Intraspecies Variation Research Articles

Exploring the versatility of sesquiterpene biosynthesis in guava plants: a comparative genome-wide analysis of two cultivars

Psidium guajava L., a fruit crop belonging to the Myrtaceae family, is highly valued for its nutritional and medicinal properties. The family exhibits a diverse chemical profile of essential oils and serves as a valuable resource due to its ecological interactions, adaptability, and dispersal capacity. The Myrtaceae family has been extensively studied for its terpenoids. Genetic studies have focused on foliar terpene yield in species from the Eucalypteae and Melaleucaceae tribes. To understand the evolutionary trends in guava breeding, this study predicted terpene synthase genes (TPS) from different cultivars. Through this analysis, 43 full-length TPS genes were identified, and approximately 77% of them exhibited relative expression in at least one of the five investigated plant tissues (root, leaf, bud, flower, and fruit) of two guava cultivars. We identified intra-species variation in the terpene profile and single nucleotide polymorphisms (SNPs) in twelve TPS genes, resulting in the clustering of 62 genotypes according to their essential oil chemotypes. The high concentration of sesquiterpenes is supported by the higher number of TPS-a genes and their expression. The expansion for TPS sub-families in P. guajava occurred after the expansion of other rosids species. Providing insight into the origin of structural diversification and expansion in each clade of the TPS gene family within Myrtaceae. This study can provide insights into the diversity of genes for specialized metabolites such as terpenes, and their regulation, which can lead to a diverse chemotype of essential oil in different tissues and genotypes. This suggests a mode of enzymatic evolution that could lead to high sesquiterpene production, act as a chemical defense and contribute to the adaptive capacity of this species to different habitats.

Comparative analysis of hydrophobicity and dentin adhesion ability in Candida albicans strains.

Adhesion to dentin is a first step for a successful microbial root canal colonization. Cell hydrophobicity seems to have some influence in the Candida species adhesion to surfaces. To measure cell surface hydrophobicity and to investigate the adherence ability to human dentin among Candida albicans strains isolated from root canal and lingual dorsum via an in vitro study. adhesion was quantified in function of dentin area covered by blastospores and/or hyphae presence detected by epifluorescence microscope. Cell surface hydrophobicity was estimated by assessing the percentage migration of cells from an aqueous phase to a hydrocarbon phase. Contact angles were measured by the sessile drop technique on the dentin surface using a contact angle measurements apparatus. We also examined the correlation between adhesion ability and hydrophobicity. although there was some intra-species variation in cell surface hydrophobicity, most isolates were characterized by moderate hydrophobicity. There was no significant difference in this parameter when the isolation niche was considered. Both root canal and lingual dorsum yeasts were able to adhere to dentin. No association was found between the strains' site of isolation and adhesion. Moreover, cell surface hydrophobicity and adhesion ability were not correlated. although hydrophobicity can influence Candida albicans virulence in many ways, this study suggests that this parameter by itself was not a good predictor of adhesion to dentin.

Genotypic Differences in Photosynthetic Limitations to Carbon Assimilation in Peanut under Drought at the Onset of Flowering

Drought can greatly limit carbon assimilation in plants. However, different species have distinct photosynthetic components governing limitations to photosynthesis exposed to drought conditions. Furthermore, intra-species variations in photosynthetic response to drought is also expected. Information on underlying limitations to carbon assimilation in peanut (Arachis hypogaea L.) has been controversial. Therefore, this study aimed to verify potential drought tolerance associated with the photosynthetic process within ten diverse peanut genotypes grown under drought as well as to determine the limitation to carbon assimilation in these genotypes and identify parameter(s) that can be used as a reference indicator of photosynthesis response to drought intensity. Experiments were conducted in 2017 and 2018 using rainout shelters to impose drought for 40 days starting 34 days after planting. Ten peanut genotypes were planted in two blocks, one fully irrigated and one under drought stress during reproductive development. Photosynthetic measurements were taken at 25 and 40 days after onset of stress. C76-16 was identified as the most tolerant genotype due to improved plasticity by downregulating photosynthesis under mild drought stress (25 progressive days under drought) and upregulating multiple photosynthetic component processes under more severe drought (40 days under drought) to sustain photosynthesis. The primary limitation to photosynthesis across all peanut genotypes was stomatal conductance, whereas non-stomatal factors (photochemical reactions) were nearly unaffected by mild drought. In addition, stomatal conductance and electron flux to CO2 assimilation contributed most to drought tolerance in peanut genotypes. Moreover, these two photosynthetic component processes can be jointly used as reference indicators of photosynthetic status of peanut under varying drought intensities.

Testing intra-species variation in allocation to growth and defense in rubber tree (Hevea brasiliensis).

Plants allocate resources to growth, defense, and stress resistance, and resource availability can affect the balance between these allocations. Allocation patterns are well-known to differ among species, but what controls possible intra-specific trade-offs and if variation in growth vs. defense potentially evolves in adaptation to resource availability. We measured growth and defense in a provenance trial of rubber trees (Hevea brasiliensis) with clones originating from the Amazon basin. To test hypotheses on the allocation to growth vs. defense, we relate biomass growth and latex production to wood and leaf traits, to climate and soil variables from the location of origin, and to the genetic relatedness of the Hevea clones. Contrary to expectations, there was no trade-off between growth and defense, but latex yield and biomass growth were positively correlated, and both increased with tree size. The absence of a trade-off may be attributed to the high resource availability in a plantation, allowing trees to allocate resources to both growth and defense. Growth was weakly correlated with leaf traits, such as leaf mass per area, intrinsic water use efficiency, and leaf nitrogen content, but the relative investment in growth vs. defense was not associated with specific traits or environmental variables. Wood and leaf traits showed clinal correlations to the rainfall and soil variables of the places of origin. These traits exhibited strong phylogenetic signals, highlighting the role of genetic factors in trait variation and adaptation. The study provides insights into the interplay between resource allocation, environmental adaptations, and genetic factors in trees. However, the underlying drivers for the high variation of latex production in one of the commercially most important tree species remains unexplained.

Compositional and functional alteration of gut microbiota profiles in response to anti-TNF-α therapy in inflammatory bowel disease: A Pilot study

Background and aimInflammatory bowel disease (IBD) is a chronic and relapsing disorder that is strongly linked to intestinal microbiota alteration (dysbiosis). Anti-tumor necrosis factor-alpha (anti-TNF-α) therapies have revolutionized IBD treatment over the last two decades. Clinical response to anti-TNF-α treatment generally involves alteration of the gut microbiota composition, although change in the microbiome following therapy has generated some contradictory theories. We examine the composition and function of the intestinal microbiota following treatment with TNF-α inhibitors and examine this relationship in the context of clinical and endoscopic response in a cohort of IBD patients in Saudi Arabia. MethodAn analysis of fecal-derived microbiota in 20 human samples was performed using 16S rRNA gene-based microbiota profiling and next generation sequencing, utilizing Illumina MiSeq. Ten samples were collected at baseline prior to treatment with TNF-α antagonists and ten samples were collected following treatment. Inter- and intra-species variation was tested using ɑ-diversity and β-diversity metrics along with appropriate statistical analysis. An examination of functional metagenomic profile variation was performed following biologics exposure. ResultsA total of 5 087 721 clean-paired sequence reads were generated across subjects before and after biologics treatment and assigned to 401 different operational taxonomic units (OTUs). The two taxonomic microbial groups (before and after treatment) demonstrated no clear separation. Anti-TNF-α treatments induced more specific variation, rather than involving a global impact on the gastrointestinal (GI) microbiota profiles, with a statistically significant increase in the Firmicutes (P = 0.01) and a statistically significant decrease in Proteobacteria (P = 0.04). This was accompanied by a remarkable increase in protective taxa, responsible for short-chain fatty acids production, such as the Lachnospiraceae family, which belongs to the Clostridiales order (P = 0.005). A notable increase in F. prausnitzii and a decrease in the relative abundance of E. coli were observed. At the functional level, an up-regulation in the carbohydrate metabolism pathway was shown in addition to a down-regulation in cellular process and signaling pathways (P = 0.04, P = 0.006, respectively). ConclusionTNF-α antagonists reduced GI microbiota with pro-inflammatory capacity enabling protective bacteria to thrive. The biologics caused specific compositional and functional variation rather than a global alteration of the gut microbiota profile in biologic-responsive IBD patients, leading to an improvement in treatment efficacy.

A simple method for Eucalyptus species discrimination: FTIR spectroscopy and machine learning

Wood sample classification is crucial in forestry, woodworking, and conservation efforts. It involves categorizing wood species based on physical characteristics like grain patterns, color, texture, and density. However, there are scientific gaps that hinder its effectiveness. One challenge is the difficulty in differentiating wood species with similar characteristics. To address this, we propose using FTIR spectroscopy and machine learning algorithms. In our study, we focused on the accurate classification of Corymbia citriodora (CIT), Eucalyptus grandis (GRA), and the hybrid species GG100 (GG). We evaluated bark and sapwood samples to determine the best for such a purpose. Using FTIR spectroscopy and Quadratic Discriminant Analysis with only seven PCs, we achieved 100% accuracy in bark sample classification. This approach offers advantages because FTIR spectroscopy captures unique chemical fingerprints, providing rapid and non-destructive analysis of wood samples. Machine learning algorithms learn from these spectral patterns for accurate species prediction. Notably, bark samples, easily obtained without tree damage, showed excellent classification results. By incorporating FTIR spectroscopy and machine learning, we can overcome the challenges of inter-species similarities and intra-species variations. This improves reliability and accuracy, supporting and ensuring high-quality wood products. Integrating FTIR spectroscopy and machine learning presents a promising solution for enhancing wood sample classification. Further research can expand species classification and improve wood identification processes.

Methodological pipeline for monitoring post-harvest quality of leafy vegetables

Plants are primary source of nutrients for humans. However, the nutritional value of vegetables tends to decrease once organ and tissue sinks are detached from the plant. Minimal processing of leafy vegetables involves cutting and washing before packaging and storage. These processing procedures result in stressful conditions and post-harvest disorders senescence-related can also occur. The aim of this work is to define a methodological pipeline to evaluate the “quality” changes of fresh cut leafy vegetables over their shelf-life. At this purpose, intra-species variability has been investigated considering two varieties of Lactuca sativa (var. longifolia and capitata), showing different susceptibility to browning. Since browning mainly depends on phenol oxidation, redox parameters as well as the activity of the enzymes involved in phenol biosynthesis and oxidation have been monitored over storage time. At the same time, the metabolic changes of the lettuce leaves have been estimated as response patterns to chemical sensors. The obtained sensor outputs were predictive of browning-related biological features in a cultivar-dependent manner. The integration of the results obtained by this multivariate methodological approach allowed the identification of the most appropriate quality markers in lettuce leaves from different varieties. This methodological pipeline is proposed for the identification and subsequent monitoring of post-harvest quality of leafy vegetables.

Mosaic environment-driven evolution of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont

BackgroundThe within-species diversity of symbiotic bacteria represents an important genetic resource for their environmental adaptation, especially for horizontally transmitted endosymbionts. Although strain-level intraspecies variation has recently been detected in many deep-sea endosymbionts, their ecological role in environmental adaptation, their genome evolution pattern under heterogeneous geochemical environments, and the underlying molecular forces remain unclear.ResultsHere, we conducted a fine-scale metagenomic analysis of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont collected from distinct habitats: hydrothermal vent and methane seep. Endosymbiont genomes were assembled using a pipeline that distinguishes within-species variation and revealed highly heterogeneous compositions in mussels from different habitats. Phylogenetic analysis separated the assemblies into three distinct environment-linked clades. Their functional differentiation follows a mosaic evolutionary pattern. Core genes, essential for central metabolic function and symbiosis, were conserved across all clades. Clade-specific genes associated with heavy metal resistance, pH homeostasis, and nitrate utilization exhibited signals of accelerated evolution. Notably, transposable elements and plasmids contributed to the genetic reshuffling of the symbiont genomes and likely accelerated adaptive evolution through pseudogenization and the introduction of new genes.ConclusionsThe current study uncovers the environment-driven evolution of deep-sea symbionts mediated by mobile genetic elements. Its findings highlight a potentially common and critical role of within-species diversity in animal-microbiome symbioses.CVLZncxgEcwzSBxr2fsxJvVideo

Pathogenicity and progression of Botryosphaeriaceae associated with dieback in walnut orchards in Australia

AbstractDieback of the fruiting spurs of walnut (Juglans regia) results in yield losses in walnut orchards in Australia. Botryosphaeriaceae spp. have been implicated as the causative agents, with Diplodia seriata and Neofusicoccum parvum reported as the most prevalent species. Pathogenicity assays demonstrated inter- and intra-species variation with N. parvum more virulent than D. seriata. Both species were re-isolated beyond the dieback lesion. At 12 months post-inoculation on one-year-old trunks, N. parvum and D. seriata were re-isolated at 31.5 and 9 mm respectively beyond lesion edges. The lesion length as well as pathogen progression beyond the lesion increased over time. The pathogen progressed faster acropetally than basipetally. Following wound healing at the site of inoculation, and in the absence of any external lesion, both pathogens continued to move through the xylem, causing internal discolouration of the vascular tissues. Both mycelia and conidia were pathogenic, with mycelia showing higher infection rates. There was a strong linear relationship between the dieback length caused by the two types of inocula. As little as two conidia were able to infect wounded tissues. Although wounds were susceptible to infection for more than 4 months post-wounding for N. parvum and 1 month for D. seriata, the highest disease incidence occurred in the first week following wounding. The implications for the walnut industry for appropriate control strategies are discussed.

Phyloproteomic study by MALDI-TOF MS in view of intraspecies variation in a significant homogenous phytopathogen Dickeya solani

Dickeya solani is an economically significant pectinolytic phytopathogen belonging to the Pectobacteriaceae family, which causes soft rot and blackleg diseases. Despite its notable impact on global potato production, there are no effective methods to control this pest. Here, we undertook a phyloproteomic study on 20 D. solani strains, of various origin and year of isolation, with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) supported by an in-depth characterization of the strains in terms of the virulence-associated phenotype. In spite of high homogeneity in this species, we herein revealed for the first time intraspecies variation in the MALDI-TOF MS protein profiles among the studied D. solani isolates. Finally, representative mass spectra for the four delineated clades are presented. A majority of the analysed D. solani strains showed high virulence potential, while two strains stood out in their growth dynamics, virulence factors production and ability to macerate plant tissue. Nonetheless, the metabolic profiles of D. solani strains turned out to be uniform, except for gelatinase activity. Given that all D. solani isolates distinctly grouped from the other Dickeya species in the MALDI-TOF MS analysis, there is strong evidence supporting the potential routine use of this method for fast and reliable to-species identification of D. solani isolates of environmental origin.

Deriving aquatic PNECs of endocrine disruption effects for PFOS and PFOA by combining species sensitivity weighted distributions and adverse outcome pathway networks

Perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA), as emerging endocrine-disrupting chemicals (EDCs), pose adverse effects on aquatic organisms. Conventional ecological risk assessment (ERA) not fully considering the mode of toxicity action of PFOS and PFOA, may result in an underestimation of risks and confuse decision-makers. In the study, we developed species sensitivity weighted distribution (SSWD) models based on adverse outcome pathway (AOP) networks for deriving predicted no-effect concentrations (PNECs). Three kinds of weighting criteria (intraspecies variation, trophic level abundance, and data quality) and weighted log-normal distribution methods were adopted. The developed models considered the inter/intraspecies variation and integrated nontraditional endpoints of endocrine-disrupting effects. The PNECs of endocrine disruption effects were derived as 2.52 μg/L (95% confidence intervals 0.667–9.85 μg/L) for PFOS and 18.7 μg/L (5.40–71.0 μg/L) for PFOA, which were more conservative than those derived from the SSD method and were comparable with the values in the literature based on the chronic toxicity data. For PFOS, the effect of growth and development was the most sensitive; however, for PFOA, the effect of reproduction was the most sensitive in the effects of growth and development, reproduction, biochemistry and genetics, and survival. The endocrine-disrupting effects of PFOS and PFOA are significant and need to be fully recognized in the ERA. This study provided an ERA framework that can improve the ecological relevance and reduce the uncertainty of PNECs of EDCs.

Taphonomic analysis of microfossil bonebeds from Western Gondwana: a case study from the late Permian Corumbataí Formation (Paraná Basin, Brazil)

ABSTRACT Storm deposits are common in geological records and encompass a variety of fossil assemblages affected by taphonomic processes that can biased fossil preservation. Here, we describe a microfossil bonebed to demonstrate the role played by certain filters in the final composition of storm-generated fossil accumulations. These layers are recurrent in the Paraná Basin and possibly in other localities of Gondwana, outcropping over 1000 km in the Permian units of the basin. Thirty samples were systematically collected from the state of São Paulo and their components were analysed. These samples consisted of clay matrix, coprolites, scales, and teeth of lower actinopterygian (Palaeonisciformes) and Xenacanthiformes fish. The taphonomic signatures demonstrated that the layer formed as a lag deposit in a distal aquatic environment. Two major taphonomic filters were recognised. The first filter selected bioclasts according to size and density, whereas the second filter preserved only the original phosphatic elements. The third and minor filter were related to breakage, which occured during reworking and diagenesis, respectively. All of these processes contributed to the generation of an assemblage with limited composition and species richness. Thus, distal tempestites might not be useful for estimating palaeodiversity, but may still offer some valuable information about intraspecies variation.

How Different Molecular Markers Estimate the Diversity of European Species of the Ganoderma Genus.

Based on published anatomical-morphological and ecological characteristics and phylogenetic evidence, six species of the Ganoderma genus are known to occur in Europe, namely, G. applanatum (Pers.) Pat., G. adspersum (Schulzer) Donk, G. pfeifferi Bres., G. resinaceum Boud., G. carnosum Pat., and G. lucidum (Curtis) P. Karst. Molecular markers (DNA sequences of selected genes or intergenic spacers) revolutionized our view of fungal variability. Every one of the four most frequently used molecular markers (ITS (internal transcribed spacer) and partial sequences of LSU (rRNA large subunit), tef1-α (translation elongation factor 1-alpha), and Rpb2 (RNA polymerase II second largest subunit)) provides a different view on the variability of European species of the Ganoderma genus. Both the lowest intraspecies variability and the best species differentiation (interspecies divergence) were observed for the LSU marker, and based on our data, this marker could be recommended for identification and species delineation in European Ganoderma spp. The sequences of the most frequently used ITS marker were unable to discriminate between G. lucidum and G. carnosum, and in general, this species pair showed the lowest interspecies divergence using all markers tested. Surprisingly, up to now, hidden variability has been detected in several Ganoderma spp., indicating the existence of possible cryptic taxa within the European Ganoderma morphospecies.

Unraveling the Polysaccharide Biosynthesis Potential of Ganoderma lucidum: A Chromosome-Level Assembly Using Hi-C Sequencing.

Ganoderma lucidum exhibits the ability to synthesize a diverse range of biologically active molecules with significant pharmaceutical potential, including xylomannan and fucogalactan, which have demonstrated antitumor activity. However, there exists considerable intra-species variability in the capacity to produce these metabolites at high concentrations, likely reflecting the high genomic diversity observed from a limited number of strains sequenced to date. We employed high-throughput shotgun sequencing to obtain the complete genome sequence of G. lucidum strain 5.1, which is distinguished by its remarkable xylomannan synthesis capabilities. Through the utilization of semi-automatic reordering based on conformation capture (Hi-C) data, we substantially enhanced the assembly process, resulting in the generation of 12 chromosome-level scaffolds with a cumulative length of 39 Mbp. By employing both de novo and homology-based approaches, we performed comprehensive annotation of the genome, thereby identifying a diverse repertoire of genes likely involved in polysaccharide biosynthesis. The genome sequence generated in this study serves as a valuable resource for elucidating the molecular mechanisms underlying the medicinal potential of Ganoderma species, discovering novel pharmaceutically valuable compounds, and elucidating the ecological mechanisms of the species. Furthermore, the chromosome contact map obtained for the first time for this species extends our understanding of 3D fungal genomics and provides insights into the functional and structural organization within the fungal kingdom.

IDENTIFICATION OF LENS CULTIVARS IN MARKET BY MOLECULAR TOOLS: DNA BARCODING AND SSRs

Substitution of plant cultivars of high commercial value with a cheaper, lower quality one is a common fraud committed against consumers and producers. Since it is one of the most widely grown legumes, lentil (Lens culinaris Medik.) is suitable for such frauds. This study aimed to identify lentil cultivars which are registered and authorized in the market in Türkiye by using current molecular methods. For this purpose, 26 lentil cultivars were analyzed for 15 SSR markers and two DNA barcode regions (trnH-psbA and matK). A high allele diversity was observed by 12 scorable SSR markers, and the average number of alleles was determined to be 16. One of the important findings was the presence of “cultivar-specific alleles” that can be used to identify each cultivar in the lentil market in Türkiye. At least one “cultivar-specific allele” was obtained for each cultivar. The lentil cultivars were also analyzed by two DNA barcode regions as trnH-psbA and matK. While it was observed that the rate of the intra-species variation for the trnH-psbA region was low and 26 varieties were divided into 7 groups, higher rate was found for matK and samples were distributed into 14 groups. Nevertheless, it was observed that intra-species discrimination can be made more effective when both loci are used together and 26 species were distributed into 18 different groups. We expect that the results of this study, especially the cultivar-specific SSR alleles and DNA barcoding sequence data may be used routinely to identify production and packaged products that are commercially available in markets.

Molecular biomarkers for sperm quality in an economically important fish: Blue catfish, Ictalurus furcatus

Intraspecies variability in sperm quality is common among aquaculture species, thus necessitating an urgent need to establish reliable molecular biomarkers to screen for males with high-quality sperm. The channel catfish (Ictalurus punctatus) ♀ × blue catfish (I. furcatus) ♂ hybrid accounts for >50% of United States catfish production. Blue catfish sperm cannot be collected using non-lethal methods, and thus, males must be sacrificed to determine reproductive quality. To establish gene expression biomarkers of sperm quality, we characterized important sperm traits, ranked blue catfish males based on the curvilinear velocity of their sperm, and sequenced testicular tissue for mRNAs and sRNAs. Of the 43 males characterized, testicular tissue from 4 individuals with low-velocity (155.70 mm/s ± 1.49 SD) and 4 with high-velocity (205.01 mm/s ± 4.63 SD) were chosen for sequencing. No differentially expressed sRNAs were detected between the two sperm performance groups. However, we identified two differentially expressed mRNA transcripts between the low-velocity and high-velocity groups, aqp3a and ly97.3, both upregulated in the high-velocity group compared to the low-velocity group. These molecular biomarkers of sperm quality in testicular tissue are linked to gamete quality and may be applied for more efficient catfish aquaculture.

Harnessing Variabilities in Digital Melt Curves for Accurate Identification of Bacteria.

Digital PCR combined with high resolution melt (HRM) is an emerging method for identifying pathogenic bacteria with single cell resolution via species-specific digital melt curves. Currently, the development of such digital PCR-HRM assays entails first identifying PCR primers to target hypervariable gene regions within the target bacteria panel, next performing bulk-based PCR-HRM to examine whether the resulting species-specific melt curves possess sufficient interspecies variability (i.e., variability between bacterial species), and then digitizing the bulk-based PCR-HRM assays with melt curves that have high interspecies variability via microfluidics. In this work, we first report our discovery that the current development workflow can be inadequate because a bulk-based PCR-HRM assay that produces melt curves with high interspecies variability can, in fact, lead to a digital PCR-HRM assay that produces digital melt curves with unwanted intraspecies variability (i.e., variability within the same bacterial species), consequently hampering bacteria identification accuracy. Our subsequent investigation reveals that such intraspecies variability in digital melt curves can arise from PCR primers that target nonidentical gene copies or amplify nonspecifically. We then show that computational in silico HRM opens a window to inspect both interspecies and intraspecies variabilities and thus provides the missing link between bulk-based PCR-HRM and digital PCR-HRM. Through this new development workflow, we report a new digital PCR-HRM assay with improved bacteria identification accuracy. More broadly, this work can serve as the foundation for enhancing the development of future digital PCR-HRM assays toward identifying causative pathogens and combating infectious diseases.

A general methodology for the quantification of crop canopy nitrogen across diverse species using airborne imaging spectroscopy

Accurate monitoring of crop nitrogen (N) across spatial and temporal scales is a fundamental goal for meeting precision agriculture requirements and promoting sustainable agriculture. The planning and implementation of several spaceborne imaging spectroscopy missions in recent years holds great promise for such large scale and intricate monitoring. Several N retrieval models have been developed for specific crop species, but a generalized model across diverse species is lacking. By leveraging imaging spectroscopy data collected by the Global Airborne Observatory (GAO), and leaf samples collected from commercial and research farms, we used partial least squares regression to calibrate and validate the retrieval of mass-based crop canopy N concentrations across diverse species and several major agricultural regions in the contiguous United States. The performance statistics indicated high precision and accuracy of the model results, suggesting that the development of a generalized N retrieval model is possible (R2: 0.78; RMSE: 0.49% N). Maps derived from GAO data provided quantitative crop N information at fine spatial resolution (i.e., 0.6 m), capturing both inter- and intra-species variations across agricultural locations. The algorithm was also successfully tested on simulated moderate resolution (i.e., 30 m) imagery, corresponding to data to be collected by forthcoming spaceborne imaging spectroscopy missions. Imaging spectroscopy offers an effective approach to quantify crop N concentration that could be incorporated to promote sustainable agriculture and improve global food security.

Genetic and phenotypic intra-species diversity of alga Tisochrysis lutea reveals original genetic structure and domestication potential

ABSTRACT Oceanic phytoplankton species are generally composed of many strains, with intra-species diversity consisting of genetic and phenotypic variability. Despite its importance in ecological and biotechnological contexts, this intra-species diversity and variation among strains has been little studied. We investigated the intra-species diversity of the microalga Tisochrysis lutea, a haptophyte of the Isochrysidales order. Inter-strain diversity of T. lutea was studied because of the economic importance of the species as a feed in aquaculture and for antioxidant metabolite production, particularly fucoxanthin and other carotenoids, which have health benefits. We analysed Tara Ocean datasets which revealed that T. lutea was present in the Pacific, Atlantic and Indian Oceans but not in the Arctic or Austral Oceans. We next made phenotypic and genotypic comparisons of 11 strains of T. lutea from worldwide algal collections. All strains were cultivated in the same controlled conditions for one week, and several phenotypic traits were measured, notably antioxidant content. In parallel, the genomes of each strain were sequenced, and genetic variants identified. At the genetic and phenotypic levels, the strains were distinct from each other and our analysis revealed natural trait variations of interest in relation to further exploitation in domestication programmes. A large number of genetic variations were identified among the strains, but no major differences in genome size were observed. Moreover, limited genetic structure was observed among these strains, which could be a consequence of the complex life history of species within the Isochrysidales. Our study provides new knowledge on the intra-species diversity that should be considered in future environmental studies and breeding programmes.

Selection of lactic acid bacteria for biopreservation of salmon products applying processing-dependent growth kinetic parameters and antimicrobial mechanisms

Biopreservation using lactic acid bacteria (LAB) is a promising technology to prevent the growth of pathogenic microorganisms in fresh and mildly processed food. The main aim of this study was to select LAB, originally isolated from ready-to-eat (RTE) seafood, for biopreservation of fresh salmon and processed salmon products. Ten LAB strains (five Carnobacterium and five Leuconostoc) were selected based on previously demonstrated bioprotective properties to investigate their antimicrobial mechanisms and temperature-dependent growth kinetics in a sterile salmon juice model system. Furthermore, five strains (three Carnobacterium and two Leuconostoc) were selected to test process-dependent growth kinetic parameters relevant to the secondary processing of salmon. Two strains (Carnobacterium maltaromaticum 35 and C. divergens 468) showed bacteriocin-like activity against Listeria innocua, while inhibitory effect of cell-free supernatants (CFS) was not observed against Escherichia coli. All selected strains were able to grow in sterile salmon juice at tested temperatures (4, 8, 12 and 16 °C), with specific growth rates (μ) ranging from 0.01 to 0.04/h at 4 °C and reaching a maximum population density of 8.4–9 log CFU/ml. All five strains tested for process-dependent growth kinetic parameters were able to grow in the range of 0.5–5% NaCl and 0.13–0.26% purified condensed smoke (VTABB and JJT01), with inter- and intraspecies variation in growth kinetics. According to the temperature-dependent growth kinetics and antimicrobial assay results, two strains, Leuconostoc mesenteroides 68 (Le.m.68) and C. divergens 468 (C d.468), were selected for in situ test to validate their ability to grow in vacuum-packed fresh salmon at 4 °C. Both strains were able to grow at maximum growth rates of 0.29 ± 0.04/d for Le. m.68 and 0.39 ± 0.06/d for C.d.468, and their final concentrations were 7.91 ± 0.31 and 8.02 ± 0.25 log CFU/g, respectively. This study shows that LAB, originally isolated from RTE seafood, have promising potential as bioprotective strains in fresh and processed salmon products.