Intraspecies Variation Research Articles

Bradyrhizobium xenonodulans sp. nov. isolated from nodules of Australian Acacia species invasive to South Africa

A genealogical concordance approach was used to delineate strains isolated from Acacia dealbata and Acacia mearnsii root nodules in South Africa. These isolates form part of Bradyrhizobium based on 16S rRNA sequence similarity. Phylogenetic analysis of six housekeeping genes (atpD, dnaK, glnII, gyrB, recA and rpoB) confirmed that these isolates represent a novel species, while pairwise average nucleotide identity (ANIb) calculations with the closest type strains (B. cosmicum 58S1T, B. betae PL7HG1T, B. ganzhouense CCBAU 51670 T, B. cytisi CTAW11T and B. rifense CTAW71T) resulted in values well below 95–96%. We further performed phenotypic tests which revealed that there are high levels of intraspecies variation, while an additional analysis of the nodA and nifD loci indicated that the symbiotic loci of the strains are closely related to those of Bradyrhizobium isolates with an Australian origin. Strain 14ABT (=LMG 31415 T = SARCC-753 T) is designated as the type strain of the novel species for which we propose the name Bradyrhizobium xenonodulans sp. nov.

Trophic Position of the Species and Site Trophic State Affect Diet Niche and Individual Specialization: From Apex Predator to Herbivore.

Intra-species variability in isotopic niches, specifically isotopic total niche width (ITNW), isotopic individual niche width (IINW), and isotopic individual specialization (IIS), was studied using an innovative approach without sacrificing the vertebrates. Stable isotopes (δ13C, δ15N) in four body tissues differing in isotopic half-life were analyzed from four freshwater fish species representing different trophic positions. ITNW was widest for the apex predator (European catfish) and narrowest for the obligate predator (Northern pike). IINW exhibited a polynomial trend for the European catfish, Northern pike, and Eurasian perch (mesopredator), decreasing with body mass and increasing again after exceeding a certain species-dependent body mass threshold. Thus, for ectotherms, apex predator status is linked rather to its size than to the species. In herbivores (rudd), IINW increased with body mass. The IIS of predators negatively correlated with site trophic state. Therefore, eutrophication can significantly change the foraging behavior of certain species. We assume that the observed trends will occur in other species at similar trophic positions in either aquatic or terrestrial systems. For confirmation, we recommend conducting a similar study on other species in different habitats.

Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome

BackgroundCumulative sequencing efforts have yielded enough genomes to construct pangenomes for dozens of bacterial species and elucidate intraspecies gene conservation. Given the diversity of organisms for which this is achievable, similar analyses for ancestral species are feasible through the integration of pangenomics and phylogenetics, promising deeper insights into the nature of ancient life.ResultsWe construct pangenomes for 183 bacterial species from 54,085 genomes and identify their core genomes using a novel statistical model to estimate genome-specific error rates and underlying gene frequencies. The core genomes are then integrated into a phylogenetic tree to reconstruct the core genome of the last bacterial common ancestor (LBCA), yielding three main results: First, the gene content of modern and ancestral core genomes are diverse at the level of individual genes but are similarly distributed by functional category and share several poorly characterized genes. Second, the LBCA core genome is distinct from any individual modern core genome but has many fundamental biological systems intact, especially those involving translation machinery and biosynthetic pathways to all major nucleotides and amino acids. Third, despite this metabolic versatility, the LBCA core genome likely requires additional non-core genes for viability, based on comparisons with the minimal organism, JCVI-Syn3A.ConclusionsThese results suggest that many cellular systems commonly conserved in modern bacteria were not just present in ancient bacteria but were nearly immutable with respect to short-term intraspecies variation. Extending this analysis to other domains of life will likely provide similar insights into more distant ancestral species.

Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines

BackgroundClimate change threatens Earth’s ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea ice brine, similar in subzero temperature and high salinity but different in temporal stability, are inhabited by microbes adapted to these extreme conditions. However, little is known about their viruses (community composition, diversity, interaction with hosts, or evolution) or how they might respond to geologically stable cryopeg versus fluctuating sea ice conditions.ResultsWe used long- and short-read viromics and metatranscriptomics to study viruses in Arctic cryopeg brine, sea ice brine, and underlying seawater, recovering 11,088 vOTUs (~species-level taxonomic unit), a 4.4-fold increase of known viruses in these brines. More specifically, the long-read-powered viromes doubled the number of longer (≥25 kb) vOTUs generated and recovered more hypervariable regions by >5-fold compared to short-read viromes. Distribution assessment, by comparing to known viruses in public databases, supported that cryopeg brine viruses were of marine origin yet distinct from either sea ice brine or seawater viruses, while 94% of sea ice brine viruses were also present in seawater. A virus-encoded, ecologically important exopolysaccharide biosynthesis gene was identified, and many viruses (~half of metatranscriptome-inferred “active” vOTUs) were predicted as actively infecting the dominant microbial genera Marinobacter and Polaribacter in cryopeg and sea ice brines, respectively. Evolutionarily, microdiversity (intra-species genetic variations) analyses suggested that viruses within the stable cryopeg brine were under significantly lower evolutionary pressures than those in the fluctuating sea ice environment, while many sea ice brine virus-tail genes were under positive selection, indicating virus-host co-evolutionary arms races.ConclusionsOur results confirmed the benefits of long-read-powered viromics in understanding the environmental virosphere through significantly improved genomic recovery, expanding viral discovery and the potential for biological inference. Evidence of viruses actively infecting the dominant microbes in subzero brines and modulating host metabolism underscored the potential impact of viruses on these remote and underexplored extreme ecosystems. Microdiversity results shed light on different strategies viruses use to evolve and adapt when extreme conditions are stable versus fluctuating. Together, these findings verify the value of long-read-powered viromics and provide foundational data on viral evolution and virus-microbe interactions in Earth’s destabilized and rapidly disappearing cryosphere.B3KUN5MJ8EAz4vqucsgZtLVideo

Deciphering the growth responses and genotypic diversity of bioluminescent Photobacterium phosphoreum on chicken meat during aerobic refrigerated storage

The advent of high-throughput sequencing technologies in recent years has revealed the unexpected presence of genus Photobacterium within the chicken meat spoilage ecosystem. This study was undertaken to decipher the occurrence, the growth patterns and the genotypic biodiversity of Photobacterium phosphoreum on chicken breast fillets stored aerobically at 4 °C through conventional microbiological methods and molecular techniques. Samples were periodically cultured on marine broth agar (MA; supplemented with meat extract and vancomycin) for the enumeration of presumptive bioluminescent Photobacterium spp. In total, 90 bioluminescent bacteria were recovered from the initial (time of first appearance), middle and end stages of storage. Concomitantly, 95 total psychrotrophic/psychrophilic bacteria were isolated from the same medium to assess the presence and diversity of non-luminous photobacteria. Genetic diversity between bioluminescent isolates was assessed with two PCR-based DNA fingerprinting methods, i.e. RAPD and rep-PCR. Moreover, the characterization of selected bacterial isolates at the genus and/or species level was performed by sequencing of the 16S rRNA and/or gyrB gene. Bioluminescent bacteria were scarcely encountered in fresh samples at population levels of ca. 2.0 log CFU/g, whilst total psychrotrophic/psychrophilic bacteria were found at levels of ca. 4.4 log CFU/g. As time proceeded and close to shelf-life end, bioluminescent bacteria were encountered at higher populations, and were found at levels of 5.3 and 7.0 log CFU/g in samples from the second and third batch, respectively. In the first batch their presence was occasional and at levels up to 3.9 log CFU/g. Accordingly, total psychrotrophic/psychrophilic bacteria exceeded 8.4 log CFU/g at the end of storage, suggesting the possible underestimation of bioluminescent populations following the specific cultivation conditions. Sequence analysis assigned bioluminescent isolates to Photobacterium phosphoreum, while genetic fingerprinting revealed high intra-species variability. Respectively, total psychrotrophs/psychrophiles were assigned to genera Pseudomonas, Shewanella, Psychrobacter, Acinetobacter, Vibrio and Photobacterium. Non-luminous photobacteria were not identified within the psychrotrophs/psychrophiles. Results of the present study reveal the intra- and inter-batch variability on the occurrence and growth responses of P. phosphoreum and highlight its potential role in the chicken meat spoilage consortium.

DNA metabarcoding Passerine bird feces at tree-line uncovers little intra- and inter-species dietary overlap

High-elevation insectivorous birds are currently confronted with the reality of a changing climate, land use shifts, and the decline of many prey groups. The diet dynamics among many imperiled animals in this group are still unresolved. Examining the diets of tree-line Passerine birds to the species level of the prey allows for stronger population predictions. This study uses DNA metabarcoding to identify prey arthropods from adult Passerine bird feces at and slightly below tree-line in a Pyrenean forest. Our objective was to quantify the intra-and inter-species richness and overlap of Passerine bird diet over time and space. The results showed that adult Passerine diets have high inter- and intra-species dietary variability and low inter- and intra-species dietary overlap. The lack of association between dietary richness and open space, season, and elevation and lack of differences between dietary overlap and open space and elevation suggest high-elevation Passerine birds have very high dietary flexibility. The results also showed that aphids known to be pests to conifers, and other conifer pests, were prevalent in the birds’ diets. The Passerine diets and high rate of rare dietary items are mainly in line with other recent DNA metabarcoding studies. Implications for the long-term projections relative to tree-line Passerine populations are discussed.

Intra-species variation of ovipositor morphology and oviposition preference in Drosophila suzukii (Diptera: Drosophilidae)

Females of Drosophila suzukii have an enlarged and sclerotized ovipositor (oviscapt, hypogynium), which is a key evolutionary trait that enabled D. suzukii to lay eggs through the skin of ripening fruits. We investigated the intra-species variation of D. suzukii in ovipositor morphology and oviposition preference for substrate hardness among 27 strains recently established from local populations in Japan. A significant difference between strains was observed in the length of the ovipositor as well as in the number of bristles on it. Further analysis using representative strains revealed that the ovipositor size variation among strains was independent of the body size variation, suggesting that the proportion between the ovipositor and other body parts was different among the strains. In the two-choice oviposition assay using 2% and 7% agar substrates, four strains preferred the soft substrates, and one strain preferred the hard substrates. Competitive cross-modal assay between substrate hardness and surface curvature revealed that the preference for curvature overrode the preference for hardness in all the tested strains.

Uncharacterized and lineage-specific accessory genes within the Proteus mirabilis pan-genome landscape.

Proteus mirabilis is a Gram-negative bacterium recognized for its unique swarming motility and urease activity. A previous proteomic report on four strains hypothesized that, unlike other Gram-negative bacteria, P. mirabilis may not exhibit significant intraspecies variation in gene content. However, there has not been a comprehensive analysis of large numbers of P. mirabilis genomes from various sources to support or refute this hypothesis. We performed comparative genomic analysis on 2,060 Proteus genomes. We sequenced the genomes of 893 isolates recovered from clinical specimens from three large US academic medical centers, combined with 1,006 genomes from NCBI Assembly and 161 genomes assembled from Illumina reads in the public domain. We used average nucleotide identity (ANI) to delineate species and subspecies, core genome phylogenetic analysis to identify clusters of highly related P. mirabilis genomes, and pan-genome annotation to identify genes of interest not present in the model P. mirabilis strain HI4320. Within our cohort, Proteus is composed of 10 named species and 5 uncharacterized genomospecies. P. mirabilis can be subdivided into three subspecies; subspecies 1 represented 96.7% (1,822/1,883) of all genomes. The P. mirabilis pan-genome includes 15,399 genes outside of HI4320, and 34.3% (5,282/15,399) of these genes have no putative assigned function. Subspecies 1 is composed of several highly related clonal groups. Prophages and gene clusters encoding putatively extracellular-facing proteins are associated with clonal groups. Uncharacterized genes not present in the model strain P. mirabilis HI4320 but with homology to known virulence-associated operons can be identified within the pan-genome. IMPORTANCE Gram-negative bacteria use a variety of extracellular facing factors to interact with eukaryotic hosts. Due to intraspecies genetic variability, these factors may not be present in the model strain for a given organism, potentially providing incomplete understanding of host-microbial interactions. In contrast to previous reports on P. mirabilis, but similar to other Gram-negative bacteria, P. mirabilis has a mosaic genome with a linkage between phylogenetic position and accessory genome content. P. mirabilis encodes a variety of genes that may impact host-microbe dynamics beyond what is represented in the model strain HI4320. The diverse, whole-genome characterized strain bank from this work can be used in conjunction with reverse genetic and infection models to better understand the impact of accessory genome content on bacterial physiology and pathogenesis of infection.

Host-specific sensing of coronaviruses and picornaviruses by the CARD8 inflammasome.

Hosts have evolved diverse strategies to respond to microbial infections, including the detection of pathogen-encoded proteases by inflammasome-forming sensors such as NLRP1 and CARD8. Here, we find that the 3CL protease (3CLpro) encoded by diverse coronaviruses, including Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), cleaves a rapidly evolving region of human CARD8 and activates a robust inflammasome response. CARD8 is required for cell death and the release of pro-inflammatory cytokines during SARS-CoV-2 infection. We further find that natural variation alters CARD8 sensing of 3CLpro, including 3CLpro-mediated antagonism rather than activation of megabat CARD8. Likewise, we find that a single nucleotide polymorphism (SNP) in humans reduces CARD8's ability to sense coronavirus 3CLpros and, instead, enables sensing of 3C proteases (3Cpro) from select picornaviruses. Our findings demonstrate that CARD8 is a broad sensor of viral protease activities and suggests that CARD8 diversity contributes to inter- and intraspecies variation in inflammasome-mediated viral sensing and immunopathology.

Design of a line-of-sight fluorescence-based imaging diagnostic for classification of microbe species

Fluorescence imaging of certain biochemicals, including flavins and pyridine nucleotides, has utility in characterizing the metabolic state of tissue and in discriminating between microbial species. There is significant clinical utility in this class of imaging techniques but most measurements reported to date require specialized training and equipment rendering most implementations unsuitable for routine medical imaging. Here, a low-cost and robust imaging technique is designed using ultraviolet-induced fluorescence of pyridine nucleotides (primarily NADH) and flavins (primarily FAD) in microbial samples. The diagnostic is optimized to distinguish between different microbial species based on previously reported spectral data using a ratiometric imaging approach. A detailed performance analysis is provided that relates the measured fluorescence intensity ratio (FIR) to the relative concentration ratio of NADH to FAD using a simplified spectroscopic model. Analysis suggests the technique is sensitive to changes in the NADH/FAD concentration ratio over several orders of magnitude, with better than 10% FIR precision on a per-pixel basis for microbial smears as thin as 10 s of microns at a resolution of 30 mm−1 and exposures of 20 ms. Representative microbe samples from eight species were imaged to demonstrate the proposed technique. Results show that the FIR varies by an order of magnitude across different species but the intra-species variation is only ∼5% for the conditions used here. An additional imaging band may be necessary to classify species that contain red pigments or bacteriochlorophyll. Radiative trapping was discussed as a possible limitation of the technique, but no clear evidence for radiative trapping was observed here. Overall, the results suggest that the proposed approach is feasible for rapid, low-cost, and robust characterization of microbial samples.

Diatom community dynamics in a tropical brackish coastal ecosystem from an ecological and biogeochemical perspective: A size-fractionated approach

Diatoms are a major, ubiquitous photosynthetic group representing most aquatic ecosystem’s microalgal communities. The species composition encompasses a wide range of cell sizes. Although cell size is vital in aquatic ecology and biogeochemistry, size-based diatom community studies are sparse, especially in tropical ecosystems. This study assesses the size-fractionated brackish diatom community based on the microscopic cell abundance and carbon-biomass metrics. Despite sufficient nutrient availability, the seasonal and spatial relative proportion of abundance and biomass of the three diatom size fractions declined under high turbidity. It increased under higher light and nutrient availability with lower turbidity. Turbulence was a favorable factor irrespective of the size groups. Light availability, increased nutrients, and lower temperature resulted in a higher contribution from the larger size group to the total diatom carbon biomass. The smaller size group dominance during highly turbid conditions could be attributed to the higher surface-to-volume ratios. The intermediate-size groups thrived under reduced turbidity. Seasonal intra-species size variations reflected changes induced either due to life-cycle stages or environmental stress. The size-based metrics permitted an in-depth understanding of the diatom responses at the community and species level, which could have implications on their ecological and biogeochemical roles in aquatic ecosystems.

Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex.

Mitochondria are essential organelles in the eukaryotic cells and responsible for the energy production but are also involved in many other functions including virulence of some fungal species. Although the evolution of fungal mitogenomes have been studied at some taxonomic levels there are still many things to be learned from studies of closely related species. In this study, we have analyzed 60 mitogenomes in the five species of the Heterobasidion annosum sensu lato complex that all are necrotrophic pathogens on conifers. Compared to other fungal genera the genomic and genetic variation between and within species in the complex was low except for multiple rearrangements. Several translocations of large blocks with core genes have occurred between the five species and rearrangements were frequent in intergenic areas. Mitogenome lengths ranged between 108 878 to 116 176 bp, mostly as a result of intron variation. There was a high degree of homology of introns, homing endonuclease genes, and intergenic ORFs among the five Heterobasidion species. Three intergenic ORFs with unknown function (uORF6, uORF8 and uORF9) were found in all five species and was located in conserved synteny blocks. A 13 bp long GC-containing self-complementary palindrome was discovered in many places in the five species that were optional in presence/absence. The within species variation is very low, among 48 H. parviporum mitogenomes, there was only one single intron exchange, and SNP frequency was 0.28% and indel frequency 0.043%. The overall low variation in the Heterobasidion annosum sensu lato complex suggests a slow evolution of the mitogenome.

Genotypic and phenotypic uniformity among the population of Pectobacterium atrosepticum strains isolated during three growing seasons from potato fields in Poland

Pectobacterium atrosepticum (Pba)are phytopathogenic, pectinolytic, non-sporulating, gram-negative rods causing blackleg and soft rot diseases in potato. They are ubiquitously present under temperate climate conditions and contribute to significant economic losses. Currently, there are no efficient control methods against soft rot Pectobacteriaceae (SRP). As limitation of the spread of SRP is solely prevention-based, we undertook broad characterization on both genotypic and phenotypic levels of the P. atrosepticum isolates acquired during monitoring of potato fields in Poland in 2013, 2014 and 2016. Of REP, ERIC and BOX-based genomic fingerprinting, the BOX-based approach turned out to be the most informative and allowed for classification of 118 Pba strains into six groups. The present study indicated that IV and I BOX profiles dominated among the investigated population. Finally, 23 Pba strains representing all BOX groups and originating from various growing seasons were selected for genotypic, phylogenetic and phenotypic studies. rpoS-based phylogeny revealed intraspecies variation (16 SNP sites) among the studied Pba strains, in contrast to the analyses relying on gyrA (1 SNP) and recA (0 SNP) sequences. Pba strains showed higher potency to macerate potato tissue at 20 °C than 28 °C. These isolates exhibited rather uniform production of plant cell wall degrading enzymes (pectinases, cellulases and proteases), lipases, siderophores and biofilm, however in the majority of cases inferior in comparison to Dickeya solani and Pectobacterium carotovorum strains. In conclusion, this study revealed genotypic and phenotypic uniformity in addition to high virulence potential of Pba strains isolated from potato fields during several growing seasons in Poland.

Derivation and validation of soil total and extractable cadmium criteria for safe vegetable production

Determining the appropriate soil cadmium (Cd) criteria for vegetable production is important for ensuring that the Cd concentrations of the vegetables meet food safety standards. The soil extractable Cd criteria for vegetable production are also essential for both food safety and environmental management, especially in areas with a high natural background level. In the present study, soil total and extractable Cd criteria were derived using the approach of species sensitivity distribution integrated with soil aging and bioavailability as affected by soil properties. A dataset of 90 vegetable species planted in different soils was compiled by screening the published in literature in five bibliographic databases using designated search strings. The empirical soil–plant transfer model was applied to normalize the bioaccumulation data. After normalization, the intra-species variability was reduced by 18.3 to 84.4%. The soil Cd concentration that would protect 95% (HC5) of the species was estimated by species sensitivity distribution curves that were fitted by the Burr III function. The soil Cd criteria derived from the added approach for risk assessment were proposed as continuous criteria based on a combination of organic carbon and pH in the soil. Criteria for total Cd and EDTA-extractable Cd in the soil ranged from 0.23 to 0.61 mg kg−1 and from 0.09 to 0.25 mg kg−1, respectively. Field experimental data were used to validate the applicability and validity of these criteria. Most of the predicted HC5 values in the field experimental sites were below the 1:1 line. These results provide a scientific basis for soil Cd criteria for vegetable production that will ensure food safety.

Effect of pearl guinea fowl eggshell ultrastructure and microstructure on keets hatchability

Variability in shell structure is an evolutionary mechanism in birds that enables them to adapt to specific environmental conditions. This variability may also occur within the same species under the influence of individual indicators, such as the age or health status of females. While interspecies variation is quite obvious and easy to interpret, the reasons for intraspecies variation remain unclear. In this study, we examined the ultra- and microstructure of guinea fowl eggshells to identify the association between variations in shell structure and hatchability outcomes. We analyzed the visual differences between shells with low (L), intermediate (I), and high (H) external porosity using scale invariant feature transform analysis with NaturePatternMatch software. We found that the external pore image was closely related to the overall porosity of the shell before incubation. The total pore area, total porosity, and diffusion index (GH2O) were highest in group H shells (P < 0.001). Posthatching shells were characterized by an increased diameter and total surface area, decreased pore number (P < 0.001), as well as shortened mammillary layer (P < 0.001) and decreased total consumption of mammillary knobs (P < 0.001). The porosity indices of posthatching H shells had intermediate values between L and I. Although the effect of shell structure parameters on hatching was not confirmed, we assumed that all categories (L, I, and H) of shells were ideal for incubation. This suggests that the shell structure adapts to the metabolic rate of developing embryos; however, differences in shell structure affect the duration of incubation and synchronization of hatching. Both L and H shells showed delayed and prolonged hatching. Therefore, we recommended that guinea fowl eggs with different external porosity parameters should be incubated separately for better hatching synchronization. Differences in GH2O between L, I, and H eggs suggest that the shell porosity characteristics of guinea fowl eggs may be a key determinant of the rate of water loss during storage before incubation.

Adverse effects of polystyrene nanoplastics on sea cucumber Apostichopus japonicus and their association with gut microbiota dysbiosis

The mariculture environment is a sink of microplastics (MPs) due to its enclosed nature and mass use of plastics. Nanoplastics (NPs) are MPs with a diameter <1 μm that have a more toxic effect on aquatic organisms than other MPs. However, little is known about the underlying mechanisms of NP toxicity on mariculture species. Here, we performed a multi-omics investigation to explore gut microbiota dysbiosis and associated health problems induced by NPs in juvenile sea cucumber Apostichopus japonicus, a commercially and ecologically important marine invertebrate. We observed significant differences in gut microbiota composition after 21 days of NP exposure. Ingestion of NPs significantly increased core gut microbes, especially Rhodobacteraceae and Flavobacteriaceae families. Additionally, gut gene expression profiles were altered by NPs, especially those related to neurological diseases and movement disorders. Correlation and network analyses indicated close relationships between transcriptome changes and gut microbiota variation. Furthermore, NPs induced oxidative stress in sea cucumber intestines, which may be associated with intraspecies variation in Rhodobacteraceae in the gut microbiota. The results suggested that NPs were harmful to the health of sea cucumbers, and they highlighted the importance of the gut microbiota in the responses to NP toxicity in marine invertebrates.

Host Specificity of Soilborne Pathogens in Hordeum Species and Their Relatives.

Soilborne pathogens destabilize the yields of Triticeae crops, including barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.). Although genetic resistance derived from relatives of these species has been utilized to prevent rust diseases (i.e., in the wheat-rye 1BL-1RS translocation line), research on resistance against soilborne pathogens remains limited. Here, we performed field trials using 76 genotypes representing 28 Hordeum, six Triticum, and two Aegilops species to examine resistance against three soilborne bymoviruses: barley yellow mosaic virus (BaYMV), barley mild mosaic virus (BaMMV), and wheat yellow mosaic virus (WYMV). We also performed greenhouse tests using the soilborne fungal pathogen Fusarium pseudograminearum, which causes Fusarium crown rot (FCR). Using RT-PCR, we detected BaMMV and BaYMV in several Hordeum species, whereas WYMV induced systemic infection in the Triticum and Aegilops species. The identification of FCR susceptibility in all species examined suggests that F. pseudograminearum is a facultative fungal pathogen in Triticeae. Intraspecies variation in FCR disease severity was observed for several species, pointing to the possibility of exploring host resistance mechanisms. Therefore, by unlocking the host specificity of four soilborne pathogens in Hordeum species and their relatives, we obtained insights for the further exploration of wild sources of soilborne pathogen resistance for future wheat and barley improvement programs.

Intra-Species Variations of Bioactive Compounds of Two Dictyota Species from the Adriatic Sea: Antioxidant, Antimicrobial, Dermatological, Dietary, and Neuroprotective Potential.

The marine environment has a significant impact on life on Earth. Organisms residing in it are vital for the ecosystem but also serve as an inexhaustible source of biologically active compounds. Herein, the biodiversity of two brown seaweeds, Dictyota dichotoma and Dictyota fasciola from the Adriatic Sea, was evaluated. The aim of the study was the determination of differences in compound composition while comparing their activities, including antioxidant, antimicrobial, and enzyme inhibition, in connection to human digestion, dermatology, and neurological disorders. Chemical analysis revealed several terpenoids and steroids as dominant molecules, while fucoxanthin was the main identified pigment in both algae. D. dichotoma had higher protein, carbohydrate, and pigment content. Omega-6 and omega-3 fatty acids were identified, with the highest amount of dihomo-γ-linolenic acid and α-linolenic acid in D. dichotoma. Antimicrobial testing revealed a dose-dependent inhibitory activity of methanolic fraction against Escherichia coli and Staphylococcus aureus. Moderate antioxidant activity was observed for both algae fractions, while the dietary potential was high, especially for the D. fasciola dichloromethane fraction, with inhibition percentages of around 92% for α-amylase and 57% for pancreatic lipase at 0.25 mg/mL. These results suggest that Dictyota species might be a potent source of naturally derived agents for obesity and diabetes.

Bacterial communities and toxin profiles of Ostreopsis (Dinophyceae) from the Pacific island of Okinawa, Japan

Variations in toxicity of the benthic dinoflagellate Ostreopsis Schmidt 1901 have been attributed to specific molecular clades, biogeography of isolated strains, and the associated bacterial community. Here, we attempted to better understand the biodiversity and the basic biology influencing toxin production of Ostreopsis. Nine clonal cultures were established from Okinawa, Japan, and identified using phylogenetic analysis of the ITS-5.8S rRNA and 28S rRNA genes. Morphological analysis suggests that the apical pore complex L/W ratio could be a feature for differentiating Ostreopsis sp. 2 from the O. ovata species complex. We analyzed the toxicity and bacterial communities using liquid chromatography-mass spectrometry, and PCR-free metagenomic sequencing. Ovatoxin was detected in three of the seven strains of O. cf. ovata extracts, highlighting intraspecies variation in toxin production. Additionally, two new potential analogs of ovatoxin-a and ostreocin-A were identified. Commonly associated bacteria clades of Ostreopsis were identified from the established cultures. While some of these bacteria groups may be common to Ostreopsis (Rhodobacterales, Flavobacteria-Sphingobacteria, and Enterobacterales), it was not clear from our analysis if any one or more of these plays a role in toxin biosynthesis. Further examination of biosynthetic pathways in metagenomic data and additional experiments isolating specific bacteria from Ostreopsis would aid these efforts.

A multivariate analysis of phenotypic traits of strains of Fusarium graminearum and F. meridionale supports structure by species

AbstractFusarium head blight (FHB) of wheat and Gibberella ear and stalk rot (GER and GSR) of maize are diseases of worldwide importance. Several phylogenetic species belonging to the Fusarium graminearum species complex (FGSC) cause FHB and GER/GSR in Brazil, but the dominant species varies depending on host. Fusarium graminearum is the most frequent cause of FHB, while F. meridionale is more often associated with GER/GSR. These two species are distinguished based on fixed sequence variations at a few genetic loci; however, relevance of these differences to reproduction, pathogenicity and toxigenicity has not been fully explored. A range of phenotypic traits were evaluated for a group of strains of F. graminearum and F. meridionale from wheat and maize. These included radial growth on agar plates, sexual and asexual reproduction, fungicide sensitivity, toxigenicity and pathogenicity on wheat and maize. Although intraspecies variation was observed for most traits, a multivariate analysis showed the strains were strongly structured by species, regardless of host origin. Increased sexual or asexual reproduction, deoxynivalenol production and aggressiveness on wheat heads were most important for distinguishing strains of F. graminearum, while faster mycelial growth in culture, nivalenol production and reduced colonization on detached maize silks were most important for distinguishing strains of F. meridionale. Thus, the phylogenetic distinction between F. graminearum and F. meridionale is supported by phenotypic differences that are relevant for pathogenicity (aggressiveness and mycotoxin production on wheat heads and maize silks, mycelial growth and sexual and asexual reproduction) and disease management (tebuconazole sensitivity).