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DOE OSTI2025

Microbial secondary metabolites: advancements to accelerate discovery towards application

Microbial secondary metabolites not only have key roles in microbial processes and relationships but are also valued in various sectors of today’s economy, especially in human health and agriculture. The advent of genome sequencing has revealed a previously untapped reservoir of biosynthetic capacity for secondary metabolites indicating that there are new biochemistries, roles and applications of these molecules to be discovered. New predictive tools for biosynthetic gene clusters (BGCs) and their associated pathways have provided insights into this new diversity. Advanced molecular and synthetic biology tools and workflows including cell-based and cell-free expression facilitate the study of previously uncharacterized BGCs, accelerating the discovery of new metabolites and broadening our understanding of biosynthetic enzymology and the regulation of BGCs. These are complemented by new developments in metabolite detection and identification technologies, all of which are important for unlocking new chemistries that are encoded by BGCs. This renaissance of secondary metabolite research and development is catalysing toolbox development to power the bioeconomy.

Dinglasan, Jaime Lorenzo N↗

DOE OSTI2025

Targeted seed EMS mutagenesis reveals a basic helix–loop–helix transcription factor underlying male sterility in sorghum

Abstract Forward genetic screens of mutant populations are fundamental for functional genomics studies. However, isolating independent mutant alleles to molecularly identify causal genes is challenging in species recalcitrant to genetic manipulation. Here, we demonstrate that classic seed ethyl methanesulfonate (EMS) mutagenesis coupled with genome sequencing can overcome this limitation in sorghum. We used this method to generate new mutant alleles of sorghum MALE STERILE 8 (MS8) and identified the causal locus for the ms8 phenotype as Sobic.004G270900, which encodes the sorghum ortholog of maize bhlh122, a basic helix–loop–helix (bHLH) transcription factor required for male fertility in maize. Bulked segregant analysis mapped ms8-1 to a region on chromosome 4 containing Sobic.004G270900. Seeds from heterozygous MS8/ms8-1 plants were mutagenized and screened for chimeric inflorescences containing sectors with white, sterile anthers resembling the ms8-1 homozygous phenotype. DNA sequencing of sterile and fertile sectors from a single chimeric inflorescence revealed two mutations in Sobic.004G270900 within the sterile sector, but not the fertile sector. Isolation of this loss-of-function allele (ms8-2) established Sobic.004G270900 as the causative locus for male sterility in the ms8 mutant. We generated additional alleles of MS8 in a different genetic background using CRISPR/Cas9-based gene editing, where deletions in Sobic.004G270900 also resulted in male sterility. Our work identified a gene underlying male sterility in sorghum and provides a novel and straightforward genetic tool for researchers who lack access to advanced transformation facilities to validate gene candidates. Unlike gene editing, no prior knowledge of candidate genes is required for targeted seed EMS mutagenesis to aid identification of causal loci.

Genetics & Heredity↗

DOE OSTI2025

The HIGH CHLOROPHYLL FLUORESCENCE 244 homolog CrHCF244 is required for psbA (D1) translation in Chlamydomonas reinhardtii

Translation of psbA, the chloroplast gene that encodes the D1 subunit of PSII, is important for both PSII biogenesis and repair. The translation of psbA transcripts in the chloroplast is under the control of nuclear gene products. Using a forward genetic screen and whole-genome sequencing of the alga Chlamydomonas reinhardtii , we found a mutant defective in PSII activity and mapped the causative gene to be the homolog of Arabidopsis HIGH CHLOROPHYLL FLUORESCENCE 244 (HCF244) , namely CrHCF244 . We then demonstrated that CrHCF244 is required for psbA translation in the alga, consistent with the function of HCF244 in Arabidopsis, and found that AtHCF244 also partially complemented the algal mutant. These results experimentally support the functional conservation of the homologs in green algae and land plants. Intriguingly, the CrHCF244 mutant also exhibited a relatively high rate of suppressor mutants, pointing to the presence of alternative factor(s)/pathway(s) for D1 translational control. The establishment of CrHCF244 as a psbA translation factor in C. reinhardti i shows the similarities in psbA translation regulation in algae and plants. The future identification of the alternative factor(s) in this alga will provide insights on psbA translation in plants.

Arabidopsis↗

DOE OSTI2024

CO2 response screen in grass Brachypodium reveals the key role of a MAP kinase in CO2-triggered stomatal closure

Abstract Plants respond to increased CO2 concentrations through stomatal closure, which can contribute to increased water use efficiency. Grasses display faster stomatal responses than eudicots due to dumbbell-shaped guard cells flanked by subsidiary cells working in opposition. However, forward genetic screening for stomatal CO2 signal transduction mutants in grasses has yet to be reported. The grass model Brachypodium distachyon is closely related to agronomically important cereal crops, sharing largely collinear genomes. To gain insights into CO2 control mechanisms of stomatal movements in grasses, we developed an unbiased forward genetic screen with an EMS-mutagenized B. distachyon M5 generation population using infrared imaging to identify plants with altered leaf temperatures at elevated CO2. Among isolated mutants, a “chill1” mutant exhibited cooler leaf temperatures than wild-type Bd21-3 parent control plants after exposure to increased CO2. chill1 plants showed strongly impaired high CO2-induced stomatal closure despite retaining a robust abscisic acid-induced stomatal closing response. Through bulked segregant whole-genome sequencing analyses followed by analyses of further backcrossed F4 generation plants and generation and characterization of sodium azide and CRISPR-cas9 mutants, chill1 was mapped to a protein kinase, Mitogen-Activated Protein Kinase 5 (BdMPK5). The chill1 mutation impaired BdMPK5 protein-mediated CO2/HCO3− sensing together with the High Temperature 1 (HT1) Raf-like kinase in vitro. Furthermore, AlphaFold2-directed structural modeling predicted that the identified BdMPK5-D90N chill1 mutant residue is located at the interface of BdMPK5 with the BdHT1 Raf-like kinase. BdMPK5 is a key signaling component that mediates CO2-induced stomatal movements and is proposed to function as a component of the primary CO2 sensor in grasses.

Lopez, Bryn N. K. (ORCID:0009000937288216)↗

DOE OSTI2024

Packaging “vegetable oils”: Insights into plant lipid droplet proteins

Abstract Plant neutral lipids, also known as “vegetable oils”, are synthesized within the endoplasmic reticulum (ER) membrane and packaged into subcellular compartments called lipid droplets (LDs) for stable storage in the cytoplasm. The biogenesis, modulation, and degradation of cytoplasmic LDs in plant cells are orchestrated by a variety of proteins localized to the ER, LDs, and peroxisomes. Recent studies of these LD-related proteins have greatly advanced our understanding of LDs not only as steady oil depots in seeds but also as dynamic cell organelles involved in numerous physiological processes in different tissues and developmental stages of plants. In the past 2 decades, technology advances in proteomics, transcriptomics, genome sequencing, cellular imaging and protein structural modeling have markedly expanded the inventory of LD-related proteins, provided unprecedented structural and functional insights into the protein machinery modulating LDs in plant cells, and shed new light on the functions of LDs in nonseed plant tissues as well as in unicellular algae. Here, we review critical advances in revealing new LD proteins in various plant tissues, point out structural and mechanistic insights into key proteins in LD biogenesis and dynamic modulation, and discuss future perspectives on bridging our knowledge gaps in plant LD biology.

Cai, Yingqi (ORCID:0000000203575809)↗

DOE OSTI2024

Biomass yields, reproductive fertility, compositional analysis, and genetic diversity of newly developed triploid giant miscanthus hybrids

Abstract Miscanthus × giganteus (giant miscanthus), first found as a naturally occurring hybrid, has shown promise as a bioenergy/biomass crop throughout much of the temperate world. This allotriploid (2 n = 3 x = 57) hybrid resulted from a cross between tetraploid Miscanthus sacchariflorus (2 n = 4 x = 76) and diploid Miscanthus sinensis (2 n = 2 x = 38) and is particularly desirable due to its low fertility that minimizes reseeding and potential invasiveness. However, there is limited genetic diversity in commonly grown cultivars of triploid M. × giganteus and breeding and development efforts to improve and domesticate this crop have been minimal. Here, we report on newly developed M. × giganteus hybrids compared with the industry standard M. × giganteus '1993‐1780'. Dry biomass yields of new hybrids ranged from 19.5 to 32.4 Mg/ha/year for the fourth growing season, compared with 21.0 Mg/ha/year for M. × giganteus '1993‐1780'. Plant reproductive fertility remained low for all accessions with overall fertility [(seed set × seed germination)/100] ranging from 0.3% to 4.5% for new hybrids compared to 0.4% for M. × giganteus '1993‐1780'. Culm density and height varied among accessions and were positively correlated with increased biomass. Based on compositional analyses, theoretical ethanol yields ranged from 9, 740 to 16,278 L/ha/year for new hybrids compared to 10,406 L/ha/year for M. × giganteus '1993‐1780'. Relative feed value indices were low overall and ranged between 66.0 and 72.8 for new hybrids compared to M. × giganteus '1993‐1780' with 71.3. The genetic diversity of new hybrids, compared with existing cultivars, was characterized using whole genome sequences. Based on pair‐wise distances, cluster analysis clearly showed increased diversity of new hybrids compared with earlier selections. These results document new triploid hybrids of M. × giganteus with enhanced biomass and theoretical ethanol yields in combination with broader genetic diversity and lowreproductive fertility.

Touchell, Darren H.↗

DOE OSTI2024

Cyanobacteria newly isolated from marine volcanic seeps display rapid sinking and robust, high-density growth

Cyanobacteria are photosynthetic organisms that play important roles in carbon cycling and are promising bioproduction chassis. Here, we isolate two novel cyanobacteria with 4.6Mbp genomes, UTEX 3221 and UTEX 3222, from a unique marine environment with naturally elevated CO₂. We describe complete genome sequences for both isolates and, focusing on UTEX 3222 due to its planktonic growth in liquid, characterize biotechnologically relevant growth and biomass characteristics. UTEX 3222 outpaces other fast-growing model strains on a solid medium. It can double every 2.35 hours in a liquid medium and grows to high density (>31 g/L biomass dry weight) in batch culture, nearly double that of Synechococcus sp. PCC 11901, whose high-density growth was recently reported. In addition, UTEX 3222 sinks readily, settling more quickly than other fast-growing strains, suggesting favorable economics of harvesting UTEX 3222 biomass. These traits may make UTEX 3222 a compelling choice for marine carbon dioxide removal (CDR) and photosynthetic bioproduction from CO₂. Overall, we find that bio-prospecting in environments with naturally elevated CO₂ may uncover novel CO₂-metabolizing organisms with unique characteristics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Alternate routes to acetate tolerance lead to varied isoprenol production from mixed carbon sources in Pseudomonas putida

ABSTRACT Lignocellulose is a renewable resource for the production of a diverse array of platform chemicals, including the biofuel isoprenol. Although this carbon stream provides a rich source of sugars, other organic compounds, such as acetate, can be used by microbial hosts. Here, we examined the growth and isoprenol production in a Pseudomonas putida strain pre-tolerized (“PT”) background where its native isoprenol catabolism pathway is deleted, using glucose and acetate as carbon sources. We found that PT displays impaired growth in minimal medium containing acetate and often fails to grow in glucose-acetate medium. Using a mutant recovery-based approach, we generated tolerized strains that overcame these limitations, achieving fast growth and isoprenol production in the mixed carbon feed. Changes in the glucose and acetate assimilation routes, including an upregulation in PP_0154 (SpcC, succinyl-CoA:acetate CoA-transferase) and differential expression of the gluconate assimilation pathways, were key for higher isoprenol titers in the tolerized strains, whereas a different set of mechanisms were likely enabling tolerance phenotypes in media containing acetate. Among these, a coproporphyrinogen-III oxidase (HemN) was upregulated across all tolerized strains and in one isolate required for acetate tolerance. Utilizing a defined glucose and acetate mixture ratio reflective of lignocellulosic feedstocks for isoprenol production in P. putida allowed us to obtain insights into the dynamics and challenges unique to dual carbon source utilization that are obscured when studied separately. Together, this enabled the development of a P. putida bioconversion chassis able to use a more complex carbon stream to produce isoprenol. IMPORTANCE Acetate is a relatively abundant component of many lignocellulosic carbon streams and has the potential to be used together with sugars, especially in microbes with versatile catabolism such as P. putida . However, the use of mixed carbon streams necessitates additional optimization. Furthermore, the use of P. putida for the production of the biofuel target, isoprenol, requires the use of engineered strains that have additional growth and production constraints when cultivated in acetate and glucose mixtures. In this study, we generate acetate-tolerant P. putida strains that overcome these challenges and examine their ability to produce isoprenol. We show that acetate tolerance and isoprenol production, although independent phenotypes, can both be optimized in a given P. putida strain. Using proteomics and whole genome sequencing, we examine the molecular basis of both phenotypes and show that tolerance to acetate can occur via alternate routes and result in different impacts on isoprenol production.

de Siqueira, Guilherme M. V. (ORCID:00000002364563↗

DOE OSTI2025

Complete genome of Erwinia spp. str . LJJL01 isolated from waste charcoal

We present the complete genome sequence of Erwinia spp. str. LJJL01, isolated from waste charcoal in Colorado, USA, using Oxford Nanopore sequencing. This sequence provides important insights into this bacterium’s metabolic and catabolic robustness to utilize sugars, acids, and aromatics, highlighting its potential as a bio-industrial strain for various feedstocks.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Characterization of Pseudomonas aeruginosa and Acinetobacter calcoaceticus-baumannii complex traumatic wound isolates

Healing of traumatic wounds is complicated by infecting pathogens, with Pseudomonas aeruginosa and members of the Acinetobacter calcoaceticus-baumannii complex among the most common infectious agents. However, a full understanding of genotypic and phenotypic differences between circulating wound isolates is lacking. To address this, traumatic wounds were sampled at Emory University Hospital, and 24 isolates were characterized; we focused on P. aeruginosa and Acinetobacter due to their prevalence and tendency for antibiotic resistance. Even though these species are renowned for antibiotic resistance, only two of the tested isolates could be classified as multidrug resistant. Whole-genome sequencing and analysis revealed that isolates from different patients were genetically distinct; however, longitudinal isolates from the same patient were closely related and appeared to represent chronic colonization by the same strain. Phylogenetic analysis revealed that laboratory strains (PAO1 and AB5075) that were isolated decades previously and from different locations grouped closely to subsets of the recent wound isolates. Given the importance of biofilm formation in infection, the ability of the isolates to form biofilms was assessed; all isolates formed biofilms but showed temporal and magnitude differences. Analysis of a subset of isolates revealed that planktonic P. aeruginosa was resistant to human serum-mediated killing. While the same was true for the majority of Acinetobacter isolates, one showed planktonic sensitivity that was abrogated when grown in a biofilm. Taken together, these data reveal genotypic and phenotypic differences in circulating isolates of P. aeruginosa and A. baumannii.

Acinetobacter↗

DOE OSTI2024

raogroupuiuc/yl_variantcalling

NGS analysis for mutation analysis in Yarrowia lipolytica evolved strains. Yarrowia lipolytica, an oleaginous yeast, shows promise for industrial fermentation due to its robust acetyl-CoA flux and well-developed genetic engineering tools. However, its lack of an active xylose metabolism restricts the conversion of cellulosic sugars to valuable products. To address this, metabolic engineering, and adaptive laboratory evolution (ALE) were applied to the Y. lipolytica PO1f strain, resulting in an efficient xylose-assimilating strain (XEV). Whole-genome sequencing (WGS) of the XEV followed by reverse engineering revealed that the amplification of the heterologous oxidoreductase pathway and a mutation in the GTPase-activating protein gene (YALI0B12100g) might be the primary reasons for improved xylose assimilation in the XEV strain. When a sorghum hydrolysate was used, the XEV strain showed superior xylose consumption and lipid production compared to its parental strain (X123). This study advances our understanding of xylose metabolism in Y. lipolytica and proposes effective metabolic engineering strategies for optimizing lignocellulosic hydrolysates.

Deewan, Anshu↗

DOE OSTI2026

Poxvirus infection triggers remodeling of host m⁶A epitranscriptome and benefits from the m⁶A regulatory responses

Understanding how host gene regulation responds to viral infection is essential for developing effective antiviral strategies. Emerging evidence suggests that host transcripts undergo dynamic chemical modifications to counteract viral invasion. Conversely, viruses that rely on nuclear transcription exploit host RNA methyltransferases to enhance mRNA export and translation. Orthopoxviruses, however, complete their entire replication cycle within compartmentalized cytoplasmic “factories” utilizing enzymes encoded by their large double-stranded viral DNA genomes. The dynamic interplay between host and poxviral epitranscriptome remains poorly characterized. Using a temporally resolved model of Vaccinia virus (VV) infection, we investigated host-virus interactions through transcriptome and N6-methyladenosine (m⁶A) epitranscriptome whole genome sequencing. We found that host m⁶A modifications respond rapidly to VV infection, preceding the delayed transcriptional changes that emerge at later stages. Early m⁶A signatures included key innate immunity factors as well as host genes involved in transcriptional regulation, post-transcriptional modification, and protein ubiquitination. Functional assays validated two host factors with early m⁶A modification changes that are essential for VV infection: a m⁶A reader, YTHDF1, and a component of the SCF E3 ubiquitin ligase complex, FBXO31. The m⁶A gain on YTHDF1 enhanced its protein expression and promoted efficient VV replication. In addition, we identified previously unrecognized roles of FBXO31 and the SCF E3 ligase complex in supporting VV infection. Temporal profiling of the m⁶A epitranscriptome reveals how VV exploits host post-transcriptional regulatory pathways, specifically m⁶A RNA modification and protein ubiquitination. These findings highlight critical host factors co-opted during poxvirus infection and identify potential targets for therapeutic intervention.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection

Abstract Background Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer death among women globally. Despite advances, there is considerable variation in clinical outcomes for patients with non-luminal A tumors, classified as difficult-to-treat breast cancers (DTBC). This study aims to delineate the proteogenomic landscape of DTBC tumors compared to luminal A (LumA) tumors. Methods We retrospectively collected a total of 117 untreated primary breast tumor specimens, focusing on DTBC subtypes. Breast tumors were processed by laser microdissection (LMD) to enrich tumor cells. DNA, RNA, and protein were simultaneously extracted from each tumor preparation, followed by whole genome sequencing, paired-end RNA sequencing, global proteomics and phosphoproteomics. Differential feature analysis, pathway analysis and survival analysis were performed to better understand DTBC and investigate biomarkers. Results We observed distinct variations in gene mutations, structural variations, and chromosomal alterations between DTBC and LumA breast tumors. DTBC tumors predominantly had more mutations inTP53,PLXNB3, Zinc finger genes, and fewer mutations inSDC2,CDH1,PIK3CA,SVIL, andPTEN. Notably, Cytoband 1q21, which contains numerous cell proliferation-related genes, was significantly amplified in the DTBC tumors. LMD successfully minimized stromal components and increased RNA–protein concordance, as evidenced by stromal score comparisons and proteomic analysis. Distinct DTBC and LumA-enriched clusters were observed by proteomic and phosphoproteomic clustering analysis, some with survival differences. Phosphoproteomics identified two distinct phosphoproteomic profiles for high relapse-risk and low relapse-risk basal-like tumors, involving several genes known to be associated with breast cancer oncogenesis and progression, includingKIAA1522,DCK,FOXO3,MYO9B,ARID1A,EPRS,ZC3HAV1, andRBM14. Lastly, an integrated pathway analysis of multi-omics data highlighted a robust enrichment of proliferation pathways in DTBC tumors. Conclusions This study provides an integrated proteogenomic characterization of DTBC vs LumA with tumor cells enriched through laser microdissection. We identified many common features of DTBC tumors and the phosphopeptides that could serve as potential biomarkers for high/low relapse-risk basal-like BC and possibly guide treatment selections.

Oncology↗

DOE OSTI2025

Sodium azide mutagenesis induces a unique pattern of mutations

The nature and effect of mutations are of fundamental importance to the evolutionary process. The generation of mutations with mutagens has also played important roles in genetics. Applications of mutagens include dissecting the genetic basis of trait variation, inducing desirable traits in crops, and understanding the nature of genetic load. Previous studies of sodium azide-induced mutations have reported single nucleotide variants (SNVs) found in individual genes. To characterize the nature of mutations induced by sodium azide, we analyze whole-genome sequencing (WGS) of 11 barley lines derived from sodium azide mutagenesis, where all lines were selected for diminution of plant fitness owing to induced mutations. We contrast observed mutagen-induced variants with those found in standing variation in WGS of 13 barley landraces. Here, we report indels that are two orders of magnitude more abundant than expected based on nominal mutation rates. We found induced SNVs are very specific, with C → T changes occurring in a context followed by another C on the same strand (or the reverse complement). The codons most affected by the mutagen include the sodium azide-specific CC motif (or the reverse complement), resulting in a handful of amino acid changes and few stop codons. The specific nature of induced mutations suggests that mutagens could be chosen based on experimental goals. Sodium azide would not be ideal for gene knockouts but will create many missense mutations with more subtle effects on protein function.

Genetics & Heredity↗

DOE OSTI2024

Domestication of Algae for Increasing Biomass Productivity

Microalgae cultivation processes have been developed for the production of a variety of bioproducts, however currently only a few species are used in commercial applications. Their domestication, that is strain improvements, is still in its infancy, with major advances required, specifically to maximize biomass productivity a limiting factor in microalgae production. This requires a deep understanding of algal biology, in particular to develop superior strains without the need of genetic technologies that would require lengthy regulatory permits, and often limit consumer acceptance. Adaptive Laboratory Evolution techniques, alone or in conjunction with sexual recombination, can allow for rapid develop of improved strains and their industrial production. Light harvesting antenna reduction has been a major approach to achieve increased photon utilization efficiency by cultures operating under full sunlight conditions due to higher light saturation levels, allowing for higher productivities under outdoor conditions. Decades of research yielded some promising results under controlled conditions with a few specific mutant strains. However, these failed to achieve the anticipated higher productivities in actual algal mass cultures, in part due to the inability of single mutations to overcome photoinhibition, reactive oxygen species, and other pleiotropic impacts on the complex metabolic processes of photosynthesis. Higher productivity strains will require multiple genetic improvements. We report on recent Adaptive Laboratory Evolution with the green alga Scenedesmus obliquus resulting in higher biomass productivity in open pond cultivation. Coupling our approach with sexual recombination and genome sequencing provides a path to algal domestication suitable for large-scale, low-cost biomass production.

09 BIOMASS FUELS↗

DOE OSTI2026

Bacterial Bioleaching and Biorecovery for Biomining Unconventional Rare Earth Element Feedstocks

Bacterial metabolic interactions with rare earth elements (REEs) can be harnessed for biomining unconventional feedstocks like abandoned coal-mine drainage (AMD). Pennsylvania has ~500 AMD passive remediation systems that can precipitate REE rich solids. REEs include yttrium and the lanthanide series that are used in modern energy and technology. Bacteria that metabolically interact with REEs can be used for biomining in an affordable efficient process that does not require hazardous chemical additives. Currently, the microbial metal mechanisms that contribute to REE biorelease and biorecovery are poorly understood. Our work shows acidogenic bacterial isolates (Bacillus mycoides JR07 and Bacillus pseudomycoides KB7) successfully bioleach a mixed REE solution from AMD solids by their organic acid production and biofilm formation. Further, our work shows the potential for bacterial lanthanide-dependent enzymes to recover lanthanides from a mixed REE solution; here we have bacterial isolate Methylobacterium sp. B3 that can recover soluble lanthanum. Whole genome sequencing of Methylobacterium sp. B3 predict lanthanide-dependent methanol dehydrogenase XoxF. Understanding the microbial metabolism and genes involved in the REE release and recovery is crucial to optimize the biomining of AMD solids. Our work addresses the growing need to develop novel REE mining methods from unconventional feedstocks.

biogeochemistry↗

DOE OSTI2024

Genetic Complexity of CC5 Staphylococcus aureus Isolates Associated with Sternal Bursitis in Chickens: Antimicrobial Resistance, Virulence, Plasmids, and Biofilm Formation

Sternal bursitis, a common inflammatory condition in poultry, poses significant challenges to both animal welfare and public health. This study aimed to investigate the prevalence, antimicrobial resistance, and genetic characteristics of Staphylococcus aureus isolates associated with sternal bursitis in chickens. Ninety-eight samples were collected from affected chickens, and 24 S. aureus isolates were identified. Antimicrobial susceptibility testing revealed resistance to multiple agents, with a notable prevalence of aminoglycoside resistance genes. Whole genome sequencing elucidated the genetic diversity and virulence profiles of the isolates, highlighting the predominance of clonal complex 5 (CC5) strains. Additionally, biofilm formation assays demonstrated moderate biofilm production capacity among the isolates. These findings underscore the importance of vigilant monitoring and targeted interventions to mitigate the impact of sternal bursitis in poultry production systems.

Silva, Vanessa (ORCID:0000000194068433)↗

DOE OSTI2025

Phylodynamics of SARS-CoV-2 Lineages B.1.1.7, B.1.1.529 and B.1.617.2 in Nigeria Suggests Divergent Evolutionary Trajectories

Background: The early months of the COVID-19 pandemic were characterized by high transmission rates and mortality, compounded by the emergence of multiple SARS-CoV-2 lineages, including Variants of Concern (VOCs). This study investigates the phylodynamic and spatio-temporal trends of VOCs during the peak of the pandemic in Nigeria. Methods: Whole-genome sequencing (WGS) data from three major VOCs circulating in Nigeria, B.1.1.7 (Alpha), B.1.617.2 (Delta), and B.1.1.529 (Omicron), were analyzed using tools such as Nextclade, R Studio v 4.2.3, and BEAST X v 10.5.0. The spatial distribution, evolutionary history, viral ancestral introductions, and geographic dispersal patterns were characterized. Results: Three major lineages following WHO nomenclature were identified: Alpha, Delta, and Omicron. The Delta variant exhibited the widest geographic spread, detected in 14 states, while the Alpha variant was the least distributed, identified in only eight states but present across most epidemiological weeks studied. Evolutionary rates varied slightly, with Alpha exhibiting the slowest rate (2.66 × 10 −4 substitutions/site/year). Viral population analyses showed distinct patterns: Omicron sustained elevated population growth over time, while Delta declined after initial expansion. The earliest Times to Most Recent Common Ancestor (TMRCA) were consistent with the earliest outbreaks of SARS-CoV-2 globally. Geographic transmission analysis indicated a predominant coastal-to-inland spread for all variants, with Omicron showing the most diffuse dispersal, highlighting commercial routes as significant drivers of viral diffusion. Conclusion: The SARS-CoV-2 epidemic in Nigeria was characterized by multiple variant introductions and a dominant coastal-to-inland spread, emphasizing that despite lockdown measures, commercial trade routes played a critical role in viral dissemination. These findings provide insights into pandemic control strategies and future outbreak preparedness.

Nigeria↗