Search Results (11)

As one of the four primary evolutionary groups within myriapods, centipedes (Chilopoda) comprise approximately 3150 valid species. Recent molecular studies have begun to elucidate the phylogeny and time to divergence in Chilopoda; yet, identifying scutigeromorphs at the species level remains a notoriously challenging task. In this study, we obtained seven new complete mitogenomes of Thereuopoda clunifera (Wood, 1862) to investigate the phylogeny and divergence times of Chilopoda. Both maximum likelihood (ML) and Bayesian inference (BI) analyses recovered the relationship of (Scutigeromorpha + (Scolopendromorpha + (Lithobiomorpha + Geophilomorpha))). For Scutigeromorpha, seven newly sequenced mitogenomes of T. clunifera were divided into four distinct clades. Divergence time estimates suggest that the basal split of Chilopoda occurred during the Middle Ordovician period, with the origins of Scolopendromorpha, Lithobiomorpha, and Geophilomorpha dating to the Devonian period. Factors such as warm climates, coevolution between predator and prey, and the rifting of the Hainan Island may have driven the diversification of Scutigeromorpha. Based on genetic distance, the delimitation of molecular species, phylogenetic relationships, and divergence time analyses, we identified three cryptic species that existed within T. clunifera. This exceptionally high degree of hidden diversity can be ascribed to the morphological stasis that has occurred since the Paleozoic era and taxonomic impediment. Full article

Micropterigidae and Eriocraniidae are poorly investigated in Southern Europe. Despite the richness of the Italian territory, studies devoted to investigating their molecular diversity are lacking. Furthermore, knowledge concerning the diversity and species distribution of these families in southern Italian regions is very poor. The aim of this paper is to contribute to filling the gaps in knowledge on the diversity of Micropterigidae and Eriocraniidae in southern Italian regions by analysing, through DNA barcoding, the samples collected in this geographic area by the authors in recent years. In total, 37 specimens were submitted to DNA barcoding analysis. The sequences were subsequently identified by comparing them with those available in the Barcoding of Life Data Systems. The results provided the first record and the first sequences of the Eriocraniidae family for southern Italy, the first record in continental Italy of a formerly Sicilian endemic species, the first sequences of an endemic species, and the first sequence belonging either to a previously described but unsequenced species or to an undescribed species. In conclusion, DNA barcoding of these families in southern Italy provided very interesting insights, improving their molecular libraries and the knowledge on the fauna of this territory. Daytime studies can further improve these results, but addressing the gaps concerning immature stages should be the major goal of future research. Full article

Only 1.2 million out of an estimated 8.7 million species on Earth have been fully classified through taxonomy. As biodiversity loss accelerates, ecologists are urgently revising conservation strategies, but the “taxonomic impediment” remains a significant barrier, limiting effective access to and understanding of taxonomic data for many researchers. As sequencing technologies advance, short DNA sequence fragments increasingly serve as DNA barcodes for species identification. Rapid acquisition of DNA sequences from diverse organisms is now possible, highlighting the increasing significance of DNA sequence analysis tools in species identification. This study introduces a new approach for species classification with DNA barcodes based on an ensemble of deep neural networks (DNNs). Several techniques are proposed and empirically evaluated for converting raw DNA sequence data into images fed into the DNNs. The best-performing approach is obtained by representing each pair of DNA bases with the value of a related physicochemical property. By utilizing different physicochemical properties, we can create an ensemble of networks. Our proposed ensemble obtains state-of-the-art performance on both simulated and real datasets. Full article

In this first field survey of an entire bee fauna for any part of Peru, we report a total of 1796 bees belonging to 181 species or morphospecies in four families. The taxonomic impediment was pronounced with only 80 species of 181 that could be named. With such a high proportion of undetermined species, it is not possible to adequately compare pollinator communities across different studies, assess historical changes or analyze endemism patterns to document ecology, behavior and evolution of the species and genera. This information is required to provide a sound basis for policymakers to protect habitats for the conservation of native pollinators. Full article

Weeds are a major threat to agriculture and horticulture cropping systems that reduce yield. Weeds have a better ability to compete for resources compared to the main crops of various agro-ecosystems and act as a major impediment in reducing overall yield. They often act as energy drains in the managed agroecosystems. We studied weed infestation for five different agro-ecosystems in the part of Indian Western Himalayas represented by paddy, maize, mustard, apple and vegetable orchards. Systematic random sampling was done to record flowering phenology and diversity of weeds during the assessment period 2015–2020. We recorded 59 weed species, taxonomically distributed among 50 genera in 24 families. The Asteraceae family has the most species (15% species), followed by Poaceae (14% species), and Brassicaceae (12% species). The Therophytes were the dominant life form followed by Hemicryptophytes. The majority of the weeds were shown to be at their most blooming in the summer (predominantly from June to July). The Shannon index based diversity of weeds ranged from 2.307–3.325 for the different agro-ecosystems. The highest number of weeds was in the horticulture systems (apple > vegetable) followed by agriculture fields (maize > paddy > mustard). Agriculture and horticulture cropping systems were distinguished using indicator species analysis, which was supported by high and significant indicator values for a number of species. Persicaria hydropiper, Cynodon dactylon, Poa annua, Stellaria media, and Rorippa palustris had the highest indicator value in agriculture cropping systems, while Trifolium repens, Phleum pratense, and Trifolium pratense had the highest indicator value in horticulture cropping systems. We found that eleven weed species were unique to apple gardens followed by nine in maize, four in vegetables, two in mustard and one in paddy fields. Spatial turnover (βsim) and nestedness-resultant components (βsne) of species dissimilarity revealed dissimilarity lower than 50% among the five cropping systems. The study is expected to assist in formulating an appropriate management strategy for the control of weed infestation in the study region. Full article

The study of human microbiomes has yielded insights into basic science, and applied therapeutics are emerging. However, conflicting definitions of what microbiomes are and how they affect the health of the “host” are less understood. A major impediment towards systematic design, discovery, and implementation of targeted microbiome therapeutics is the continued reliance on taxonomic indicators to define microbiomes in health and disease. Such reliance often confounds analyses, potentially suggesting associations where there are none, and conversely failing to identify significant, causal relationships. This review article discusses recent discoveries pointing towards a molecular understanding of microbiome “dysbiosis” and away from a purely taxonomic approach. We highlight the growing role of systems biological principles in the complex interrelationships between the gut microbiome and host cells, and review current approaches commonly used in targeted microbiome therapeutics, including fecal microbial transplant, bacteriophage therapies, and the use of metabolic toxins to selectively eliminate specific taxa from dysbiotic microbiomes. These approaches, however, remain wholly or partially dependent on the bacterial taxa involved in dysbiosis, and therefore may not capitalize fully on many therapeutic opportunities presented at the bioactive molecular level. New technologies capable of addressing microbiome-associated diseases as molecular problems, if solved, will open possibilities of new classes and categories of targeted microbiome therapeutics aimed, in principle, at all dysbiosis-driven disorders. Full article

Soil salinity is considered to be a major impediment to the production of rice among other abiotic stresses. In this study, 16S rRNA Illumina amplicon sequencing was performed to characterise the halophilic communities entrapped in rice rhizosphere soil cultivated in different planting systems (conventional, aerobic and System of Rice Intensification (SRI)) under saline conditions. The physicochemical properties and urease, soil dehydrogenase, alkaline phosphatase and arylsulphatase activity of soil samples were evaluated to understand their influence on the bacterial communities of the soil. Electrical conductivity (EC) of soil was lower in SRI soil samples, while the available major soil nutrients (nitrogen, phosphorous and potassium) content and soil enzyme activities such as dehydrogenase, alkaline phosphatase, urease and arylsulphatase were higher. A total of 2,516,700 reads were generated by amplicon sequencing of the hypervariable V3–V4 regions of bacterial 16S rRNA gene and were clustered into 273,447 OTU operational taxonomic units. The total number of Operational Taxonomic Units (OTUs) was higher in the conventional soil samples compared to the SRI and aerobic soil samples. Metagenomic analysis revealed that Proteobacteria was the most dominant phyla in all the planting systems followed by Actinobacteria, Firmicutes and Chloroflexi. The alpha diversity index was higher in conventional soil samples compared to other samples and more species diversity was found in SRI soil samples. KEGG analysis revealed that bacterial communities in different soil samples showed varied functional properties. The bacterial diversity of saline soil in this study can be utilised to identify microbial communities with biotechnological potential that can be employed for plant growth promotion in saline environments. Full article

One of the major impediments to the commercialization of biodegradable plastic is the high cost of substrate. Consequently, there is a continuous search for effective microorganisms and cheaper carbon substrates to reduce the high production cost. In this study, waste transformer oil-degrading bacteria were isolated from soil, wastewater, and sediment samples, using a mineral salt medium (MSM) supplemented with 1% waste transformer oil as the sole carbon source. The isolates were screened for polyhydroxyalkanoates (PHA) production using Nile red staining and fluorescence microscopy. PHA granules accumulation was confirmed using transmission electron microscopy. Oil degradation analysis was accomplished using solvent extraction and gravimetric methods whereas, the bacteria were identified using 16S DNA sequence homology. A total of 62 transformer oil-degrading bacteria were isolated, out of which 16 (26%) showed positive results for Nile red fluorescence microscopy. The identified organisms belong to four different taxonomic genera of Acinetobacter, Bacillus, Proteus, and Serratia. The percentage of oil degradation observed among the different isolates ranged between 19.58% and 57.51%. Analysis of the PHA extracted from the selected isolate revealed the presence of medium chain length polyhydroxyalkanoates (mcl-PHA). The findings of this work have further highlighted the diversity of the bacteria capable of utilizing waste streams such as waste transformer oil. Consequently, the isolates can be explored as agents of converting waste transformer oil into bioplastics. Full article

Taxonomic impediment is one of the main roadblocks to managing the current biodiversity crisis. Insect taxonomy is the biggest contributor to the taxonomic impediment, both in terms of the knowledge gap and the lack of experts. With this study, we tried to size the knowledge gap by analyzing taxonomical studies on the subfamily Aphidiinae (Hymenoptera: Braconidae) conducted from 2010 to 2021. All available taxonomic knowledge gathered in this period is critically summarized: newly described species, detection of alien species, published identification keys, etc. All findings are discussed relative to the current state of general taxonomy. Future prospects for taxonomy are also discussed. Full article

Determining the size of the German insect fauna requires better knowledge of several megadiverse families of Diptera and Hymenoptera that are taxonomically challenging. This study takes the first step in assessing these “dark taxa” families and provides species estimates for four challenging groups of Diptera (Cecidomyiidae, Chironomidae, Phoridae, and Sciaridae). These estimates are based on more than 48,000 DNA barcodes (COI) from Diptera collected by Malaise traps that were deployed in southern Germany. We assessed the fraction of German species belonging to 11 fly families with well-studied taxonomy in these samples. The resultant ratios were then used to estimate the species richness of the four “dark taxa” families (DT families hereafter). Our results suggest a surprisingly high proportion of undetected biodiversity in a supposedly well-investigated country: at least 1800–2200 species await discovery in Germany in these four families. As this estimate is based on collections from one region of Germany, the species count will likely increase with expanded geographic sampling. Full article

Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction. Full article