Taxonomic Classification Research Articles

Macromorphological and foliar epidermal anatomical characteristics of Lilium rosthornii (Liliaceae): Implications for morphological adaptations and taxonomic significance.

This research is to examine the macromorphological and foliar epidermal anatomical features of Lilium rosthornii Diels and its ability to plastically adapt to environmental forces, which is crucial for its taxonomic classification. L. rosthornii has macromorphological characteristics such as linear to lanceolate leaves of up to 20 cm in length and 2-3 cm in breadth, grouped in a whorled pattern. The blooms are voluminous and conspicuous, measuring up to 15 cm in diameter and are supported by a towering stalk that grows up to 1 m in height. The foliar epidermal structure of L. rosthornii exhibits a stomatal length of 82.02 ± 5.77 μm and a width of 29.19 ± 1.39 μm. These measurements suggest that the plant's stomata are influenced by its ploidy levels and may serve as adaptive mechanisms to enhance water consumption efficiency. The leaf structure shows a significant thickness of 398.74 ± 97.96 μm, which might potentially contribute to its ability to withstand environmental challenges. Additionally, the presence of defensive adaptations in the top and lower epidermal layers further supports this observation. The palisade tissue measurement (58.87 ± 9.56 m) and spongy tissue measurement (32.42 ± 12.72 μm) indicate a potential for photosynthetic optimization. Furthermore, there is a possible correlation between the vascular bundle width (28.15 ± 6.52 °m) and the efficiency of nutrition delivery. The results of this study emphasize the notable diversity in the foliar structures of L. rosthornii, offering valuable understanding of its morphological adaptations that have ecological and taxonomic significance. The findings provide a deeper comprehension of the potential impact of anatomical characteristics on plant function and categorization, hence providing significant insights to the domain of plant morphology and systematics. RESEARCH HIGHLIGHTS: Examines Lilium rosthornii's anatomical features and environmental adaptability for taxonomic relevance. Leaf thickness and epidermal defenses indicate resilience to environmental stress. Highlights the diversity in L. rosthornii's foliar structures, with implications for ecological and taxonomic significance Offers insights into the impact of anatomical characteristics on plant function and classification.

Molecular phylogeny and biogeography of the aquatic dance fly subfamily Clinocerinae (Diptera: Empididae)

AbstractThis study presents the first molecular phylogenetic analysis of the Clinocerinae, challenging the traditionally accepted monophyly of this subfamily. DNA was extracted from fresh and museum specimens representing all biogeographical regions. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic analyses were performed based on sequences from two mitochondrial genes, cytochrome c oxidase subunit I (COI) and cytochrome β, and three nuclear genes, carbomoylphosphate synthase domain of rudimentary, elongation factor‐1α and isocitrate dehydrogenase. Through molecular data and morphological examination, our results reveal a division within Clinocerinae, distinguishing ‘typical’ or Clinocerinae (s.s.) from several genera, specifically Afroclinocera Sinclair, Asymphyloptera Collin and Proagomyia Collin, possibly lending support for a reclassification of these genera outside Clinocerinae. Bergenstammia Mik is proposed as a junior synonym of Phaeobalia Mik, syn. n., and the following new combinations are recognized: Phaeobalia albanica (Wagner) comb. n., Phaeobalia aurinae (Pusch & Wagner) comb. n., Phaeobalia carniolica (Horvat) comb. n., Phaeobalia frigida (Vaillant) comb. n., Phaeobalia glacialis (Palaczyk & Słowińska) comb. n., Phaeobalia multiseta (Strobl) comb. n., Phaeobalia nudimana (Vaillant) comb. n., Phaeobalia nudipes (Loew) comb. n., Phaeobalia pulla (Vaillant & Wagner) comb. n., Phaeobalia pyrenaica (Vaillant & Vinçon) comb. n., Phaeobalia slovaca (Wagner) comb. n. and Phaeobalia thomasi (Vaillant & Vinçon) comb. n. Re‐evaluation of the genus Roederiodes resulted in the following new combinations: Clinocerella macedonicus (Wagner & Horvat) comb. n. and Clinocerella montenegrinus (Wagner & Horvat) comb. n. The origins of Clinocerinae (s.s.) are traced back to the Holarctic region, Laurasian origin, with a likely complex history of dispersal events into the Southern Hemisphere. Based on current knowledge, the greatest generic and species richness is confined to the Palaearctic Region. These findings provide valuable insights into the evolutionary relationships and distribution patterns of Clinocerinae (s.s.), challenging existing taxonomic classifications and shedding light on their historical biogeography.

Unveiling the hidden diversity and functional role of Chloroflexota in full-scale wastewater treatment plants through genome-centric analyses

Abstract The phylum Chloroflexota has been found to exhibit high abundance in the microbial communities from wastewater treatment plants (WWTPs) in both aerobic and anaerobic systems. However, its metabolic role has not been fully explored due to the lack of cultured isolates. To address this gap, we use publicly available metagenome datasets from both activated sludge (AS) and methanogenic (MET) full-scale wastewater treatment reactors to assembled genomes. Using this strategy, 264 dereplicated, medium- and high-quality metagenome-assembled genomes (MAGs) classified within Chloroflexota were obtained. Taxonomic classification revealed that AS and MET reactors harbored distinct Chloroflexota families. Nonetheless, the majority of the annotated MAGs (166 MAGs with >85% completeness and < 5% contamination) shared most of the metabolic potential features, including the ability to degrade simple sugars and complex polysaccharides, fatty acids and amino acids, as well as perform fermentation of different products. While Chloroflexota MAGs from MET reactors showed the potential for strict fermentation, MAGs from AS harbored the potential for facultatively aerobic metabolism. Metabolic reconstruction of Chloroflexota members from AS unveiled their versatile metabolism and suggested a primary role in hydrolysis, carbon removal and involvement in nitrogen cycling, thus establishing them as fundamental components of the ecosystem. Microbial reference genomes are essential resources for understanding the potential functional role of uncultured organisms in WWTPs. Our study provides a comprehensive genome catalog of Chloroflexota for future analyses aimed at elucidating their role in these ecosystems.

Assessment of Plant-Growth Promoting Potential of Bacteria Isolated from Amazonian Black Pepper Roots

AbstractPurpose: In the Amazon, farmers use chemical fertilizers on a large scale to meet the nutritional requirements of some crops. Plant-growth promoting bacteria (PGPB) offer a sustainable alternative to enhance crop productivity. This study aimed to prospect novel PGPB from Amazonian black pepper (Piper nigrum L.) roots. Methods: Bacterial isolates were obtained from plant roots, evaluated for their biofertilizing potential, and the most promising strain was selected for genome sequencing. Taxonomic classification was based on 16 S rRNA gene sequencing. ACC deaminase activity, phosphate solubilization, and nitrogen fixation were assessed. Genome sequencing was performed using the Ion GeneStudio S5 platform. Results: The 20 isolates were affiliated to Enterobacter (7 isolates), Klebsiella (4 isolates), Kosakonia (5 isolates), Bacillus (2 isolates), and two unclassified bacteria. Seven isolates were positive for ACC deaminase activity, while four were positive for the presence of the nifH gene. Nitrogenase gene was found only in Kosakonia isolates. Ninety isolates were able to solubilize phosphate. The isolate Pn16 was the most promising and presented a genome of 6,432,985 bp, GC content of 55%, 6,465 Coding Sequences, 10 Symbiotic Islands, 28 biosynthetic gene clusters, and several genes involved in plant-growth promotion such as phoU-pstSCAB-phoBR, oqxAB, ipdC, speADEGF, nifHDK. Conclusions: We were able to isolate a bacterium with potential for biofertilization. Based on phylogeny and Average Nucleotide Identity, we propose the classification of the Pn16 isolate as Kosakonia pseudosacchari Pn16.

The phylogeny of ceutorhynchine weevils (Ceutorhynchinae, Curculionidae): Mitogenome data improve the resolution of tribal relationships

AbstractCeutorhynchinae Gistel are a diverse weevil subfamily of almost worldwide distribution and considerable economic importance. Nevertheless, the classification of Ceutorhynchinae and their phylogenetic relationships are not yet fully resolved. Here, we sequenced the mitogenomes of 54 ceutorhynchine species. Phylogenetic analyses by maximum likelihood and Bayesian inference were performed on a dataset of 13 protein‐coding and two ribosomal genes. All analyses recovered three well supported clades A–C. A principal component analysis shows that codon usage differs considerably between these clades, indicating a compositional asymmetry in ceutorhynchine mitogenomes. This increased the challenge of resolving the early relationships among the three clades. The resolution of the later diversification was more robust, and the resulting topologies were largely compatible with each other and with the current taxonomic classification. Exceptions are the genera Micrelus Thomson, which is transferred from the tribe Ceutorhynchini to Egriini Pajni and Kohli (new position) and Amalus Schoenherr, which is transferred to Phytobiini Gistel (new position). Amalini Wagner 1936 is a junior synonym of Phytobiini Gistel 1848 (syn. n.). Coeliodini Lacordaire (new status), a tribe previously regarded as junior synonym of Ceutorhynchini, is re‐established. Our analyses also clarified the difficult assignments of taxa to the tribes Scleropterini Schultze and Phytobiini. All taxa with the ability to jump as adult beetles belong to clade B, which comprises the tribes Cnemogonini Colonnelli, Hypurini Schultze, Mecysmoderini Wagner and Phytobiini. With dense taxon sampling and appropriate analytical methods, mitogenome data provide a phylogeny well suited to improve the traditional classification of this neglected and species‐rich taxon.

Pollen morphology of the genera Basananthe, Deidamia and Efulensia of the tribe Passifloreae (Passifloraceae sensu stricto)

Passifloreae is the largest tribe of the family Passifloraceae sensu stricto. Within the tribe, palynological studies are mostly restricted to the largest genus, Passiflora, given its expressive number of species. Consequently, other genera within the tribe are frequently underexplored, particularly in terms of pollen characters. Given the importance of pollen morphology for the taxonomic classification of Passifloraceae s.s., it is necessary to describe the pollen characters of Basananthe Peyr., Deidamia Noronha ex Thouars, and Efulensia C.H.Wright. The analyzed characters included dispersion unit, polarity, size, shape, aperture number, aperture type, operculum type, and sexine ornamentation. Subsequently, 10 metric variables were subjected to principal component analysis. The results showed that the studied genera could be easily distinguished based on pollen characters, confirming the importance of palynology. The pollen of all studied species, regardless of the genus, had the same aperture number and type, namely 3-colporate. Sexine ornamentation ranged from microreticulate to reticulate, without spines. Here, pollen characters of Basananthe, Deidamia, and Efulensia were compared with those of closely related genera and Passiflora, contributing to a more comprehensive and up-to-date understanding of the group. The results confirmed the importance of analyzing pollen attributes for the taxonomy of Passiflora s.s.

Fungal phthalimidines-chemodiversity, bioactivity and biosynthesis of a unique class of natural products

AbstractA wide range of natural products important for the engineering and drug design of pharmaceuticals comprise largely of nitrogen-based heterocycles. Fungal natural products have proven to be a rich source of the industrially-important molecules, many of which are promising drug leads. Although, natural products containing a phthalimidine core tends not to be given distant classification, but compounds containing these structures exhibit antimicrobial, anthelmintic, antimalarial and insecticidal activities, and are among the potential target for discovering new drug candidates. Intriguingly, these are primarily isolated from fungal sources and to a very lesser extent from plants or bacteria. This review surveys fungal-derived phthalimidine metabolites published until the end of 2022, isolated from both terrestrial and aquatic or marine sources with emphasis on their unique chemistry, bioactivities, biogenesis and taxonomic classification. Their unique chemistry and diverse bioactivities (including antiviral, antiproliferative, antioxidant and antimicrobial) provide a chemical library with high medicinal potential, representing a treasure trove for synthetic chemists. Graphical Abstract

Deep learning workflow to support in-flight processing of digital aerial imagery for wildlife population surveys.

Deep learning shows promise for automating detection and classification of wildlife from digital aerial imagery to support cost-efficient remote sensing solutions for wildlife population monitoring. To support in-flight orthorectification and machine learning processing to detect and classify wildlife from imagery in near real-time, we evaluated deep learning methods that address hardware limitations and the need for processing efficiencies to support the envisioned in-flight workflow. We developed an annotated dataset for a suite of marine birds from high-resolution digital aerial imagery collected over open water environments to train the models. The proposed 3-stage workflow for automated, in-flight data processing includes: 1) image filtering based on the probability of any bird occurrence, 2) bird instance detection, and 3) bird instance classification. For image filtering, we compared the performance of a binary classifier with Mask Region-based Convolutional Neural Network (Mask R-CNN) as a means of sub-setting large volumes of imagery based on the probability of at least one bird occurrence in an image. On both the validation and test datasets, the binary classifier achieved higher performance than Mask R-CNN for predicting bird occurrence at the image-level. We recommend the binary classifier over Mask R-CNN for workflow first-stage filtering. For bird instance detection, we leveraged Mask R-CNN as our detection framework and proposed an iterative refinement method to bootstrap our predicted detections from loose ground-truth annotations. We also discuss future work to address the taxonomic classification phase of the envisioned workflow.

Characterization of the complete chloroplast genome of Eutrema deltoideum (Brassicaceae)

Eutrema deltoideum (Hook. f. et Thoms.) has been recognized as a potentially important vegetable and medicinal resource. In this study, we present the complete chloroplast genome of E. deltoideum and conduct a phylogenetic analysis. The chloroplast genome is 154,051 bp long and consists of a large single-copy (LSC) region of 84,149 bp, two inverted repeat (IR) regions of 26,065 bp each, and a small single-copy (SSC) region of 17,772 bp. It contains 132 complete genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 37 tRNA genes. Additionally, we identified 78 simple sequence repeats (SSRs). The phylogenetic tree reveals that E. deltoideum is closely related to E. heterophyllum, and the Eutrema genus is monophyletic. This study provides valuable information about E. deltoideum and enhances our understanding of its taxonomic classification.

Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus.

Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense data set of 710 fungal genomes from the biomedically and technologically important genus Aspergillus. To do so, we generated a novel set of 1,362 high-quality molecular markers specific for Aspergillus and provided profile Hidden Markov Models for each, facilitating their use by others. Examining the resulting phylogeny helped resolve ongoing taxonomic controversies, identified new ones, and revealed extensive strain misidentification (7.59% of strains were previously misidentified), underscoring the importance of population-level sampling in species classification. These findings were corroborated using the current standard, taxonomically informative loci. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the Tree of Life.IMPORTANCEIdentification of fungal species relies on the use of molecular markers. Advances in genomic technologies have made it possible to sequence the genome of any fungal strain, making it possible to use genomic data for the accurate assignment of strains to fungal species (and for the discovery of new ones). We examined the usefulness and current limitations of genomic data using a large data set of 710 publicly available genomes from multiple strains and species of the biomedically, agriculturally, and industrially important genus Aspergillus. Our evolutionary genomic analyses revealed that nearly 8% of publicly available Aspergillus genomes are misidentified. Our work highlights the usefulness of genomic data for fungal systematic biology and suggests that systematic genome sequencing of multiple strains, including reference strains (e.g., type strains), of fungal species will be required to reduce misidentification errors in public databases.

POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy.

Sequence technology advancements have led to an exponential increase in bacterial genomes, necessitating robust taxonomic classification methods. The Percentage Of Conserved Proteins (POCP), proposed initially by Qin et al. (2014), is a valuable metric for assessing prokaryote genus boundaries. Here, I introduce a computational pipeline for automated POCP calculation, aiming to enhance reproducibility and ease of use in taxonomic studies. The POCP-nf pipeline uses DIAMOND for faster protein alignments, achieving similar sensitivity to BLASTP. The pipeline is implemented in Nextflow with Conda and Docker support and is freely available on GitHub under https://github.com/hoelzer/pocp. The open-source code can be easily adapted for various prokaryotic genome and protein datasets. Detailed documentation and usage instructions are provided in the repository.

The Landscape and Perspectives of the Human Gut Metaproteomics

The human gut microbiome is closely associated with human health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of the gut microbiome by analyzing the entire proteins present in microbial communities. Recent advancements in liquid chromatography and tandem mass spectrometry (LC-MS/MS) techniques have expanded the detection range of metaproteomics. However, the overall coverage of the proteome in metaproteomics is still limited. While metagenomics studies have revealed substantial microbial diversity and functional potential of the human gut microbiome, few studies have summarized and studied the human gut microbiome landscape revealed with metaproteomics.In this paper, we present the current landscape of human gut metaproteomics studies by re-analyzing the identification results from fifteen published studies. We quantified the limited proteome coverage in metaproteomics and revealed a high proportion of annotation coverage of metaproteomics-identified proteins. We conducted a preliminary comparison between the metaproteomics view and the metagenomics view of the human gut microbiome, identifying key areas of consistency and divergence. Based on the current landscape of human gut metaproteomics, we discuss the feasibility of using metaproteomics to study functionally unknown proteins and propose a whole workflow peptide-centric analysis. Additionally, we suggest enhancing metaproteomics analysis by refining taxonomic classification and calculating confidence scores, as well as developing tools for analyzing the interaction between taxonomy and function.

Impact of temperature stress on Pyropia yezoensis and its inhabitant microbiota to promote aquaculture

The diverse inhabitant microbiota of Pyropia yezoensis can establish both beneficial and harmful interactions that effect community structure. It is complex to understand the seaweed microbial diversity and their ecological and functional regulations which are affected by numerous environmental factors. In this study, temperature stress was focused to understand the metagenomics of P. yezoensis microbiota, its functional annotation and the metabolites regulation of P. yezoensis. The samples of P. yezoensis from yellow sea of China were divided into two groups i.e low temperature 5°C (LT) and High temperature 25°C (HT). The genes and functional level analysis were followed by using metagenomic sequencing analysis and sequencing of 16sRNA gene. The Pyropia yezoensis samples were also analyzed through LCMS for metabolites regulation due to effects of microbiota and temperature stress. According to taxonomic classification analysis, Proteobacteria, Bacteroidetes, and Firmicutes were predominant in both samples with over-representation of these species in high temperature stress samples. A diverse relationship between the bacterial communities residing in the LT and HT samples was explored through discriminant analysis. The functional prediction of bacterial communities from KEGG analysis revealed a notable increase in HT predicted genes associated to amino acid metabolism, carbohydrate metabolism, energy metabolism, co-factors and vitamins metabolism, membrane transport, and nucleotide metabolism. The provoked chemical signaling and transportation response from the bacterial community, leading to activation of metabolic genes to utilize the available substrates of seaweed. The LCMS illustrated that the primary metabolites of Pyropia yezoensis were down regulated due to effect of high temperature which indicates a negative effect on the growth and health of Pyropia, while the secondary metabolites were up-regulated showing the defensive mechanism against unbearable stress. These up and down regulated metabolites also activated their respective pathways, suggesting the adoptive mechanism of P. yezoensis in response of high temperature.

Molecular identification and genetic diversity of ten Pierid butterflies based on mitochondrial COI gene

The IUCN Bangladesh has documented a total of 31 species belonging to the Pieridae family in Bangladesh. There is currently limited knowledge regarding the genetic diversity and molecular relationships among these butterflies. The present investigation involved the generation of mitochondrial COI (mtCOI) gene sequences for ten species of butterflies belonging to the Pierid family. After that, BLAST analysis showed 96% to 100% similarity, and then the sequences were submitted to NCBI’s GenBank. MEGA10 and BioEdit were used to identify a 584 bp COI gene fragment with 179 variable sites and 128 parsimony-informative sites. The COI sequences' average base compositions were 38.56% T, 17.12% C, 30.18% A, and 14.12% G. While a significant AT bias (68.74%) existed among the Pierid species. The genetic distance between ten Pierid species was assessed using the Kimura 2-Parameter (K2P) algorithm, and the nucleotide differences ranged from 0.00172% to 0.24261%. Afterwards, the Maximum Likelihood (ML) method was used to construct a phylogenetic tree using ten sequences of Pierid species. These species belongs to two subfamilies, Pierinae and Coliadinae in Bangladesh. On the tree, the Pierinae subfamily of Pieridae formed a paraphyletic arrangement whereas the Coliadinae subfamily was shown to be monophyletic. The data analyses support the following relationships between the two subfamilies as follows: [(Appias + Leptosia) + (Pieris + Appias) + (Delias) + (Eurema + Catopsilia) + (Pareronia)]. This supported the theory that Pierinae and Coliadinae are sister taxa. Nonetheless, Pareronia hippia remains outside the main Pierinae group, requiring further study to resolve this issue. Finally, these studies generated ten mtCOI gene sequences that have the potential to serve as valuable references for the accurate identification of Pierid species. In addition, this result could be used in the future to reveal the subfamily relationships within the Pieridae taxonomic classification. Bangladesh J. Zool. 51(3): 289-299, 2023  

Quantitative grain size estimation on airless bodies from the negative polarization branch

This work explores characteristics of the negative polarization branch (NPB), which occurs in scattered light from rough surfaces, with particular focus on the effects of fine particles. Factors such as albedo, compression, roughness, and the refractive index are considered to determine their influence on the NPB. This study compiles experimental data and lunar observations to derive insights from a wide array of literature. Employing our proposed methodology, we estimate the representative grain sizes on the lunar surface to be D ~ 1–2 µm, with D ≲ 2–4 µm, consistent with observed grain size frequency distributions in laboratory settings for lunar fines. Considering Mars, we propose that the finest particles are likely lacking (D ≫ 10 µm), which matches previous estimations. This study highlights the potential of multiwavelength, particularly near-infrared, polarimetry for precisely gauging small particles on airless celestial bodies. The conclusions provided here extend to cross-validation with grain sizes derived from thermal modeling, asteroid taxonomic classification, and regolith evolution studies.

Genomic and Phenotypic Analysis of Salmonella enterica Bacteriophages Identifies Two Novel Phage Species

Bacteriophages (phages) are potential alternatives to chemical antimicrobials against pathogens of public health significance. Understanding the diversity and host specificity of phages is important for developing effective phage biocontrol approaches. Here, we assessed the host range, morphology, and genetic diversity of eight Salmonella enterica phages isolated from a wastewater treatment plant. The host range analysis revealed that six out of eight phages lysed more than 81% of the 43 Salmonella enterica isolates tested. The genomic sequences of all phages were determined. Whole-genome sequencing (WGS) data revealed that phage genome sizes ranged from 41 to 114 kb, with GC contents between 39.9 and 50.0%. Two of the phages SB13 and SB28 represent new species, Epseptimavirus SB13 and genera Macdonaldcampvirus, respectively, as designated by the International Committee for the Taxonomy of Viruses (ICTV) using genome-based taxonomic classification. One phage (SB18) belonged to the Myoviridae morphotype while the remaining phages belonged to the Siphoviridae morphotype. The gene content analyses showed that none of the phages possessed virulence, toxin, antibiotic resistance, type I–VI toxin–antitoxin modules, or lysogeny genes. Three (SB3, SB15, and SB18) out of the eight phages possessed tailspike proteins. Whole-genome-based phylogeny of the eight phages with their 113 homologs revealed three clusters A, B, and C and seven subclusters (A1, A2, A3, B1, B2, C1, and C2). While cluster C1 phages were predominantly isolated from animal sources, cluster B contained phages from both wastewater and animal sources. The broad host range of these phages highlights their potential use for controlling the presence of S. enterica in foods.

An in-depth evaluation of metagenomic classifiers for soil microbiomes

BackgroundRecent endeavours in metagenomics, exemplified by projects such as the human microbiome project and TARA Oceans, have illuminated the complexities of microbial biomes. A robust bioinformatic pipeline and meticulous evaluation of their methodology have contributed to the success of these projects. The soil environment, however, with its unique challenges, requires a specialized methodological exploration to maximize microbial insights. A notable limitation in soil microbiome studies is the dearth of soil-specific reference databases available to classifiers that emulate the complexity of soil communities. There is also a lack of in-vitro mock communities derived from soil strains that can be assessed for taxonomic classification accuracy.ResultsIn this study, we generated a custom in-silico mock community containing microbial genomes commonly observed in the soil microbiome. Using this mock community, we simulated shotgun sequencing data to evaluate the performance of three leading metagenomic classifiers: Kraken2 (supplemented with Bracken, using a custom database derived from GTDB-TK genomes along with its own default database), Kaiju, and MetaPhlAn, utilizing their respective default databases for a robust analysis. Our results highlight the importance of optimizing taxonomic classification parameters, database selection, as well as analysing trimmed reads and contigs. Our study showed that classifiers tailored to the specific taxa present in our samples led to fewer errors compared to broader databases including microbial eukaryotes, protozoa, or human genomes, highlighting the effectiveness of targeted taxonomic classification. Notably, an optimal classifier performance was achieved when applying a relative abundance threshold of 0.001% or 0.005%. The Kraken2 supplemented with bracken, with a custom database demonstrated superior precision, sensitivity, F1 score, and overall sequence classification. Using a custom database, this classifier classified 99% of in-silico reads and 58% of real-world soil shotgun reads, with the latter identifying previously overlooked phyla using a custom database.ConclusionThis study underscores the potential advantages of in-silico methodological optimization in metagenomic analyses, especially when deciphering the complexities of soil microbiomes. We demonstrate that the choice of classifier and database significantly impacts microbial taxonomic profiling. Our findings suggest that employing Kraken2 with Bracken, coupled with a custom database of GTDB-TK genomes and fungal genomes at a relative abundance threshold of 0.001% provides optimal accuracy in soil shotgun metagenome analysis.

Population genetic structure of bottlenose and whitespotted wedgefishes from the Southwest Indian Ocean using a dual marker approach

Wedgefishes (Rhinidae) are threatened by unsustainable fishing globally, and especially in the Southwest Indian Ocean (SWIO), due to their high-value fins in the shark trade. The whitespotted wedgefish Rhynchobatus djiddensis and the bottlenose wedgefish R. australiae are both classified as Critically Endangered on the IUCN Red List of Threatened Species, yet a lack of species-specific knowledge and taxonomic uncertainty still exists within this genus. Genetic approaches aid in taxonomic classification and identifying distinct populations for targeted conservation. Morphological specimen identification of samples (n = 189) collected across the SWIO was confirmed based on the cytochrome oxidase c subunit I (COI) and/or nicotinamide adenine dehydrogenase subunit 2 (ND2) gene regions. The genetic diversity and population structure within and between species and sampling locations were investigated using a dual marker approach: (1) 2 concatenated mitochondrial gene regions, namely COI and the control region (n = 117), and (2) 9 nuclear microsatellite markers (n = 146). The overall genetic diversity was moderate, with an indication that different evolutionary forces are at play on a mitochondrial versus nuclear level. The 2 species were delineated based on both marker types, and for R. djiddensis, the sampling locations of South Africa and Mozambique were genetically homogeneous. For R. australiae, significant differentiation was found between sampling locations, with Madagascar and Tanzania being genetically the most similar. This information provides critical insights into the distribution range and population structure of the whitespotted wedgefish species complex that can support the sustainable management of wedgefishes.

Dependability of Network Services in the Context of NFV: A Taxonomy and State of the Art Classification

Dependability of Network Services in the Context of NFV: A Taxonomy and State of the Art Classification

Decoupled response of microbial taxa and functions to nutrients: The role of stoichiometry in plantations

The resource quantity and elemental stoichiometry play pivotal roles in shaping belowground biodiversity. However, a significant knowledge gap remains regarding the influence of different plant communities established through monoculture plantations on soil fungi and bacteria's taxonomic and functional dynamics. This study aimed to elucidate the mechanisms underlying the regulation and adaptation of microbial communities at the taxonomic and functional levels in response to communities formed over 34 years through monoculture plantations of coniferous species (Japanese larch, Armand pine, and Chinese pine), deciduous forest species (Katsura), and natural shrubland species (Asian hazel and Liaotung oak) in the temperate climate. The taxonomic and functional classifications of fungi and bacteria were examined for the mineral topsoil (0–10 cm) using MiSeq-sequencing and annotation tools of microorganisms (FAPROTAX and Funguild). Soil bacterial (6.52 ± 0.15) and fungal (4.46 ± 0.12) OTUs' diversity and richness (5.83*103±100 and 1.12*103±46.4, respectively) were higher in the Katsura plantation compared to Armand pine and Chinese pine. This difference was attributed to low soil DOC/OP (24) and DON/OP (11) ratios in the Katsura, indicating that phosphorus availability increased microbial community diversity. The Chinese pine plantation exhibited low functional diversity (3.34 ± 0.04) and richness (45.2 ± 0.41) in bacterial and fungal communities (diversity 3.16 ± 0.15 and richness 56.8 ± 3.13), which could be attributed to the high C/N ratio (25) of litter. These findings suggested that ecological stoichiometry, such as of enzyme, litter C/N, soil DOC/DOP, and DON/DOP ratios, was a sign of the decoupling of soil microorganisms at the genetic and functional levels to land restoration by plantations. It was found that the stoichiometric ratios of plant biomass served as indicators of microbial functions, whereas the stoichiometric ratios of available nutrients in soil regulated microbial genetic diversity. Therefore, nutrient stoichiometry could serve as a strong predictor of microbial diversity and composition during forest restoration.