Pub Date : 2025-12-01Epub Date: 2025-08-30DOI: 10.1016/j.egg.2025.100400
Md Imran Khan , Abdur Rahman Al Akil
Acinetobacter venetianus is a gram-negative, aerobic, and non-motile bacterium commonly found in marine and oil-contaminated environments due to its ability to degrade hydrocarbons. The studied Acinetobacter venetianus JKSF06 strain was originally isolated from sediment collected in La Porte, Texas, near the southern terminus of the Houston Ship Channel, into the Gulf of Mexico. The genome of JKSF06 spans 3,462,857 bp and encodes 3232 protein-coding sequences. ResFinder (v4.6.0) identified a β-lactamase-encoding antimicrobial resistance gene, blaOXA-266, while RGI (v6.0.3) detected four antimicrobial resistance genes, including adeF (RND-type efflux pump) and blaOXA-266, both sharing >90 % sequence similarity. Furthermore, a heavy metal resistance system, czcCBA system (Cobalt-Zinc-Cadmium) was identified in the JKSF06 strain, which may indicate its adaptability in sediment environments. Notably, it also showed 100 % similarity with the Baumannoferrin AB-producing NI-siderophore type biosynthetic gene cluster. Additionally, two intact bacteriophages from the Caudoviricetes class were identified in its genome, indicating possible horizontal gene transfer. Phylogenetic analysis demonstrated a close evolutionary relationship between A. venetianus JKSF06 and other sediment-derived isolates, suggesting a potential common ancestry and adaptation to sediment environments.
{"title":"Genome analysis of Acinetobacter venetianus JKSF06 strain providing insight into evolutionary features and adaptative potential in marine sediment environment","authors":"Md Imran Khan , Abdur Rahman Al Akil","doi":"10.1016/j.egg.2025.100400","DOIUrl":"10.1016/j.egg.2025.100400","url":null,"abstract":"<div><div><em>Acinetobacter venetianus</em> is a gram-negative, aerobic, and non-motile bacterium commonly found in marine and oil-contaminated environments due to its ability to degrade hydrocarbons. The studied <em>Acinetobacter venetianus</em> JKSF06 strain was originally isolated from sediment collected in La Porte, Texas, near the southern terminus of the Houston Ship Channel, into the Gulf of Mexico. The genome of JKSF06 spans 3,462,857 bp and encodes 3232 protein-coding sequences. ResFinder (v4.6.0) identified a β-lactamase-encoding antimicrobial resistance gene, <em>blaOXA-266</em>, while RGI (v6.0.3) detected four antimicrobial resistance genes, including <em>adeF</em> (RND-type efflux pump) and <em>blaOXA-266</em>, both sharing >90 % sequence similarity. Furthermore, a heavy metal resistance system, czcCBA system (Cobalt-Zinc-Cadmium) was identified in the JKSF06 strain, which may indicate its adaptability in sediment environments. Notably, it also showed 100 % similarity with the Baumannoferrin AB-producing NI-siderophore type biosynthetic gene cluster. Additionally, two intact bacteriophages from the Caudoviricetes class were identified in its genome, indicating possible horizontal gene transfer. Phylogenetic analysis demonstrated a close evolutionary relationship between <em>A. venetianus</em> JKSF06 and other sediment-derived isolates, suggesting a potential common ancestry and adaptation to sediment environments.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100400"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144926256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The soil is one of the most important components of Earth and provides the greatest nutrient reservoir to support the diverse groups of microbes due to its heterogeneous nature. Often, pedigree shifts of microbial communities are seen in soil samples due to the influence of biotic and abiotic factors. Apart from the soil, organic matter is the main driver of acquiring new traits as well as physiological adaptability in microbes. Therefore, it encourages us to make a clear understanding of microbes and their functions from diverse habitats of soil. As is well known, the inhabiting microbes play a crucial role in biogeochemical cycles, plant growth promotion (PGP), bioremediation, and several other interactions. However, we have limited knowledge about the hidden microbial potential that is continuously at work inside the soil system, due to a lack of precise methods for total microbe identification and functional annotation. Omics approaches alone are insufficient to reveal real-time functional information due to several limitations. However, due to the emergence of meta-omics approaches, it is now possible to unlock the complete functioning of soil. In contrast, we can explore multiple facts at a time by minimizing barriers associated with molecular soil microbiology. So far, critical analysis of soil microbes has yielded unique findings, as well as insights into microbial strength, inter- and intra-dependent mechanisms, pathways, and novel biomolecules with industrial applications. This review can provide valuable insights into soil microbial functioning and challenges.
{"title":"Soil meta-omics: Current status, challenges, and applications","authors":"Vivek Kumar , Durgesh Kumar Jaiswal , Pramod Kumar Sahu , Rajan Chaurasia , Shraddha Kasoundhan , Ayushi Patel , Digvijay Verma","doi":"10.1016/j.egg.2025.100411","DOIUrl":"10.1016/j.egg.2025.100411","url":null,"abstract":"<div><div>The soil is one of the most important components of Earth and provides the greatest nutrient reservoir to support the diverse groups of microbes due to its heterogeneous nature. Often, pedigree shifts of microbial communities are seen in soil samples due to the influence of biotic and abiotic factors. Apart from the soil, organic matter is the main driver of acquiring new traits as well as physiological adaptability in microbes. Therefore, it encourages us to make a clear understanding of microbes and their functions from diverse habitats of soil. As is well known, the inhabiting microbes play a crucial role in biogeochemical cycles, plant growth promotion (PGP), bioremediation, and several other interactions. However, we have limited knowledge about the hidden microbial potential that is continuously at work inside the soil system, due to a lack of precise methods for total microbe identification and functional annotation. Omics approaches alone are insufficient to reveal real-time functional information due to several limitations. However, due to the emergence of meta-omics approaches, it is now possible to unlock the complete functioning of soil. In contrast, we can explore multiple facts at a time by minimizing barriers associated with molecular soil microbiology. So far, critical analysis of soil microbes has yielded unique findings, as well as insights into microbial strength, inter- and intra-dependent mechanisms, pathways, and novel biomolecules with industrial applications. This review can provide valuable insights into soil microbial functioning and challenges.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100411"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145266104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lake Chitu and Shala, two Ethiopian soda lakes, are polyextreme environments characterized by high salinity and alkalinity. These conditions support diverse haloalkaliphilic microbial communities that regulate critical biogeochemical cycles. However, their MicroTrait bioelement profiles remain poorly characterized. In this study, shotgun metagenomic sequencing was employed to investigate taxonomic composition and bioelement-associated functional genes derived from MicroTrait analysis in Lakes Chitu and Shala, providing insights into microbial contributions to biogeochemical cycling. Environmental samples were collected, and DNA was extracted and sequenced to generate comprehensive metagenomic datasets. Taxonomic annotation revealed substantial phylogenetic diversity in both lakes. Bacteria dominated the communities (89 % in Chitu, 92 % in Shala), with Archaea present in lower abundances (4 % in Chitu, 0.8 % in Shala), alongside minor fractions of eukaryotes and viruses. The presence of unclassified and unassigned clades suggests potentially novel microbial lineages. Dominant bacterial phyla included Pseudomonadota, Actinomycetota, and Gemmatimonadota, while Euryarchaeota and Nitrososphaerota were the main archaeal groups. MicroTrait-based comparative metagenomic profiling usingAnnotated-Metagenome-Assemblies (AMAs)revealed both shared and distinct elemental cycling potentials in microbial communities from Lake Chitu and Shala. While Chitu exhibited higher gene hits for nitrogen, carbon fixation, and methane metabolism, Shala showed greater functional capacity in oxygen respiration, sulfur oxidation, C1metabolism, and trace element detoxification, highlighting ecosystem-specific biogeochemical specializations. These findings reveal distinct MicroTrait bioelement gene abundance profiles, uncovering metabolic strategies and genetic potential in these extreme ecosystems. This underscores the importance of linking microbial diversity to functional traits and highlights potential biotechnological applications.
{"title":"Metagenomic profiling reveals microbial diversity and MicroTrait bioelement signatures in Ethiopian soda lakes","authors":"Gessesse Kebede Bekele , Ebrahim M. Abda , Abu Feyisa Meka , Ermias Sissay Balcha , Zuriash Mamo Nademo , Fassil Assefa Tuji , Mesfin Tafesse Gemeda","doi":"10.1016/j.egg.2025.100403","DOIUrl":"10.1016/j.egg.2025.100403","url":null,"abstract":"<div><div><em>Lake Chitu and Shala, two Ethiopian soda lakes, are polyextreme environments characterized by high salinity and alkalinity. These conditions</em> support <em>diverse haloalkaliphilic microbial communities that regulate critical biogeochemical cycles. However, their MicroTrait bioelement profiles remain poorly characterized. In this study, shotgun metagenomic sequencing was employed to investigate taxonomic composition and bioelement-associated functional genes derived from MicroTrait analysis in Lakes Chitu and Shala, providing insights into microbial contributions to biogeochemical cycling. Environmental samples were collected, and DNA was extracted and sequenced to generate comprehensive metagenomic datasets. Taxonomic annotation revealed substantial phylogenetic diversity in both lakes. Bacteria dominated the communities (89 % in Chitu, 92 % in Shala), with Archaea present in lower abundances (4 % in Chitu, 0.8 % in Shala), alongside minor fractions of eukaryotes and viruses. The presence of unclassified and unassigned clades suggests potentially novel microbial lineages. Dominant bacterial phyla included Pseudomonadota, Actinomycetota, and Gemmatimonadota, while Euryarchaeota and Nitrososphaerota were the main archaeal groups. MicroTrait-based comparative metagenomic profiling using</em> <em>Annotated-Metagenome-Assemblies (AMAs)</em> <em>revealed both shared and distinct elemental cycling potentials in microbial communities from Lake Chitu and Shala. While Chitu exhibited higher gene hits for nitrogen, carbon fixation, and methane metabolism, Shala showed greater functional capacity in oxygen respiration, sulfur oxidation, C</em><sub><em>1</em></sub> <em>metabolism, and trace element detoxification, highlighting ecosystem-specific biogeochemical specializations</em>. <em>These findings reveal distinct MicroTrait bioelement gene abundance profiles, uncovering metabolic strategies and genetic potential in these extreme ecosystems. This underscores the importance of linking microbial diversity to functional traits and highlights potential biotechnological applications.</em></div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100403"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145010777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plastic pollution, particularly in the form of microplastics, has emerged as one of the most pressing global environmental challenges due to the persistence and accumulation of synthetic polymers in terrestrial and aquatic ecosystems. Recent studies highlight the remarkable ability of superworms (Zophobas atratus) to consume and degrade various plastics, a process largely facilitated by their gut microbiota. This review synthesizes current knowledge on the diversity and enzymatic functions of gut microorganisms, such as Pseudomonas, Enterobacter, Citrobacter, and Enterococcus, which play pivotal roles in the oxidative and hydrolytic breakdown of polystyrene, polyethylene, polypropylene, and other polymers. Enzymes including oxygenases, dehydrogenases, and alkane hydroxylases enable the conversion of complex polymers into smaller monomers and organic acids, thereby reducing the formation of secondary microplastics. Beyond environmental benefits, by-products such as frass and larval biomass present opportunities for integration into a circular bio-economy as fertilizer or feed ingredients. Nevertheless, challenges remain regarding enzyme stability, the sustainability of microbial consortia, and potential risks associated with plastic additives. This review provides novel insights by emphasizing gut microbiota-mediated mechanisms in superworms, distinguishing it from prior reviews that predominantly focused on larval feeding behavior. The implications extend to biotechnological innovations in bio-augmentation, synthetic microbial consortia, and bioreactor engineering, offering promising strategies for sustainable plastic waste management.
{"title":"Gut microbiota of superworm (Zophobas atratus) in plastic biodegradation: Implications for microplastic mitigation and circular bio-economy","authors":"Adi Sutanto , Iswahyudi Iswahyudi , Marchel Putra Garfansa , Siti Alfiatul Amani , Imbang Dwi Rahayu , Asmah Hidayati , Annisa Dwi Puspitarini , Sri Utami Lestari , Moh Subhan","doi":"10.1016/j.egg.2025.100425","DOIUrl":"10.1016/j.egg.2025.100425","url":null,"abstract":"<div><div>Plastic pollution, particularly in the form of microplastics, has emerged as one of the most pressing global environmental challenges due to the persistence and accumulation of synthetic polymers in terrestrial and aquatic ecosystems. Recent studies highlight the remarkable ability of superworms (<em>Zophobas atratus</em>) to consume and degrade various plastics, a process largely facilitated by their gut microbiota. This review synthesizes current knowledge on the diversity and enzymatic functions of gut microorganisms, such as <em>Pseudomonas</em>, <em>Enterobacter</em>, <em>Citrobacter</em>, and <em>Enterococcus</em>, which play pivotal roles in the oxidative and hydrolytic breakdown of polystyrene, polyethylene, polypropylene, and other polymers. Enzymes including oxygenases, dehydrogenases, and alkane hydroxylases enable the conversion of complex polymers into smaller monomers and organic acids, thereby reducing the formation of secondary microplastics. Beyond environmental benefits, by-products such as frass and larval biomass present opportunities for integration into a circular bio-economy as fertilizer or feed ingredients. Nevertheless, challenges remain regarding enzyme stability, the sustainability of microbial consortia, and potential risks associated with plastic additives. This review provides novel insights by emphasizing gut microbiota-mediated mechanisms in superworms, distinguishing it from prior reviews that predominantly focused on larval feeding behavior. The implications extend to biotechnological innovations in bio-augmentation, synthetic microbial consortia, and bioreactor engineering, offering promising strategies for sustainable plastic waste management.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100425"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145614537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01Epub Date: 2025-09-26DOI: 10.1016/j.egg.2025.100408
Mandakini Kabi , Suvalaxmi Palei , Snehasish Routray , Islavath Suresh Naik , Mahipal Singh Kesawat , Vidadala Rajendra , Rajneesh Kumar , Mehdi Rahimi
Crop improvement requires precise modification of genotypes to enhance their usefulness for human need that encompasses a broad range of techniques. It started with conventional plant breeding techniques like domestication, selection, hybridization breeding, mutation breeding, and passes through molecular breeding. These techniques have pros and cons in terms of their procedure, application, and outcome. Therefore, efficient desirable manipulation of genotypes can achieve through genome editing techniques that includes inactivation of target gene, replacement or addition of new gene with new function to the genome. In the recent past, emergence of new approach of genome editing enables researcher to manipulate gene. It uses artificial nucleases to modify genome rapidly which allow reverse genetics, genome engineering and targeted transgene integration in to one experiment in an efficient, precise and predictable manner. Tools used for genome editing are, programmable sequence specific nucleases which includes Mega nucleases, ZFN, TALEN and CRISPR-cas9 and base editor. Use of this genome editing tools to get desirable characters has been reported in many crops. This review paper has elaborately focused on genome editing tools and desirable modification of characters for crop improvements.
{"title":"Engineering crop genomes: A review of editing tool evolution, applications, and future trajectories","authors":"Mandakini Kabi , Suvalaxmi Palei , Snehasish Routray , Islavath Suresh Naik , Mahipal Singh Kesawat , Vidadala Rajendra , Rajneesh Kumar , Mehdi Rahimi","doi":"10.1016/j.egg.2025.100408","DOIUrl":"10.1016/j.egg.2025.100408","url":null,"abstract":"<div><div>Crop improvement requires precise modification of genotypes to enhance their usefulness for human need that encompasses a broad range of techniques. It started with conventional plant breeding techniques like domestication, selection, hybridization breeding, mutation breeding, and passes through molecular breeding. These techniques have pros and cons in terms of their procedure, application, and outcome. Therefore, efficient desirable manipulation of genotypes can achieve through genome editing techniques that includes inactivation of target gene, replacement or addition of new gene with new function to the genome. In the recent past, emergence of new approach of genome editing enables researcher to manipulate gene. It uses artificial nucleases to modify genome rapidly which allow reverse genetics, genome engineering and targeted transgene integration in to one experiment in an efficient, precise and predictable manner. Tools used for genome editing are, programmable sequence specific nucleases which includes Mega nucleases, ZFN, TALEN and CRISPR-cas9 and base editor. Use of this genome editing tools to get desirable characters has been reported in many crops. This review paper has elaborately focused on genome editing tools and desirable modification of characters for crop improvements.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100408"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145220613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01Epub Date: 2025-10-06DOI: 10.1016/j.egg.2025.100414
Achmad Zamroni, Muhammad Taufik, Tri Ernawati, Erfind Nurdin, Pratiwi Lestari, Moh Fauzi
This study investigates the genetic architecture and demographic history of two commercial snapper species, Lutjanus erythropterus and Pinjalo pinjalo, in Indonesian waters to fill a knowledge gap regarding the evolutionary responses of co-distributed species within a complex marine landscape. By analyzing 450 base pairs of mitochondrial DNA control region (D-loop) sequences from 29 L. erythropterus and 26 P. pinjalo samples from five locations, this study reveals starkly different genetic patterns. The results show that L. erythropterus possesses very high genetic diversity (Hd = 0.98030; π = 0.01817) and exhibits no significant population structure (Φst = 0.00777; P > 0.05), consistent with a model of a single panmictic population that has undergone a past demographic expansion. Conversely, P. pinjalo exhibits substantially lower genetic diversity (Hd = 0,52615; π = 0,01068) and no signal of expansion, indicating a stable long-term demographic history and potential complex population dynamics. These findings conclude that these two sympatric species exhibit fundamentally different evolutionary trajectories, likely mediated by intrinsic biological differences in responding to the same historical environmental changes. The implications of these findings are highly significant for fisheries management, rejecting a "one-size-fits-all" approach and underscoring the urgent need to develop species-specific management strategies to ensure the sustainability of vital fishery resources in Indonesia.
{"title":"Divergent genetic diversity reveals contrasting demographic histories in two commercially important snappers","authors":"Achmad Zamroni, Muhammad Taufik, Tri Ernawati, Erfind Nurdin, Pratiwi Lestari, Moh Fauzi","doi":"10.1016/j.egg.2025.100414","DOIUrl":"10.1016/j.egg.2025.100414","url":null,"abstract":"<div><div>This study investigates the genetic architecture and demographic history of two commercial snapper species, <em>Lutjanus erythropterus</em> and <em>Pinjalo pinjalo</em>, in Indonesian waters to fill a knowledge gap regarding the evolutionary responses of co-distributed species within a complex marine landscape. By analyzing 450 base pairs of mitochondrial DNA control region (D-loop) sequences from 29 <em>L. erythropterus</em> and 26 <em>P. pinjalo</em> samples from five locations, this study reveals starkly different genetic patterns. The results show that <em>L. erythropterus</em> possesses very high genetic diversity (Hd = 0.98030; π = 0.01817) and exhibits no significant population structure (Φst = 0.00777; P > 0.05), consistent with a model of a single panmictic population that has undergone a past demographic expansion. Conversely, <em>P. pinjalo</em> exhibits substantially lower genetic diversity (Hd = 0,52615; π = 0,01068) and no signal of expansion, indicating a stable long-term demographic history and potential complex population dynamics. These findings conclude that these two sympatric species exhibit fundamentally different evolutionary trajectories, likely mediated by intrinsic biological differences in responding to the same historical environmental changes. The implications of these findings are highly significant for fisheries management, rejecting a \"one-size-fits-all\" approach and underscoring the urgent need to develop species-specific management strategies to ensure the sustainability of vital fishery resources in Indonesia.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100414"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145266103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01Epub Date: 2025-09-03DOI: 10.1016/j.egg.2025.100402
Christopher Alphonce Mduda , Faraja Samwel Makwinja , Juma Mahmud Hussein
Accurate taxonomic identification of stingless bees is critical for their conservation and sustainable management, yet morphological methods are often limited by species complexity and lack of expertise. This study employed DNA barcoding targeting a 650 bp fragment of the mitochondrial cytochrome oxidase I (COI) gene to identify stingless bee specimens collected from 19 locations across mainland Tanzania. A total of 28 specimens from wild colonies were analyzed, yielding reliable species-level identification (>97 % similarity to reference sequences in the BOLD database) for 53.6 % of the samples. Identified species included Plebeina armata, Hypotrigona gribodoi, Axestotrigona ferruginea, and Dactylurina schmidti. Specimens with barcode similarity between 95 and 97 % were assigned to the genus Axestotrigona, with their taxonomic status remaining unresolved. Despite reliable identification, we observed significant morphological diversity among P. armata and H. gribodoi specimens, with average within-group genetic distances of 3.5 and 4.1 %, respectively. Phylogenetic analysis corroborated these identifications and revealed potential cryptic speciation and genetic structuring consistent with geographical locations. The findings underscore the utility of DNA barcoding to complement traditional taxonomic approaches, and highlight the underexplored diversity of Afrotropical stingless bees. Further molecular and morphological studies are recommended to clarify species boundaries within the genus Axestotrigona, resolve taxonomic discrepancies in Afrotropical stingless bees, and improve regional biodiversity assessments.
{"title":"Taxonomic identification of stingless bees (Hymenoptera: Apidae: Meliponini) from selected locations of Tanzania using DNA barcoding","authors":"Christopher Alphonce Mduda , Faraja Samwel Makwinja , Juma Mahmud Hussein","doi":"10.1016/j.egg.2025.100402","DOIUrl":"10.1016/j.egg.2025.100402","url":null,"abstract":"<div><div>Accurate taxonomic identification of stingless bees is critical for their conservation and sustainable management, yet morphological methods are often limited by species complexity and lack of expertise. This study employed DNA barcoding targeting a 650 bp fragment of the mitochondrial cytochrome oxidase I (COI) gene to identify stingless bee specimens collected from 19 locations across mainland Tanzania. A total of 28 specimens from wild colonies were analyzed, yielding reliable species-level identification (>97 % similarity to reference sequences in the BOLD database) for 53.6 % of the samples. Identified species included <em>Plebeina armata</em>, <em>Hypotrigona gribodoi</em>, <em>Axestotrigona ferruginea</em>, and <em>Dactylurina schmidti</em>. Specimens with barcode similarity between 95 and 97 % were assigned to the genus <em>Axestotrigona</em>, with their taxonomic status remaining unresolved. Despite reliable identification, we observed significant morphological diversity among <em>P. armata</em> and <em>H. gribodoi</em> specimens, with average within-group genetic distances of 3.5 and 4.1 %, respectively. Phylogenetic analysis corroborated these identifications and revealed potential cryptic speciation and genetic structuring consistent with geographical locations. The findings underscore the utility of DNA barcoding to complement traditional taxonomic approaches, and highlight the underexplored diversity of Afrotropical stingless bees. Further molecular and morphological studies are recommended to clarify species boundaries within the genus <em>Axestotrigona</em>, resolve taxonomic discrepancies in Afrotropical stingless bees, and improve regional biodiversity assessments.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100402"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145010776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Drought is a significant environmental challenge that restricts crop growth and development. Aegilops tauschii, the source of the DD genome (2n = 2x = 14), is an important genetic resource for enhancing drought tolerance in wheat. This study investigated 15 native ecotypes of Ae. tauschii under three levels of water availability: non-stress (100 % field capacity), moderate stress (60 % FC), and severe stress (30 % FC). We evaluated various traits, including shoot dry weight (SDW), tiller number (TN), plant length (PL), dry root weight (DRW), and root volume (RV), along with activities of peroxidase (POD) and polyphenol oxidase (PPO) to assess drought tolerance. Significant variability in drought responses was observed; growth metrics declined under water stress, especially during severe conditions. POD and PPO activities increased notably during drought, indicating differences between control and stressed plants. Based on Membership Function Value (MFV), the ecotype E6 showed the highest drought tolerance (MFV >0.83), and E8 placed in second order (MFV >0.70), while E1, E3, and E12 were the most drought-sensitive (MFV <0.30). Other ecotypes exhibited moderate to varying levels of tolerance. Based on the heatmap and cluster analysis, the 15 Ae. tauschii ecotypes were grouped into four main clusters according to their responses to drought stress. These results highlight E6 and E8 as promising candidates for improving drought tolerance in wheat, due to their stable growth, high antioxidant enzyme activity, and consistent ranking across both MFV and clustering analyses.
{"title":"Growth and antioxidant enzymes responses of Aegilops tauschii ecotypes to drought stress: Identifying tolerant genotypes","authors":"Elnaz Nozari , Rasool Asghari-Zakaria , Nasser Zare , Parisa Sheikhzadeh","doi":"10.1016/j.egg.2025.100405","DOIUrl":"10.1016/j.egg.2025.100405","url":null,"abstract":"<div><div>Drought is a significant environmental challenge that restricts crop growth and development. <em>Aegilops tauschii</em>, the source of the DD genome (2<em>n</em> = 2<em>x</em> = 14), is an important genetic resource for enhancing drought tolerance in wheat. This study investigated 15 native ecotypes of <em>Ae. tauschii</em> under three levels of water availability: non-stress (100 % field capacity), moderate stress (60 % FC), and severe stress (30 % FC). We evaluated various traits, including shoot dry weight (SDW), tiller number (TN), plant length (PL), dry root weight (DRW), and root volume (RV), along with activities of peroxidase (POD) and polyphenol oxidase (PPO) to assess drought tolerance. Significant variability in drought responses was observed; growth metrics declined under water stress, especially during severe conditions. POD and PPO activities increased notably during drought, indicating differences between control and stressed plants. Based on Membership Function Value (MFV), the ecotype E6 showed the highest drought tolerance (MFV >0.83), and E8 placed in second order (MFV >0.70), while E1, E3, and E12 were the most drought-sensitive (MFV <0.30). Other ecotypes exhibited moderate to varying levels of tolerance. Based on the heatmap and cluster analysis, the 15 <em>Ae. tauschii</em> ecotypes were grouped into four main clusters according to their responses to drought stress. These results highlight E6 and E8 as promising candidates for improving drought tolerance in wheat, due to their stable growth, high antioxidant enzyme activity, and consistent ranking across both MFV and clustering analyses.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100405"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145010778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Halophilic bacteria thrive in environments with high concentrations of sodium chloride, such as salt mines, solar salterns, and hypersaline lakes. They survive extreme salinity by balancing osmotic pressure, preventing cellular damage. Extreme halophiles require up to 30 % salt for growth and structural integrity, making their proteins uniquely stable and functional in high-salt conditions. Understanding the molecular mechanisms behind halophilic protein stability is crucial for biotechnology. Investigating halotolerant proteins can lead to novel industrial applications, including enzymes for food processing, bioremediation, and pharmaceuticals. Proteomics, the large-scale study of proteins, helps characterize the proteomes of halophilic bacteria. Recent advancements in proteomic techniques allow deeper insights into protein structure, function, and adaptation in hypersaline environments. Modern methods, such as mass spectrometry and two-dimensional gel electrophoresis, facilitate the identification and analysis of halophilic proteins. This review explores advanced proteomic tools for studying halophilic bacteria, shedding light on protein stability, molecular mechanisms, and biotechnological potential. Understanding these proteins paves the way for innovations in enzyme engineering, industrial biotechnology, and synthetic biology. By leveraging cutting-edge proteomics, researchers can unlock new applications for halophilic proteins across industries, enhancing sustainability and efficiency in extreme environments.
{"title":"Advanced proteomic approaches for characterizing halophilic bacteria: Insights into protein stability and industrial applications","authors":"Pavithran Kumar , Pasiyappazham Ramasamy , Manjunathan Jagadeesan","doi":"10.1016/j.egg.2025.100431","DOIUrl":"10.1016/j.egg.2025.100431","url":null,"abstract":"<div><div>Halophilic bacteria thrive in environments with high concentrations of sodium chloride, such as salt mines, solar salterns, and hypersaline lakes. They survive extreme salinity by balancing osmotic pressure, preventing cellular damage. Extreme halophiles require up to 30 % salt for growth and structural integrity, making their proteins uniquely stable and functional in high-salt conditions. Understanding the molecular mechanisms behind halophilic protein stability is crucial for biotechnology. Investigating halotolerant proteins can lead to novel industrial applications, including enzymes for food processing, bioremediation, and pharmaceuticals. Proteomics, the large-scale study of proteins, helps characterize the proteomes of halophilic bacteria. Recent advancements in proteomic techniques allow deeper insights into protein structure, function, and adaptation in hypersaline environments. Modern methods, such as mass spectrometry and two-dimensional gel electrophoresis, facilitate the identification and analysis of halophilic proteins. This review explores advanced proteomic tools for studying halophilic bacteria, shedding light on protein stability, molecular mechanisms, and biotechnological potential. Understanding these proteins paves the way for innovations in enzyme engineering, industrial biotechnology, and synthetic biology. By leveraging cutting-edge proteomics, researchers can unlock new applications for halophilic proteins across industries, enhancing sustainability and efficiency in extreme environments.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100431"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145614390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lentil, one of the most important legume crops, is well known for its high nutritional and economic values. Ethiopia fails to meet its domestic lentil demand, although it is one of the centers of lentil diversity. Thus, understanding the existing genetic diversity of lentil accessions is essential to develop effective breeding programs. There is dearth of information on the genetic diversity of landrace and released varieties in Ethiopia using SSR markers. Therefore, the genetic diversity of 130 lentil accessions was assessed using 12 simple sequence repeat (SSR) markers. A total of 57 alleles with overall average of 4.75 alleles per locus were detected. The results revealed the existence of considerable genetic variation within and among lentil populations with an overall mean value of 0.49 gene diversity (h) and the highest (0.51) polymorphic information content (PIC). The resolving power of markers, PIC, indicated that all markers used in this study were highly informative, with average values of 0.40. SSR 317–2 and SSR 28 were the most informative loci with the highest (0.51) PIC value. Analysis of molecular variance revealed moderate genetic variation of within (95 %) and among (5 %) populations. The principal coordinate analysis showed the overall variation of 53.67 % and grouped the populations into three clusters. The UPGMA, neighbor-joining tree, and STRUCTURE analysis grouped the populations into four clusters. The population structure revelated that the lentil populations under the study were shared alleles from 4 subgroups (K = 4), showing higher genetic admixture. The overall genetic variations within landrace populations were larger than released variety and ICARDA populations. In this study, significant genetic variations across lentil populations which can serve as a starting point for upcoming breeding initiatives have been obtained.
{"title":"Genetic diversity analysis and population structure of Ethiopian lentil (Lens culinaris Medik.) using SSR markers","authors":"Shiferaw Teshome , Alemneh Mideksa , Tsegaye Getahun , Tileye Feyissa , Demsachew Guadie","doi":"10.1016/j.egg.2025.100430","DOIUrl":"10.1016/j.egg.2025.100430","url":null,"abstract":"<div><div>Lentil, one of the most important legume crops, is well known for its high nutritional and economic values. Ethiopia fails to meet its domestic lentil demand, although it is one of the centers of lentil diversity. Thus, understanding the existing genetic diversity of lentil accessions is essential to develop effective breeding programs. There is dearth of information on the genetic diversity of landrace and released varieties in Ethiopia using SSR markers. Therefore, the genetic diversity of 130 lentil accessions was assessed using 12 simple sequence repeat (SSR) markers. A total of 57 alleles with overall average of 4.75 alleles per locus were detected. The results revealed the existence of considerable genetic variation within and among lentil populations with an overall mean value of 0.49 gene diversity (h) and the highest (0.51) polymorphic information content (PIC). The resolving power of markers, PIC, indicated that all markers used in this study were highly informative, with average values of 0.40. SSR 317–2 and SSR 28 were the most informative loci with the highest (0.51) PIC value. Analysis of molecular variance revealed moderate genetic variation of within (95 %) and among (5 %) populations. The principal coordinate analysis showed the overall variation of 53.67 % and grouped the populations into three clusters. The UPGMA, neighbor-joining tree, and STRUCTURE analysis grouped the populations into four clusters. The population structure revelated that the lentil populations under the study were shared alleles from 4 subgroups (K = 4), showing higher genetic admixture. The overall genetic variations within landrace populations were larger than released variety and ICARDA populations. In this study, significant genetic variations across lentil populations which can serve as a starting point for upcoming breeding initiatives have been obtained.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100430"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145614538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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