This study presents the first exploratory assessment of antibiotic resistance genes (ARGs) and antibiotic residues in agricultural environments on Reunion Island, a French tropical territory in the south-western Indian Ocean. Sixteen samples from diverse matrices (manure, soil, water, and vegetables) across different agroecosystems were analyzed using high-throughput qPCR targeting 332 ARGs and chemical methods targeting 58 antibiotic compounds and trace elements. ARGs were widely detected across all matrices, with highest abundance observed in amended soils and manure. Surprisingly, ARG profiles, in terms of both abundance and average number, were comparable between unamended soils and natural soils. Antibiotic residues were found in only five manure and soil samples, with no clear correlation between the presence of these residues, trace elements and ARG abundance. Organic amendments significantly increased ARG levels in soils and non-metric multidimensional scaling revealed that ARG profiles clustered primarily by matrix type rather than by location. High-risk ARGs were widely prevalent, with 86% detected and 23% ubiquitous across all samples, and their occurrence in water and raw vegetables suggests potential human exposure through the food chain. This study highlights the influence of agricultural practices on environmental antimicrobial resistance in tropical island contexts and supports the need for expanded One Health surveillance integrating the environmental, animal and human compartments. ### Competing Interest Statement E. Doelsch and M. N. Bravin reports financial support was provided by Veolia Water. The other authors declare no conflicts of interest.

Mealybug wilt disease of pineapple (MWP) poses a significant threat to global pineapple production, yet its etiology remains poorly understood. The disease is believed to involve mealybugs, multiple pineapple mealybug wilt-associated viruses (PMWaVs, genus Ampelovirus), and possibly other viruses from the Badnavirus, Secovirus, and Vitivirus genera. This study examines the distribution and prevalence of three ampeloviruses (PMWaV1, PMWaV2, PMWaV3) and two badnaviruses (PBERV, PBCOV), previously associated to MWP symptoms, across 15 pineapple plots of the 'Queen Victoria' cultivar in Reunion Island. A total of 450 symptomatic and asymptomatic leaf samples were analyzed using PCR and RT-PCR-based diagnostics. Globally, 93 % of samples were infected with at least one virus, and 76 % were co-infected with two to four viruses. PMWaV1 (78 %) and PBCOV (87 %) were the most prevalent, while PBERV was not detected. Virus presence was associated with leaf dieback, wilting, and curling. Leaf reddening and yellowing, commonly associated with MWP, were not associated with viral infection, suggesting that other biotic or abiotic factors may be responsible for these symptoms. Viral infections and MWP symptoms were significantly lower in plots planted with vitroplants (VPs) compared to those using suckers, highlighting the potential of VPs in reducing viral infections. These findings highlight the complexity of MWP and underscore the potential benefits of using virus-free VPs to manage the disease.

In this work, we monitored the flowering phenology of two vanilla varieties (Ordinary V. planifolia and a V. planifolia X V. pompona hybrid) cultivated under intensive conditions in Mauritius. Thirty-three vine and stem development parameters were monitored during the first three flowering cycles. Data analyses at the plot, plant and stem scales, shed light on the vanilla development parameters influencing flowering probability and intensity. Thus, the effectiveness of manual decapitation to promote flowering, a practice commonly adopted empirically by vanilla growers, was formally confirmed. Flowering was hastened by one year (∼46 % increase in plant flowering probability in the cycle 2 for both varieties), and the quantity of inflorescences increased by 5 to 178 % at plot scale, fluctuating notably with the flowering year and stem rot prevalence caused by a fungus of the genus Fusarium. The high beneficial impact of apex decapitation on flowering intensity the year following the decapitation was highlighted, with decapitated stems aged 16–20 months showing the greatest flowering rates compared to decapitated stems aged 4–8 months or 28–32 months. Thus, practicing manual decapitation starting from the second year after planting should be recommended, as it reduces the time to first flowering and increases the number of inflorescences. Additionally, May was identified as the month during which apex decapitation was most effective in inducing flowering. However, given the complex interactions observed between the parameters studied, further research is needed to evaluate the long-term effects of apex decapitation in different environmental and agronomic conditions.

The invasive psyllid Acizzia uncatoides poses a critical threat to the biodiversity of La Réunion Island by colonizing Acacia heterophylla, a strictly endemic keystone tree. To unravel the drivers of this invasion, we analyzed a five-year time series (2017–2022) of psyllid abundance across an elevational gradient using Seasonal Autoregressive Integrated Moving Average (SARIMA/SARIMAX) modeling. The psyllid population displayed extreme seasonality and high-amplitude outbreaks (peaking at > 35,000 individuals per minute of vacuum sampling), consistent with a lack of effective top-down regulation in their introduced range, as confirmed by the absence of natural enemies documented at these sites (Baujeu et al. 2025). Spatially, infestation severity supported the Resource Concentration Hypothesis: monoculture-like stands at high altitudes sustained massive outbreaks, whereas structurally complex forests conferred significant associational resistance. Modeling identified host phenology, specifically the proportion of trees exhibiting green flush (young growing tissues), as the primary bottom-up driver, exhibiting a strict trophic synchronization. Conversely, abiotic factors played a secondary role; temperature imposed delayed negative feedback (2–3 month lag), likely by accelerating leaf sclerification rather than through direct thermal stress. These findings confirmed the high susceptibility of this insular plant host of Acizzia uncatoides and provided a crucial baseline for the implementation of classical biological control to mitigate the decline of this cloud forest ecosystem. While SARIMA models provided robust predictive tools for outbreak forecasting, SARIMAX models elucidated proximate ecological mechanisms. These findings underscore the urgent need for integrated management, including biological control, to protect this endemic keystone tree species.

The distribution and abundance of insect pests are influenced by landscape structure and composition, particularly through modifications to biocontrol services and the proportion of suitable habitats within the landscape. In addition, pest populations are affected by agricultural practices at different landscape scales, ranging from field-by-field to area-wide. Our study focuses on one of the world's most invasive and polyphagous pests of fruits and vegetables: the Oriental fruit fly, Bactrocera dorsalis (Hendel, 1912) (Diptera: Tephritidae). We analysed how farmer practices, landscape composition, and mango varieties were related to B. dorsalis infestation in an insular tropical agroecosystem with disparate farming systems, where crop plots are of modest size and interconnected with various habitat types. Fruit infestations were regularly recorded during 18 months in different plots on all mango varieties of the study area. Agricultural practices were determined through semi-structured interviews and categorised according to the farm structure and practices related to B. dorsalis management. Landscape composition was determined from high-resolution satellite imagery and local surveys, and the area of landscape cover was calculated within a 500 m buffer around each sampled orchard plot. We demonstrate that both landscape and local factors influence the infestation indexes of B. dorsalis in mango orchards. At a landscape scale, B. dorsalis was favoured by habitat diversity, which probably provided complementary larval food resources and enabled populations to maintain throughout the year. On a local scale, individual farmers' practices had a significant influence on infestation indexes. The proportion of infested fruits was lower in plots managed by farmers who practised sanitation.

This study examines the community composition and structure of psyllophagous ladybirds in a tropical environment, focusing on their interactions with psyllids as a food resource. It investigates the effects of prey availability and landscape composition on the structure of all ladybird species associated with psyllids and on the presence and abundance of species whose life cycles depend on psyllids. Sampling was conducted in Reunion island on two psyllid-infested plant species, Leucaena leucocephala and Acacia heterophylla. Ladybirds and psyllids were regularly collected during two years using a thermal aspirator, and visual inspection was conducted at eleven sites visited monthly. In this study, 16 ladybird species were identified, and only juveniles from Coccinella septempunctata, Exochomus laeviusculus, and Olla v-nigrum were frequently present, suggesting they can complete their biological cycle on psyllids. The structure of psyllophagous ladybird communities in a tropical environment is driven by the psyllid host plant and the monthly average temperature. When studied separately, food resources or landscape variables did not affect significantly the communities. The distribution of Coccinella septempunctata is limited to high elevations, where it is recognized as an aphid-eating species, mainly in its juvenile form. Conversely, at low elevation, we encountered juvenile individuals of the generalist species Exochomus laeviusculus and the specialist species Olla v-nigrum. The presence and abundance of the generalist was positively influenced by the landscape and the presence of the specialist positively by prey abundance only.

Given the risk of zoonotic disease emergence, including new SARS-CoV-2 variants of COVID-19, rapid diagnostic tools are urgently needed to improve the control of the spread of infectious diseases. A one-pot triplex real-time RT-LAMP (reverse-transcription-loop-mediated isothermal amplification) assay, based on two regions of the genome SARS-CoV-2-specifically the Orf1ab and N genes-along with one internal control, the human RNase P gene, was developed. The multiplexing relies on the distinct melting peaks produced during an annealing step. This tool, named RUNCOV, was compared to the gold-standard reverse-transcription real-time quantitative PCR (RT-qPCR) assay. A simple sample preparation step was designed alongside the assay, making it ready for use on site, as a point-of-care diagnostic tool. RUNCOV is rapid (typically less than 40 minutes), highly sensitive and specific. When tested on clinical samples with known SARS-CoV-2 status, its limit of detection (LOD) ranges between 5 and 20 copies per reaction and its diagnostic sensitivity (97.44%) and specificity (100%) values are high compared to the RT-qPCR gold standard. These results were supported with an extensive in silico analysis of over 14 million genomes, demonstrating this tool was capable of detecting all known SARS-CoV-2 variants, including the most recent ones KP.3.1.1 and BA2.86.1. This molecular assay is portable, as demonstrated when it was used successfully in La R & eacute;union in different contexts outside the laboratory.

Mealybug wilt of pineapple (MWP) is a destructive disease worldwide caused by a parasitic complex that includes Pineapple Mealybug Wilt-associated Viruses (PMWaVs) and mealybugs (Dysmicoccus brevipes), which concurrently act as vectors for these viruses. Reducing the mealybug population is key to managing MWP, which is achieved in intensive production systems through the use of insecticides. SA (salicylic acid), ASM (acibenzolar-S-methyl), BABA (β-aminobutyric acid), and MeSA (methyl salicylate) are key components of systemic acquired resistance (SAR), the defense mechanism of plants against biotrophic agents such as mealybugs. In this study, these compounds were applied either as pure chemicals and/or as a major constituent of plant extracts. Both the Hawaiian hybrid MD-2 and Queen Victoria tissue culture plants, as well as suckers used for vegetative propagation, were treated with these compounds by direct application on the soil of pineapple pots. Subsequently, five mealybugs were released on each plant or each daughter plant in case of a transgenerational experiment; then, after 45 days, the number of mealybugs was counted. Exogenous SA, ASM, and MeSA reduced the population of mealybugs by a minimum of 50% and up to 80%. These SAR-inducing treatments could be an interesting alternative for controlling mealybugs and are already used in other pathosystems. The SAR mechanisms behind this effect are yet to be confirmed by molecular and enzymatic markers. ASM and MeSA are promising treatments for pineapples using tissue culture plants or traditional shoots.

The increase in human-mediated introduction of plant species to new regions has resulted in a rise of invasive exotic plant species (IEPS) that has had significant effects on biodiversity and ecosystem processes. One commonly accepted mechanism of invasions is that proposed by the enemy release hypothesis (ERH), which states that IEPS free from their native herbivores and natural enemies in new environments can outcompete indigenous species and become invasive. We here propose the virome release hypothesis (VRH) as a virus-centered variant of the conventional ERH that is only focused on enemies. The VRH predicts that vertically transmitted plant-associated viruses (PAV, encompassing phytoviruses and mycoviruses) should be co-introduced during the dissemination of the IEPS, while horizontally transmitted PAV of IEPS should be left behind or should not be locally transmitted in the introduced area due to a maladaptation of local vectors. To document the VRH, virome richness and composition as well as PAV prevalence, co-infection, host range, and transmission modes were compared between indigenous plant species and an invasive grass, cane bluestem (Bothriochloa barbinodis), in both its introduced range (southern France) and one area of its native range (Sonoran Desert, Arizona, USA). Contrary to the VRH, we show that invasive populations of B. barbinodis in France were not associated with a lower PAV prevalence or richness than native populations of B. barbinodis from the USA. However, comparison of virome compositions and network analyses further revealed more diverse and complex plant-virus interactions in the French ecosystem, with a significant richness of mycoviruses. Setting mycoviruses apart, only one putatively vertically transmitted phytovirus (belonging to the Amalgaviridae family) and one putatively horizontally transmitted phytovirus (belonging to the Geminiviridae family) were identified from B. barbinodis plants in the introduced area. Collectively, these characteristics of the B. barbinodis-associated PAV community in southern France suggest that a virome release phase may have immediately followed the introduction of B. barbinodis to France in the 1960s or 1970s, and that, since then, the invasive populations of this IEPS have already transitioned out of this virome release phase, and have started interacting with several local mycoviruses and a few local plant viruses.

Motivation Molecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. Importantly, such inferences should only be performed on datasets displaying sufficient temporal signal, a feature important to test prior to any tip-dating inference. For this purpose, the most popular method considered to-date has been the ‘root-to-tip regression’ which consist in fitting a linear regression of the number of substitutions accumulated from the root to the tips of a phylogenetic tree as a function of sampling times. The main limitation of the regression method, in its current implementation, relies in the fact that the temporal signal can only be tested at the whole-tree scale (i.e. its root). Results To overcome this limitation we introduce Phylostems, a new graphical user-friendly tool developed to investigate temporal signal within every clade of a phylogenetic tree. We provide a ‘how to’ guide by running Phylostems on an empirical dataset and supply guidance for results interpretation. Availability and implementation Phylostems is freely available at https://pvbmt-apps.cirad.fr/apps/phylostems.

Fusarium oxysporum f. sp. radicis-vanillae (Forv), the causal agent of root and stem rot disease, is the main pathogen affecting vanilla production. Sources of resistance have been reported in Vanilla planifolia G. Jackson ex Andrews, the main cultivated vanilla species. In this study, we developed the first high-density genetic map in this species with 1,804 genotyping-by-sequencing (GBS)-generated single nucleotide polymorphism (SNP) markers using 125 selfed progenies of the CR0040 traditional vanilla cultivar. Sixteen linkage groups (LG) were successfully constructed, with a mean of 113 SNPs and an average length of 207 cM per LG. The map had a high density with an average of 5.45 SNP every 10 cM and an average distance of 1.85 cM between adjacent markers. The first three LG were aligned against the first assembled chromosome of CR0040, and the other 13 LG were correctly associated with the other 13 assembled chromosomes. The population was challenged with the highly pathogenic Forv strain Fo072 using the root-dip inoculation method. Five traits were mapped, and 20 QTLs were associated with resistance to Fo072. Among the genes retrieved in the CR0040 physical regions associated with QTLs, genes potentially involved in biotic resistance mechanisms, coding for kinases, E3 ubiquitin ligases, pentatricopeptide repeat-containing proteins, and one leucine-rich repeat receptor underlying the qFo72_08.1 QTL have been highlighted. This study should provide useful resources for marker-assisted selection in V. planifolia.

Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).

Aim:The effectiveness of thermotherapy in managing cassava mosaic disease (CMD) was studied on a susceptible local cultivar in the field in the epidemiological conditions.Study Design: The field was laid out in randomized complete block design Place and Duration: Field experiment was conducted in forest zone at Kapou located in south west of Central African Republic according to University of Bangui during August 2010 and July 2011.Methodology: Diseased cassava cuttings were treated in a heated water bath at temperatures ranging from 43ºC to 51ºC for 30 min before being grown for 12 months in the field.

This datasheet on Xanthomonas axonopodis pv. allii covers Identity, Distribution, Hosts/Species Affected, Diagnosis, Further Information.

Whiteflies are one of the major pests of tomato under greenhouses, and their control partly relies on biocontrol strategies. Among those biocontrol agents, parasitoids or predators are widely used. However, the introduction of a biocontrol agent in a new area is not trivial. For that reason, we investigated the use of a tropical native mirid, Nesidiocoris volucer (Hemiptera: Miridae), for the biological control of whiteflies among other insect pests on tomato crops under greenhouses in the subtropical island of La Réunion, France. Nesidiocoris volucer life history traits and plant injury were examined. Nymphs developed and survived between 15 and 30°C and required on average 49.41 days at 15°C and on average 10.50 days at 30°C to develop (nymph survival >94%). At 25°C, each female produced on average 65 eggs. Nesidiocoris volucer was able to feed on several prey species, but performed better on whiteflies than on spider mites or thrips. No N. volucer feeding injury was observed on tomato. Nesidiocoris volucer has also been found in tropical countries of Africa, and we believe that the data presented on this natural enemy could be of great importance for the biocontrol of whiteflies in tropical areas.

A previous study demonstrated that the color of 4 mm mango slices is altered very slightly by drying for 5 h at 60 °C, 30% RH and 1 m/s. The objectives of this complementary study were to determine the impact of various drying procedures encountered in the drying units on color alterations of sulfite-free mango slices from heterogeneous raw material due to variable maturity degrees of mangoes. Drying procedures with various temperature/humidity/duration combinations were performed to analyze their effects on the color of natural dried mangoes according to the degree of fruit maturity. They were dried at an air speed of 1.0 m/s for 5 h according to 3 schemes: standard drying (SD) at 60 °C and 30% RH; wet drying (WD) for 1 h at 60 °C and 60% RH, followed by 4 h SD; and finally, hot drying (HD) for 4 h SD, followed by 1 h at 80 °C and 30% RH. The color of the mango slices was analyzed before and after drying. SD preserves the color of fresh mangoes very well, whatever their maturity stage. A relatively slow drying onset corresponding to WD has a highly adverse impact, which becomes greater as the degree of maturity increases. There is already significant browning on mangoes with near-optimum quality (L* = 75; H* = 92). Applying high temperature at the end of the drying procedure (HD) for 20% of the time has a more limited adverse impact with immature mangoes that are the most sensitive. Linear regressions were assessed to represent the relationships of color differences between drying schemes according to mango maturity degrees. These statistical models showed a significant increase in color degradation in the case of WD and a decrease in color differences in the case of HD with the advance in fruit maturity.

Introduction Huanglonbing (HLB) is the most serious disease of citrus in the world, associated with three non-cultivable phloem-restricted bacteria Candidatus Liberibacter asiaticus (CLas), Ca L. africanus (CLaf) and Ca L. americanus (CLam). CLas is transmitted by the Asian citrus psyllid Diaphorina citri, and has spread to several countries. The African psyllid Trioza erytreae, the vector of CLaf occurs in Africa and neighbouring islands. Only two major citrus-growing regions - Australia/New Zealand and the Mediterranean Basin - are still HLB-free in the world. However, T. erytreae has recently been introduced into continental Europe (Portugal and Spain) and has become a potential threat to citrus production. The transmission of CLas by T. erytreae had been postulated but never tested. To evaluate the risk of T. erytreae transmitting CLas, comparative transmissions of CLas by T. erytreae and D. citri were assessed. Methods Transmission tests were performed on excised leaves and seedlings of Citrus volkameriana with different inoculation access periods (in series) for both insect species. Quantifications of bacterial titers were made in excised leaves, seedlings three and six months after inoculation and on individual insects. Results Our results showed that T. erytreae was able to efficiently acquire CLas. Furthermore, T. erytreae carried significantly higher bacterial titers than D. citri, and was able to efficiently transmit the bacteria to seedlings at a similar rate that D. citri highlighting the high risk of spread of the most aggressive variant of HLB (CLas) by T. erytreae in Europe. Discussion Thus, extreme precautions to prevent any entry of CLas into Europe should be adopted.

In recent decades, a legion of monopartite begomoviruses transmitted by the whitefly Bemisia tabaci has emerged as serious threats to vegetable crops in Africa. Recent studies in Burkina Faso (West Africa) reported the predominance of pepper yellow vein Mali virus (PepYVMLV) and its frequent association with a previously unknown DNA-B component. To understand the role of this DNA-B component in the emergence of PepYVMLV, we assessed biological traits related to virulence, virus accumulation, location in the tissue and transmission. We demonstrate that the DNA-B component is not required for systemic movement and symptom development of PepYVMLV (non-strict association), but that its association produces more severe symptoms including growth arrest and plant death. The increased virulence is associated with a higher viral DNA accumulation in plant tissues, an increase in the number of contaminated nuclei of the phloem parenchyma and in the transmission rate by B. tabaci . Our results suggest that the association of a DNA-B component with the otherwise monopartite PepYVMLV is a key factor of its emergence.