Biology subjects

Palma, L.

Publications and source records attributed to Palma, L..

12 recordsLinked to original sources

bioRxiv2026

Genomic and proteomic insights into the virulence of a native Heterorhabditis indica-Photorhabdus akhurstii complex active against Spodoptera spp.

A native entomopathogenic nematode isolate, Heterorhabditis indica Che4.1, was recovered from soils in Valencia (Spain), and its symbiotic bacterium, Photorhabdus akhurstii Che4.1, was isolated and characterized. Nematode identification was confirmed by ITS and 28S rDNA sequencing, while genome-based analyses supported the taxonomic assignment of the bacterial symbiont. The nematode-bacterium complex exhibited insecticidal activity against Spodoptera exigua and Spodoptera littoralis. H. indica Che4.1 showed an LC of 53.7 infective juveniles (IJs)/mL against S. exigua, comparable to that of the commercial reference Larvanem (54.3 IJs/mL). Against S. littoralis, Che4.1 exhibited an approximately twofold lower LC than Larvanem (77.3 versus 155.9 IJs/mL), with non-overlapping 95% confidence intervals. The complete genome of P. akhurstii Che4.1 consists of a single circular chromosome of 5.66 Mb encoding a diverse repertoire of putative virulence factors, including toxin complex (Tc) components, YenTc-like proteins, Mcf toxins, App-family proteins, Pra/Prb proteins, and chitinases, together with several predicted secondary metabolite biosynthetic gene clusters. LC-MS/MS analyses of bacterial culture supernatants and infected insect cadavers detected multiple predicted virulence-associated proteins, including Tc-related, YenTc-like, App-family, and Pra/Prb proteins. In addition, bacterial cell-free supernatants caused 68.8-81.3% mortality in S. exigua neonates under laboratory conditions. Together, these findings reveal a diverse repertoire of potential virulence determinants in P. akhurstii Che4.1 and demonstrate the insecticidal potential of its native nematodebacterium complex. The performance of H. indica Che4.1 relative to a commercial reference supports further evaluation of this isolate for biological control of Spodoptera spp., particularly under greenhouse and field conditions.

microbiology↗

bioRxiv2026

Comparative genomics reveals extensive genomic conservation and limited microdiversification among Xenorhabdus bovienii isolates recovered from a single Steinernema feltiae isolation event.

Xenorhabdus bovienii is a symbiotic bacterium associated with entomopathogenic nematodes of the genus Steinernema. Comparative genomic analyses of closely related isolates provide an opportunity to investigate fine-scale diversification, genome plasticity, and the evolutionary processes shaping symbiotic bacterial populations. Here, we analyzed four X. bovienii isolates (XenUTI4.1-XenUTI4.4) recovered from a single Steinernema feltiae isolation event using comparative genomics approaches integrating average nucleotide identity (ANI), single-nucleotide polymorphism (SNP) analyses, pangenome reconstruction, biosynthetic gene cluster (BGC) prediction, and mobile element-associated annotation screening. Whole-genome comparisons revealed extremely high genomic similarity among isolates, with ANI values exceeding 99.84%. Read-based SNP analyses identified only 23-36 annotated variants relative to the XenUTI4.1 reference genome, indicating limited sequence divergence despite detectable microvariation. Functional annotation of these variants showed that most corresponded to missense or synonymous substitutions affecting a small number of coding sequences. Pangenome analysis identified 4,712 orthologous gene clusters, including a highly conserved core genome of 4,256 clusters (90.3%) shared by all isolates and a relatively small accessory genome comprising 456 clusters. antiSMASH analyses revealed broadly conserved secondary metabolite biosynthetic potential across the four genomes, whereas screening of genome annotations identified abundant phage-related, transposase-associated, and recombination-associated genes consistent with ongoing genome plasticity. Collectively, these results demonstrate that the analyzed X. bovienii isolates represent a highly conserved population exhibiting limited but detectable genomic microdiversification. The coexistence of a large core genome, a modest accessory gene complement, and numerous mobile element-associated functions suggests that localized sequence variation and mobile genetic elements contribute to genomic diversification within S. feltiae-associated X. bovienii populations.

genetics↗

bioRxiv2026

Unlocking the (Coleoptera: Tenebrionidae)-Combatting Capabilities of INTA Mo4-4 through genomic and phenotypic characterization

Bacillus thuringiensis INTA Mo4-4 was characterized phenotypically, genomically, and for insecticidal activity against Alphitobius diaperinus. Microscopy revealed rare flat rectangular parasporal crystals, and SDS-PAGE identified a ca. 67 kDa protein, similar to B. thuringiensis serovar morrisoni strain tenebrionis DSM-2803, which was proteolytically processed to a ca. 55 kDa fragment. Genomic analysis showed a 5.99 Mb genome with 99.43% completeness, clustering phylogenetically with B. cereus and B. thuringiensis. High genomic similarity was observed with B. thuringiensis svar. morrisoni BGSC 4AA1, confirmed by MLST analysis assigning it to ST-23. The genome encodes an interesting arsenal of pesticidal proteins showing significant similarity to Cry3Aa, Mpp23Aa, Xpp37Aa, Mpp5Ab, Vpb1Ad, Vpb1Ae, Vpa2Ab, Vpa2Ba, Vpa2Bb and Spp1Aa, with demonstrated toxicity against coleopteran pests. Biosynthetic gene clusters for toyoncin, fengycin, and bacillibactin were identified. Dose-response bioassays showed that INTA Mo4-4 was nearly four times more toxic to A. diaperinus larvae (LC50 136.9 {micro}g/ml) than DSM-2803 (LC50 540.5 {micro}g/ml), with the difference being statistically significant. No teratological effects were observed on Musca domestica. These findings suggest that INTA Mo4-4 is a promising candidate for the biological control of A. diaperinus.

microbiology↗

bioRxiv2026

Secretome analysis of Bacillus toyonensis Bto_UNVM-42 reveals extracellular pesticidal protein homologs and enzymes consistent with its nematicidal activity.

Previous studies demonstrated that cell-free supernatants of Bacillus toyonensis biovar Thuringiensis Bto_UNVM-42 exhibit nematicidal activity against Panagrellus redivivus, although the molecular basis of this phenotype remains unclear. While pesticidal proteins in Bacillus thuringiensis and related species are classically considered intracellular and associated with parasporal crystals, their occurrence in extracellular fractions remains poorly explored. Here, we characterized the extracellular protein repertoire of biologically active supernatants and evaluated their effects on Caenorhabditis elegans N2. LC-MS/MS analysis of LB-derived cell-free supernatants revealed the presence of pesticidal protein homologs related to Cry32-, Cyt1, and Mpp3-like protein families, together with degradative enzymes including collagenases, chitinases, proteases, phospholipases, and cytolysins. Signal peptide prediction suggested classical secretion pathways for several proteins, whereas others may reach extracellular fractions through alternative localization mechanisms. Comparative DIA-based proteomic analyses of LB and CCY supernatants revealed marked medium-dependent differences in the extracellular protein repertoire, including differential enrichment of Bt-like pesticidal homologs and degradative enzymes associated with distinct physiological states. Exposure assays showed that concentrated cell-free supernatants from both conditions caused severe loss of mobility and morphological alterations consistent with tissue disruption in C. elegans. Together, these findings provide proteomic evidence for the extracellular occurrence of pesticidal and degradative protein homologs in Bto_UNVM-42 and identify candidate extracellular factors potentially associated with the nematicidal activity of this strain. More broadly, the results support the view that soluble extracellular components may contribute to the biological activity of Bt-related bacteria beyond the classical spore-crystal paradigm.

microbiology↗

bioRxiv2026

A 16S rRNA gene-based analysis of microbial communities in compost-bedded pack barns from dairy farms in Argentina.

Microbial communities play a central role in compost-bedded pack (CBP) systems by driving organic matter decomposition and nutrient cycling. The objective of this study was to characterize and compare the bacterial community structure of CBP from two dairy farms in Cordoba, Argentina, using 16S rRNA gene sequencing. Two CBP systems were evaluated: Martin Bono (MB; 30 months in operation) and Angela Teresa (AT; 20 months). The MB system was established on natural soil without bedding addition and included concrete feed alleys, whereas AT was initiated with peanut shell bedding and lacked concrete alleys. In both systems, compost was tilled twice daily. Two samples per farm were collected at a depth of 30 cm during winter 2019. Raw Illumina reads were processed using the DADA2 pipeline, including quality filtering, error modeling, denoising, and chimera removal. A total of four samples yielded 2,503 amplicon sequence variants (ASVs), with approximately 76% of reads retained after filtering and chimera removal, indicating high-quality sequencing data. Taxonomic analysis revealed that bacterial communities in both systems were dominated by phyla typically associated with compost environments, including Actinobacteriota, Proteobacteria, and Firmicutes. Differences in relative abundance between systems suggested shifts in community composition associated with management conditions.

microbiology↗

bioRxiv2026

Draft Genome Sequence of Bacillus pergaminensis sp. nov. strain Bva_UNVM-123: A Promising Candidate for Bioremediation.

The Bacillus genus comprises physiologically versatile, endospore-forming bacteria widely distributed in natural environments. In this study, we report the isolation and genomic characterization of strain Bva_UNVM-123, recovered from agricultural soil in Pergamino, Argentina. Whole-genome sequencing using Illumina technology yielded a 5.1 Mbp draft genome assembled in 67 contigs with a GC content of 36%. Comparative genomic analyses using the TYGS server and digital DNA-DNA hybridization (dDDH) values supported its classification as a potentially novel species within the Bacillus sensu lato (s.l.) group. Genome annotation revealed 4,866 protein-coding genes, including multiple determinants conferring resistance to antibiotics (e.g., fosfomycin, tetracycline, beta-lactams) and toxic heavy metals (e.g., arsenic, cadmium, mercury), supporting its potential application in bioremediation. Additionally, PathogenFinder predicted a low probability of human pathogenicity (0.207), reinforcing its safety for environmental use. Functional classification based on Swiss-Prot further supported a metabolically versatile profile and revealed the presence of resistance-related categories associated with environmental adaptation. This study adds to the growing knowledge of environmental Bacillus species and their biotechnological potential.

microbiology↗

bioRxiv2026

Exploratory 16S rRNA Metagenomic Analysis of Soil Microbial Communities in Agroecosystems of North-Central Argentina

Agriculture has modified the soil structure due to the influence of external factors and processes that affect microbial biodiversity. Metagenomics is a fundamental tool for the study of soil microbial diversity because it provides information about the ecosystem diversity, including both the microorganisms that cannot be isolated in culture media and those that are no longer viable in the analyzed sample. In this work, six soil samples obtained from agroecosystems of central and northern Argentina were subjected to a preliminary 16S metagenomic analysis. Copiotrophic bacteria (Proteobacteria and Actinobacteriota) were dominant and one of the samples had a dominance of an oligotrophic Phylum (Acidobacteria). Our findings support previous evidence from traditionally managed agroecosystems and provide new insights into the diversity of soil microbiomes in Argentine regions outside the Pampas. Finally, we analyzed the most common genera with relevant species to agronomy, both beneficial and pathogenic, and their abundance and diversity in the sequenced samples.

genetics↗

bioRxiv2025

Forest conversion to cashew orchards delays the diel activity of diurnal mammals in West Africa

Land-use change is the main driver of biodiversity loss worldwide. However, less is known about how species adapt their behavior to persist in human-altered habitats. We addressed this gap by examining mammal responses in terms of habitat use and diel activity patterns to forest conversion into cashew orchards in West Africa. We surveyed mammals using camera-trapping in 12 forest sites and 12 cashew orchards in the Cantanhez National Park in southwest Guinea-Bissau, West Africa. We grouped mammals into (1) diurnal and cathemeral and (2) nocturnal species according to their diel activity periods and assessed their use and diel activity between habitat types. Based on 709 trap-days, we obtained 842 records of 12 diurnal or cathemeral species (18.3% of the records) and 13 nocturnal species (81.7%). Mammal habitat use was similar between forests and cashew orchards for both diurnal/cathemeral and nocturnal species. However, the peak of diurnal/cathemeral species shifted from the morning period ([~]11h00) in the forests to the afternoon period in the cashew orchards ([~]16h30), resulting in little overlap in activity of diurnal/cathemeral species between habitat types. No differences were observed in the diel activity of nocturnal mammals. Although mammals can make use of altered habitats, diurnal species are able to delay their activity, probably to avoid direct contact with humans. Our study highlights the ability of species in adapting their behaviour to persist in newly human-modified landscapes in the tropics.

ecology↗

bioRxiv2025

Mammal responses to habitat degradation induced by cashew expansion in West Africa

Tropical landscapes are perishing due to high rates of land-use change. In West Africa, Guinea-Bissau lost 77% of its closed-canopy forest over the last 25 years, mostly to the expansion of cashew monoculture. To date, understanding how species cope with such changes remains a conservation priority for the region. Here we examine mammal species composition, richness, and abundance, in addition to trophic-guild abundance across closed-canopy sub-humid forests and cashews orchards in the Cantanhez National Park, southwest Guinea-Bissau. Mammals were surveyed using one camera trap at each of the 24 sites, half in forest and half in cashew orchards, and their local and landscape-scale variables were measured. Based on 709 trap-nights, we collected 842 records from 25 mammal species. Local habitat structure--including canopy openness, floor obstruction, density of both lianas, palms and trees, tree species richness and height--sharply contrasted between forests and cashew orchards. As expected, mammal species composition differed between forests and cashew orchards, and the estimated, but not the observed, species richness declined towards cashew-like habitats. Although overall mammal abundance remained unaffected by the variables considered, carnivores were more abundant in cashew-like habitats, whereas insectivores and herbivores were more abundant in forest-like habitats. Human activity and distance to forest did not affect the response variables considered. Forest conversion into cashew orchards negatively affects mammals by profoundly changing the local habitat structure. Guild-level responses further unveiled specificity in their vulnerability to this form of land-use change, alerting for a potential disruption in the ecosystem functioning. We emphasize the need for policies that limit monoculture expansion, while safeguarding the remaining forests, thus maximising biodiversity persistence across the Afrotropics.

ecology↗

bioRxiv2024

Bacillus toyonensis biovar Thuringiensis: an overlooked entomopathogen?

Horizontal gene transfer (HGT) significantly influences prokaryotic genome evolution. Bacillus cereus and Bacillus thuringiensis are nearly identical at the chromosomal level, except for B. thuringiensis producing parasporal crystals. The genes for these crystal proteins (e.g., cry1A), along with other encoded insecticidal proteins (e.g., vip3A), are located on megaplasmids and can be horizontally transferred. Recently, Sauka et al. (2022) reported a Bacillus toyonensis strain that produces parasporal crystals with dual insecticidal activity. This strain was classified as Bacillus toyonensis biovar Thuringiensis (NCBI: txid2923195) following Carroll et al.s (2020) nomenclature. Misclassified B. toyonensis strains, previously identified as B. thuringiensis (e.g., strain MC28), encode cry and cyt genes toxic to lepidopteran and dipteran insects. Advances in genome sequencing and bioinformatics tools now reduce misidentifications, enabling accurate reclassification in databases like GenBank. These findings highlight the need for genome-based taxonomic reassessment within the Bacillus cereus group and clarify the chromosomal placement of crystal-forming B. toyonensis strains.

evolutionary biology↗

bioRxiv2022

Adult Hox gene expression promotes periosteal stem cell maintenance and mediates reprogramming in a regionally restricted manner

Periosteal stem and progenitor cells are pivotal to the growth and lifelong turnover of bone and underpin its capacity to regenerate. Adjusting the potency of this cell population will therefore be critical to the successful generation and application of new bone repair therapies. Following their role in patterning the embryonic skeleton, Hox genes remain regionally expressed in mesenchymal stromal cell populations of the adult skeleton. Here we show that Hoxa10 is most expressed in the most uncommitted periosteal stem cell and that Hox maintains these skeletal stem cells in a multipotential, uncommitted state, thereby preventing their differentiation into bone. We demonstrate that Hoxa10 mediates the reprogramming of periosteal progenitors towards a stem cell state with greater self-renewal capacity and also establish that region-specific Hox genes mediate cell reprogramming in distinct anatomical regions, demonstrating the continued functional relevance of the embryonic Hox profile in adult stem cells. Together, our data describe a master regulator role of Hox in skeletal stem and progenitor cells and help provide insight into the development of cell-based therapies for treatment of at-risk bone fractures and other bone-related ailments.

molecular biology↗

bioRxiv2021

Cysteine induces mitochondrial reductive stress in glioblastoma through hydrogen peroxide production

Glucose and amino acid metabolism are critical for glioblastoma (GBM) growth, but little is known about the specific metabolic alterations in GBM that are targetable with FDA-approved compounds. To investigate tumor metabolism signatures unique to GBM, we interrogated The Cancer Genome Atlas for alterations in glucose and amino acid signatures in GBM relative to other human cancers and found that GBM exhibits the highest levels of cysteine and methionine pathway gene expression of 32 human cancers. Treatment of patient-derived GBM cells with the FDA-approved cysteine compound N-acetylcysteine (NAC) reduce GBM cell growth and mitochondrial oxygen consumption, which was worsened by glucose starvation. Mechanistic experiments revealed that cysteine compounds induce rapid mitochondrial H2O2 production and reductive stress in GBM cells, an effect blocked by oxidized glutathione, thioredoxin, and redox enzyme overexpression. These findings indicate that GBM is uniquely susceptible to NAC-driven reductive stress and could synergize with glucose-lowering treatments for GBM.

cancer biology↗