Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center

Abstract In perennial agroecosystems, pest management outcomes are influenced by herbivore ecology and farming practices that shape arthropod activity. Yet, across many systems, information on taxonomic composition, spatiotemporal dynamics, and sensitivity of herbivore groups to crop management is sparse. In perennial tree crops, Auchenorrhyncha (Hemiptera) are abundant herbivores, notable for causing feeding damage and transmitting plant pathogens. Here, to strengthen the ecological understanding of Auchenorrhyncha activity in managed tree systems, we tracked the seasonal abundance and within-canopy distribution of Auchenorrhyncha in a mature pecan ( Carya illinoinensis ) orchard over two seasons and evaluated how these patterns interact with common canopy management interventions: hedge pruning and calendar-based pesticide applications of insecticide and fungicide. We collected 5882 Auchenorrhyncha, representing seven families. The assemblage was dominated by Cicadellidae, with over 95% of individuals belonging to the subfamily Typhlocybinae. Auchenorrhyncha abundance increased from June to September, and the lower canopy consistently harbored fewer insects. Calendar-based pesticide applications reduced community abundance, although effects varied across dates and canopy location, highlighting potential spatial constraints of pesticide use in tall trees. In contrast, hedge pruning significantly increased Auchenorrhyncha abundance, independently of pesticide use or canopy location. This study not only establishes a baseline for the taxa composition and spatiotemporal activity of Auchenorrhyncha in pecan systems but also advances our understanding of how common farming practices interact with herbivore community patterns. Together, these findings support the refinement of more ecologically grounded, spatially informed strategies for pest management in pecan and other tree-based systems.

This study aimed to evaluate the effectiveness of a sustainable pest management program for controlling the coffee berry borer (CBB), Hypothenemus hampei, at La Catalina coffee farm (Pereira, Risaralda, Colombia) and compare it with the historical conventional control approach (2012-2022), a period during which the management of CBB was based primarily on the application of synthetic chemical insecticides. The working hypothesis was that integrating biological control agents (Phymastichus coffea, Prorops nasuta, and Beauveria bassiana) with cultural and monitoring practices would significantly reduce infestation levels and insecticide dependence while maintaining or improving economic profitability. From 2023 to 2024, GIS-based hotspot mapping, targeted parasitoid release, and fungal application triggered when infestation thresholds were reached were incorporated into sustainable pest management. Infestation, flight activity, and parasitism rates were monitored, and climatic variables were analyzed to determine their relationships with pest dynamics. The results showed that a sustainable pest management program reduced field infestation from a historical average of 3.3 ± 0.15% to 1.7 ± 0.2%, remaining below the 2% action threshold (F-test, p < 0.05). Prorops nasuta reduced the number of CBB life stages by 32.1%, falling from 10.9 ± 0.3 individuals per berry in non-parasitized fruits to 7.0 ± 0.7 in parasitized berries, while parasitism by P. coffea peaked at 70%. CBB flight activity decreased markedly compared to historical averages. The shift from a chemical approach to sustainable pest management resulted in a 26% increase in net income per hectare and a Marginal Rate of Return (MRR) of 18.06. Overall, the results confirm that a sustainable pest management program effectively suppresses CBB populations, minimizes pesticide use, and enhances the economic and environmental sustainability of coffee production systems.

ABSTRACTThe fumigant toxicity of 6 essential oils (EOs) (Mediterranean, Southern, citrus, cinnamon, Asian, and savory thyme), 2 citrus extracts (CEs: organic OCE and natural NCE), and 2 active formulations (microfluidized nanoemulsions AF‐1 and AF‐2) was investigated for control of rice weevil (Sitophilus oryzae), a stored product pest. In bioassays, AF‐1 and AF‐2 at 0.6 µL/mL exhibited higher insecticidal efficacy compared to single EOs and CEs after 72 h of exposure. AF‐2 showed higher acetylcholinesterase enzyme inhibition in rice weevils than AF‐1. Oil‐in‐water nanoemulsions (NEs) of AF‐1 and AF‐2 were prepared by microfluidization, resulting in a decrease in droplet size (DS) from 232 to 116 nm and 230 to 40 nm, and an increase in encapsulation efficiency (EE) from 30% to 77% and from 11% to 79% respectively. To exploit the insecticidal attributes of these NEs, 6 nanocomposite bioactive diffusion films (BDFs) were prepared based on chitosan (CH), poly(butylene adipate‐co‐terephthalate (PBAT), or polylactic acid (PLA), all reinforced with cellulose nanocrystals (CNC), and containing either AF‐1 or AF‐2. Films were evaluated as diffusion devices in bags of rice infested with weevils. CH films induced the highest insect mortality (78%–83%) after 14 days, compared to 6% in controls. Gamma irradiation at 200 Gy alone caused 62% mortality, which increased to 82%100% after combination with the BDFs after 14 days. The presence of CNC in BDFs reduced the % release of bioactive NEs by 12%–27% compared to the films without CNC.Practical ApplicationsNanocomposite BDFs developed in this study could be applied as diffusion devices of insecticidal natural compounds for the control of rice weevils in packaged rice. The active formulations (AF‐1 and AF‐2 based on nanoemulsions of CEs and EOs), combined with low‐dose irradiation treatments, could be used in the food industry for controlling insect proliferation in the sector of stored cereals.

Hi-C characterizes three-dimensional chromatin organization, facilitates haplotype phasing, and enables genome-assembly scaffolding, but encounters difficulties across complex regions. By coupling chromosome conformation capture (3C) with PacBio HiFi long-read sequencing, here we develop a method (CiFi) that enables analysis of genomic interactions across repetitive regions. Starting with as little as 60,000 cells (sub-microgram DNA), the method produces multi-kilobasepair HiFi reads that contain multiple interacting, concatenated segments (~350 bp to 2 kbp). This multiplicity and increase in segment length versus standard short-read-based Hi-C improves read-mapping efficiency and coverage in repetitive regions and enhances haplotype phasing. CiFi pairwise interactions are largely concordant with Hi-C from a human lymphoblastoid cell line, with gains in assigning topologically associating domains across centromeres, segmental duplications, and human disease-associated genomic hotspots. As CiFi requires less input versus established methods, we apply the approach to characterize single small insects: assaying chromatin interactions across the genome from an Anopheles coluzzii mosquito and producing a chromosome-scale scaffolded assembly from a Ceratitis capitata Mediterranean fruit fly. Together, CiFi enables assessment of chromosome-scale interactions of previously recalcitrant low-complexity loci, low-input samples, and small organisms.

Abstract Tephritid fruit flies are invasive species of ripening fruit and vegetables. The olive fly (Bactrocera oleae) a specialist of olives, harbors a symbiotic gut bacterium Candidatus Erwinia dacicola, which is crucial to the olive fly’s exploitation of Oleaceae. This study characterized the genome of Ca. E. dacicola to investigate functional pathways that facilitate its obligate symbiosis. We used an extremely high-quality Ca. E. dacicola genome produced in tandem with an olive fly genome and paired that reference with transcriptomics. Of 4,675 genes, 1,783 (38.13%) were classified as pseudogenes. Overall, many pathways are complete, mostly associated with nutritional components. The symbiont also has genes encoding hypothetical proteins to degrade the phenolics in olives. Some pathways were heavily pseudogeneized, suggesting that Ca. E. dacicola have impaired functions in generalized metabolism, carbon utilization, pathogenicity, and signaling systems. Gene selection analyses in Ca. E. dacicola compared to related organisms, indicated positive selection on genes related to amino acid metabolism, carbon utilization, secretion and transport, and energy production. Our results indicate that the main service likely provided by Ca. E. dacicola is the production of amino acids and metabolism of oleuropein. The high pseudogenization rate implies incipient erosion of a formerly free-living symbiont.

Coffea arabica L. var. 'Kona Typica' is renowned for its premium cup quality, but its vulnerability to pests and diseases limits production. To accelerate cultivar improvement, we generated a chromosome-level genome assembly of 'Kona Typica' using PacBio HiFi sequencing and Hi-C scaffolding technology. The final assembly spans 1.13 Gb, with a scaffold N50 of 50.50 Mb, organized into 22 chromosomes. BUSCO assessment indicated a high completeness at 99.1%. We annotated 65,458 protein-coding genes and identified 1,073,545 interspersed repeats, accounting for 65.16% of the genome. Analysis of transposon insertion ages revealed that most long terminal repeat retrotransposons proliferated after the polyploidization event. This high-quality genome assembly of 'Kona Typica' provides a valuable resource for exploring coffee genomic evolution and genetic mechanisms of complex traits, facilitating genomics studies and the development of improved coffee cultivars with enhanced disease resistance and quality traits.

ABSTRACTMonarchs and their milkweed hosts are well studied for mechanisms of plant defence and insect counter‐defence, but little is known about their associated microbiomes in this iconic system. It is unclear how herbivore‐induced changes in milkweed microbiomes are linked to chemical defensive responses (i.e., plant secondary metabolites). Metagenomics was used to characterise functional gene profiles of bacterial communities associated with plant tissues and monarch caterpillars feeding in milkweed spp. (Asclepias curassavica L., 1753, Asclepias syriaca L., 1762, and Asclepias tuberosa subsp. tuberosa). We compared the influence of monarch feeding and milkweed spp. on phyllosphere and rhizosphere communities. Shotgun metagenomic sequencing was used to profile microbial diversity, predict annotative functions, assess microbial plant secondary metabolite (PSM) degradation potential, and look for enrichment of PSM degradation pathways. Findings show phyllosphere and rhizosphere microbiomes have distinct functional gene profiles and the presence of potential PSM metabolism genes that varied across milkweed spp. Rhizosphere metagenomes had more genes and metabolic pathways involved in degradation/detoxification of known classes of PSMs. In relation to milkweed defensive chemical profiles, we saw an inverse pattern of PSM metabolism pathways and enzymes. Overall, results suggested greater potential for PSM metabolism in rhizosphere compared to phyllosphere communities.