Genus-level Classification Research Articles

Systematics of Apatelodidae Neumoegen & Dyar, 1894 (Lepidoptera: Bombycoidea) based on molecular and morphological data.

Apatelodidae is a family of New World bombycoids distributed mainly in the Neotropical region, with 14 genera, 222 valid species and 8 subspecies. These moths are medium-sized with a wingspan ranging from 2 to 8cm, generally greyish, straw-yellow or reddish-brown, with darker spots and lines on the dorsal side of the wings. We combine adult morphology and molecular data to test, under a probabilistic framework, the monophyly of apatelodid genera and the placement of Tamphana (Bombycidae). We sampled the type species of 12 of the 14 valid genera of Apatelodidae, including the type species of synonymised genera. We sampled ~75% of the species from all valid genera in the family and outgroups from Bombycidae, Brahmaeidae, Eupterotidae and Phiditiidae, totalling 195 terminals. Examination of the specimens resulted in a matrix of 138 morphological characters (116 from male; 22 from female) from the head (7 from male; 1 from female), thorax (37 from male; 4 from female), abdomen (5 from male) and genitalia (66 from male; 17 from female). For the molecular analyses, we used four genes: DDC (647bp) for 14% of terminals; CAD (2486bp) for 23% of terminals, Wgl (409bp) for 38% of terminals and COI (658bp) for 75% of terminals. Species of Tamphana were recovered in Apatelodidae as two independent clades. The genera Arotros , Crastolliana , Drepatelodes , Pantelodes , and Prothysana were recovered as monophyletic. The remaining apatelodid genera were polyphyletic. We propose a new genus-level classification: Tamphana is transferred to Apatelodidae; 16 new genera are proposed: Aymara gen. nov. , Campesina gen. nov. , Caribas gen. nov. , Cecile gen. nov. , Kaweskar gen. nov. , Lempira gen. nov. , Misak gen. nov. , Mocambo gen. nov. , Nhanderu gen. nov. , Peabiru gen. nov. , Raoni gen. nov. , Tapuia gen. nov. , Tibira gen. nov. , Tupac gen. nov. , Tuyvae gen. nov. and Zapata gen. nov. Two new species are described: Mocambo lauracensis sp. nov. , and Nhanderu takua sp. nov. We revalidate the genus Hygrochroa stat. rev. and three species: Carnotena perlineata stat. rev., Tupac bombycina stat. rev., comb. nov. and Zanola vivax stat. rev. Overall, we propose 82 new generic combinations, synonymise 16 species, and restore the status of 3 species: Apatelodes floramia stat. rest. , Carnotena rectilinea comb. nov. , stat. rest. and Ephoria nubilosa stat. rest. Additionally, we summarise data on the natural history and distribution of each Apatelodidae species. ZooBank: urn:lsid:zoobank.org:pub:254AA924-30B3-48A8-AB15-CCF2745C3B8E.

VirTAXA: enhancing RNA virus taxonomic classification with remote homology search and tree-based validation.

RNA viruses are ubiquitous across a broad spectrum of ecosystems. Therefore, beyond their significant implications for public health, RNA viruses are also key players in ecological processes. High-through sequencing has accelerated the discovery of RNA viruses. Nevertheless, many of these viruses lack taxonomic annotation, posing a challenge to functional inference and evolutionary study. In particular, virus classification at the genus level remains difficult due to the limited reference data and ambiguous boundaries between some closely related genera. We introduce VirTAXA, a robust classification tool that combines remote homology search and tree-based validation to enhance the genus-level taxonomic classification of RNA viruses. VirTAXA is able to predict the genus label of an assembled viral contig and provide evidence type for each prediction. It achieves comparable accuracy to state-of-the-art methods while assigning genus labels to a greater number of sequences. Specifically, on the Global Ocean RNA metatranscriptomic data, VirTAXA can assign genus labels for 18% more contigs than the second-best classification tool. Furthermore, we demonstrated that VirTAXA can be conveniently extended to other types of viruses. The source code and data of VirTAXA are available via https://github.com/JudithEllyn/VirTAXA.

Fine-scale characterization of the soybean rhizosphere microbiome via synthetic long reads and avidity sequencing

BackgroundThe rhizosphere microbiome displays structural and functional dynamism driven by plant, microbial, and environmental factors. While such plasticity is a well-evidenced determinant of host health, individual and community-level microbial activity within the rhizosphere remain poorly understood, due in part to the insufficient taxonomic resolution achieved through traditional marker gene amplicon sequencing. This limitation necessitates more advanced approaches (e.g., long-read sequencing) to derive ecological inferences with practical application. To this end, the present study coupled synthetic long-read technology with avidity sequencing to investigate eukaryotic and prokaryotic microbiome dynamics within the soybean (Glycine max) rhizosphere under field conditions.ResultsSynthetic long-read sequencing permitted de novo reconstruction of the entire 18S-ITS1-ITS2 region of the eukaryotic rRNA operon as well as all nine hypervariable regions of the 16S rRNA gene. All full-length, mapped eukaryotic amplicon sequence variants displayed genus-level classification, and 44.77% achieved species-level classification. The resultant eukaryotic microbiome encompassed five kingdoms (19 genera) of protists in addition to fungi – a depth unattainable with conventional short-read methods. In the prokaryotic fraction, every full-length, mapped amplicon sequence variant was resolved at the species level, and 23.13% at the strain level. Thirteen species of Bradyrhizobium were thereby distinguished in the prokaryotic microbiome, with strain-level identification of the two Bradyrhizobium species most reported to nodulate soybean. Moreover, the applied methodology delineated structural and compositional dynamism in response to experimental parameters (i.e., growth stage, cultivar, and biostimulant application), unveiled a saprotroph-rich core microbiome, provided empirical evidence for host selection of mutualistic taxa, and identified key microbial co-occurrence network members likely associated with edaphic and agronomic properties.ConclusionsThis study is the first to combine synthetic long-read technology and avidity sequencing to profile both eukaryotic and prokaryotic fractions of a plant-associated microbiome. Findings herein provide an unparalleled taxonomic resolution of the soybean rhizosphere microbiota and represent significant biological and technological advancements in crop microbiome research.

Identification of pathogen composition in a Chinese population with iatrogenic and native vertebral osteomyelitis by using mNGS

Background Early antimicrobial therapy is crucial regarding the prognosis of vertebral osteomyelitis, but early pathogen diagnosis remains challenging. Objective In this study, we aimed to differentiate the types of pathogens in iatrogenic vertebral osteomyelitis (IVO) and native vertebral osteomyelitis (NVO) to guide early antibiotic treatment. Methods A total of 145 patients, who had confirmed spinal infection and underwent metagenomic next-generation sequencing (mNGS) testing, were included, with 114 in the NVO group and 31 in the IVO group. Using mNGS, we detected and classified 53 pathogens in the 31 patients in the IVO group and 169 pathogens in the 114 patients in the NVO group. To further distinguish IVO from NVO, we employed machine learning algorithms to select serum biomarkers and developed a nomogram model. Results The results revealed that the proportion of the Actinobacteria phylum in the NVO group was approximately 28.40%, which was significantly higher than the 15.09% in the IVO group. Conversely, the proportion of the Firmicutes phylum (39.62%) in the IVO group was markedly increased compared to the 21.30% in the NVO group. Further genus-level classification demonstrated that Staphylococcus was the most common pathogen in the IVO group, whereas Mycobacterium was predominant in the NVO group. Through LASSO regression and random forest algorithms, we identified 5 serum biomarkers including percentage of basophils (BASO%), percentage of monocytes (Mono%), platelet volume (PCT), globulin (G), activated partial thromboplastin time (APTT) for distinguishing IVO from NVO. Based on these biomarkers, we established a nomogram model capable of accurately discriminating between the two conditions. Conclusion The results of this study hold promise in providing valuable guidance to clinical practitioners for the differential diagnosis and early antimicrobial treatment of vertebral osteomyelitis.

Comparing DNA isolation and sequencing strategies for 16S rRNA gene amplicon analysis in biofilm containing environments

Bacteria are primarily responsible for biological water treatment processes in constructed wetland systems. Gravel in constructed wetlands serves as an essential substrate onto which complex bacterial biofilms may successfully grow and evolve. To fully understand the bacterial community in these systems it is crucial to properly isolate biofilms and process DNA from such substrates. This study looked at how best to isolate bacterial biofilms from gravel substrates in terms of bacterial richness. It considered factors including the duration of agitation during extraction, extraction temperature, and enzyme usage. Further, the 16S taxonomy data subsequently produced from Illumina MiSeq reads (using the SILVA 132 ribosomal RNA (rRNA) database on the DADA2 pipeline) were compared with the 16S data produced from Oxford Nanopore Technologies (ONT) MinION reads (using the NCBI 16S database on the EPI2ME pipeline). Finally, performance was tested by comparing the taxonomy data generated from the Illumina MiSeq and ONT MinION reads using the same (SILVA 132) database. We found no significant differences in the effective number of species observed when using different bacterial biofilm detachment techniques. However, enzyme treatment enhanced the total concentration of DNA. In terms of wetland community profiles, relative abundance differences within each sample type were clearer at the genus level. For genus-level taxonomic classification, MinION sequencing with the EPI2ME pipeline (NCBI database) produced bacterial abundance information that was poorly correlated with that from the Illumina MiSeq and DADA2 pipelines (SILVA132 database). When using the same database for each sequencing technology (SILVA132), the correlation between relative abundances at genus-level improved from negligible to moderate. This study provides detailed information of value to researchers working on constructed wetlands regarding efficient biofilm detachment techniques for DNA isolation and 16 s metabarcoding platforms for sequencing and data analysis.

Mitochondrial genomes of Nemourinae species (Plecoptera: Nemouridae) and the phylogenetic implications.

Currently, the classification system of 2 subfamilies within Nemouridae has been widely accepted. However, monophyly of 2 subfamilies has not been well supported by molecular evidence. To date, only mitogenomes from genus Nemoura of the subfamily Nemourinae were used in previous phylogenetic studies and produced conflicting results with morphological studies. Herein, we analyzed mitogenomes of 3 Nemourinae species to reveal their mitogenomic characteristics and to examine genus-level classification among Nemouridae. In this study, the genome organization of 3 mitogenomes is highly conserved in gene order, nucleotide composition, codon usage, and amino acid composition. In 3 Nemourinae species, there is a high variation in nucleotide diversity among the 13 protein-coding genes (PCGs). The Ka/Ks values for all PCGs were far lower than 1, indicating that these genes were evolving under purifying selection. The phylogenetic analyses highly support Nemurella as the sister group to Ostrocerca. Meanwhile, Nemoura is recovered as the sister group of Malenka; they are grouped with other Amphinemurinae and emerged from a paraphyletic Nemourinae. More molecular data from different taxonomic groups are needed to understand stoneflies phylogeny and evolution.

Toward Characterizing Environmental Sources of Non-tuberculous Mycobacteria (NTM) at the Species Level: A Tutorial Review of NTM Phylogeny and Phylogenetic Classification.

Nontuberculous mycobacteria (NTM) are any mycobacteria that do not cause tuberculosis or leprosy. While the majority of NTM are harmless and some of them are considered probiotic, a growing number of people are being diagnosed with NTM infections. Therefore, their detection in the environment is of interest to clinicians, environmental microbiologists, and water quality researchers alike. This review provides a tutorial on the foundational approaches for taxonomic classifications, with a focus on the phylogenetic relationships among NTM revealed by the 16S rRNA gene, rpoB gene, and hsp65 gene, and by genome-based approaches. Recent updates on the Mycobacterium genus taxonomy are also provided. A synthesis on the habitats of 189 mycobacterial species in a genome-based taxonomy framework was performed, with attention paid to environmental sources (e.g., drinking water, aquatic environments, and soil). The 16S rRNA gene-based classification accuracy for various regions was evaluated (V3, V3-V4, V3-V5, V4, V4-V5, and V1-V9), revealing overall excellent genus-level classification (up to 100% accuracy) yet only modest performance (up to 63.5% accuracy) at the species level. Future research quantifying NTM species in water systems, determining the effects of water treatment and plumbing conditions on their variations, developing high throughput species-level characterization tools for use in the environment, and incorporating the characterization of functions in a phylogenetic framework will likely fill critical knowledge gaps. We believe this tutorial will be useful for researchers new to the field of molecular or genome-based taxonomic profiling of environmental microbiomes. Experts may also find this review useful in terms of the selected key findings of the past 30 years, recent updates on phylogenomic analyses, as well as a synthesis of the ecology of NTM in a phylogenetic framework.

PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification.

Features extraction methods, such as k-mer-based methods, have recently made up a significant role in classifying and analyzing approaches for metagenomics data. But, they are challenged by various bottlenecks, such as performance limitations, high memory consumption, and computational overhead. To deal with these challenges, we developed an innovative features extraction and sequence profiling method for DNA/RNA sequences, called PC-mer, taking advantage of the physicochemical properties of nucleotides. PC-mer in comparison with the k-mer profiling methods provides a considerable memory usage reduction by a factor of 2k while improving the metagenomics classification performance, for both machine learning-based and computational-based methods, at the various levels and also archives speedup more than 1000x for the training phase. Examining ML-based PC-mer on various datasets confirms that it can achieve 100% accuracy in classifying samples at the class, order, and family levels. Despite the k-mer-based classification methods, it also improves genus-level classification accuracy by more than 14% for shotgun dataset (i.e. achieves accuracy of 97.5%) and more than 5% for amplicon dataset (i.e. achieves accuracy of 98.6%). Due to these improvements, we provide two PC-mer-based tools, which can actually replace the popular k-mer-based tools: one for classifying and another for comparing metagenomics data.

A revised genus-level classification for Cerrenaceae (Polyporales, Agaricomycetes).

Cerrenaceae is a small family of polypores and hydnoid fungi in the order Polyporales (Basidiomycota). The family consists of white-rot fungi, some of which are serious tree pathogens. Combining morphological evidence with a phylogenetic dataset of six genetic markers, we revise generic concepts in the family and propose a seven-genus classification system for the family. Two genera are introduced as new: the monotypic Acanthodontia for Radulodon cirrhatinus, and Lividopora for the Rigidoporus vinctus complex. We re-introduce the name Somion for the Spongipellis delectans complex. Other recognized genera in the family are Cerrena, Irpiciporus, Pseudolagarobasidium, and Radulodon. New species introduced are Irpiciporus branchiformis from Tanzania, Lividopora armeniaca, and L. facilis from Southeast Asia, and Somion strenuum from East Asia. We provide nomenclatural comments on all the names combined to the above Cerrenaceae genera and typify Cerrena unicolor, C. zonata, Polyporus carneopallens (= L. vincta), Somion occarium, and S. unicolor. The genus Hyphoradulum belongs to Cystostereaceae (Agaricales), and we transfer the type species H. conspicuum to Crustomyces. Our study highlights the importance of integrating different basidiocarp types in analyses when revising genus classification in macrofungi. Citation: Miettinen O, Vlasák J, Larsson E, Vlasák J Jr., Seelan JSS, Hernawati, Levicky Q, Larsson K-H, Spirin V (2023). A revised genus-level classification for Cerrenaceae (Polyporales, Agaricomycetes). Fungal Systematics and Evolution 12: 271-322. doi: 10.3114/fuse.2023.12.14.

MONITORING THE MANGROVES OF INDIAN SUNDARBANS USING GEOSPATIAL TECHNIQUES

Abstract. The world’s largest mangrove ecosystem Sundarbans lies in the southwestern part of the Ganges-Brahmaputra Delta. The health, function, and ecosystem services of the mangrove forest depend on the availability of freshwater flow within the deltaic system. The rivers, which used to feed the delta and nourish the mangrove ecosystem now stand disconnected from their upstream freshwater sources. The unavailability of freshwater restricts the growth of freshwater-loving mangroves and has the potential to affect the health of the existing mangroves limiting their ability to provide ecosystem services. Due to the high salinity, the natural reproduction of these valuable freshwater-loving floral species gradually got ceased. High salinity is considered a stress factor influencing the health, growth, productivity, and distribution of mangrove plants. In this circumstance, the main objective of the study is to monitor the spatiotemporal change of the mangrove ecosystem of Sundarbans in terms of species assemblage, floral diversity, biomass, canopy cover, forest health, etc. Remote sensing techniques and field measurements were used to perform an in-depth mangrove genus-level classification (Maximum Likelihood Classifier). To assess the plant species diversity, Shannon-Wiener Index was used in different plots of the Sundarbans to get an idea of the rich biodiversity of these coastal ecosystems. Different vegetation indices such as NDVI, OSAVI, SAVI, TDVI, etc. were estimated to assess the health of the mangrove forest. The biomass and carbon sequestration potential of the mangrove forest was assessed using field data and microwave remote sensing techniques. The result shows the declining trend of freshwater-loving mangroves from the central section of Sundarbans and an increasing trend of saline water-loving mangroves by replacing the others.

Recent studies on aero-aquatic fungi, with special reference to diversity of conidial morphology and convergent evolution.

Aero-aquatic fungi compose an ecological group of saprophytes inhabiting the submerged decaying substrates in stagnant freshwater environment. They produce three-dimensional shaped, multi-cellular conidia, which float on water surface by holding air between conidial cells. Because the conidia show diverse morphology, genus and species level classification have been based on their features. They are mostly known as asexual morphs of Ascomycota or Basidiomycota. Recent phylogenetic study revealed the aero-aquatic fungi appeared mainly in the lineages of Leotiomycetes, Dothideomycetes, and Sordariomycetes. Furthermore, the phylogenetic tree showed the aero-aquatic fungi have polyphyletic origins and similar three-dimensional conidial morphology generated as a convergent evolution among different lineages of fungi by the selection pressure for inhabiting freshwater environment. Recent studies suggested the ancestors of the aero-aquatic fungi were terrestrial fungi.

PhaGenus: genus-level classification of bacteriophages using a Transformer model.

Bacteriophages (phages for short), which prey on and replicate within bacterial cells, have a significant role in modulating microbial communities and hold potential applications in treating antibiotic resistance. The advancement of high-throughput sequencing technology contributes to the discovery of phages tremendously. However, the taxonomic classification of assembled phage contigs still faces several challenges, including high genetic diversity, lack of a stable taxonomy system and limited knowledge of phage annotations. Despite extensive efforts, existing tools have not yet achieved an optimal balance between prediction rate and accuracy. In this work, we develop a learning-based model named PhaGenus, which conducts genus-level taxonomic classification for phage contigs. PhaGenus utilizes a powerful Transformer model to learn the association between protein clusters and support the classification of up to 508 genera. We tested PhaGenus on four datasets in different scenarios. The experimental results show that PhaGenus outperforms state-of-the-art methods in predicting low-similarity datasets, achieving an improvement of at least 13.7%. Additionally, PhaGenus is highly effective at identifying previously uncharacterized genera that are not represented in reference databases, with an improvement of 8.52%. The analysis of the infants' gut and GOV2.0 dataset demonstrates that PhaGenus can be used to classify more contigs with higher accuracy.

Molecular phylogeny of the Orthalicoidea land snails: Further support and surprises.

The superfamily Orthalicoidea comprises approximately 2,000 species of terrestrial gastropods, mostly concentrated in the Neotropics but also present in southern Africa and Oceania. We provide a multi-marker molecular phylogeny of this superfamily, reassessing its family- and genus-level classification. We exclude two families from the group, Odontostomidae and Vidaliellidae, transferring them to Rhytidoidea based on their phylogenetic relationships as recovered herein. Two new families are recognized herein as members of Orthalicoidea, Tomogeridae and Cyclodontinidae fam. nov. The family Megaspiridae and the subfamily Prestonellinae are paraphyletic but are retained herein for taxonomic stability. The subfamily Placostylinae is synonymized with Bothriembryontinae. The new genera Alterorhinus gen. nov. and Sanniostracus gen. nov. containing some Brazilian species are described here to better reflect the phylogeny. The fossil record and paleobiogeographic history of the group is explored under the new phylogenetic framework.

UCE phylogenomics, biogeography, and classification of long-horned bees (Hymenoptera: Apidae: Eucerini), with insights on using specimens with extremely degraded DNA

AbstractLong-horned bees (Apidae, Eucerini) are found in different biomes worldwide and include some important crop pollinators. In the Western Hemisphere, Eucerini received extensive taxonomic study during the twentieth century, resulting in several revisions of its genera. In contrast, progress on eucerine phylogenetic research and the genus-level classification has been slow, primarily due to the relatively homogeneous external morphology within the tribe and the rarity of many of its species in collections. Here, we present a comprehensive phylogenetic study of Eucerini based on ultraconserved elements, including 153 species from nearly all genera and subgenera and from all biogeographic regions where they occur. Many of these specimens are from museums and were collected as far back as 1909. We discuss the challenges of working with specimens with highly degraded DNA, present insights into improving phylogenetic results for both species-tree and concatenation approaches, and present a new pipeline for UCE curation (Curation of UltraconseRved Elements—CURE). Our results show the existence of seven main lineages in Eucerini and most of the genera and subgenera to be reciprocally monophyletic. Using a comprehensive and up-to-date phylogenetic framework, we: (1) propose taxonomic changes, including a new subtribal classification and reorganized generic and subgeneric limits; (2) estimate divergence times; and (3) conduct a detailed exploration of historical biogeography of long-horned bees. We find that eucerine lineages expanded their range onto most continents only after their initial diversification in southern South America during the Eocene.

Integrated characterisation of nine species of the Schistorchiinae (Trematoda: Apocreadiidae) from Indo-Pacific fishes: two new species, a new genus, and a resurrected but ‘cryptic’ genus

We report nine species of the Schistorchiinae Yamaguti, 1942 (Apocreadiidae Skrjabin, 1942) from Indo-Pacific marine fishes. Molecular data (ITS2 and 28S rDNA and cox1 mtDNA) are provided for all species and the genus-level classification of the subfamily is revised. For Schistorchis Lühe, 1906, we report the type-species Sch. carneus Lühe, 1906 and Sch. skrjabini Parukhin, 1963. For Sphinteristomum Oshmarin, Mamaev & Parukhin, 1961 we report the type-species, Sph. acollum Oshmarin, Mamaev & Parukhin, 1961. We report and re-recognise Lobatotrema Manter, 1963, for the type and only species, L. aniferum Manter, 1963, previously a synonym of Sph. acollum. Lobatotrema aniferum is phylogenetically distant from, but morphologically similar to, Sph. acollum and Lobatotrema is recognised as a ‘cryptic genus’. We propose Blendiellan. gen. for B. trigintatestisn. sp. and B. tridecimtestisn. sp. These species are broadly consistent with the present morphological concept of Schistorchis but are phylogenetically distant from the type-species; a larger number of testes and some other subtle morphological characters in species of Blendiella serve to distinguish the two genera. We report three species of Paraschistorchis Blend, Karar & Dronen, 2017: P. stenosoma (Hanson, 1953) Blend, Karar & Dronen, 2017 (type-species), P. seychellesiensis (Toman, 1989) Blend, Karar & Dronen, 2017, and P. zancli (Hanson, 1953) Blend, Karar & Dronen, 2017. Lobatotrema aniferum, P. stenosoma, and Sch. carneus each have two distinct cox1 populations either over geographical range or in sympatry. Available evidence suggests that most of these species, but not all, are widespread in the tropical Indo-Pacific.

Effects of Water Potential on Anaerobic Methane Production and a Microbial Consortium

This study probed the effect of the water potential (Ψ) on anaerobic methane production and a microbial consortium. The Ψ level of the investigated anaerobic digester (n = 20) was in the range from −0.10 to −2.09 MPa with a mean value of −1.23 MPa, and the Ψ level of the anaerobic digester was significantly correlated with the SCOD, TKN, NH4+-N, alkalinity, salinity (SPS), NH4+, Na+, K+, Cl−, NO3−, and PO43− (p < 0.001). The maximum methane production rate (Rm) of the Control (−0.40 MPa) was 8.11 mL day−1 and decreased to 1.70 mL day−1 at −3.91 MPa (K5), and the lag growth phase time (λ) was delayed to 35.96 and 25.34 days at −2.85 MPa (K4) and −3.91 MPa (K5), respectively. The ultimate methane potential (Bu) was 0.264 Nm3 kg−1-VSadded for the Control, and when Ψ was adjusted, Bu increased to 0.278 Nm3 kg−1-VSadded at −1.49 MPa (K3) but decreased to 0.203 and 0.172 Nm3 kg−1-VSadded at −2.85 MPa (K4) and −3.91 MPa (K5), respectively. Therefore, the methane yield was inhibited due to the decrease in Ψ, and the methane yield is predicted to be inhibited from about −1.65 MPa. In the genus-level taxonomic classification of the microbial community, the relative abundance of Methanosarcina decreased significantly to 36.76% at −3.91 MPa (K5) compared to 58.15% for the Control; however, the relative abundance of Methanoculleus significantly increased to 35.16% at −3.91 MPa (K5) compared to 14.85% for the Control.

Plastome evolution and phylogeny of the tribe Ruteae (Rutaceae).

Rutaceae is a large family, and the genus-level classification in the subfamilies or tribes of this family is not unified based on different taxonomic treatments. Until now, phylogenetic relationships of some genera in traditional tribe Ruteae have not been clearly resolved. In this study, seven new complete plastomes of this tribe were sequenced, and a comparative analysis was performed to investigate their plastome characteristics and evolution. In addition, we inferred the phylogenetic relationships of Ruteae based on complete plastome and nuclear ITS data. All plastomes exhibited a typical quadripartite structure and were relatively conserved in their structure and gene arrangement. Their genome sizes ranged from 154,656 bp to 160,677 bp, and the size variation was found to be associated with differences in IR expansion and gene loss. A total of 112 to 114 genes were identified in the genomes, including 78 to 79 protein-coding genes, 30 tRNA genes, 4 rRNA genes, and 2 pseudogenes. Sequence divergence analysis indicated that non-coding regions exhibited a higher percentage of variable characters, and nine non-coding and six coding regions were identified as divergent hotspots. Phylogenetic results based on different datasets showed that this tribe was divided into three reciprocally exclusive groups. The phylogenetic analyses between plastome and nuclear ITS data were partly incongruent with each other. This study provides new insights into plastome evolution of Ruteae as well as Rutaceae. The availability of these plastomes provides useful genomic resources for molecular DNA barcodes and phylogenetically informative markers and deepens our understanding of the phylogeny in Ruteae.

Effect of inoculum pretreatment on the microbial and metabolic dynamics of food waste dark fermentation

This study systematically evaluated and compared different inoculum pretreatment methods to quickly select dark fermentative bacteria from anaerobic sludge for the bioconversion of food waste. The hydrogen (H2) production rate was found to be highest for 'heat + CO2′ treated inoculum at 140.75 ± 2.61 mL/L/h compared to control experiments (60.27 ± 2.61 mL/L/h). At the same time, H2 yield was found to be highest for alkali-treated inoculum at 157.25 ± 7.62 mL/g of volatile solids (VS) added compared to control experiments (91.61 ± 1.93 mL/g VS). Analysis of organic acids suggests a Clostridial-type fermentation with acetate (0.52 to 1.60 g/L) and butyrate (1.69 to 2.42 g/L) being the major by-products. The microbial data analysis showed that Firmicutes (63.64–90.39%), Bacteroidota (1.16–21.88%), and Proteobacteria (2.09–9.93%) were dominant at the phylum level, whereas genus-level classification showed Clostridium sensu stricto 1 (6.37–42.63%), Streptococcus (1.87–28.96%), Prevotella (0.57–16.59%), and Enterococcus (0.56–14.51%) dominated under different experimental conditions.

MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants

Microbial communities are responsible for biological wastewater treatment, but our knowledge of their diversity and function is still poor. Here, we sequence more than 5 million high-quality, full-length 16S rRNA gene sequences from 740 wastewater treatment plants (WWTPs) across the world and use the sequences to construct the ‘MiDAS 4’ database. MiDAS 4 is an amplicon sequence variant resolved, full-length 16S rRNA gene reference database with a comprehensive taxonomy from domain to species level for all sequences. We use an independent dataset (269 WWTPs) to show that MiDAS 4, compared to commonly used universal reference databases, provides a better coverage for WWTP bacteria and an improved rate of genus and species level classification. Taking advantage of MiDAS 4, we carry out an amplicon-based, global-scale microbial community profiling of activated sludge plants using two common sets of primers targeting regions of the 16S rRNA gene, revealing how environmental conditions and biogeography shape the activated sludge microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 966 genera and 1530 species that represent approximately 80% and 50% of the accumulated read abundance, respectively. Finally, we show that for well-studied functional guilds, such as nitrifiers or polyphosphate-accumulating organisms, the same genera are prevalent worldwide, with only a few abundant species in each genus.

Multilocus phylogeny, natural history traits and classification of natricine snakes (Serpentes: Natricinae)

Abstract Natricine snakes are geographically widespread, species rich (with ~250 extant species) and both morphologically and ecologically diverse. We present a multilocus DNA sequence phylogeny for 249 natricine specimens representing 189 named species, including 69 specimens and 21 species not previously sampled. Our inferred Bayesian and maximum likelihood trees form the basis for evaluations of genus-level classification, historical biogeography, lineage diversification, and dietary, habit and reproductive-mode diversity and evolution, although several, mostly deeper, relationships remain poorly resolved. The optimal trees support natricine origins in Asia, with dispersals to Australo-Melanesia, sub-Saharan Africa (including Seychelles Archipelago, excluding Aldabra), Europe and North Africa and into North and Central America. Viviparity appears to have evolved independently three times in Natricinae but was not significantly associated with an aquatic habit. We found limited associations between habit and diet categories. We propose generic reallocations for four natricine species and highlight other points of uncertainty in natricine classification.