbiont SFA1 was precultured in minimal medium (20 mM phosphate buffer [pH 7.0], 0.01% yeast, 0.1% (NH4)2SO4, 0.02% NaCl, 0.01% MgSO4⋅7H2O, 0.005% CaCl2⋅2H2O, 0.00025% FeSO4⋅7H2O, and 0.00033% EDTA⋅2Na) containing 1.0 mM of MEP on a gyratory shaker (210 rpm) at 30 °C overnight, and subcultured in newly prepared MEP-containing minimal medium under the same conditions for 5 h. As a control, SFA1 was precultured in minimal medium containing 0.1% citrate overnight, and then the overnighter was subcultured in a newly prepared citrate-containing minimal medium under the same conditions for 10 h. The culture was mixed with an equal amount of RNAprotect Bacteria Regent (Qiagen, Valencia, CA, USA), then centrifuged to harvest the cells for the RNA-seq analysis.Preparation of midgut symbiont cells for RNA-seqThe oral administration of the symbiont strain SFA1 was performed as described19,44. The symbiont was inoculated to 2nd instar nymphs, and three days after molting to the 3rd instar, nymphs were transdermally administered with 1 µl of 0.2 µM or 20 µM of MEP (dissolved in acetone). One- or three days after the treatment, insects were dissected and the crypt-bearing symbiotic gut region was subjected to the RNA extraction and RNA-seq analysis. As a control, untreated insects were analyzed.RNA-seq analysisTotal RNA was extracted from triplicate samples from cultures by the hot-phenol method as previously described45 or from the midgut symbiont cells by using RNAiso Plus (Takara Bi, Kusatsu, Shiga, Japan) and the RNeasy mini kit (Qiagen). The extracted total RNA was purified by phenol–chloroform extraction and digestion by DNase (RQ1 RNase-Free DNase, Promega, Fitchburg, WI, USA) and repurified by using a RNeasy Mini Kit. The mRNA in the samples was further enriched by the RiboMinus Transcriptome Isolation Kit bacteria (Thermo Fisher Scientific, Waltham, MA, USA) and the RiboMinus Eukaryote Kit for RNA-Seq (Thermo Fisher Scientific), and purified by using an AMPure XP kit (Beckman Coulter, Brea, CA, USA). The cDNA libraries were constructed from approximately 100 ng of rRNA-depleted RNA samples by the use of a NextUltraRNA library prep kit (New England Biolabs, Ipswich, MA, USA). Size selection of cDNA (200–300 bp) and determination of the size distribution and concentration of the purified cDNA samples were performed as described previously46. In total, 21 cDNA libraries were constructed and sequenced by MiSeq (Illumina, Inc., San Diego, CA, USA). To ensure high sequence quality, the remaining sequencing adapters and the reads with a cutoff Phred score of 15 (for leading and tailing sequences, Phred score of >20) and a length of less than 80 bp in the obtained RNA-seq data were removed by the program Trimmomatic v0.30 using Illumina TruSeq3 adapter sequences for the clipping47. The remaining paired reads were analyzed by FastQC version 0.11.9 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) for quality control, and Bowtie2 ver. 2.2.248 for mapping on the symbiont genome (DDBJ/EMBL/GenBank accession: AP022305–AP022312). After the conversion of the output BAM files to BED files using the bamtobed program in BEDTools ver. 2.14.349, gene expression levels were calculated in TPM (transcripts per kilobase million) values by using in-house scripts46.Gene deletion and complementationMEP-degrading genes (mpd, pnpA1, and pnpA2) were deleted by the homologous-recombination-based deletion method using pK18mobsacB or pUC18, as previously described50,51. Primers used for the mutagenesis are listed in Supplementary Table 1. For mpd gene deletion, pK18mobsacB was used to construct a markerless mutant. For single deletion of pnpA1 and pnpA2 genes, pUC18 was used to substitute each gene locus with a kanamycin-resistance gene cassette. The double deletion of pnpA1 and pnpA2 genes was performed by substituting pnpA2 gene locus with a tetracycline-resistance gene cassette in the pnpA1-deletion mutant. Gene complementation of mpd was also performed by homologous recombination using plasmid pUC18 with primers listed in Supplementary Table 1. To investigate growth profiles of the wild-type SFA1, the gene-deletion mutants (Δmpd, ΔpnpA1, ΔpnpA2, and ΔpnpA1/ΔpnpA2), and the mph-complement mutant (Δmpd/mpd+) in the MEP-containing minimal medium, the strains were precultured in minimal medium containing 1.0 mM MEP on a gyratory shaker (210 rpm) at 30 °C overnight, and then cultured in newly prepared MEP-containing minimal medium under the same condition. The growth of cultures was estimated by OD600 measurements. To confirm the basic growth abilities of the mutants, these bacterial strains were pre- and subcultured in minimal medium containing 0.1% glucose under the same conditions. These symbiont strains and mutants were inoculated to the bean bug as described above.Quantitative PCRSymbiont titers in the midgut crypts were evaluated by quantitative PCR (qPCR) of bacterial dnaA gene copies. The qPCR was performed by using a KAPA SYBR Fast qPCR Master Mix (Kapa Biosystems) and the LightCycler 96 System (Roche Applied Science) with the following primers: BSdnaA–F (5′-AGC GCG AGA TCA GAC GGT CGT CGA T-3′) and BSdnaA–R (5′-TCC GGC AAG TCG CGC ACG CA-3′).MEP treatment of insectsMEP treatment of R. pedestris was performed as previously described19. Soybean seeds were dipped in 0.2 mM MEP for 5 s and dried at room temperature. In each clean plastic container, 15 individuals of 3rd-instar nymphs were reared on three seeds of the MEP-treated soybean and DWA at 25 °C under the long-day regime, and the number of dead insects was counted 24 h after the treatments. The survival rate of the insects was analyzed under Fisher’s exact test by use of the program R ver. 3.6.3 (available at https://www.R-project.org/). Multiple comparisons were corrected by the Bonferroni method.Bactericidal activities of MEP and its degradation product 3M4NTo measure bactericidal activities of MEP and 3M4N on cultured cells of SFA1, 104 cells of log-phase growing bacteria were mixed with a defined concentration of MEP or 3M4N, and spotted on a YG agar plate. To measure the bactericidal activity against midgut crypt-colonizing cells, the symbiotic organs infected with SFA1 were dissected from 3rd-instar insects, homogenized in PBS, and purified by a 5-µm-size pore Syringe filter to harvest colonizing symbiont cells50. MEP or 3M4N was added to approximately 104 cells of the harvested cells and spotted on a YG agar plate. Bactericidal activities of the chemical compounds were then checked in 24 h after incubation at 30 °C.HPLC detection of in vitro and in vivo MEP-degrading activities of the symbiontTo determine in vitro MEP-degradation activity, cultured cells of SFA1 were prepared as above, and 106 cells were incubated at 25 °C in 200 µl of MEP solution (2 mM MEP in Tris-Hcl [pH 8.5] with 0.1% Triton X-100) in a 1.5-ml microtube. To determine in vivo MEP-degradation activity, the midgut of a 5th-instar insect infected with SFA1 was dissected, the posterior and anterior parts of the crypt-bearing symbiotic region were closed with 0.2-mm polyethylene fishline (Supplementary Fig. 6a), and incubated at 25 °C in 200 µl of the MEP solution. For the in vivo determination, 250 mM of trehalose, known as a major sugar source of insects’ hemolymph52, was added to the MEP solution to keep the tissue fresh. After incubation for different times, the reaction was stopped by adding 400 µl of methanol. After centrifugation, supernatants were subjected to high-performance liquid chromatography (HPLC) analyses to detect MEP and 3M4N, as previously reported21, and precipitated cells and tissues were subjected to DNA extraction and qPCR to estimate symbiont-cell numbers of each reaction.LC–ESI–MS detection of 3M4N in feces from 3M4N-fed insectsAn insect-rearing system for feeding 3M4N and collecting feces is shown in Supplementary Fig. 7. Insects were fed with DW or DW containing 10 mM 3M4N in a plastic container, in which the solution supplier was covered by 0.5-mm mesh, so that insects were able to drink the solution by probing with their proboscis, but did not directly touch the solution by their legs or body. Twenty insects were reared per container and their feces were accumulated on the bottom of the container for five days. The collected feces (DW- or 3M4N-treated) were suspended in 1 ml of MilliQ water, and the water-soluble fractions were extracted by thorough vortexing. Solids and insoluble fractions were removed from the suspension by centrifugation and subsequent filtration using a cellulose-acetate membrane (Φ, 0.20 μm, ADVANTEC, Tokyo, Japan). The resultant fraction was diluted 10-fold by MilliQ water and analyzed by liquid chromatography–electrospray-ionization mass spectrometry (LC–ESI–MS) according to a previous report53,54,55. HPLC was performed using the Nexera X2 system (Shimadzu, Kyoto, Japan) composed of LC-30AD pump, SPD-M30A photodiode-array detector, and SIL-30AC autosampler. Develosil HB ODS-UG column (ID 2.0 mm × L 75 mm, Nomura Chemical Co., Ltd, Aichi, Japan) was employed with a flow rate of 0.2 mL/min. The following gradient system was used for analysis of metabolites: MilliQ water (solvent A) and methanol (solvent B), 90% A and 10% B at 0–5 min, linear gradient from 90% A and 10% B to 20% A and 80% B at 5–15 min, 20% A and 80% B at 15–20 min, and 90% A and 10% B at 20–25 min. Retention time of 3M4N standard reagent was 14.2 min. Electrospray-ionization mass spectrometry (ESI–MS) in positive and negative ion modes was simultaneously performed using amaZon SL (Bruker, Billerica, MA, USA). 3M4N (MW = 153.14) standard showed a clear peak in negative mode at m/z of 151.53.Reporting summaryFurther information on research design is available in the Nature Research Reporting Summary linked to this article. More