Abundance Analysis Research Articles

Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa.

Our 24-month study used metagenomics to investigate antimicrobial resistance (AMR) abundance in raw sewage from wastewater treatment works (WWTWs) in two municipalities in Gauteng Province, South Africa. At the AMR class level, data showed similar trends at all WWTWs, showing that aminoglycoside, beta-lactam, sulfonamide and tetracycline resistance was most abundant. AMR abundance differences were shown between municipalities, where Tshwane Metropolitan Municipality (TMM) WWTWs showed overall higher abundance of AMR compared to Ekurhuleni Metropolitan Municipality (EMM) WWTWs. Also, within each municipality, there were differing trends in AMR abundance. Notably, within TMM, certain AMR classes (macrolides and macrolides_streptogramin B) were in higher abundance at a WWTW serving an urban high-income area, while other AMR classes (aminoglycosides) were in higher abundance at a WWTW serving a semi-urban low income area. At the AMR gene level, all WWTWs samples showed the most abundance for the sul1 gene (encoding sulfonamide resistance). Following this, the next 14 most abundant genes encoded resistance to sulfonamides, aminoglycosides, macrolides, tetracyclines and beta-lactams. Notably, within TMM, some macrolide-encoding resistance genes (mefC, msrE, mphG and mphE) were in highest abundance at a WWTW serving an urban high-income area; while sul1, sul2 and tetC genes were in highest abundance at a WWTW serving a semi-urban low income area. Differential abundance analysis of AMR genes at WWTWs, following stratification of data by season, showed some notable variance in six AMR genes, of which blaKPC-2 and blaKPC-34 genes showed the highest prevalence of seasonal abundance differences when comparing data within a WWTW. The general trend was to see higher abundances of AMR genes in colder seasons, when comparing seasonal data within a WWTW. Our study investigated wastewater samples in only one province of South Africa, from WWTWs located within close proximity to one another. We would require a more widespread investigation at WWTWs distributed across all regions/provinces of South Africa, in order to describe a more comprehensive profile of AMR abundance across the country.

The Response of Murine Gut Microbiome in the Presence of Altered rpoS Gene of Klebsiella pneumoniae.

The murine model is invaluable for studying intricate interactions among gut microbes; hosts; and diseases. However; the impact of genetic variations in the murine microbiome; especially in disease contexts such as Klebsiella pneumoniae (Kp) infection; still needs to be explored. Kp; an opportunistic global pathogen; is becoming increasingly prevalent in regions like Asia; especially China. This study explored the role of the gut microbiota during Kp infection using mouse model; including wild-type and rpoS mutants of Kp138; KpC4; and KpE4 from human; maize; and ditch water; respectively. Under stress conditions; RpoS reconfigures global gene expression in bacteria; shifting the cells from active growth to survival mode. Our study examined notable differences in microbiome composition; finding that Lactobacillus and Klebsiella (particularly in WKp138) were the most abundant genera in mice guts at the genus level in all wild-type treated mice. In contrast; Firmicutes were predominant in the healthy control mice. Furthermore; Clostridium was the dominant genus in all mutants; mainly in ∆KpC4; and was absent in wild-type treated mice. Differential abundance analysis identified that these candidate taxa potentially influence disease progression and pathogen virulence. Functional prediction analysis showed that most bacterial groups were functionally involved in biosynthesis; precursor metabolites; degradation; energy generation; and metabolic cluster formation. These findings challenge the conventional understanding and highlight the need for nuanced interpretations in murine studies. Additionally; this study sheds light on microbiome-immune interactions in K. pneumoniae infection and proposes new potential therapeutic strategies.

Modulation of Metabolomic Profile in Sepsis According to the State of Immune Activation.

To investigate the metabolomic profiles associated with different immune activation states in sepsis patients. Subgroup analysis of the PROVIDE (a Personalized Randomized trial of Validation and restoration of Immune Dysfunction in severe infections and Sepsis) prospective clinical study. Results of the PROVIDE study showed that patients with sepsis may be classified into three states of immune activation: 1) macrophage-activation-like syndrome (MALS) characterized by hyperinflammation, sepsis-induced immunoparalysis, and 3) unclassified or intermediate patients without severe immune dysregulation. Two hundred ten patients from 14 clinical sites in Greece meeting the Sepsis-3 definitions with lung infection, acute cholangitis, or primary bacteremia. During our comparison, we did not perform any intervention. Untargeted metabolomics analysis was performed on plasma samples from 210 patients (a total of 1394 products). Differential abundance analysis identified 221 significantly different metabolites across the immune states. Metabolites were enriched in pathways related to ubiquinone biosynthesis, tyrosine metabolism, and tryptophan metabolism when comparing MALS to immunoparalysis and unclassified patients. When comparing MALS to unclassified, 312 significantly different metabolites were found, and pathway analysis indicated enrichment in multiple pathways. Comparing immunoparalysis to unclassified patients revealed only two differentially regulated metabolites. Findings suggest distinct metabolic dysregulation patterns associated with different immune dysfunctions in sepsis: the strongest metabolic dysregulation is associated with MALS.

Rich diversity of RNA viruses in the biological control agent, Orius laevigatus

Orius laevigatus (Hemiptera, Anthocoridae) is a generalist predator extensively used for the biocontrol of diverse agricultural pests. Previous studies on O. laevigatus have focused on the improvement of insect genetic traits, but little is known about its association with microbes, especially viruses that may influence its production and efficacy. More than 280 RNA viruses have been described in other Hemiptera insects, in line with the continuous discovery of insect-specific viruses (ISVs) boosted by next-generation sequencing. In this study, we characterized the repertoire of RNA viruses associated with O. laevigatus. Its virome comprises 27 RNA viruses, classified within fourteen viral families, of which twenty-three viruses are specific to O. laevigatus and four are likely associated with fungal microbiota. The analysis of viral abundance in five O. laevigatus populations confirmed the presence of simultaneous viral infections and highlighted the ubiquitous presence and high abundance of one solinvivirus and three totiviruses. Moreover, we identified 24 non-retroviral endogenous viral elements (nrEVEs) in the genome of O. laevigatus, suggesting a long-term relationship between the host and its virome. Although no symptoms were described in the insect populations under study, the high diversity of viral species and the high abundance of certain RNA viruses identified indicate that RNA viruses may be significant for the applicability and efficacy of O. laevigatus in biocontrol programs.

Clinical Investigation of Bacteriome in Primary Endodontic Infections With Apical Periodontitis Using High-Throughput Sequencing Analysis

IntroductionThis study characterized the bacteriome in primary endodontic infection (PEI) with apical periodontitis (AP), identified core and rare bacteriome species and community diversity metrics, and analyzed the relationship between the bacteriome composition, diversity and features, and patient variables. MethodsTwenty-seven patients with PEI and AP were sampled. The DNA was extracted and quantified using quantitative polymerase chain reaction. Raw V3-V4 amplicon sequencing data were processed with the DADA2 pipeline to generate amplicon sequence variants, and taxonomic assignment of the amplicon sequence variants up to the species level was done against the Human Oral Microbiome Database. Core bacteriome and differential abundance analyses were performed using ANCOM. Alpha diversity was determined using Chao1, Shannon, and Simpson indexes. LeFse analysis was used to identify abundant taxa. Sparse Estimation of Correlations among Microbiomes analysis estimated linear and nonlinear relationships among bacteria. ResultsOf 27, 24 root canal samples were analyzed, and 3 root canal sampling were filtered out with a low read count. The bacterial phyla with top mean relative abundance were Bacteroidetes, Firmicutes, Synergistetes, Fusobacteria, and Actinobacteria. A total of 113 genera and 215 species were identified. The samples were gathered into 3 clusters. LefSe analysis identified differences in abundant taxa between distinct age, gender, symptomatology, and lesion size groups. Sparse Estimation of Correlations among Microbiomes distance analysis indicated Slackia exigua as the node with the highest degree. ConclusionsThe bacteriome in PEI with AP among the patients in this study was complex and displayed high microbial heterogeneity. Moreover, age, gender, symptomatology, and lesion size were associated with differences in bacteriome features in PEI with AP.

Mating frequency estimation and its importance for colony abundance analyses in eusocial pollinators: a case study of Bombus impatiens (Hymenoptera: Apidae).

The genus Bombus (bumble bees) includes approximately 265 species, many of which are in decline in North America and Europe. To estimate colony abundance of bumble bees in natural and agricultural habitats, sibship relationships are often reconstructed from genetic data with the assumption that colonies have 1 monandrous queen. However, some species such as the North American common eastern bumble bee (Bombus impatiens Cresson) can display low levels of polyandry, which may bias estimates of colony abundance based on monandrous sibship reconstructions. To accurately quantify rates of polyandry in wild and commercially mated queens of this species, we empirically estimated mating frequencies using a novel statistical model and genotypes from 730 bees. To genotype individuals, we used a highly polymorphic set of microsatellites on colonies established from 20 wild-caught gynes and 10 commercial colonies. We found multiple fathers in 3 of the wild colonies and 3 of the commercial colonies. This resulted in average effective mating frequencies of 1.075 ± 0.18 and 1.154 ± 0.25 for wild and commercial colonies, respectively. These findings agree with previous reports of low rates of polyandry for B. impatiens. Using a large empirical dataset, we demonstrate that assuming monandry for colony abundance estimation in species that violate this assumption results in an overestimation of the number of colonies. Our results emphasize the importance of studying mating frequencies in social species of conservation concern and economic importance for the accuracy of colony abundance estimation and for understanding their ecology and sociobiology.

TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data.

State-of-the-art mass spectrometers combined with modern bioinformatics algorithms for peptide-to-spectrum matching (PSM) with robust statistical scoring allow for more variable features (i.e., post-translational modifications) being reliably identified from (tandem-) mass spectrometry data, often without the need for biochemical enrichment. Semi-specific proteome searches, that enforce a theoretical enzymatic digestion to solely the N- or C-terminal end, allow to identify of native protein termini or those arising from endogenous proteolytic activity (also referred to as "neo-N-termini" analysis or "N-terminomics"). Nevertheless, deriving biological meaning from these search outputs can be challenging in terms of data mining and analysis. Thus, we introduce TermineR, a data analysis approach for the (1) annotation of peptides according to their enzymatic cleavage specificity and known protein processing features, (2) differential abundance and enrichment analysis of N-terminal sequence patterns, and (3) visualization of neo-N-termini location. We illustrate the use of TermineR by applying it to tandem mass tag (TMT)-based proteomics data of a mouse model of polycystic kidney disease, and assess the semi-specific searches for biological interpretation of cleavage events and the variable contribution of proteolytic products to general protein abundance. The TermineR approach and example data are available as an R package at https://github.com/MiguelCos/TermineR.

Identification of novel cattle (Bos taurus) genes and biological insights of their function in pre-implantation embryo development

BackgroundAppropriate regulation of genes expressed in oocytes and embryos is essential for acquisition of developmental competence in mammals. Here, we hypothesized that several genes expressed in oocytes and pre-implantation embryos remain unknown. Our goal was to reconstruct the transcriptome of oocytes (germinal vesicle and metaphase II) and pre-implantation cattle embryos (blastocysts) using short-read and long-read sequences to identify putative new genes.ResultsWe identified 274,342 transcript sequences and 3,033 of those loci do not match a gene present in official annotations and thus are potential new genes. Notably, 63.67% (1,931/3,033) of potential novel genes exhibited coding potential. Also noteworthy, 97.92% of the putative novel genes overlapped annotation with transposable elements. Comparative analysis of transcript abundance identified that 1,840 novel genes (recently added to the annotation) or potential new genes were differentially expressed between developmental stages (FDR < 0.01). We also determined that 522 novel or potential new genes (448 and 34, respectively) were upregulated at eight-cell embryos compared to oocytes (FDR < 0.01). In eight-cell embryos, 102 novel or putative new genes were co-expressed (|r|> 0.85, P < 1 × 10–8) with several genes annotated with gene ontology biological processes related to pluripotency maintenance and embryo development. CRISPR-Cas9 genome editing confirmed that the disruption of one of the novel genes highly expressed in eight-cell embryos reduced blastocyst development (ENSBTAG00000068261, P = 1.55 × 10–7).ConclusionsOur results revealed several putative new genes that need careful annotation. Many of the putative new genes have dynamic regulation during pre-implantation development and are important components of gene regulatory networks involved in pluripotency and blastocyst formation.

LAMOST J1010+2358 is not a Pair-Instability Supernova Relic

The discovery of a star formed out of pair-instability supernova ejecta would have massive implications for the Population III star initial mass function and the existence of stars over 100 Msun, but none have yet been found. Recently, the star LAMOST J1010+2358 was claimed to be a star that formed out of gas enriched by a pair-instability supernova. We present a non-LTE abundance analysis of a new high-resolution Keck/HIRES spectrum of J1010+2358. We determined the carbon and aluminum abundances needed to definitively distinguish between enrichment by a pair-instability and core-collapse supernova. Our new analysis demonstrates that J1010+2358 does not have the unique abundance pattern of a a pair-instability supernova, but was instead enriched by the ejecta of a low mass core-collapse supernova. Thus, there are still no known stars displaying unambiguous signatures of pair-instability supernovae.

Gut microbial composition is altered in sarcopenia: A systematic review and meta-analysis of clinical studies.

Increasing evidence has shown that gut microbiota (GM) was involved in the pathophysiology of musculoskeletal disorders through multiple pathways such as protein anabolism, chronic inflammation and immunity, and imbalanced metabolism. We performed a systematic review and meta-analysis of human studies to evaluate GM diversity differences between individuals with and without sarcopenia, and explore bacteria with potential to become biomarkers. PubMed, Embase and Cochrane library were systematically searched from inception to February 16, 2024. Studies were included if they (1) sampled adults with sarcopenia, and (2) performed GM analysis and reported α-diversity, β-diversity or relative abundance. The methodological quality of included studies and the certainty of evidence were assessed through the Joanna Briggs Institute critical appraisal checklist for analytical cross-sectional studies and the Grades of Recommendation, Assessment, Development and Evaluation (GRADE) Working Group system, respectively. Weighted standardized mean differences (SMDs) and corresponding 95% confidence intervals (CIs) were estimated for α-diversity indices using a fixed-effects and a random-effects model. Beta diversity and the relative abundance of GM were summarized qualitatively. A total of 19 studies involving 6,565 participants were included in this study. Compared with controls, significantly moderate decrease in microbial richness in participants with sarcopenia were found (Chao1: SMD = -0.44; 95%CI, -0.64 to -0.23, I2 = 57.23%, 13 studies; observed species: SMD = -0.68; 95%CI, -1.00 to -0.37, I2 = 66.07%, 5 studies; ACE index: SMD = -0.30; 95%CI, -0.56 to -0.04, I2 = 8.12%, 4 studies), with very low certainty of evidence. Differences in β-diversity were consistently observed in 84.6% of studies and 97.3% of participants. The detailed analysis of the gut microbial differential abundance identified a loss of Prevotellaceae, Prevotella, and Megamonas in sarcopenia compared with non-sarcopenia. In conclusion, sarcopenia was found to be associated with reduced richness of GM, and supplementing intestinal bacteria described above may contribute to preventing and treating this muscle disease. The research protocol was registered and approved in PROSPERO (CRD42023412849).

Associations of upper respiratory mucosa microbiota with Rheumatoid arthritis, autoantibodies, and disease activity.

The lung is recognized as a site for initiating the formation of self-antigen and autoimmune responses in rheumatoid arthritis (RA). We aimed to investigate the association of upper respiratory microbiota with RA, autoantibody production, and disease activity. Forty-six patients with RA and 17 controls were examined. Nasopharyngeal swab samples were sequenced for microbiome profiling using the V3-V4 region of the 16S rRNA gene. The microbial diversity and relative abundance were compared between RA patients and controls. Correlation analyses were conducted to evaluate the relationship between microbial abundance and clinical markers such as autoantibodies and disease activity. Microbial diversity analysis revealed no major differences between RA patients and healthy controls. However, beta diversity analysis indicated a subtle distinction in microbial composition (unweighted UniFrac distance) between the two groups (P = 0.03), hinting at a minor subset of microbiota associated with disease status. Differential abundance analysis uncovered specific taxa at various taxonomic levels, including Saccharibacteria (TM7) [O-1] (PFDR = 2.53 × 10-2), TM7 [F-1] (PFDR = 5.20 × 10-3), Microbacterium (PFDR = 3.37 × 10-4), and Stenotrophomonas (PFDR = 2.57 × 10-3). The relative abundance of ten genera correlated significantly with anti-cyclic citrullinated peptide (anti-CCP) antibody levels (PFDR < 0.05) and 11 genera were significantly associated with disease activity markers, including ESR, CRP, DAS28-ESR, and DAS-CRP (PFDR < 0.05). In particular, Saccharibacteria TM7 [G-3] and Peptostreptococcaceae [XI] [G-1] were correlated with all disease activity biomarkers. Dysbiosis in the upper respiratory mucosa is associated with RA, anti-CCP antibody levels, and disease activity.

Reduced Gut Bacterial Diversity in Early Life Predicts Feeding Intolerance in Preterm Neonates.

Microbiota plays a crucial role in intestinal maturation in preterm newborns. The clinical manifestation of the immaturity of the gastro-intestinal tract is called feeding intolerance (FI). This condition may resolve spontaneously or dramatically evolve into necrotizing enterocolitis. One of the most challenging tasks for the neonatologist is to identify those neonates that will develop the disease early in order to adequately provide nutrition to these patients, from the very first hours of life. A close interplay between the maturity of the gastro-intestinal tract and gut microbiota has been described; however, in preterm neonates, this relationship is still undefined. We analyzed the bacterial composition of stool samples, collected early in life, from 30 preterm newborns classified as intolerant or tolerant according to the degree of readiness of the gastro-intestinal tract to receive enteral nutrition. The Pielou evenness index was significantly increased in intolerant compared with tolerant newborns. Data corrected for confounding variables confirmed that the occurrence of gut maturation was independently influenced by Pielou evenness at birth. A lower bacterial diversity very early in life is associated with improved feeding tolerance in preterm newborns. The abundance analysis showed that neonates not ready to receive enteral nutrition for feeding intolerance show, after birth, an increased abundance of Proteobacteria, Lachnospiracae, Enterobacter and Acinetobacter. We can argue that those are the taxa that prevent the establishment of pioneer bacteria. A lower alpha-diversity, in the first days of life, may facilitate the seeding of beneficial pioneer bacteria that, in turn, drive healthy microbial colonization during neonatal life.

Compositional profiling of the rhizosphere microbiome of Canada thistle reveals consistent patterns across the United States northern Great Plains

Canada thistle is a pervasive perennial weed, causing challenges to agricultural and natural ecosystems globally. Although research has focused on the phenology, genetics, and control of Canada thistle, little is known about the rhizosphere microbiome and the role plant–microbe interactions play in invasion success. This study investigated the rhizosphere microbiome of Canada thistle across diverse climates, soils, and crops in the U.S. northern Great Plains. Soil and rhizosphere samples were collected and bacterial 16S and fungal ITS2 sequencing were performed to characterize the core microbiome and identify potential factors contributing to invasion success. Amplicon sequencing revealed a stable core microbiome that was detected in the Canada thistle rhizosphere across all locations. The core microbiome was dominated by the bacterial phyla Actinobacteriota and Proteobacteria and fungal phyla Ascomycota and Basidiomycota. Differential abundance analysis showed rhizosphere fungal communities were enriched in pathogen-containing genera with a 1.7-fold greater abundance of Fusaria and a 2.6-fold greater abundance of Gibberella compared to bulk soil. Predictive functional profiling showed rhizosphere communities were enriched (p < 0.05, FDR corrected) in plant pathogen fungal guilds which represented 19% of the fungal community. The rhizosphere microbiome was similar in composition across environments, highlighting the stable association between Canada thistle and specific microbial taxa. This study characterized the core microbiome of Canada thistle, and the findings highlight plant–microbe interactions shaping invasive behavior. These findings are important for understanding the ecological impacts of plant invasion and soil-microbe ecological processes.

Ant-observer: A new approach for automatic acquisition and autonomous analyses of individual species abundance and interactions

Traditional methods, such as direct observations or manually photographing bait stations, are limited in both data collection efficiency and accuracy. Consequently, they fail to capture the dynamic changes and complex relationships between ant species. We developed a novel system as a potential solution that combines processed consumer-grade camera equipment and software that acquires data needed for in situ experiments. This software features a user-friendly graphics user interface (GUI) for data collection and post-hoc analysis from videos captured by the camera equipment. Researchers can use this system to (1) count species abundance per frame; (2) calculate species speed; (3) detect ant interactions; and (4) count the abundance of different subcastes within species on baits. To demonstrate the complete workflow, we applied this system on ant videos collected in Hong Kong. Practical guides (supplement materials) detailing suggestions for camera equipment and software operations in both field and laboratory studies are provided. We present the results of ten in situ experiments of ants (each lasting 1–1.5 h) conducted in Hong Kong though processed consumer-grade camera equipment, with videos analyzed using the newly developed software. The analysis captured a range of variables related to ant foraging behavior, including resource discovery time, nestmate recruitment rate, and interspecific interactions. Our results confirm that the developed software provides an integrated and efficient approach for data collection, extraction, and analysis in in situ experiments, enhancing the capabilities of insect ecology research.

Li Evolution among Stars of Low/Intermediate Mass: the Metal-deficient Open Cluster NGC 2204

We have analyzed high-dispersion spectra in the Li 6708 Å region for 167 stars within the anticenter cluster NGC 2204. From 105 probable members, abundance analysis of 45 evolved stars produces [Fe/H] = −0.40 ± 0.12, [Si/Fe] = 0.14 ± 0.12, [Ca/Fe] = 0.29 ± 0.07, and [Ni/Fe] = −0.12 ± 0.10, where quoted errors are standard deviations. With E(B − V) = 0.07 and (m − M)0 = 13.12, appropriate isochrones provide an excellent match from the main sequence through the tip of the giant branch for an age of 1.85 ± 0.05 Gyr. Li spectrum synthesis produces A(Li) below 1.4 at the base of the red giant branch to a detectable value of −0.4 at the tip. Six probable asymptotic giant branch stars and all but one red clump star have only Li upper limits. A rapidly rotating red giant is identified as a possible Li-rich giant, assuming it is a red clump star. Main-sequence turnoff stars have a well-defined A(Li) = 2.83 ± 0.03 (sem) down to the Li-dip wall at the predicted mass of 1.29 M ☉. Despite having the same isochronal age as the more metal-rich NGC 2506, the luminosity distribution of red giants reflects a younger morphology similar to NGC 7789, possibly indicating a deeper impact of metallicity on stellar structure and A(Li) than previously assumed. As in NGC 2506 and NGC 7789, the NGC 2204 turnoff exhibits a broad range of rotation speeds, making abundance estimation impossible for some stars. The place of the cluster within Galactic A(Li) evolution is discussed.

CHAOS. VIII. Far-ultraviolet Spectra of M101 and the Impact of Wolf–Rayet Stars* ∗Based on observations made with the NASA/ESA Hubble Space Telescope, obtained from the Data Archive at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555.

We investigate the stellar and nebular properties of nine H ii regions in the spiral galaxy M101 with far-ultraviolet (FUV; ∼900–2000 Å) and optical (∼3200–10,000 Å) spectra. We detect significant C iii] λλ1907,1909 nebular emission in seven regions, but O iii] λ1666 only in the lowest-metallicity region. We produce new analytic functions of the carbon ionization correction factors as a function of metallicity in order to perform a preliminary C/O abundance analysis. The FUV spectra also contain numerous stellar emission and P-Cygni features that we fit with luminosity-weighted combinations of single-burst Starburst99 and BPASS models. We find that the best-fit Starburst99 models closely match the observed very-high-ionization P-Cygni features, requiring very hot, young (≲3 Myr), metal-enriched massive stars. The youngest stellar populations are strongly correlated with broad He ii emission, nitrogen Wolf–Rayet (WR) FUV and optical spectral features, and enhanced N/O gas abundances. Thus, the short-lived WR phase may be driving excess emission in several N P-Cygni wind features (λ955, λ991, λ1720) that bias the stellar continuum fits to higher metallicities relative to the gas-phase metallicities. Accurate characterization of these H ii regions requires additional inclusion of WR stars in the stellar population synthesis models. Our FUV spectra demonstrate that the ∼900–1200 Å FUV can provide a strong test bed for future WR atmosphere and evolution models.

Decoding the end of message: PASTA provides food for thought on mechanisms of alternative polyadenylation

In a recent publication in Cell, Kowalski etal.1 developed an interdisciplinary and multiplexed approach to uncover regulatory modules of alternative polyadenylation, involving single-cell-based gene perturbation, isoform abundance analysis, machine learning of RNA motifs, and massively parallel reporter assays.

The largest metallicity difference in twin systems: High-precision abundance analysis of the benchmark pair Krios and Kronos

Aims. We conducted a high-precision differential abundance analysis of the remarkable binary system HD 240429/30 (Krios and Kronos, respectively), whose difference in metallicity is one of the highest detected to date in systems with similar components (~0.20 dex). A condensation temperature TC trend study was performed to search for possible chemical signatures of planet formation. In addition, other potential scenarios are proposed to explain this disparity. Methods. Fundamental atmospheric parameters (Teff, log g, [Fe/H], υturb) were calculated using the latest version of the FUNDPAR code in conjunction with ATLAS12 model atmospheres and the MOOG code, considering the Sun and then Kronos as references, employing high-resolution MAROON-X spectra. We applied a full line-by-line differential technique to measure the abundances of 26 elements in both stars with equivalent widths and spectral synthesis taking advantage of the non-solar-scaled opacities to achieve the highest precision. Results. We find a difference in metallicity of ~0.230 dex: Kronos is more metal rich than Krios. This result denotes a challenge for the chemical tagging method. The analysis encompassed the examination of the diffusion effect and primordial chemical differences, concluding that the observed chemical discrepancies in the binary system cannot be solely attributed to any of these processes. The results also show a noticeable excess of Li of approximately 0.56 dex in Kronos, and an enhancement of refractories with respect to Krios. A photometric study with TESS data was carried out, without finding any signal of possible transiting planets around the stars. Several potential planet formation scenarios were also explored to account for the observed excess in both metallicity and lithium in Kronos; none was definitively excluded. While planetary engulfment is a plausible explanation, considering the ingestion of an exceptionally high mass, approximately ~27.8 M⊕, no scenario is definitively ruled out. We emphasize the need for further investigations and refinements in modelling; indispensable for a comprehensive understanding of the intricate dynamics within the Krios and Kronos binary system.

WIYN Open Cluster Study. XC. Barium Surface Abundances of Blue Straggler Stars in the Open Clusters NGC 7789 and M67

We investigate barium (Ba) abundances in blue straggler stars (BSSs) in two open clusters, NGC 7789 (1.6 Gyr) and M67 (4 Gyr), as signatures of asymptotic-giant-branch (AGB) mass transfer. We combine our findings with previous Ba abundance analyses of NGC 6819 (2.5 Gyr) and NGC 188 (7 Gyr). Out of 35 BSSs studied in NGC 7789, NGC 6819, and M67, 15 (43% ± 11%) are Ba enriched; no BSSs in NGC 188 are Ba enriched. The Ba abundances of enriched BSSs show an anticorrelation with cluster age, ranging from an enrichment of [Ba/Fe] ∼ +1.5 dex in NGC 7789 to [Ba/Fe] ∼ +1.0 dex in M67. The Ba-enriched BSSs all lie in the same region of the H-R diagram, irrespective of cluster age or distance from the main-sequence turnoff. Our data suggest a link between AGB donor mass and mass-transfer efficiency in BSSs, in that less massive AGB donors tend to undergo more conservative mass transfer. We find that 40% ± 16% of the Ba-enriched BSSs are in longer-period spectroscopic binaries with orbital periods less than 5000 days. Those Ba-enriched BSSs that do not exhibit radial-velocity variability suggest AGB mass transfer in wide binaries by either wind mass transfer or wind Roche-lobe overflow. Given the preponderance of long orbital periods in the BSSs of M67 and NGC 188 and the frequency of Ba enrichment in NGC 7789, NGC 6819, and M67, it may be that AGB mass transfer is the dominant mechanism of BSS formation in open clusters older than 1 Gyr.

Root-soil-microbiome interaction in the rhizosphere of Masson pine (Pinus massoniana) under different levels of heavy metal pollution

Heavy metal pollution of the soil affects the environment and human health. Masson pine is a good candidate for phytoremediation of heavy metal in mining areas. Microorganisms in the rhizosphere can help with the accumulation of heavy metal in host plants. However, studies on its rhizosphere bacterial communities under heavy metal pollution are still limited. Therefore, in this study, the chemical and bacterial characteristics of Masson pine rhizosphere under four different levels of heavy metal pollution were investigated using 16 S rRNA gene sequencing, soil chemistry and analysis of plant enzyme activities. The results showed that soil heavy metal content, plant oxidative stress and microbial diversity damage were lower the farther they were from the mine dump. The co-occurrence network relationship of slightly polluted soils (C1 and C2) was more complicated than that of highly polluted soils (C3 and C4). Relative abundance analysis indicated Sphingomonas and Pseudolabrys were more abundant in slightly polluted soils (C1 and C2), while Gaiella and Haliangium were more abundant in highly polluted soils (C3 and C4). LEfSe analysis indicated Burkholderiaceae, Xanthobacteraceae, Gemmatimonadaceae, Gaiellaceae were significantly enriched in C1 to C4 site, respectively. Mantel analysis showed that available cadmium (Cd) contents of soil was the most important factor influencing the bacterial community assembly. Correlation analysis showed that eight bacterial genus were significantly positively associated with soil available Cd content. To the best of our knowledge, this is the first study to investigate the rhizospheric bacterial community of Masson pine trees under different degrees of heavy metal contamination, which lays the foundation for beneficial bacteria-based phytoremediation using Masson pines in the future.