Dictyostelium discoideum-assisted pharmacognosy of plant resources for discovering antivirulence molecules targeting Klebsiella pneumoniae.

The rise of antibiotic-resistant bacterial strains represents an important challenge for global health, underscoring the critical need for innovative strategies to confront this threat. Natural products and their derivatives have emerged as a promising reservoir for drug discovery. The social amoeba Dictyostelium discoideum is a potent model organism in this effort. Employing this invertebrate model, we introduce a novel perspective to investigate natural plant extracts in search of molecules with potential antivirulence activity. Our work established an easy-scalable developmental assay targeting a virulent strain of Klebsiella pneumoniae, with Helenium aromaticum as the representative plant. The main objective was to identify tentative compounds from the Helenium aromaticum extract that attenuate the virulence of K. pneumoniae virulence without inducing cytotoxic effects on amoeba cells. Notably, the methanolic root extract of H. aromaticum fulfilled these prerequisites compared to the dichloromethane extract. Using UHPLC Q/Orbitrap/ESI/MS/MS, 63 compounds were tentatively identified in both extracts, 47 in the methanolic and 29 in the dichloromethane, with 13 compounds in common. This research underscores the potential of employing D. discoideum-assisted pharmacognosy to discover new antivirulence agents against multidrug-resistant pathogens.

Enhanced radiation use efficiency and grain filling rate as the main drivers of grain yield genetic gains in the CIMMYT elite spring wheat yield trial.

Common wheat (Triticum aestivum L.) is a major staple food crop, providing a fifth of food calories and proteins to the world's human population. Despite the impressive growth in global wheat production in recent decades, further increases in grain yield are required to meet future demands. Here we estimated genetic gain and genotype stability for grain yield (GY) and determined the trait associations that contributed uniquely or in combination to increased GY, through a retrospective analysis of top-performing genotypes selected from the elite spring wheat yield trial (ESWYT) evaluated internationally during a 14-year period (2003 to 2016). Fifty-six ESWYT genotypes and four checks were sown under optimally irrigated conditions in three phenotyping trials during three consecutive growing seasons (2018-2019 to 2020-2021) at Norman E. Borlaug Research Station, Ciudad Obregon, Mexico. The mean GY rose from 6.75 (24th ESWYT) to 7.87 t ha-1 (37th ESWYT), representing a cumulative increase of 1.12 t ha-1. The annual genetic gain for GY was estimated at 0.96% (65 kg ha-1 year-1) accompanied by a positive trend in genotype stability over time. The GY progress was mainly associated with increases in biomass (BM), grain filling rate (GFR), total radiation use efficiency (RUE_total), grain weight per spike (GWS), and reduction in days to heading (DTH), which together explained 95.5% of the GY variation. Regression lines over the years showed significant increases of 0.015 kg m-2 year-1 (p < 0.01), 0.074 g m-2 year-1 (p < 0.05), and 0.017 g MJ-1 year-1 (p < 0.001) for BM, GFR, and RUE_total, respectively. Grain weight per spike exhibited a positive but no significant trend (0.014 g year-1, p = 0.07), whereas a negative tendency for DTH was observed (- 0.43 days year-1, p < 0.001). Analysis of the top ten highest-yielding genotypes revealed differential GY-associated trait contributions, demonstrating that improved GY can be attained through different mechanisms and indicating that no single trait criterion is adopted by CIMMYT breeders for developing new superior lines. We conclude that CIMMYT's Bread Wheat Breeding Program has continued to deliver adapted and more productive wheat genotypes to National partners worldwide, mainly driven by enhancing RUE_total and GFR and that future yield increases could be achieved by intercrossing genetically diverse top performer genotypes.

Carbapenem-resistant hypervirulent ST23 Klebsiella pneumoniae with a highly transmissible dual-carbapenemase plasmid in Chile.

BACKGROUND: The convergence of hypervirulence and carbapenem resistance in the bacterial pathogen Klebsiella pneumoniae represents a critical global health concern. Hypervirulent K. pneumoniae (hvKp) strains, frequently from sequence type 23 (ST23) and having a K1 capsule, have been associated with severe community-acquired invasive infections. Although hvKp were initially restricted to Southeast Asia and primarily antibiotic-sensitive, carbapenem-resistant hvKp infections are reported worldwide. Here, within the carbapenemase production Enterobacterales surveillance system headed by the Chilean Public Health Institute, we describe the isolation in Chile of a high-risk ST23 dual-carbapenemase-producing hvKp strain, which carbapenemase genes are encoded in a single conjugative plasmid. RESULTS: Phenotypic and molecular tests of this strain revealed an extensive resistance to at least 15 antibiotic classes and the production of KPC-2 and VIM-1 carbapenemases. Unexpectedly, this isolate lacked hypermucoviscosity, challenging this commonly used hvKp identification criteria. Complete genome sequencing and analysis confirmed the K1 capsular type, the KpVP-1 virulence plasmid, and the GIE492 and ICEKp10 genomic islands carrying virulence factors strongly associated with hvKp. Although this isolate belonged to the globally disseminated hvKp clonal group CG23-I, it is unique, as it formed a clade apart from a previously reported Chilean ST23 hvKp isolate and acquired an IncN KPC-2 plasmid highly disseminated in South America (absent in other hvKp genomes), but now including a class-I integron carrying blaVIM-1 and other resistance genes. Notably, this isolate was able to conjugate the double carbapenemase plasmid to an E. coli recipient, conferring resistance to 1st -5th generation cephalosporins (including combinations with beta-lactamase inhibitors), penicillins, monobactams, and carbapenems. CONCLUSIONS: We reported the isolation in Chile of high-risk carbapenem-resistant hvKp carrying a highly transmissible conjugative plasmid encoding KPC-2 and VIM-1 carbapenemases, conferring resistance to most beta-lactams. Furthermore, the lack of hypermucoviscosity argues against this trait as a reliable hvKp marker. These findings highlight the rapid evolution towards multi-drug resistance of hvKp in Chile and globally, as well as the importance of conjugative plasmids and other mobile genetic elements in this convergence. In this regard, genomic approaches provide valuable support to monitor and obtain essential information on these priority pathogens and mobile elements.

Inorganic Polyphosphate Affects Biofilm Assembly, Capsule Formation, and Virulence of Hypervirulent ST23 Klebsiella pneumoniae.

The emergence of hypervirulent Klebsiella pneumoniae (hvKP) strains poses a significant threat to public health due to high mortality rates and propensity to cause severe community-acquired infections in healthy individuals. The ability to form biofilms and produce a protective capsule contributes to its enhanced virulence and is a significant challenge to effective antibiotic treatment. Polyphosphate kinase 1 (PPK1) is an enzyme responsible for inorganic polyphosphate synthesis and plays a vital role in regulating various physiological processes in bacteria. In this study, we investigated the impact of polyP metabolism on the biofilm and capsule formation and virulence traits in hvKP using Dictyostelium discoideum amoeba as a model host. We found that the PPK1 null mutant was impaired in biofilm and capsule formation and showed attenuated virulence in D. discoideum compared to the wild-type strain. We performed a proteomic analysis to gain further insights into the underlying molecular mechanism. The results revealed that the PPK1 mutant had a differential expression of proteins involved in capsule synthesis (Wzi-Ugd), biofilm formation (MrkC-D-H), synthesis of the colibactin genotoxin precursor (ClbB), as well as proteins associated with the synthesis and modification of lipid A (ArnB-LpxC-PagP). These proteomic findings corroborate the phenotypic observations and indicate that the PPK1 mutation is associated with impaired biofilm and capsule formation and attenuated virulence in hvKP. Overall, our study highlights the importance of polyP synthesis in regulating extracellular biomolecules and virulence in K. pneumoniae and provides insights into potential therapeutic targets for treating K. pneumoniae infections.

Climate change impacts on crop breeding: Targeting interacting biotic and abiotic stresses for wheat improvement.

Wheat (Triticum aestivum L.) as a staple crop is closely interwoven into the development of modern society. Its influence on culture and economic development is global. Recent instability in wheat markets has demonstrated its importance in guaranteeing food security across national borders. Climate change threatens food security as it interacts with a multitude of factors impacting wheat production. The challenge needs to be addressed with a multidisciplinary perspective delivered across research, private, and government sectors. Many experimental studies have identified the major biotic and abiotic stresses impacting wheat production, but fewer have addressed the combinations of stresses that occur simultaneously or sequentially during the wheat growth cycle. Here, we argue that biotic and abiotic stress interactions, and the genetics and genomics underlying them, have been insufficiently addressed by the crop science community. We propose this as a reason for the limited transfer of practical and feasible climate adaptation knowledge from research projects into routine farming practice. To address this gap, we propose that novel methodology integration can align large volumes of data available from crop breeding programs with increasingly cheaper omics tools to predict wheat performance under different climate change scenarios. Underlying this is our proposal that breeders design and deliver future wheat ideotypes based on new or enhanced understanding of the genetic and physiological processes that are triggered when wheat is subjected to combinations of stresses. By defining this to a trait and/or genetic level, new insights can be made for yield improvement under future climate conditions.

Molecular Forecasting of Domoic Acid during a Pervasive Toxic Diatom Bloom.

In 2015, the largest recorded harmful algal bloom (HAB) occurred in the Northeast Pacific, causing nearly 100 million dollars in damages to fisheries and killing many protected marine mammals. Dominated by the toxic diatom Pseudo-nitzschia australis , this bloom produced high levels of the neurotoxin domoic acid (DA). Through molecular and transcriptional characterization of 52 near-weekly phytoplankton net-tow samples collected at a bloom hotspot in Monterey Bay, California, we identified active transcription of known DA biosynthesis ( dab ) genes from the three identified toxigenic species, including P. australis as the primary origin of toxicity. Elevated expression of silicon transporters ( sit1 ) during the bloom supports the previously hypothesized role of dissolved silica (Si) exhaustion in contributing to bloom physiology and toxicity. We find that co-expression of the dabA and sit1 genes serves as a robust predictor of DA one week in advance, potentially enabling the forecasting of DA-producing HABs. We additionally present evidence that low levels of iron could have co-limited the diatom population along with low Si. Iron limitation represents a previously unrecognized driver of both toxin production and ecological success of the low iron adapted Pseudo-nitzschia genus during the 2015 bloom, and increasing pervasiveness of iron limitation may fuel the escalating magnitude and frequency of toxic Pseudo-nitzschia blooms globally. Our results advance understanding of bloom physiology underlying toxin production, bloom prediction, and the impact of global change on toxic blooms. Significance: Pseudo-nitzschia diatoms form oceanic harmful algal blooms that threaten human health through production of the neurotoxin domoic acid (DA). DA biosynthetic gene expression is hypothesized to control DA production in the environment, yet what regulates expression of these genes is yet to be discovered. In this study, we uncovered expression of DA biosynthesis genes by multiple toxigenic Pseudo-nitzschia species during an economically impactful bloom along the North American West Coast, and identified genes that predict DA in advance of its production. We discovered that iron and silica co-limitation restrained the bloom and likely promoted toxin production. This work suggests that increasing iron limitation due to global change may play a previously unrecognized role in driving bloom frequency and toxicity.

Antimicrobial resistance, pathogenic potential, and genomic features of carbapenem-resistant Klebsiella pneumoniae isolated in Chile: high-risk ST25 clones and novel mobile elements.

Multidrug- and carbapenem-resistant Klebsiella pneumoniae (CR-Kp) are critical threats to global health and key traffickers of resistance genes to other pathogens. Despite the sustained increase in CR-Kp infections in Chile, few strains have been described at the genomic level, lacking details of their resistance and virulence determinants and the mobile elements mediating their dissemination. In this work, we studied the antimicrobial susceptibility and performed a comparative genomic analysis of 10 CR-Kp isolates from the Chilean surveillance of carbapenem-resistant Enterobacteriaceae. High resistance was observed among the isolates (five ST25, three ST11, one ST45, and one ST505), which harbored 44 plasmids, most carrying genes for conjugation and resistance to several antibiotics and biocides. Ten plasmids encoding carbapenemases were characterized, including novel plasmids or variants with additional resistance genes, a novel genetic environment for blaKPC-2, and plasmids widely disseminated in South America. ST25 K2 isolates belonging to CG10224, a clone traced back to 2012 in Chile, which recently acquired blaNDM-1, blaNDM-7, or blaKPC-2 plasmids stood out as high-risk clones. Moreover, this corresponds to the first report of ST25 and ST45 Kp producing NDM-7 in South America and ST505 CR-Kp producing both NDM-7 and KPC-2 worldwide. Also, we characterized a variety of genomic islands carrying virulence and fitness factors. These results provide baseline knowledge for a detailed understanding of molecular and genetic determinants behind antibiotic resistance and virulence of CR-Kp in Chile and South America. IMPORTANCE In the ongoing antimicrobial resistance crisis, carbapenem-resistant strains of Klebsiella pneumoniae are critical threats to public health. Besides globally disseminated clones, the burden of local problem clones remains substantial. Although genomic analysis is a powerful tool for improving pathogen and antimicrobial resistance surveillance, it is still restricted in low- to middle-income countries, including Chile, causing them to be underrepresented in genomic databases and epidemiology surveys. This study provided the first 10 complete genomes of the Chilean surveillance for carbapenem-resistant K. pneumoniae in healthcare settings, unveiling their resistance and virulence determinants and the mobile genetic elements mediating their dissemination, placed in the South American and global K. pneumoniae epidemiological context. We found ST25 with K2 capsule as an emerging high-risk clone, along with other lineages producing two carbapenemases and several other resistance and virulence genes encoded in novel plasmids and genomic islands.

A cross-regional examination of patterns and environmental drivers of Pseudo-nitzschia harmful algal blooms along the California coast.

Pseudo-nitzschia species with the ability to produce the neurotoxin domoic acid (DA) are the main cause of harmful algal blooms (HABs) along the U.S. West Coast, with major impacts on ecosystems, fisheries, and human health. While most Pseudo-nitzschia (PN) HAB studies to date have focused on their characteristics at specific sites, few cross-regional comparisons exist, and mechanistic understanding of large-scale HAB drivers remains incomplete. To close these gaps, we compiled a nearly 20-year time series of in situ particulate DA and environmental observations to characterize similarities and differences in PN HAB drivers along the California coast. We focus on three DA hotspots with the greatest data density: Monterey Bay, the Santa Barbara Channel, and the San Pedro Channel. Coastwise, DA outbreaks are strongly correlated with upwelling, chlorophyll-a, and silicic acid limitation relative to other nutrients. Clear differences also exist across the three regions, with contrasting responses to climate regimes across a north to south gradient. In Monterey Bay, PN HAB frequency and intensity increase under relatively nutrient-poor conditions during anomalously low upwelling intensities. In contrast, in the Santa Barbara and San Pedro Channels, PN HABs are favored under cold, nitrogen-rich conditions during more intense upwelling. These emerging patterns provide insights on ecological drivers of PN HABs that are consistent across regions and support the development of predictive capabilities for DA outbreaks along the California coast and beyond.

Coastal upwelling drives ecosystem temporal variability from the surface to the abyssal seafloor.

Long-term biological time series that monitor ecosystems across the ocean's full water column are extremely rare. As a result, classic paradigms are yet to be tested. One such paradigm is that variations in coastal upwelling drive changes in marine ecosystems throughout the water column. We examine this hypothesis by using data from three multidecadal time series spanning surface (0 m), midwater (200 to 1,000 m), and benthic (~4,000 m) habitats in the central California Current Upwelling System. Data include microscopic counts of surface plankton, video quantification of midwater animals, and imaging of benthic seafloor invertebrates. Taxon-specific plankton biomass and midwater and benthic animal densities were separately analyzed with principal component analysis. Within each community, the first mode of variability corresponds to most taxa increasing and decreasing over time, capturing seasonal surface blooms and lower-frequency midwater and benthic variability. When compared to local wind-driven upwelling variability, each community correlates to changes in upwelling damped over distinct timescales. This suggests that periods of high upwelling favor increase in organism biomass or density from the surface ocean through the midwater down to the abyssal seafloor. These connections most likely occur directly via changes in primary production and vertical carbon flux, and to a lesser extent indirectly via other oceanic changes. The timescales over which species respond to upwelling are taxon-specific and are likely linked to the longevity of phytoplankton blooms (surface) and of animal life (midwater and benthos), which dictate how long upwelling-driven changes persist within each community.

Impact of different on-farm management practices on bread wheat quality: a case study in the Yaqui Valley.

BACKGROUND: Continuous development of new wheat varieties is necessary to satisfy the demands of farmers, industry, and consumers. The evaluation of candidate genotypes for commercial release under different on-farm conditions is a strategy that has been strongly recommended to assess the performance and stability of new cultivars in heterogeneous environments and under different farming systems. The main objectives of this study were to evaluate the grain yield and quality performance of ten different genotypes across six contrasting farmers' field conditions with different irrigation and nitrogen fertilization levels, and to develop suggestions to aid breeding programs and farmers to use resources more efficiently. Genotype and genotype by environment (GGE) interaction biplot analyses were used to identify the genotypes with the strongest performance and greatest stability in the Yaqui Valley. RESULTS: Analyses showed that some traits were mainly explained by the genotype effect, others by the field management conditions, and the rest by combined effects. The most representative and diverse field conditions in the Yaqui Valley were also identified, a useful strategy when breeders have limited resources. The independent effects of irrigation and nitrogen levels and their interaction were analyzed for each trait. The results showed that full irrigation was not always necessary to maximize grain yield in the Yaqui Valley. Other suggestions for more efficient use of resources are proposed. CONCLUSIONS: The combination of on-farm trials with GGE interaction analyses is an effective strategy to include in breeding programs to improve processes and resources. Identifying the most outstanding and stable genotypes under real on-farm systems is key to the development of novel cultivars adapted to different management and environmental conditions. © 2023 Society of Chemical Industry.

On-farm assessment of yield and quality traits in durum wheat.

BACKGROUND: Durum wheat is key source of calories and nutrients for many regions of the world. Demand for it is predicted to increase. Further efforts are therefore needed to develop new cultivars adapted to different future scenarios. Developing a novel cultivar takes, on average, 10 years and advanced lines are tested during the process, in general, under standardized conditions. Although evaluating candidate genotypes for commercial release under different on-farm conditions is a strategy that is strongly recommended, its application for durum wheat and particularly for quality traits has been limited. This study evaluated the grain yield and quality performance of eight different genotypes across five contrasting farmers' fields over two seasons. Combining different analysis strategies, the most outstanding and stable genotypes were identified. RESULTS: The analyses revealed that some traits were mainly explained by the genotype effect (thousand kernel weight, flour sodium dodecyl sulfate sedimentation volume, and flour yellowness), others by the management practices (yield and grain protein content), and others (test weight) by the year effect. In general, yield showed the highest range of variation across genotypes, management practices, and years and test weight the narrowest range. Flour yellowness was the most stable trait across management conditions, while yield-related traits were the most unstable. We also determined the most representative and discriminative field conditions, which is a beneficial strategy when breeders are constrained in their ability to develop multi-environment experiments. CONCLUSIONS: We concluded that assessing genotypes in different farming systems is a valid and complementary strategy for on-station trials for determining the performance of future commercial cultivars in heterogeneous environments to improve the breeding process and resources. © 2023 Society of Chemical Industry.

Exotic alleles contribute to heat tolerance in wheat under field conditions.

Global warming poses a major threat to food security and necessitates the development of crop varieties that are resilient to future climatic instability. By evaluating 149 spring wheat lines in the field under yield potential and heat stressed conditions, we demonstrate how strategic integration of exotic material significantly increases yield under heat stress compared to elite lines, with no significant yield penalty under favourable conditions. Genetic analyses reveal three exotic-derived genetic loci underlying this heat tolerance which together increase yield by over 50% and reduce canopy temperature by approximately 2 °C. We identified an Ae. tauschii introgression underlying the most significant of these associations and extracted the introgressed Ae. tauschii genes, revealing candidates for further dissection. Incorporating these exotic alleles into breeding programmes could serve as a pre-emptive strategy to produce high yielding wheat cultivars that are resilient to the effects of future climatic uncertainty.

Prediction of ACE-I Inhibitory Peptides Derived from Chickpea (Cicer arietinum L.): In Silico Assessments Using Simulated Enzymatic Hydrolysis, Molecular Docking and ADMET Evaluation.

Chickpea (Cicer arietinum L.) peptides have shown in vitro potential to inhibit the angiotensin I-converting enzyme (ACE-I). However, the potential molecular interactions between chickpea peptides (CP) and ACE-I as well as their ADMET (absorption/distribution/metabolism/excretion/toxicity) characteristics remain unknown. Thus, our aim was to study the in silico interactions of CP with ACE-I and the CP ADMET characteristics. Legumin and provicilin sequences were submitted to in silico analysis to search for ACE-I inhibitory peptides. Simulated enzymatic hydrolysis was performed using the BIOPEP-UWM database, and the ACE-I inhibitory peptides generated (EC50 ≤ 200 µM) were selected to perform molecular docking and ADMET analysis. After hydrolysis, 59 out of 381 peptides with ACE-I inhibitory potential were released. Based on A and B parameters, the legumin peptides showed better ACE-I inhibitory potential than the provicilin ones. CP mainly interact with residues from pocket S1 (Ala354/Glu384) and S2 (His353/His513) through hydrogen bonds (distances < 3.0 Å) and hydrophobic interactions (binding energy from −5.7 to −9.2 kcal/mol). Through ADMET analysis, CP showed optimal values for inhibiting ACE-I in vivo. ACE-I inhibitory peptides from legumin and provicilin can bind strongly and tightly to the active site of ACE-I. Further studies to evaluate in vivo the antihypertensive effects of CP are warranted.

Pelagic calcifiers face increased mortality and habitat loss with warming and ocean acidification.

Global change is impacting the oceans in an unprecedented way, and multiple lines of evidence suggest that species distributions are changing in space and time. There is increasing evidence that multiple environmental stressors act together to constrain species habitat more than expected from warming alone. Here, we conducted a comprehensive study of how temperature and aragonite saturation state act together to limit Limacina helicina, globally distributed pteropods that are ecologically important pelagic calcifiers and an indicator species for ocean change. We co-validated three different approaches to evaluate the impact of ocean warming and acidification (OWA) on the survival and distribution of this species in the California Current Ecosystem. First, we used colocated physical, chemical, and biological data from three large-scale west coast cruises and regional time series; second, we conducted multifactorial experimental incubations to evaluate how OWA impacts pteropod survival; and third, we validated the relationships we found against global distributions of pteropods and carbonate chemistry. OWA experimental work revealed mortality increases under OWA, while regional habitat suitability indices and global distributions of L. helicina suggest that a multi-stressor framework is essential for understanding pteropod distributions. In California Current Ecosystem habitats, where pteropods are living close to their thermal maximum already, additional warming and acidification through unabated fossil fuel emissions (RCP 8.5) are expected to dramatically reduce habitat suitability.

Assessment of the Route of Exposure to Ovalbumin and Cow's Milk Proteins on the Induction of IgE Responses in BALB/c Mice.

BALB/c mice can be orally sensitized to food proteins under acid suppressive medication, mimicking human exposure and triggering a human-like allergic immune response. However, the reproducibility of such an oral food allergy model remains questionable. Our aim was to evaluate the IgE responses triggered against ovalbumin (OVA) and cow's milk proteins (CMP) after intragastric (IG), either under gastric-acid suppression or not, or intraperitoneal (IP) sensitization in BALB/c mice. OVA (0.2 mg) and different concentrations of CMP were administered with/without the antacid sucralfate by the IG route. For IP sensitization, OVA or CMP (0.5 mg) were administered. ELISA was used to evaluate IgE responses. The IP sensitization protocols triggered more robust and consistent anti-OVA or anti-CMP IgE responses than the intragastric ones (with/without sucralfate) (p < 0.05). 2.7% (1/36), and 5.5% (3/54) of the mice that underwent the sucralfate-assisted IG protocol triggered IgE responses against OVA or CMP, respectively. All the mice were administered OVA or CMP via IP triggered detectable IgE responses. The IP sensitization model is more reliable than the IG one for evaluating the intrinsic sensitizing and/or allergenic potential of food proteins, even if IG immunizations are carried out under gastric-acid suppression.

The highly diverse Antarctic Peninsula soil microbiota as a source of novel resistance genes.

The rise of multiresistant bacterial pathogens is currently one of the most critical threats to global health, encouraging a better understanding of the evolution and spread of antimicrobial resistance. In this regard, the role of the environment as a source of resistance mechanisms remains poorly understood. Moreover, we still know a minimal part of the microbial diversity and resistome present in remote and extreme environments, hosting microbes that evolved to resist harsh conditions and thus a potentially rich source of novel resistance genes. This work demonstrated that the Antarctic Peninsula soils host a remarkable microbial diversity and a widespread presence of autochthonous antibiotic-resistant bacteria and resistance genes. We observed resistance to a wide array of antibiotics among isolates, including Pseudomonas resisting ten or more different compounds, with an overall increased resistance in bacteria from non-intervened areas. In addition, genome analysis of selected isolates showed several genes encoding efflux pumps, as well as a lack of known resistance genes for some of the resisted antibiotics, including colistin, suggesting novel uncharacterized mechanisms. By combining metagenomic approaches based on analyzing raw reads, assembled contigs, and metagenome-assembled genomes, we found hundreds of widely distributed genes potentially conferring resistance to different antibiotics (including an outstanding variety of inactivation enzymes), metals, and biocides, hosted mainly by Polaromonas, Pseudomonas, Streptomyces, Variovorax, and Burkholderia. Furthermore, a proportion of these genes were found inside predicted plasmids and other mobile elements, including a putative OXA-like carbapenemase from Polaromonas harboring conserved key residues and predicted structural features. All this evidence indicates that the Antarctic Peninsula soil microbiota has a broad natural resistome, part of which could be transferred horizontally to pathogenic bacteria, acting as a potential source of novel resistance genes.

The founding charter of the Omic Biodiversity Observation Network (Omic BON).

Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.

Comparative Analysis of Salmon Cell Lines and Zebrafish Primary Cell Cultures Infection with the Fish Pathogen Piscirickettsia salmonis.

Piscirickettsia salmonis is the etiologic agent of piscirickettsiosis, a disease that causes significant losses in the salmon farming industry. In order to unveil the pathogenic mechanisms of P. salmonis, appropriate molecular and cellular studies in multiple cell lines with different origins need to be conducted. Toward that end, we established a cell viability assay that is suitable for high-throughput analysis using the alamarBlue reagent to follow the distinct stages of the bacterial infection cycle. Changes in host cell viability can be easily detected using either an absorbance- or fluorescence-based plate reader. Our method accurately tracked the infection cycle across two different Atlantic salmon-derived cell lines, with macrophage and epithelial cell properties, and zebrafish primary cell cultures. Analyses were also carried out to quantify intracellular bacterial replication in combination with fluorescence microscopy to visualize P. salmonis and cellular structures in fixed cells. In addition, dual gene expression analysis showed that the pro-inflammatory cytokines IL-6, IL-12, and TNFα were upregulated, while the cytokines IL1b and IFNγ were downregulated in the three cell culture types. The expression of the P. salmonis metal uptake and heme acquisition genes, together with the toxin and effector genes ospD3, ymt, pipB2 and pepO, were upregulated at the early and late stages of infection regardless of the cell culture type. On the other hand, Dot/Icm secretion system genes as well as stationary state and nutrient scarcity-related genes were upregulated only at the late stage of P. salmonis intracellular infection. We propose that these genes encoding putative P. salmonis virulence factors and immune-related proteins could be suitable biomarkers of P. salmonis infection. The infection protocol and cell viability assay described here provide a reliable method to compare the molecular and cellular changes induced by P. salmonis in other cell lines and has the potential to be used for high-throughput screenings of novel antimicrobials targeting this important fish intracellular pathogen.

Potential of rice landraces with strong culms as genetic resources for improving lodging resistance against super typhoons.

It is generally believed that rice landraces with long culms are susceptible to lodging, and have not been utilized for breeding to improve lodging resistance. However, little is known about the structural culm strength of landraces and their beneficial genetic loci. Therefore, in this study, genome-wide association studies (GWAS) were performed using a rice population panel including Japanese rice landraces to identify beneficial loci associated with strong culms. As a result, the landraces were found to have higher structural culm strength and greater diversity than the breeding varieties. Genetic loci associated with strong culms were identified, and it was demonstrated that haplotypes with positive effects of those loci were present in a high proportion of these landraces. These results indicated that the utilization of the strong culm-associated loci present in Japanese rice landraces may further improve the lodging resistance of modern breeding varieties that have relied on semi-dwarfism.

Environmental DNA reveals the fine-grained and hierarchical spatial structure of kelp forest fish communities.

Biodiversity is changing at an accelerating rate at both local and regional scales. Beta diversity, which quantifies species turnover between these two scales, is emerging as a key driver of ecosystem function that can inform spatial conservation. Yet measuring biodiversity remains a major challenge, especially in aquatic ecosystems. Decoding environmental DNA (eDNA) left behind by organisms offers the possibility of detecting species sans direct observation, a Rosetta Stone for biodiversity. While eDNA has proven useful to illuminate diversity in aquatic ecosystems, its utility for measuring beta diversity over spatial scales small enough to be relevant to conservation purposes is poorly known. Here we tested how eDNA performs relative to underwater visual census (UVC) to evaluate beta diversity of marine communities. We paired UVC with 12S eDNA metabarcoding and used a spatially structured hierarchical sampling design to assess key spatial metrics of fish communities on temperate rocky reefs in southern California. eDNA provided a more-detailed picture of the main sources of spatial variation in both taxonomic richness and community turnover, which primarily arose due to strong species filtering within and among rocky reefs. As expected, eDNA detected more taxa at the regional scale (69 vs. 38) which accumulated quickly with space and plateaued at only ~ 11 samples. Conversely, the discovery rate of new taxa was slower with no sign of saturation for UVC. Based on historical records in the region (2000-2018) we found that 6.9 times more UVC samples would be required to detect 50 taxa compared to eDNA. Our results show that eDNA metabarcoding can outperform diver counts to capture the spatial patterns in biodiversity at fine scales with less field effort and more power than traditional methods, supporting the notion that eDNA is a critical scientific tool for detecting biodiversity changes in aquatic ecosystems.