Epidemic preparedness depends on tracking microbial evolution that drives shifts in ecological behaviors such as disease emergence. However, the genetic constraints mediating microbial emergence for generalist and specialist behaviors remain poorly described. Here, we addressed this question by combining comparative and functional genomics with phylogeny-based evolutionary analyses of the cereal pathogen Xanthomonas translucens. We show that a generalist X. translucens subgroup arose from a specialist ancestor, and the loss of a single effector gene, xopAL1, contributed to the generalist host expansion by promoting host jump from barley to wheat. Deleting barley-specialist X. translucens xopAL1 recapitulated the host jump to wheat and demonstrates risk across each globally distributed genetic lineage. However, this niche expansion via XopAL1 loss incurs a significant fitness cost to colonize barley. Moreover, the specialist lineage gained an additional effector gene, xopAJ, which enhanced virulence on barley while restricting oat infection, thereby reinforcing niche specialization. We further conducted transcriptomic analysis of wheat and determined that XopAL1 triggers a defense response that involves the reduction of photosynthetic processes. Our work provides an experimentally validated evolutionary framework to understand mechanisms of intergenera host jump. Overall, we demonstrate that single events of gene loss and gain shape ecological behaviors by creating a dynamic trade-off between niche breadth and specialization.

The ability to disperse over long distances through the atmosphere is a common trait across the tree of life, facilitating resource access and increasing long-range gene flow. Loss of dispersal mechanisms, viz . flight, can occur in animals found on islands where documented phenotypic changes like loss of wingspan impedes longer distance travel to mate with the metapopulation. Bacteria also experience atmospheric flight and descend via bioprecipitation by catalyzing the freezing of cloud droplets with protein InaZ. InaZ triggers ice nucleation at temperatures near 0 ∘ C(1). This ice nucleation activity (INA), a biophysical trait, enhances bacterial deposition through precipitation. The role of InaZ-mediated ice nucleation on bacterial dispersal is well documented, but the impact of loss of INA and thus reduction or loss of atmospheric dispersal on bacterial ecology and evolution has not been described. Here we show that the loss of the ancestral inaZ gene restricts bacterial dispersal and leads to significant genetic and ecological isolation across multiple genera. Through the analysis of available complete genomes, we demonstrate that lineages lacking functional inaZ experience major gene loss events, reduced recombination rates and a marked dependence on human-mediated or insect transmission. These INA-lacking bacteria exhibit an increased ecological signature of isolation that parallels the distribution of geographically isolated animals. Our results establish InaZ as a keystone biophysical trait that defines microbial dispersal strategies. We anticipate these findings will provide a framework for understanding how shifts in biophysical traits drive niche differentiation and changes in dispersal with downstream consequences for Earth system processes. Some microorganisms catalyze freezing of cloud droplets near 0°C via ice nucleation activity (INA) enhancing their deposition. We determined that loss of the gene encoding the INA protein in Gammaproteobacteria restricts bacterial dispersal. Bacteria that lost this ancestral trait compared to relatives with INA experienced distinct, major gene loss events, altered gene flow and marked dependence on transmission by plant tissues or insects and an increased ecological signature of isolation paralleling the geographically isolated plants and animals. We posit that gene loss for biophysical traits such as INA is a keystone example of the consequences of a biological trait defining microbial dispersal.

Turkey arthritis reovirus (TARV) causes arthritic lameness in market-age turkeys. Since 2011, highly pathogenic TARV strains have caused significant economic losses in the turkey industry due to increased culling, reduced market weights, and decreased carcass quality, necessitating more effective control measures. Autogenous vaccine prevention strategies have been inefficacious partly due to a limited understanding of age-related susceptibility of turkeys to TARV. This study investigated age-related host and gut microbiota responses to TARV infection in commercial turkeys derived from vaccinated breeder hens. Poults with known maternally derived antibody titers were orally challenged with TARV O’Neil strain at 1-, 3-, and 7- weeks of age (WOA) and monitored for cloacal virus shedding, gastrocnemius tendon viral tropism, tendon inflammation, weight gain, and changes in gut microbiota. A transient TARV-induced weight gain suppression was evident in poults infected at 1- and 3- WOA during the first 3 weeks post-infection. Age-dependent variations in cloacal viral shedding, virus isolation from tendons, and tendon inflammation severity were also observed. There was significant dissimilarity in ileal and cecal bacterial communities between mock and infected groups, but the effect of age of infection was unclear. Age dependent host response was observed to TARV based on cloacal virus shedding, weight gain suppression and viral tendon tropism. Our study also indicates that maternally derived antibodies appeared insufficient to prevent virus translocation to the tendons and subsequent pathological changes. This study lays the groundwork for future investigations of better vaccines/vaccination strategies and alternative preventive measures. Turkey arthritis reovirus (TARV) causes lameness due to arthritis and tenosynovitis, commonly in market-age turkeys, resulting in significant economic losses. As a control strategy, the turkey industry used autogenous vaccines, prepared from field TARV isolates in breeder hens, to protect the poults in the early stage of life through maternally derived antibodies (MDAs). This study establishes the level of protection provided by MDAs in young poults with age-based responses to TARV O’Neil reovirus strain. Additionally, this study reveals the dynamics of gut dysbiosis in infected poults at different timepoints, paving the way to ground-breaking investigations into gut microbiome modulation interventions that could potentially improve vaccine efficacy and reduce virus transmission and disease severity.

Insect herbivore evolution is tightly linked to changes in their host plants. Many plants have defensive traits that enable them to naturally tolerate and/or deter insect herbivory (host plant resistance; HPR). Some insects have adapted to overcome or resist these defenses (virulence). Global climate change may exacerbate insect virulence, although these interactions have not been closely examined. We tested how one abiotic stressor, flooding, affects interactions between soybeans and two different biotypes of the invasive, soybean aphid (Aphis glycines). In laboratory assays, flooding suppressed avirulent aphid population growth but had no impact on virulent conspecifics, indicating a differential fitness response between biotypes. We also used RNA sequencing to compare flooding stress impacts on gene expression in virulent and avirulent aphids. There were strong, constitutive differences between biotypes regardless of flooding stress, with virulent aphids upregulating putative effector genes and differentially expressing genes involved in epigenetic regulatory processes. Within each biotype, transcriptomic changes due to flooding were limited, but overall, fewer genes were differentially expressed in virulent aphids in response to stress treatments. Our data suggested that virulence adaptations in soybean aphids may also confer greater resiliency to abiotic stress, which could accelerate selection for virulence as climate change effects intensify.

The genetic constraints for microbial host adaptation to emerge for generalist and specialist behaviors remain unclear but is key for epidemiological preparedness. Here, we show that generalist cereal pathogen Xanthomonas translucens arose from a specialist ancestor via the loss of a single effector gene, xopAL1 . Deleting barley-specialist X. translucens xopAL1 recapitulated the host jump to wheat and demonstrates risk across each globally distributed genetic lineages. However, this niche expansion via XopAL1 loss incurs a significant pathogenic fitness cost on barley. Moreover, the specialist lineage gained additional effector genes, such as xopAJ , enhancing virulence on barley while restricting oat infection, thereby reinforcing niche specialization. We further identified and validated key host defense genes that restrict host infection, providing new, undefined targets for crop improvement. Our work provides a validated evolutionary framework of intergenera host jump, demonstrating that single loss and gain events create a dynamic trade-off between niche breadth and specialization. Teaser Evolutionary events of gene loss and gain shape the ecological niche of Xanthomonas translucens for host plant range. ### Competing Interest Statement The authors have declared no competing interest. INRAE SPE project XANTHOHS Agriculture and Food Research Initiative, SCRI grant no. 2020-51181-32154 American Malting Barley Association President’s Postdoctoral Scholars Program of The Ohio State University

Natural host-plant resistance provides a sustainable solution to control insect outbreaks but can be limited due to insect counter-adaptation. The exact mechanisms of insect adaptation to host-plant resistance remain unclear in most systems. Some insect adaptations are controlled by epigenetic mechanisms, such as through noncoding RNA. PIWI-interacting RNAs are specific noncoding RNAs that bind with PIWI proteins to control a diverse range of gene regulatory functions, particularly in insects. Previous investigation into aphid PIWI gene copies showed expansion in their abundance compared to other insects, which may suggest PIWI genes have additional functions among aphids. We first characterized PIWI gene evolution through a phylogenetic analysis, then investigated the role of PIWIs by examining gene expression in the soybean aphid (Aphis glycines), a significant insect pest of soybean which has adapted to overcome aphid-resistance in host plants. Our data indicated the presence of three PIWI ortholog groups, as well as taxon-specific gene expansions, with gene copy numbers ranging from 3 to 17 across species. To evaluate a potential role of PIWIs in overcoming host-plant resistance, we measured their gene expression in Ap. glycines with (virulent) and without (avirulent) the ability to survive on aphid-resistant soybean. We found that virulent Ap. glycines have significantly higher expression of 2 PIWI genes (Agl1.1 and Agl1.3) compared to the avirulent biotype. These data suggest that gene regulatory mechanisms related to the PIWI pathway, potentially including piRNAs, are important in aphid systems and may enable adaptation to host-plant resistance.

The breeding of disease-resistant soybeans cultivars to manage Phytophthora root and stem rot caused by the pathogen Phytophthora sojae involves combining quantitative disease resistance (QDR) and Rps gene-mediated resistance. To identify and confirm potential mechanisms of QDR toward P. sojae, we conducted a time course study comparing changes in gene expression among Conrad and M92-220 with high QDR to susceptible genotypes, Sloan, and three mutants derived from fast neutron irradiation of M92-220. Differentially expressed genes from Conrad and M92-220 indicated several shared defense-related pathways at the transcriptomic level but also defense pathways unique to each cultivar, such as stilbenoid, diarylheptanoid, and gingerol biosynthesis and monobactam biosynthesis. Gene Ontology pathway analysis showed that the susceptible fast neutron mutants lacked enrichment of three terpenoid-related pathways and two cell wall-related pathways at either one or both time points, in contrast to M92-220. The susceptible mutants also lacked enrichment of potentially important Kyoto Encyclopedia of Genes and Genomes pathways at either one or both time points, including sesquiterpenoid and triterpenoid biosynthesis; thiamine metabolism; arachidonic acid; stilbenoid, diarylheptanoid, and gingerol biosynthesis; and monobactam biosynthesis. Additionally, 31 genes that were differentially expressed in M92-220 following P. sojae infection were not expressed in the mutants. These 31 genes have annotations related to unknown proteins; valine, leucine, and isoleucine biosynthesis; and protein and lipid metabolic processes. The results of this study confirm previously proposed mechanisms of QDR, provide evidence for potential novel QDR pathways in M92-220, and further our understanding of the complex network associated with QDR mechanisms in soybean toward P. sojae.

ABSTRACT Pseudomonas syringae pv. syringae ( Pss ) is an emerging phytopathogen that causes Pseudomonas leaf spot (PLS) disease in pepper plants. Pss can cause serious economic damage to pepper production, yet very little is known about the virulence factors carried by Pss that cause disease in pepper seedlings. In this study, Pss strains isolated from pepper plants showing PLS symptoms in Ohio between 2013 and 2021 ( n = 16) showed varying degrees of virulence ( Pss populations and disease symptoms on leaves) on 6-week-old pepper seedlings. In vitro studies assessing growth in nutrient-limited conditions, biofilm production, and motility also showed varying degrees of virulence, but in vitro and in planta variation in virulence between Pss strains did not correlate. Comparative whole-genome sequencing studies identified notable virulence genes including 30 biofilm genes, 87 motility genes, and 106 secretion system genes. Additionally, a total of 27 antimicrobial resistance genes were found. A multivariate correlation analysis and Scoary analysis based on variation in gene content ( n = 812 variable genes) and single nucleotide polymorphisms within virulence genes identified no significant correlations with disease severity, likely due to our limited sample size. In summary, our study explored the virulence and antimicrobial gene content of Pss in pepper seedlings as a first step toward understanding the virulence and pathogenicity of Pss in pepper seedlings. Further studies with additional pepper Pss strains will facilitate defining genes in Pss that correlate with its virulence in pepper seedlings, which can facilitate the development of effective measures to control Pss in pepper and other related P. syringae pathovars. IMPORTANCE Pseudomonas leaf spot (PLS) caused by Pseudomonas syringae pv. syringae ( Pss ) causes significant losses to the pepper industry. Highly virulent Pss strains under optimal environmental conditions (cool–moderate temperatures, high moisture) can cause severe necrotic lesions on pepper leaves that consequently can decrease pepper yield if the disease persists. Hence, it is important to understand the virulence mechanisms of Pss to be able to effectively control PLS in peppers. In our study, in vitro , in planta , and whole-genome sequence analyses were conducted to better understand the virulence and pathogenicity characteristics of Pss strains in peppers. Our findings fill a knowledge gap regarding potential virulence and pathogenicity characteristics of Pss in peppers, including virulence and antimicrobial gene content. Our study helps pave a path to further identify the role of specific virulence genes in causing disease in peppers, which can have implications in developing strategies to effectively control PLS in peppers.

Transportation significantly impacts the health and welfare of surplus dairy calves largely due to the various stressors and pathogen exposures encountered during the process. Concurrently, the animal's microbiome is known to correlate with its health status, with stress-induced alterations in the microbiota potentially precipitating various diseases. This study aimed to compare the impacts of transportation durations of 6, 12, or 16 h on the fecal microbiota in young surplus dairy calves. We used a randomized controlled design, where surplus dairy calves aged 1–19 d old from 5 commercial dairy farms in Ontario were allocated into one of 3 (6, 12, and 16 h of continuous transportation) transportation groups. Health assessments were conducted before, immediately after, and for 2 weeks following transportation. Fecal samples were collected before, immediately after, and at 24- and 72 h post-transportation and subjected to 16S rRNA sequencing. Alpha diversity metrics showed no significant differences between the 3 transportation groups at any of the sampling time points. Although β diversity metrics revealed no clustering by transportation groups, they indicated significant differences across sampling time points within each group. The overall analysis revealed a total of 22 phyla and 353 genera, with Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria being the most abundant phyla. Bacteroides, Escherichia/Shigella, Lactobacillus, Collinsella, and Bifidobacterium were the most abundant genera. The reduction in Fusobacteria abundance before and after transport was significantly larger in the 16-h transportation group when compared with the 6-h transportation group. We also identified several genus-level and ASV-level taxa that displayed significant differences in their abundances across various transportation groups, observed at all sampling time points investigated. In conclusion, this research identifies microbiota changes due to varying transportation durations in surplus dairy calves providing a broad understanding of the microbial shifts in surplus dairy calves' post-transportation across varying durations. While these variations may not directly correlate with overall calf health or indicate dysbiosis, these results emphasize the importance of further investigating transportation practices to enhance calf health and well-being. Further studies are warranted to elucidate the relationship between microbiota and calf health.

Global biodiversity is under accelerating threats, and species are succumbing to extinction before being described. Madagascar’s biota represents an extreme example of this scenario, with the added complication that much of its endemic biodiversity is cryptic. Here we illustrate best practices for clarifying cryptic diversification processes by presenting an integrative framework that leverages multiple lines of evidence and taxon-informed cut-offs for species delimitation, while placing special emphasis on identifying patterns of isolation by distance. We systematically apply this framework to an entire taxonomically controversial primate clade, the mouse lemurs (genus Microcebus, family Cheirogaleidae). We demonstrate that species diversity has been overestimated primarily due to the interpretation of geographic variation as speciation, potentially biasing inference of the underlying processes of evolutionary diversification. Following a revised classification, we find that crypsis within the genus is best explained by a model of morphological stasis imposed by stabilizing selection and a neutral process of niche diversification. Finally, by clarifying species limits and defining evolutionarily significant units, we provide new conservation priorities, bridging fundamental and applied objectives in a generalizable framework. A spatial taxonomic framework integrating genomic, morphological, ecological, life history and acoustic data is used to clarify the cryptic evolution of the taxonomically controversial mouse lemur complex, with a view to aiding future conservation of this and other similarly cryptic clades.

Aedes aegypti is a major vector of several arboviruses that cause human mortality and morbidity. One method for controlling the spread of these viruses is to control mosquito reproduction. During mating, seminal fluid molecules and sperm are transferred and these stimuli influence female post-mating physiology and behavior. Yet, little is known about the mechanisms underlying these post-mating responses. To fill this gap, short-read RNA sequencing was used to identify differentially expressed genes between unmated (control) and mated females in the head/thorax (HT), abdomen (Ab) and the lower reproductive tract (LRT), of mosquitoes reared with 3% and 12% sucrose. The results revealed that at 3% sucrose, four, 408 and 415 significantly differential expressed genes (DEGs) were identified in the HT, Ab and LRT, respectively, at six hours post mating (hpm). The number of DEGs dropped dramatically at 24 hpm with no DEGs in the HT, three in the Ab, and 112 in the LRT. In contrast, the number of DEGs was lower at 6 hpm than 24 hpm in the LRT at 12% sucrose. Comparing our results to a similar study which used 10% sucrose revealed evidence in support of condition-dependent regulation of gene expression by mating in this species. This study shows that mating-induced transcriptional changes depend on time point after mating, body region, and diet. Our results provide foundational knowledge for future functional analyses to identify genes and pathways involved in the post-mating behavioral and physiological changes of female mosquitoes.

Salmonella is the leading cause of death associated with foodborne illnesses in the USA. Difficulty in treating human salmonellosis is attributed to the development of antimicrobial resistance and the pathogenicity of Salmonella strains. Therefore, it is important to study the genetic landscape of Salmonella, such as the diversity, plasmids, and presence antimicrobial resistance genes (AMRs) and virulence genes. To this end, we isolated Salmonella from environmental samples from small specialty crop farms (SSCFs) in Northeast Ohio from 2016 to 2021; 80 Salmonella isolates from 29 Salmonella-positive samples were subjected to whole-genome sequencing (WGS). In silico serotyping revealed the presence of 15 serotypes. AMR genes were detected in 15% of the samples, with 75% exhibiting phenotypic and genotypic multidrug resistance (MDR). Plasmid analysis demonstrated the presence of nine different types of plasmids, and 75% of AMR genes were located on plasmids. Interestingly, five Salmonella Newport isolates and one Salmonella Dublin isolate carried the ACSSuT gene cassette on a plasmid, which confers resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide, and tetracycline. Overall, our results show that SSCFs are a potential reservoir of Salmonella with MDR genes. Thus, regular monitoring is needed to prevent the transmission of MDR Salmonella from SSCFs to humans.

Soilless substrates are widely used for plant cultivation. However, little is known about how soilless substrate components, plant growth, or their interactions impact microbial communities in soilless media. The objectives of this study were to analyze microbial communities in typical pine bark substrates used for nursery crop production and determine the impacts of substituting peat with a compost substrate, and planting, on microbial community dynamics over a production cycle. Three soilless substrate mixtures were compared. The substrate mixes consisted of 80:20:0, 80:10:10, and 80:0:20 (volume:volume:volume) ratios of pine bark:peatmoss:leaf compost, respectively. One set of each treatment was planted with a single birch ( Betula nigra ‘Cully’) liner and another set was not planted. The treatments (n = 3) were maintained in a nursery production setting, and samples were taken after 0, 1, 2, 3, and 4 months. Bacterial and fungal communities were characterized by sequencing polymerase chain reaction-amplified 16s rRNA genes and internal transcribed spacer regions. Initially, the two substrate mixtures that contained compost had more phyla than the substrate mixture that only contained peat and bark. After 1 month, microbial communities in all treatments contained similar phyla, but at different relative abundances based on the amount of compost they contained. Over time, Nitrosomonadaceae and Acetobacteraceae were the most abundant bacterial families in substrate mixes containing 10% and 20% compost, but they were absent from treatments without compost. The communities were dynamic and changed the most over the first 2 months. Microbial communities and their dynamics were similar between planted and unplanted treatments. Planting had less of an effect on microbial communities than compost amendment. Among the fungal communities, differences were observed based on both compost amendment and plant presence. Ascomycota and Basidiomycota were the most abundant fungal phyla and resembled those originally in the peat and compost, respectively. These findings could be used to understand the importance and dynamics of specific microbial communities present in substrate components and how they develop during greenhouse production.

Phytophthora sansomeana was recognized as a distinct species in 2009. It has since been detected in Phytophthora surveys across the North Central region of the United States in recent years. Two isolates of P. sansomeana with moderate and high levels of pathogenicity (Psan_MP and Psan_HP, respectively), based on lesion development on soybean tap roots, were chosen for Oxford Nanopore Technologies long-read genome sequencing to allow within-species genomic comparisons between isolates with different levels of pathogenicity on soybean. The genome assembly size, number of predicted protein-encoding genes, and number of candidate effectors were greater in the highly pathogenic isolate (Psan_HP) than in the moderately pathogenic isolate (Psan_MP). Future work should more closely examine the context of P. sansomeana pathogenicity mechanisms relative to other Phytophthora species. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence of even a small amount of introgression can bias divergence time estimates when gene flow is ignored in the analysis. Using advances in analytical methods under the multispecies coalescent (MSC) model, we demonstrate that by accounting for incomplete lineage sorting and introgression using large phylogenomic data sets this problem can be avoided. The multispecies-coalescent-with-introgression (MSci) model is capable of accurately estimating both divergence times and ancestral effective population sizes, even when only a single diploid individual per species is sampled. We characterize some general expectations for biases in divergence time estimation under three different scenarios: 1) introgression between sister species, 2) introgression between non-sister species, and 3) introgression from an unsampled (i.e., ghost) outgroup lineage. We also conducted simulations under the isolation-with-migration (IM) model and found that the MSci model assuming episodic gene flow was able to accurately estimate species divergence times despite high levels of continuous gene flow. We estimated divergence times under the MSC and MSci models from two published empirical datasets with previous evidence of introgression, one of 372 target-enrichment loci from baobabs (Adansonia), and another of 1000 transcriptome loci from 14 species of the tomato relative, Jaltomata. The empirical analyses not only confirm our findings from simulations, demonstrating that the MSci model can reliably estimate divergence times but also show that divergence time estimation under the MSC can be robust to the presence of small amounts of introgression in empirical datasets with extensive taxon sampling. [divergence time; gene flow; hybridization; introgression; MSci model; multispecies coalescent].

Aedes japonicus (Diptera: Culicidae), or the Asian rock pool mosquito, is an invasive mosquito in Europe and America. It was first detected outside of Asia in 1990 in Oceania. It has since expanded to North America and Europe in 1998 and 2000, respectively. Even though it is classified as a secondary vector of pathogens, it is competent to several arboviruses and filarial worms, and it is contributing to the transmission of La Crosse virus (LACV) and West Nile virus (WNV). In this study, CDC light, BG-sentinel, and gravid traps were used to collect mosquitoes between June and October 2021, in Wooster, Northeastern Ohio, USA. Morphological identification or/and Sanger sequencing were performed to identify the collected mosquitoes. Our results revealed that (adult) Ae. japonicus mosquitoes were the most abundant mosquito species collected with gravid traps in Wooster in 2021, confirming its establishment in Ohio. Molecular analyses of Ae. japonicus showed 100% nucleotide similarity with Ae. japonicus collected in Iowa (USA) and Canada, suggesting multiple introductions. Its presence may increase the risk of future arbovirus outbreaks in Wooster, Ohio. This study stresses the importance of actively monitoring the density and distribution of all members of the Ae. japonicus complex.

The intestinal microbial population is recognized for its impact on cancer treatment outcomes. Little research has reported microbiome changes during cancer progression or the interplay of disease progression, dietary sugar/fat intake, and the microbiome through surgery and chemotherapy. In this study, the murine gut microbiome was used as a model system, and changes in microbiome diversity, richness, and evenness over the progression of the cancer and treatment were analyzed. Mice were categorized into four diet cohorts, combinations of either high or low sucrose and high or low omega-3 fatty acids, and two treatment cohorts, saline vehicle or chemotherapy, for a total of eight groups. Fecal samples were collected at specific timepoints to assess changes due to diet implementation, onset of cancer, lumpectomy, and chemotherapy. Akkermansia muciniphila abundance was very high in some samples and negatively correlated with overall Amplicon Sequence Variant (ASV) richness (r(64) = −0.55, p = 3 × 10−8). Throughout the disease progression, ASV richness significantly decreased and was impacted by diet and treatment. Alpha-diversity and differential microbial abundance were significantly affected by disease progression, diet, treatment, and their interactions. These findings help establish a baseline for understanding how cancer progression, dietary macronutrients, and specific treatments impact the murine microbiome, which may influence outcomes.

The growth-promoting fungi Trichoderma are reported to have a positive effect on the morphological and physio-chemical properties of plants under water deficit stress conditions. In the present study, transcriptomic analysis was conducted to understand the key molecular mechanisms and candidate genes involved in water deficit response in drought susceptible tomato genotype 'Jaune Flamme' when colonized by Trichoderma asperelloides NT33. The data showed that gene expression differences between irrigation treatments were more pronounced than those due to Trichoderma inoculation. Specifically, we found that more than 16,000 genes were differentially expressed between water deficit stress and irrigated plants, while only 28 genes were differentially expressed between NT33 inoculated and non-inoculated treatments under water stress conditions. Nevertheless, nine of these 28 genes have important roles in stress tolerance mechanisms. The transcriptomic study showed that the metabolic pathways involved in secondary metabolite production are one of the main mechanisms adopted by NT33 inoculated plants for maintenance of homeostasis balance under water deficit stress conditions compared to non-inoculated control plants. Among genes upregulated in inoculated (versus non-inoculated) plants under water deficit stress conditions, gene ontology categories involved in regulation of secondary metabolite biosynthetic processes, anthocyanin biosynthetic processes, phospholipase activity, cellular responses to stress, lipid catabolic processes, and regulation of stomata development were overrepresented. On the other hand, genes downregulated in NT33 inoculated samples were involved in the induction of defense response and signaling such as pathogenesis-related proteins, polyphenol oxidase, and chitinase, compared to non-inoculated control samples under water deficit stress. Overall, this study identified key molecular mechanisms involved in water deficit tolerance in the drought susceptible tomato, 'Jaune Flamme', using a novel Trichoderma asperelloides NT33.

Introduction:With more public interest in consuming locally grown produce, small specialty crop farms (SSCF) are a viable and growing segment of the food production chain in the United States.Methods:The goal of this study was to investigate the genomic diversity of Campylobacter isolated from dairy manure (n = 69) collected from 10 SSCF in Northeast Ohio between 2018 and 2020.Results:A total of 56 C. jejuni and 13 C. coli isolates were sequenced. Multi-locus sequence typing (MLST) identified 22 sequence types (STs), with ST-922 (18%) and ST-61 (13%) predominant in C. jejuni and ST-829 (62%) and ST-1068 (38%) predominant in C. coli. Interestingly, isolates with similar genomic and gene contents were detected within and between SSCF over time, suggesting that Campylobacter could be transmitted between farms and may persist in a given SSCF over time. Virulence-associated genes (n = 35) involved in the uptake and utilization of potassium and organic compounds (succinate, gluconate, oxoglutarate, and malate) were detected only in the C. jejuni isolates, while 45 genes associated with increased resistance to environmental stresses (capsule production, cell envelope integrity, and iron uptake) were detected only in the C. coli isolates. Campylobacter coli isolates were also sub-divided into two distinct clusters based on the presence of unique prophages (n = 21) or IncQ conjugative plasmid/type-IV secretion system genes (n = 15). Campylobacter coli isolates harbored genes associated with resistance to streptomycin (aadE-Cc; 54%) and quinolone (gyrA-T86I; 77%), while C. jejuni had resistance genes for kanamycin (aph3'-IIIa; 20%). Both species harbored resistance genes associated with β-lactam (especially, blaOXA-193; up to 100%) and tetracycline (tetO; up to 59%).Discussion/Conclusion:Our study demonstrated that Campylobacter genome plasticity associated with conjugative transfer might provide resistance to certain antimicrobials and viral infections via the acquisition of protein-encoding genes involved in mechanisms such as ribosomal protection and capsule modification.

Treatment of high salt wastewater is of interest for the seafood and aquaculture industries. Systems such as sequencing batch reactors, anammox, and moving bed bioreactors have been used for high strength, high salt wastewater treatment. Microbial inoculation and acclimation to salinity are research areas for improving start-up times and efficacy of biological treatment systems for high salt wastewater. The objectives of this study were to determine the impacts of salinity, inoculation, and time on the fixed-film microbial communities and predictive gene functions in intermittent sand bioreactors (ISBs). ISBs were operated at 0, 0.6, 1.3 and 3.5% salinity. At 3.5% salinity, ISBs were operated with and without inoculation utilizing intertidal marine sand. Samples for bacteria were taken at intervals during 116 days of operation to understand time-dependent shifts in the microbial community. The diversity and abundance of several bacterial genera associated with wastewater treatment and nitrification were impacted by salinity. Inoculated bioreactors had distinctly different microbial communities in mature biofilms. Nitrosomonas increased with time in ISBs treating 0-1.3% salinity wastewater and were not significantly impacted by increased salinity. The results show the effects of salinity and inoculation on established biofilms in ISB treatment of saline wastewater and suggest that stepwise acclimation to salinity in ISBs is not necessary.