Taxonomic Identification Research Articles

Isolation, Selection, and Identification of Keratinolytic Bacteria for Green Management of Keratin Waste.

The volume of difficult-to-process keratin waste is increasing as a result of rising global meat production. If not properly managed, this waste can contribute to environmental pollution and pose a threat to human and animal welfare. An interesting and more sustainable alternative is therefore the bioconversion of keratin using microorganisms and their enzymes. This work aimed to isolate bacteria from soil samples and zoonotic keratins and to evaluate their enzymatic capacity to degrade α- and β-keratin wastes. A total of 113 bacterial strains were isolated from environmental samples and subjected to taxonomic identification using the MALDI-TOF MS technique and to a two-step screening for proteolytic and keratinolytic activity. The ability to degrade a β-rich keratin substrate was observed in almost all of the strains isolated from soil and horsehairs. In contrast, when an α-rich keratin substrate was used, the highest levels of hydrolysis were observed only for Ker39, Ker66, Ker85, Ker100, and Ker101. Strains with the highest biodegradation potential were identified using molecular biology methods. Phylogenetic analysis of 16S rDNA gene sequences allowed the assignment of selected keratinolytic microorganisms to the genera Exiguobacterium, Priestia, Curtobacterium, Stenotrophomonas, Bacillus, Kocuria, or Pseudomonas. The results of this study are a promising precursor for the development of new, more sustainable methods of managing keratin waste to produce high-value hydrolysates.

AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides

BackgroundUsing next-generation sequencing technologies, scientists can sequence complex microbial communities directly from the environment. Significant insights into the structure, diversity, and ecology of microbial communities have resulted from the study of metagenomics. The assembly of reads into longer contigs, which are then binned into groups of contigs that correspond to different species in the metagenomic sample, is a crucial step in the analysis of metagenomics. It is necessary to organize these contigs into operational taxonomic units (OTUs) for further taxonomic profiling and functional analysis. For binning, which is synonymous with the clustering of OTUs, the tetra-nucleotide frequency (TNF) is typically utilized as a compositional feature for each OTU.ResultsIn this paper, we present AFIT, a new l-mer statistic vector for each contig, and AFITBin, a novel method for metagenomic binning based on AFIT and a matrix factorization method. To evaluate the performance of the AFIT vector, the t-SNE algorithm is used to compare species clustering based on AFIT and TNF information. In addition, the efficacy of AFITBin is demonstrated on both simulated and real datasets in comparison to state-of-the-art binning methods such as MetaBAT 2, MaxBin 2.0, CONCOT, MetaCon, SolidBin, BusyBee Web, and MetaBinner. To further analyze the performance of the purposed AFIT vector, we compare the barcodes of the AFIT vector and the TNF vector.ConclusionThe results demonstrate that AFITBin shows superior performance in taxonomic identification compared to existing methods, leveraging the AFIT vector for improved results in metagenomic binning. This approach holds promise for advancing the analysis of metagenomic data, providing more reliable insights into microbial community composition and function.AvailabilityA python package is available at: https://github.com/SayehSobhani/AFITBin.

Phylogenetic relationships and genetic diversity of the Korean endemic Phedimus latiovalifolius (Crassulaceae) and its close relatives

Phedimus latiovalifolius (Y.N.Lee) D.C.Son & H.J.Kim is exclusively distributed in the high mountains in the Korean Peninsula, mainly along the Baekdudaegan mountain range. Despite its morphological and distributional distinction from other Phedimus Raf. species, its taxonomic identity and phylogenetic relationship with congeneric species remain unclear. This study employs genotyping-by-sequencing-derived genome-wide single nucleotide polymorphisms to establish the monophyly of P. latiovalifolius and its relationship with closely related species. Genetic diversity and population differentiation of P. latiovalifolius are also assessed to provide baseline genetic information for future conservation and management strategies. Our phylogenetic analyses robustly demonstrate the monophyletic nature of P. latiovalifolius, with P. aizoon (L.) ‘t Hart identified as its closest sister lineage. There is no genetic evidence supporting a hybrid origin of P. latiovalifolius from P. aizoon involving either P. ellacombeanus (Praeger) ‘t Hart or P. kamtschaticus (Fisch.) ‘t Hart. Population genetic analyses reveal two major groups within P. latiovalifolius. A higher genetic variation is observed in P. ellacombeanus than in the congeneric species. Notably, most of the genetic variation exists within P. latiovalifolius populations. Given its distribution and the potential role of Baekdudaegan as an East Asian Pleistocene refugia, P. latiovalifolius could be considered rare and endemic, persisting in the refugium across glacial/interglacial cycles.

Cryptic Diversity of Barred Mudskippers, <i>Periophthalmus argentilineatus</i> (Valenciennes, 1837), from the Southern Coast of Java and East Lombok, Indonesia inferred by <i>COI</i> Mitochondrial Gene

The Barred Mudskipper (P. argentilineatus) is an amphibious fish species that displays fully terrestrial behaviour during low tides. Previous studies have indicated the existence of cryptic species of the barred mudskipper, leading to difficulties in taxonomic identification due to similarities in morphological characteristics. Therefore, this study aimed to generate DNA barcodes for Indonesian barred mudskipper populations. We collected ten specimens from Clungup Beach and Kondang Bandung Beach, representing our samples. Additionally, we incorporated 25 previously collected COI sequences from Indonesia into our analysis. The mitochondrial COI gene was amplified using PCR and analysed using various bioinformatics programs. This study provides evidence for the presence of three genetically distinct clades (A, B, and C) within the P. argentilineatus population in Indonesia, with a deep genetic divergence of 2.41% to 6.12%. Clade A showed a high genetic divergence of 5.51-6.12%, suggesting the presence of a cryptic species consistent with previous studies. The high level of haplotype diversity and low nucleotide diversity observed in each clade suggest a population bottleneck followed by a rapid expansion. The lack of geographical separation in the haplotype network analysis indicates that gene flow between populations may have been facilitated by glaciation events in the past. These findings contribute to a better understanding of the biodiversity of the barred mudskipper species in Indonesia and will aid in the accurate identification of cryptic species. This study highlights the importance of using molecular techniques to complement morphological identification in understanding the evolution and diversity of mudskipper fish species.

Combining traceological analysis and ZooMS on Early Neolithic bone artefacts from the cave of Coro Trasito, NE Iberian Peninsula: Cervidae used equally to Caprinae.

Few studies have combined the analysis of use-wear traces, traceology, and the proteomic taxonomic identification method Zooarchaeology by Mass Spectrometry (ZooMS). Traceology provides information on the usage, in this case, of bone artefacts, while ZooMS allows for taxonomic identifications where diagnostic features are otherwise gone. The approaches therefore offer complementary information on bone artefacts, allowing for insights into species selection strategies in bone tool manufacture and their subsequent use. Here we present a case study of 20 bone artefacts, mainly bone points, from the Early Neolithic cave site of Coro Trasito located on the southern slope of the Central Pyrenees. Hitherto, studies on Early Neolithic bone artefacts from the Iberian Peninsula have suggested based on morphological assessments that Ovis aries/Capra hircus constituted the majority of the bone material selected for bone tool production. However, the taxonomic identification in this study suggests that, at this site, Cervidae was selected equally to that of O. aries/C. hircus. Furthermore, bone artefacts made from Cervidae specimens seem to be utilised in a wider range of artefact types compared to O. aries/C. hircus. Coro Trasito's bone artefact species composition is probably site-specific to some degree, however, morphological assessments of bone artefacts might not be representative and could be biased towards certain species. Therefore, research on bone artefacts' usage could possibly gain new insights by implementing ZooMS in combination with traceology.

Genomic Insights into the Landfill Microbial Community: Denitrifying Activity Supporting One-Carbon Utilization.

In spite of the developments in understanding of denitrifying methylotrophy in the recent years, challenges still exist in unravelling the overall biochemistry of nitrate-dependent methane oxidation in novel or poorly characterized/not-yet-cultured bacteria. In the present study, landfill site was mined for novel C1-carbon-metabolizing bacteria which can use nitrate/nitrite as an electron acceptor. A high-throughput rapid plate assay identified three bacterial isolates with eminent ability for nitrate-dependent methane metabolism under anaerobic conditions. Taxonomic identification by whole-genome sequence-based overall genome relatedness indices accurately assigned the isolates AAK_M13, AAK_M29, and AAK_M39 at the species level to Enterobacter cloacae, Bacillus subtilis, and Bacillus halotolerans, respectively. Several genes encoding sub-components involved in alcohol utilization and denitrification pathways, such as adh, fdh, fdo, nar, nir, and nor, were identified in all the genomes. Though no gene clusters encoding MMO/AMO were annotated, sequencing of PCR amplicons revealed similarity with pMMO/AMO gene using translated nucleotide sequence of strains AAK_M29 and AAK_M39, while strain AAK_M13 showed similarity with XRE family transcriptional regulator. This suggests the horizontal gene transfer and/or presence of a truncated version of a housekeeping enzyme encoded by genes exhibiting partial sequence similarity with pMMO genes that mimicked its function at greenhouse gas emission sites. Owing to lack of conclusive evidence for presence of methane metabolism genes in the selected isolates, further experiment was performed to validate their nitrate-dependent methane oxidation capacities. Bacillus subtilis AAK_M29, Bacillus halotolerans AAK_M39, and Enterobacter cloacae AAK_M13 could oxidize 60%, 75%, and 85% of the added methane respectively accompanied by high nitrate reduction (56-62%) thus supporting the correlation between these two activities. The remarkable ability of these isolates for nitrate-dependent methane metabolism has highlighted their role in ecological contribution and biotechnological potential to serve as methane and nitrate sinks in the landfill sites.

Gambierdiscus carpenteri (Dinophyceae) from Bahía de La Paz, Gulf of California: morphology, genetic affinities, and mouse toxicity

Abstract Gambierdiscus is a marine benthic dinoflagellate genus that currently contains 19 species; some of them are toxigenic, producing ciguatoxins, maitotoxins, and other toxic compounds. The objective of this study was to document the morphological and molecular identification (ITS, 5.8S and 28S of the rDNA) of two strains of Gambierdiscus from La Gaviota Island, Gulf of California, Mexico, and a toxicity test. The shape of the 2′ plate varied between hatchet-shaped and rectangular, that complicated the differentiation between G. carpenteri and G. toxicus. Molecular markers of the three rDNA regions allowed confirmation of the taxonomic identity of G. carpenteri, separating this species from other congeners with high phylogenetic affinity, such as G. excentricus, G. toxicus and G. caribaeus. Studies of the morphological taxonomy of G. carpenteri are scarce; therefore, due to the similarity between species, the combination of morphological and molecular tools is recommended for the identification of species, such as G. carpenteri, G. excentricus, G. toxicus and G. caribaeus. The mouse bioassay showed that the examined isolate was toxic, and it is a potential etiology of ciguatera fish poisoning cases in the region. This study provides the first reliable report and ribosomal sequences of G. carpenteri for the Gulf of California, as well as data on mouse bioassay toxicity.

Cnida Morphology as Taxonomic Tools within Tube-Dwelling Anemones (Ceriantharia, Cnidaria)

Cnidome morphology appears to be a valuable tool for anthozoan (Octocarallia, Ceriantharia, and Hexacorallia) taxonomy. Ceriantharian cnidomes consist of b-mastigophores, isorhizas, spirocysts, and ptychocysts, including different subtypes. The b-mastigophores are the most valuable ceriantharian cnidae for species identification. The Ceriantharian b-mastigophore terminology is congruent to the b-mastigophores of Carlgren, b-rhabdoids, including the “faltstück” of Schmidt, spirulae, and also potentially the penicilli of den Hartog. The apical tightly folded, inverted b-mastigophore shafts, the “faltstück”, are important species-specific characteristics due to their various patterns. The mesenterial structures known as craspedonemes, cnidorages, and acontioids also have high taxonomic value. Drop-shaped b-mastigophores might be characteristic nematocysts for mesenteries. The occurrence of isorhizas and striations on the inner ptychocyst capsule walls are other species’ characteristics. The morphological similarities of spirulae and penicilli to b-mastigophores within Hexacorallia are highlighted by naming spirulae and penicilli as b-mastigophores/spirulae and b-mastigophores/penicilli subtypes, respectively. The slight morphological distinction between spirulae and penicilli will doubtfully justify the suborders Spirularia and Penicillaria. The spirocysts presence in Ceriantharia and Hexacorallia indicates a closer relationship between Ceriantharia and Hexacorallia than between Ceriantharia and Octocorallia. Octocorallia are the only anthozoans without spirocysts. This work underlines the importance of cnidome morphological analysis for taxonomic identification and classification.

Comparing Energetics and Physiological Trait Patterns of North American Birds to Support Ecological Risk Assessment

The environmental risk assessment (ERA) of plant protection products (PPPs) is commonly conducted for a number of standard laboratory species, though its scope includes all species, especially those that are vulnerable or endangered. This begs the question of how the eco-physiological and life history traits of those data-rich species compare to those of less documented species. This paper investigates the utility of a database of such traits, the Add-my-Pet collection of Dynamic Energy Budget theory, for the ERA of North American birds. We identified 72 bird species in the collection that have a federal listing status or are otherwise of interest for the ERA of PPPs and compared their eco-physiological and life history traits in relation to body size, feeding guild, and taxonomic identity to those of 446 terrestrial Holarctic birds, as well as those of standard lab species, notably the northern bobwhite, mallard, and zebra finch. The properties of standard lab species generally align with those of a similar taxonomy and size, with the notable exception of the relatively high reproductive capacity of the northern bobwhite and mallard due to the unique properties of laboratory study data. In addition, taxonomy appears to be a better predictor of eco-physiological traits than feeding guild. We conclude that, to identify representative species for the ERA of PPPs, more traits need to be included, such as those directly linked to the likelihood of exposure and those related to reproductive behavior.

Glucosinolates in non-Brassicales plant species: Critical literature evaluation and testing of two high chemical quality reports

Glucosinolates (GSLs) are secondary metabolites mainly found in the plant order Brassicales. We critically evaluate reports of GSLs in other orders of flowering plants, propose standards for future reports and subject two cases to rigorous testing. Reports of GSLs in non-Brassicales species should live up to state-of-the-art scientific standards concerning chemical evidence, botanical evidence and biological replication. Occurrence of GSLs in the family Putranjivaceae, order Malpighiales (genera Putranjiva and Drypetes) was reasonably supported, but state-of-the-art confirmation was required. Hence, the taxonomic identity of Putranjiva roxbughii seeds with the previously known GSL profile was confirmed using DNA-based methods. Similarly, good suggestive evidence exist from the family Violaceae, order Malpighiales, but in need of confirmation. No other report of any GSL in a non-Brassicales species meet the proposed scientific standards, but suggestive evidence exists for the family Phytolaccaceae, order Caryophyllales and to a lesser extent family Celastraceae, order Celastrales. A recent report of a GSL in a tropical plant suggested to be a species in the order Sapindales was subjected to a rigorous testing in terms of chemical analysis, biological replication and botanical identification including DNA sequencing. We confirmed the original report concerning chemical structure and reproducibility but revised the botanical identification to a species from the Brassicales order (family Capparidaceae). Hence this paper also reports myrosinase activity, isothiocyanate-type GSL products from roots and stems, and GSL profile of roots, stems, leaves and fruits of Capparis sepiaria L., dominated by Leu-derived 2-methylpropyl GSL in vegetative parts, Val-derived 1-methylethyl GSL and Ile-derived 1-methylpropyl GSL in fruits, and additionally Trp-derived indol-3-ylmethyl GSL and 4-hydroxyindol-3-ylmethyl GSL in immature fruits. Several other GSLs were searched for and conclusively not found above the limit of detection.

Agaricus karakensis sp. nov. (Agaricaceae, Agaricales), a new species from Pakistan

There are around 500 species of saprobic basidiomycetes in the genus Agaricus, of which 21 are reported from Pakistan. In this study, Agaricus karakensis sp. nov. is described as a new species from the tropical semi-arid District Karak, Khyber Pakhtunkhwa, Pakistan. The taxonomic identification was based on morphological features and ITS-region of rDNA. Both, field data and morpho-anatomical characterizations support that our specimens belong to a new species of Agaricus section Bivelares from family Agaricaceae, order Agaricales. In the phylogenetic tree, A. karakensis fall in section Bivelares forming a sister branch with A. bitorquis. In this paper, the nearest falling species were also compared with our novel finding in morphology.

New Technique for Identification of Ichthyoplankton and Its Application in Biomonitoring Studies, Management and Conservation of Neotropical Fish.

Despite significant advancements in ichthyoplankton collection and data processing, challenges persist in the taxonomic identification of these organisms, particularly their eggs. To overcome these challenges, a novel technique has been developed to facilitate the identification of live eggs collected directly in wild. This user-friendly technique includes the collection, processing of the material, and field incubation. Sampling must be conducted using a pelagic net towed at low speed, preferably during early evening. The material processing involves pre-sorting and sorting to remove eggs and larvae. The separated eggs, kept in an aerated bowl, can be identified based on their morphological and meristic characteristics. Unidentified eggs can be placed in plastic bags with oxygen and incubated directly in the aquatic environment for 48-72 h. After this incubation period, the hatched larvae at the yolk-sac or preflexion stage, are identified to the lowest possible taxonomic level. Depending on the study's purpose, hatched larvae and field-collected larvae can be transported to research centers for further development, released back into the natural environment, or fixed to complete the collection. The application of this technique supports management and monitoring programs by identifying spawning areas through egg identification, forming broodstock, and replenishing threatened species, thereby enhancing scientific collections of ichthyoplankton. Additionally, it reduces mortality in ichthyoplankton techniques, including endangered species. Therefore, we believe that this novel taxonomic technique for identifying live ichthyoplankton represents a paradigm shift in the monitoring, management, and conservation of fish, as well as in ecological stewardship and advances in this area of research.

Towards accurate monitoring of water content in woody tissue across tropical forests and other biomes.

Forest ecosystems face increasing drought exposure due to climate change, necessitating accurate measurements of vegetation water content to assess drought stress and tree mortality risks. Although Frequency Domain Reflectometry offers a viable method for monitoring stem water content by measuring dielectric permittivity, challenges arise from uncertainties in sensor calibration linked to wood properties and species variability, impeding its wider usage. We sampled tropical forest trees and palms in eastern Amazônia to evaluate how sensor output differences are controlled by wood density, temperature and taxonomic identity. Three individuals per species were felled and cut into segments within a diverse dataset comprising five dicotyledonous tree and three monocotyledonous palm species on a wide range of wood densities. Water content was estimated gravimetrically for each segment using a temporally explicit wet-up/dry-down approach and the relationship with the dielectric permittivity was examined. Woody tissue density had no significant impact on the calibration, but species identity and temperature significantly affected sensor readings. The temperature artefact was quantitatively important at large temperature differences, which may have led to significant bias of daily and seasonal water content dynamics in previous studies. We established the first tropical tree and palm calibration equation which performed well for estimating water content. Notably, we demonstrated that the sensitivity remained consistent across species, enabling the creation of a simplified one-slope calibration for accurate, species-independent measurements of relative water content. Our one-slope calibration serves as a general, species-independent standard calibration for assessing relative water content in woody tissue, offering a valuable tool for quantifying drought responses and stress in trees and forest ecosystems.

Lower Valanginian ammonite biostratigraphy of the Cañón de la Vaca section, Taraises Formation, Coahuila state, northern Mexico

The present work carries out a biostratigraphic analysis of the Valanginian ammonite record from the Cañón de la Vaca section in the Sierra de Parras, Coahuila, Mexico. The collection of ammonites exhibits an abundance of specimens, representing a biodiverse range of taxa, and numerous occurrences throughout the biostratigraphic section. This record in the Taraises Formation allowed a solid identification and diagnosis of the ‘Thurmanniceras’ pertransiens, Neocomites neocomiensiformis and Karakaschiceras inostranzewi zones, along with the Neocomites premolicus, Neocomites neocomiensiformis, Busnardoites campylotoxus, Karakaschiceras inostranzewi and Neocomites platycostatus subzones. These biostratigraphic units corresponds to the lower Valanginian of the Standard Mediterranean Ammonite Zonation. Among the collected ammonites, numerous specimens of significant biostratigraphic importance remain scarcely known or lack a proper taxonomic identification. This situation has been already observed in other sections, such as Peña del Águila, Zacatecas, Mexico, and in the Betic Cordillera, southeast Spain. Fortunately, these unknown taxa can be compared with other sections in Mexico and with lower Valanginian ammonites from Spain, facilitating a more comprehensive biostratigraphic analysis. The present biostratigraphic analysis is expected to contribute to an increased understanding of lower Valanginian strata, thereby enabling future taxonomic and biostratigraphic research on the lower Valanginian in Mexico and globally.

EDNA Is a Useful Environmental Monitoring Tool for Assessing Stream Ecological Health

ABSTRACTEnvironmental DNA (eDNA) is increasingly used in biodiversity assessments, but there remain uncertainties regarding its congruence with data based on traditional approaches involving habitat sampling and morphological‐based taxonomy. Using eDNA for biomonitoring has several advantages, including improved processing efficiencies and precision of taxonomic identification. In contrast, traditional biomonitoring is time‐consuming and expensive, often limiting the number of sites monitored. Establishing that eDNA‐derived metrics are congruent with their traditional equivalents on a national scale would support its wider use in biomonitoring. Our study compared ecosystem health assessments made by traditional biomonitoring techniques to those using eDNA from 53 sites throughout Aotearoa New Zealand. Because eDNA sampling was not done concurrently with benthic sampling at most sites, we used the average community composition at each site based on previous sampling occasions. We also allocated species identified by eDNA to the traditional level of identification to allow comparisons with eDNA data identified to broader taxonomic groups. We assessed similarities between the three datasets and found a high degree of correlation and convergence between biotic indices calculated from the different methods. eDNA did, however, appear to under‐represent some taxa, reflecting challenges in matching barcodes with an often‐incomplete sequence library. eDNA data did not always perform better in terms of showing the effects of land use on invertebrate community composition, but all datasets produced similar patterns. Multivariate analyses (redundancy analysis and variation partitioning) identified congruent relationships between environmental and spatial variables with the invertebrate community structure described by the three methods. eDNA data replicated the environmental responses and showed the same overall patterns in community composition as the traditionally collected data. We suggest that eDNA biomonitoring can complement traditional methods, and will perform at least as well as traditional data at detecting patterns in invertebrate community composition and ecosystem health at a national scale.

Re-evaluation of the taxonomic identity of Angelica fallax (Apiaceae) and its conservation status

A re-evaluation of the taxonomic identity of Angelica fallax H. Boissieu (Apiaceae), a species endemic to Jejudo Island is presented. A. fallax has mostly been treated as a synonym of A. polymorpha Maxim. or sometimes as neither a species nor a synonym in Korea. A. fallax should be considered a species distinct from A. polymorpha based on a detailed re-examination of the original morphological description of the type materials. It is clearly distinguishable from A. polymorpha due to its recurved rachides, obsolete calyx teeth, four or five conspicuous bractlets, slightly zygomorphic peripheral flowers, and mericarps bearing thick primary ribs with an inflated base. Especially, A. fallax has larger mericarps than A. polymorpha; the mericarps do not overlap with each other in size. Furthermore, the two species showed significant differences in leaf and mericarp epidermal characteristics, including the arrangement and shape of epidermal cells and cuticular ornamentation. The morphological differences strongly suggest that the two species are taxonomically distinct. Thus, it is recommended that A. fallax be resurrected from the synonymy of A. polymorpha. A full description, illustrations, color photographs, taxonomic note, ecology, phenology of the species, and an identification key for all Korean species of Angelica are provided. Additionally, listing A. fallax as Vulnerable (VU D2) on the International Union for the Conservation of Nature and Natural Resources Red List is recommended.

The State of the Art of the Global Distribution of the Invasive Mytilid Species Brachidontes pharaonis (P. Fischer, 1870)

The studies on the bioinvasion phenomenon focus mainly on the biological and ecological traits of a species, while scattered literature is addressed to a correct systematic assessment and an updated geographical distribution on the whole. It is noteworthy that non-indigenous species should be monitored on both sides of their range, i.e., towards the front of dispersal and beyond the original range. The backside range boundaries are not often monitored or well delimited; thus, the novel global distribution of an invasive taxon is not often accurately delimitated. A model species for highlighting criticisms about the scarce knowledge on the novel range was chosen. Brachidontes pharaonis is a mussel that has successfully colonised the Mediterranean Sea, following an immigration pathway through the Suez Canal from the Red Sea, presumably from a wider Indo-Pacific area. In this case, the Indo-Pacific boundaries have been overlooked and are still misunderstood due to diverse causes, principally as the synonymy with the congeneric B. variabilis has created confusion in the taxonomic identification. The present review demonstrates that the borders of the B. pharaonis range are still unclear and that the species should be analysed in a wider geographical area. Records of B. pharaonis from Southeast Asia should be treated with caution as this area is out of its range. The Indian and Pacific Oceans host the taxon B. variabilis, composed of two potential cryptic species. Data from the literature highlight the importance of the integrative taxonomic approach to solving various issues concerning the species group complex, morphological variations and cosmopolitan claims of species.

Diversity of genome size, endopolyploidy and SCoT markers in 20 Trigonella (Fabaceae) species.

The Trigonella species possess medicinal, nutraceutical and pharmaceutical properties due to the presence of many bioactive compounds. Its therapeutic effects are mostly valuable in medicine, cosmetics and the functional food industry. Correct genetic characterisation of plant material is needed to increase the potential of Trigonella species by breeding and conservation programs. The aim of this study was to develop a reliable marker system to support the morphological and phytochemical analysis in Trigonella taxonomic research, species identification and characterization as well as determination of the interspecific variation within this genus along with relationships between species. For this purpose, flow cytometry and SCoT molecular markers were combined. Flow cytometric analyses revealed that Trigonella species possess very small and small genomes. The range of genome sizes was from 1.10 to 5.76 pg/2C, with most species possessing very small genomes (< 2.8 pg/2C). In seeds of 14 species endopolyploid nuclei were detected. Flow cytometric analysis of genome size enabled quick identification of four out of 20 species, while combined with endopolyploidy detection in seeds, facilitated distinction of the next seven species. ScoT molecular markers helped to identify closely related species with similar genome size and cell cycle activity. Therefore, flow cytometry was proposed as the first-choice method for quick accession screening, while the more detailed genetic classification was obtained using SCoT molecular markers.

Unveiling the complete chloroplast genome of tribulus macropterus var. Arabicus (hosni) al-hemaid &amp; j. Thomas: genome structure, comparative analysis and phylogeny

The present investigation unveiled the first complete chloroplast (cp) genome of Tribulus macropterus var. arabicus (Hosni) Al-Hemaid &amp; J. Thomas (Zygophyllaceae), a medicinal herb, indigenous to Saudi Arabia. The cp genome, comprising a length of 158,179 bp and a GC content of 35.8%, exhibited the typical circular quadripartite arrangement of flowering plants, including two inverted repeat regions (25842 bp) separated by a large single-copy (88873 bp) and a small single-copy region (17622 bp). Genome annotation unraveled 132 genes, comprising of 87 protein-coding genes, 37 tRNAs and eight rRNAs. A comparative plastomics approach demonstrated a very similar genome structure and gene organization in closely related taxa. Whole-genome alignment indicated that the inverted repeat regions exhibited greater conservation when compared to the single copy zones. Repeat analysis of the cp genome identified 80 simple sequence repeats, with the majority (64) being mononucleotides. Among the longer repeats, forward repeats were frequent (20) followed by palindromic and reverse repeats. The nucleotide diversity endeavor identified some hypervariable sites (rpl22, cemA, trnL-UAG) in the small and large single copies which would offer opportunities to design molecular markers for potential application in taxonomic identification. Phylogenetic analysis with rbcL barcode elucidated the distinct position of T. macropterus var. arabicus compared to T. macropterus within Zygophyllaceae and further validated the assembly. The findings of this investigation provide significant insights into biological fields, particularly enhancing the current understanding of the genetic and evolutionary variations within Zygophyllaceae. Bangladesh J. Plant Taxon. 31(1): 1-14, 2024 (June)

Using feces to indicate plastic pollution in terrestrial vertebrate species in western Thailand.

Plastic pollution is a widespread and growing concern due to its transformation into microplastics (MPs), which can harm organisms and ecosystems. This study, aimed to identify plastic pollution in the feces of terrestrial vertebrates using convenience sampling both inside and outside protected areas in Western Thailand. We hypothesized that MPs are likely to be detectable in the feces of all vertebrate species, primarily in the form of small black fragments. We predicted varying quantities of MPs in the feces of the same species across different protected areas. Furthermore, we expected that factors indicating human presence, landscape characteristics, scat weight, and the MP abundance in water, soils, and sediments would influence the presence of plastics in feces. Among 12 terrestrial species studied, potential MPs were found in 41.11% of 90 samples, totaling 83 pieces across eight species including the Asian elephant (Elephas maximus), Eld's deer (Rucervus eldii), Dhole (Cuon alpinus), Gaur (Bos gaurus), Sambar deer (Rusa unicolor), Wild boar (Sus scrofa), Northern red muntjac (Muntiacus vaginalis), and Butterfly lizard (Leiolepis belliana). Specifically, 3.61% of all potential MPs (three pieces) were macroplastics, and the remaining 96.39% were considered potential MPs with the abundance of 0.92 ± 1.89 items.scat-1 or 8.69 ± 32.56 items.100 g-1 dw. There was an association between the numbers of feces with and without potential plastics and species (χ2 = 20.88, p = 0.012). Most potential plastics were fibers (95.18%), predominantly black (56.63%) or blue (26.51%), with 74.70% smaller than two millimeters. Although there were no significant associations between species and plastic morphologies, colors, and sizes, the abundance classified by these characteristics varied significantly. FTIR identified 52.38% as natural fibers, 38.10% as synthetic fibers (rayon, polyurethane (PUR), polyethylene terephthalate (PET), polypropylene (PP), and PUR blended with cotton), and 9.52% as fragments of PET and Polyvinyl Chloride (PVC). Human-related factors were linked to the occurrence of potential plastics found in the feces of land-dwelling wildlife. This study enhances the understanding of plastic pollution in tropical protected areas, revealing the widespread of MPs even in small numbers from the areas distant from human settlements. Monitoring plastics in feces offers a non-invasive method for assessing plastic pollution in threatened species, as it allows for easy collection and taxonomic identification without harming live animals. However, stringent measures to assure the quality are necessitated to prevent exogenous MP contamination. These findings underscore the importance of raising awareness about plastic pollution in terrestrial ecosystems, especially regarding plastic products from clothing and plastic materials used in agriculture and irrigation systems.