Re-evaluation of the phylogenetic diversity and global distribution of the genus Candidatus Accumulibacter

Candidatus Accumulibacter was the first microorganism identified as a polyphosphate-accumulating organism (PAO), important for phosphorus removal from wastewater. This genus is diverse, and the current phylogeny and taxonomic framework appears complicated, with the majority of publicly available genomes classified as Candidatus Accumulibacter phosphatis, despite notable phylogenetic divergence. The ppk1 marker gene allows for a finer scale differentiation into different types and clades, nevertheless taxonomic assignments remain confusing and inconsistent across studies. Therefore, a comprehensive re-evaluation is needed to establish a common understanding of this genus, both in terms of naming and basic conserved physiological traits. Here, we provide this re-assessment using a comparison of genome, ppk1, and 16S rRNA gene-based approaches from comprehensive datasets. We identified 15 novel species, along with the well-known Ca. A. phosphatis, Ca. A. deltensis and Ca. A. aalborgensis. To compare the species in situ, we designed new species-specific FISH probes and revealed their morphology and arrangement in activated sludge. Based on the MiDAS global survey, Ca. Accumulibacter species were widespread in WWTPs with phosphorus removal, indicating the process design as a major driver for their abundance. Genome mining for PAO related pathways and FISH-Raman microspectroscopy confirmed the potential for the PAO metabolism in all Ca. Accumulibacter species, with detection in situ of the typical PAO storage polymers. Genome annotation further revealed fine-scale differences in the nitrate/nitrite reduction pathways. This provides insights into the niche differentiation of these lineages, potentially explaining their coexistence in the same ecosystem while contributing to overall phosphorus and nitrogen removal.

Corrieopone nouragues gen. nov., sp. nov., a new Ponerinae from French Guiana (Hymenoptera, Formicidae)

This study describes the worker and queen castes of the Neotropical ponerine Corrieopone nouraguesgen. nov., sp. nov., an ant from the tropical rainforest in French Guiana. Worker morphology of the taxon is compared with those of other Ponerinae and the similarities between them are discussed, refining the definition of character states for some diagnostic characters at the generic level, providing an identification key to the Neotropical genera, and making some adjustments to the taxonomic framework within the subfamily. Descriptions, diagnosis, character discussion, identification key, and glossary are illustrated with more than 300 images and line drawings. Open science is supported by providing access to measurement data for specimens of the new genus, a matrix of character states for all ponerine taxa evaluated in this study, and specimen data for all examined material. The new or revived combinations presented here are Pachycondyla procidua Emery, comb. rev., Neoponera curiosa (Mackay and Mackay), comb. nov., Leptogenys butteli (Forel), comb. nov., and Bothroponera escherichi (Forel), comb. nov. In addition, Leptogenys butteli is synonymized with Leptogenys myops (Emery), syn. nov.

New shallow water species of Caribbean Ircinia Nardo, 1833 (Porifera: Irciniidae)

Seven Ircinia morphospecies were collected from three sites in the Caribbean (Bocas del Toro, Panama; the Mesoamerican Barrier Reef, Belize; and the Florida Keys, United States of America). Previous research used an integrative taxonomic framework (genome-wide SNP sampling and microbiome profiling) to delimit species boundaries among these Ircinia. Here, we present morphological descriptions for these species, six of which are new to science (Ircinia lowi sp. nov., Ircinia bocatorensis sp. nov., Ircinia radix sp. nov., Ircinia laeviconulosa sp. nov., Ircinia vansoesti sp. nov., Ircinia ruetzleri sp. nov.) in addition to one species conferre (Ircinia cf. reteplana Topsent, 1923).

When Imagery and Physical Sampling Work Together: Toward an Integrative Methodology of Deep-Sea Image-Based Megafauna Identification

Imagery has become a key tool for assessing deep-sea megafaunal biodiversity, historically based on physical sampling using fishing gears. Image datasets provide quantitative and repeatable estimates, small-scale spatial patterns and habitat descriptions. However, taxon identification from images is challenging and often relies on morphotypes without considering a taxonomic framework. Taxon identification is particularly challenging in regions where the fauna is poorly known and/or highly diverse. Furthermore, the efficiency of imagery and physical sampling may vary among habitat types. Here, we compared biodiversity metrics (alpha and gamma diversity, composition) based on physical sampling (dredging and trawling) and towed-camera still images (1) along the upper continental slope of Papua New Guinea (sedimented slope with wood-falls, a canyon and cold seeps), and (2) on the outer slopes of the volcanic islands of Mayotte, dominated by hard bottoms. The comparison was done on selected taxa (Pisces, Crustacea, Echinoidea, and Asteroidea), which are good candidates for identification from images. Taxonomic identification ranks obtained for the images varied among these taxa (e.g., family/order for fishes, genus for echinoderms). At these ranks, imagery provided a higher taxonomic richness for hard-bottom and complex habitats, partially explained by the poor performance of trawling on these rough substrates. For the same reason, the gamma diversity of Pisces and Crustacea was also higher from images, but no difference was observed for echinoderms. On soft bottoms, physical sampling provided higher alpha and gamma diversity for fishes and crustaceans, but these differences tended to decrease for crustaceans identified to the species/morphospecies level from images. Physical sampling and imagery were selective against some taxa (e.g., according to size or behavior), therefore providing different facets of biodiversity. In addition, specimens collected at a larger scale facilitated megafauna identification from images. Based on this complementary approach, we propose a robust methodology for image-based faunal identification relying on a taxonomic framework, from collaborative work with taxonomists. An original outcome of this collaborative work is the creation of identification keys dedicated specifically to in situ images and which take into account the state of the taxonomic knowledge for the explored sites.

The classification of dwarf mistletoes (Arceuthobium spp., Viscaceae) in section Campylopoda, series Campylopoda

The taxonomic classification of dwarf mistletoes (Arceuthobium spp., Viscaceae) is complicated due to their reduced morphology, requiring the integration of not only morphology but also phenology, geography, and host relationships. This has been particularly true for the classification of taxa in subgenus Vaginata, section Campylopoda, series Campylopoda. Most of the species in this group have been recently circumscribed in synonymy with or reduced to subspecies of Arceuthobium campylopodum Engelm; however, we contend they deserve separate species recognition. To address this question, we have conducted morphological analyses of the taxa in ser. Campylopoda using univariate and multivariate statistical analyses. Our results have demonstrated that these taxa can be determined to species using morphological data without consideration of geographic location or host specificity; however, the host specialization and geographic distribution exhibited by these taxa also supports their classification as species. Here, we discuss the evidence supporting the specific classification of ser. Campylopoda taxa. This taxonomic framework permits the treatment of several dwarf mistletoe populations with geographically restricted distributions, fewer morphological differences, and specialized host affinities as subspecies of Arceuthobium abietinum (Engelm.) Abrams, Arceuthobium microcarpum (Engelm.) Hawksw. & Wiens, and Arceuthobium tsugense (Rosend.) G.N.Jones. It is also the most practical classification for the management of these economically and ecologically important parasitic plants.

Leviviricetes: expanding and restructuring the taxonomy of bacteria-infecting single-stranded RNA viruses

The vast majority of described prokaryotic viruses have double-stranded or single-stranded DNA or double-stranded RNA genomes. Until 2020, a mere four prokaryotic single-stranded, positive-sense RNA viruses have been classified in two genera (Riboviria; Lenarviricota; Allassoviricetes; Leviviridae). Several recent metagenomic and metatranscriptomic studies revealed a vastly greater diversity of these viruses in prokaryotic soil communities than ever anticipated. Phylogenetic analysis of these newly discovered viruses prompted the reorganization of class Allassoviricetes, now renamed Leviviricetes, to include two orders, Norzivirales and Timlovirales, and a total of six families, 428 genera and 882 species. Here we outline the new taxonomy of Leviviricetes, approved and ratified in 2021 by the International Committee on Taxonomy of Viruses, and describe open-access hidden Markov models to accommodate the anticipated identification and future classification of hundreds, if not thousands, of additional class members into this new taxonomic framework.

A Framework for Understanding the Nature of Questions Asked by Audience Participants at Science Cafés

Science Cafés are events designed as public engagement tools that create the opportunity for open dialogue between members of the general public and experts on the issue being discussed at the event. This study explores the nature of questions being asked by audience participants during discussion sessions of Science Café events. It was conducted by coding audio recordings of audience participant engagements at 41 Science Café events held between 2010 and 2019. The result of this analysis produced a novel taxonomic framework to describe audience participant behaviors in terms of their learning goals. This framework was evaluated by applying it to samples of Science Café question data selected by Science Café topic theme. Comparisons between question-asking behaviors for specific Science Café topics and overall trends in question-asking behaviors for all Science Cafés revealed significant changes in audience participant learning goals when asking questions at Science Cafés centered on different topic types. Implications for understanding Science Café audiences and potential developments for Science Café events as public science engagement tools are discussed.

A phylogenomic framework for charting the diversity and evolution of giant viruses

Large DNA viruses of the phylum Nucleocytoviricota have recently emerged as important members of ecosystems around the globe that challenge traditional views of viral complexity. Numerous members of this phylum that cannot be classified within established families have recently been reported, and there is presently a strong need for a robust phylogenomic and taxonomic framework for these viruses. Here, we report a comprehensive phylogenomic analysis of the Nucleocytoviricota, present a set of giant virus orthologous groups (GVOGs) together with a benchmarked reference phylogeny, and delineate a hierarchical taxonomy within this phylum. We show that the majority of Nucleocytoviricota diversity can be partitioned into 6 orders, 32 families, and 344 genera, substantially expanding the number of currently recognized taxonomic ranks for these viruses. We integrate our results within a taxonomy that has been adopted for all viruses to establish a unifying framework for the study of Nucleocytoviricota diversity, evolution, and environmental distribution.

Fungi inhabiting attine ant colonies: reassessment of the genus Escovopsis and description of Luteomyces and Sympodiorosea gens. nov.

Escovopsis is a diverse group of fungi, which are considered specialized parasites of the fungal cultivars of fungus-growing ants. The lack of a suitable taxonomic framework and phylogenetic inconsistencies have long hampered Escovopsis research. The aim of this study is to reassess the genus Escovopsis using a taxonomic approach and a comprehensive multilocus phylogenetic analysis, in order to set the basis of the genus systematics and the stage for future Escovopsis research. Our results support the separation of Escovopsis into three distinct genera. In light of this, we redefine Escovopsis as a monophyletic clade whose main feature is to form terminal vesicles on conidiophores. Consequently, E. kreiselii and E. trichodermoides were recombined into two new genera, Sympodiorosea and Luteomyces, as S. kreiselii and L. trichodermoides, respectively. This study expands our understanding of the systematics of Escovopsis and related genera, thereby facilitating future research on the evolutionary history, taxonomic diversity, and ecological roles of these inhabitants of the attine ant colonies.

Investigating mindfulness influences on cognitive function: On the promise and potential of converging research strategies

Research investigating the effects and underlying mechanisms of mindfulness on cognitive functioning has accelerated exponentially over the past two decades. Despite the rapid growth of the literature and its influential role in garnering public interest in mindfulness, inconsistent methods in defining and measuring mindfulness have yielded variable findings, which contribute to the overall dearth of clear generalizable conclusions. The focus of this article is to address the lack of cohesion in the collective methodologies used in this domain, by providing a new perspective grounded in classic cognitive and experimental psychology principles. We leverage the concept of converging operations to demonstrate how seemingly disparate research strategies can be integrated towards a more unified and systematic approach. An organizing taxonomic framework is described to provide useful structure in how mindfulness can be operationalized, measured, and investigated. We illustrate the rationale and core organizing principles of the framework through a selective review of studies on mindfulness and cognitive control. We then demonstrate the utility of the approach by showing how it can be applied to synthesize extant methodologies and guide the development of future research. Specific suggestions and examples pertaining to experimental design and statistical analysis are provided.