Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera

Pseudomonas is a large and diverse genus broadly distributed in nature. Its species play relevant roles in the biology of earth and living beings. Because of its ubiquity, the number of new species is continuously increasing although its taxonomic organization remains quite difficult to unravel. Nowadays the use of genomics is routinely employed for the analysis of bacterial systematics. In this work, we aimed to investigate the classification of species of the genus Pseudomonas on the basis of the analyses of the type strains whose genomes are currently available. Based on these analyses, we propose the creation of three new genera (Denitrificimonas gen nov. comb. nov., Neopseudomonas gen nov. comb. nov. and Parapseudomonas gen nov. comb. nov) to encompass several species currently included within the genus Pseudomonas and the reclassification of several species of this genus in already described taxa.

Extreme philopatry and genetic diversification at unprecedented scales in a seabird

Effective conservation requires maintenance of the processes underlying species divergence, as well as understanding species’ responses to episodic disturbances and long-term change. We explored genetic population structure at a previously unrecognized spatial scale in seabirds, focusing on fine-scale isolation between colonies, and identified two distinct genetic clusters of Barau’s Petrels (Pterodroma baraui) on Réunion Island (Indian Ocean) corresponding to the sampled breeding colonies separated by 5 km. This unexpected result was supported by long-term banding and was clearly linked to the species’ extreme philopatric tendencies, emphasizing the importance of philopatry as an intrinsic barrier to gene flow. This implies that loss of a single colony could result in the loss of genetic variation, impairing the species’ ability to adapt to threats in the long term. We anticipate that these findings will have a pivotal influence on seabird research and population management, focusing attention below the species level of taxonomic organization.

A taxonomy of sustainability topics: a guide to set the corporate sustainability content on the web

PurposeThe objective of this paper is to propose a taxonomy of sustainability communication (SC) topics that provide digital content managers with a guide for setting a sustainability content agenda and for fostering stakeholder engagement mechanisms on environmental, social and economic issues that increasingly characterize conversations on social media of all stakeholder groups.Design/methodology/approachTaxonomy is a conceptual and qualitative way used to classify and represent the corporate sustainability (CS) domain of knowledge. The taxonomy categories of SC topics are both theoretically and empirically derived, combining an in-depth literature review with a thematic content analysis of 300 web pages of the corporate websites of the top ten sustainable brands selected in “The 2019 GlobeScan-SustainAbility Leaders Survey.”FindingsThe analysis of the results led to the construction of a hierarchical dictionary of tags that categorizes all sustainability topics based on a new, four-dimensional conceptual structure: planet, people, profit and governance. Each dimension is organized in four groups of sustainability themes, which, in turn, group multiple topics, considered the smallest communication unit to develop the SC content.Practical implicationsThe taxonomy provides a concise and immediate conceptual framework on all those topics of broader interest, which, suitably modulated, can act as touch points with several groups of stakeholders. Drawn upon the best practices of thematic organization of SCs via the web, the taxonomy represents a guide for programming an editorial plan based on environmental, social, economic and governance issues from a sustainability content marketing perspective. The taxonomy of sustainability topics also finds application as a framework for a content intelligent system, providing a dictionary of tags that can be used for the indexing and retrieval of SC web content.Originality/valueThe study represents the first attempt at reaching a taxonomic organization of the sustainability aspects from a communicational perspective, supporting a new way of thinking and managing SC in the digital realm. Moreover, the results highlight, for the first time, that the Triple Bottom Line (TBL) theory, applied to corporate communications, lacks the governance aspect, which is essential to pursue sustainability consistently and effectively.

An updated phylogeny of the metallo-β-lactamases

Background Metallo-β-lactamases (MBLs) are enzymes that use zinc-dependent hydrolysis to confer resistance to almost all available β-lactam antibiotics. They are hypothesized to originate from commensal and environmental bacteria, from where some have mobilized and transferred horizontally to pathogens. The current phylogeny of MBLs, however, is biased as it is founded largely on genes encountered in pathogenic bacteria. This incompleteness is emphasized by recent findings of environmental MBLs with new forms of zinc binding sites and atypical functional profiles. Objectives To expand the phylogeny of MBLs to provide a more accurate view of their evolutionary history. Methods We searched more than 16 terabases of genomic and metagenomic data for MBLs of the three subclasses B1, B2 and B3 using the validated fARGene method. Predicted genes, together with the previously known ones, were used to infer phylogenetic trees. Results We identified 2290 unique MBL genes forming 817 gene families, of which 741 were previously uncharacterized. MBLs from subclasses B1 and B3 separated into distinct monophyletic groups, in agreement with their taxonomic and functional properties. We present evidence that clinically associated MBLs were mobilized from Proteobacteria. Additionally, we identified three new variants of the zinc binding sites, indicating that the functional repertoire is broader than previously reported. Conclusions Based on our results, we recommend that the nomenclature of MBLs is refined into the phylogenetic groups B1.1–B1.5 and B3.1–B3.4 that more accurately describe their molecular and functional characteristics. Our results will also facilitate the annotation of novel MBLs, reflecting their taxonomic organization and evolutionary origin.

Phonetic Aspects of the Turkic-Mongolian Language Contacts

The purpose of the article is to identify traces of Turkic-Mongolian language contacts in the structural and taxonomic organization of consonant systems in the South Siberian Turkic languages and the Mongolian languages of Russia and the Mongolian People’s Republic. The work is based on the generalization of the results of long-term experimental phonetic studies obtained by Siberian linguists using a complex methodology that includes both linguistic methods of phonological analysis and objective methods of articulatory and acoustic phonetics. Instrumental data indicate significant structural and typological differences in the organization of Mongolian consonant systems, determined both by the processes of historical contact with the Turkic, Tungus-Manchu, and Ugro-Samoyed languages, and by the laws of immanent development. Khalkha-Mongolian and Kalmyk consonantism, which is based on a trichotomic opposition in articulatory tension (strong / weak / super-weak phonemes), is closer to the Tuva and Tofa languages – the South Siberian Turkic languages of the Sayan-Baikal branch of the Circum-Baikal language Union. This specificity can be considered as a result of the assimilating influence of the Mongolian ethnic groups on the previous Turkic-speaking population: by switching to the Mongolian language, the native Turks preserved their articulatory-acoustic base in it, focused on the relevance of the 3-step gradation of units according to the degree of tension. Another niche in the typological classification is occupied by the Hori-Buryat consonant system, structured by the binary opposition of weak and super-weak consonant phonemes. The unacceptability of highly stressed settings for the articulatory base of native speakers includes the Khori-Buryat language in one cluster with the Turkic languages of the Altai-Sayan branch of the Circum-Baikal language Union (Altai, Khakass) formed on the Ugro-Samoyed substrate. The Yakut language, which was heavily Mongolized during the ethnic fusion of the ancient Turks and Khidans, has a consonantal system with a basic orientation to the opposition on the additional vocal cords work (voiceless / voiced / sonorous), developed under the influence of active contacts with the Tungus-Manchu tribes and under the pressure of the Russian phonological system. Instrumental data show that the Turkic-Mongolian language community is heterogeneous in its composition and structure, and the obvious material and structural-typological proximity of the consonant systems of the Altaic group languages is the result of convergence, rather than divergence from a common root.

Rapid, Experience-Related Changes in the Organization of Children’s Semantic Knowledge

The organization of knowledge according to relations between concepts is crucially important for many cognitive processes, and its emergence during childhood is a key focus of cognitive development research. Prior evidence about the role of learning and experience in the development of knowledge organization primarily comes from studies investigating naturally-occurring group differenes (such as children from rural vs. ubran settings, or children who own a pet vs. children who don’t). However, we know little about whether knowledge organization can be relatively rapidly molded by shorter-term learning experiences (e.g., on a time-scale of days vs. months and years). The present study investigated whether learning experiences can drive rapid, measurable changes in knowledge organization in children by investigating the effects of a week-long Zoo summer camp (compared to a control school-based camp) on the degree to which 4- to 9-year-old children’s knowledge about animals was organized according to taxonomic relations. Although there were no differences in taxonomic organization between the Zoo and the school-based camp at pre-test, only children who participated in the Zoo camp showed increases in taxonomic organization at post-test. These findings provide novel evidence that experiences can drive rapid changes in knowledge organization.

Mapping from spatial meaning: bridging Hñahñu (Otomi) ecological knowledge and geo-information tools

Background Hñahñu (Otomi) farmers organize their experiences and ecological learning into a farmland system designed to grow food in areas of scarce water and low soil fertility. The purpose of this paper is to examine Hñahñu concepts and categories pertaining to the farming landscape and the ecological foundations underlying the system, its management implications, and categorial organization in Huitexcalco de Morelos, Mezquital Valley, Mexico. Methods Native terms and their links to landscape were recorded and discussed in various workshops. Open interviews and field trips with local experts were used to explain soil and water management practices that allow Hñahñu farmers to maintain sustained yields throughout the year. We then used participatory mapping in order to explore the semantic relations of the terms with the space and its validity in the productive landscape. Results We elicited 7 Hñahñu language terms related to landforms, 4 related to land use categories, and 17 related to their constituent components organized in two hierarchical levels. We found that mothe as a term of land usage was followed by mothee, ñut’athee, gadñhe, or muiñhe; these primarily refer to the topographic position of the parcel and the form of access to water for irrigation. Stone barriers and earth channels represent the functional structures that are most commonly used by Hñahñu farmers to retain soil and water. In the participatory mapping results, mothe muiñhe displayed a robust spatial link with the gullies. Identifying other landscape categories required a substantial understanding both of management practices of soil and water and forms of organization. Conclusions This study revealed a complex system of knowledge that contributes to the continued proper management of the local landscape. The terms and their elicited meanings are key to understand the ways in which Hñahñu farmers conceptualize and relate the reality of their landscape and its cultural meanings. Scale and perception were found to have a determining role in defining their taxonomic organization, semantic structure, and relations in space.

The Purple Sea Urchin Strongylocentrotus purpuratus Demonstrates a Compartmentalization of Gut Bacterial Microbiota, Predictive Functional Attributes, and Taxonomic Co-Occurrence

The sea urchin Strongylocentrotus purpuratus (order Camarodonta, family Strongylocentrotidae) can be found dominating low intertidal pool biomass on the southern coast of Oregon, USA. In this case study, three adult sea urchins were collected from their shared intertidal pool, and the bacteriome of their pharynx, gut tissue, and gut digesta, including their tide pool water and algae, was determined using targeted high-throughput sequencing (HTS) of the 16S rRNA genes and bioinformatics tools. Overall, the gut tissue demonstrated Arcobacter and Sulfurimonas (Epsilonproteobacteria) to be abundant, whereas the gut digesta was dominated by Psychromonas (Gammaproteobacteria), Propionigenium (Fusobacteria), and Flavobacteriales (Bacteroidetes). Alpha and beta diversity analyses indicated low species richness and distinct microbial communities comprising the gut tissue and digesta, while the pharynx tissue had higher richness, more closely resembling the water microbiota. Predicted functional profiles showed Kyoto Encyclopedia of Genes and Genomes (KEGG) Level-2 categories of energy metabolism, membrane transport, cell motility, and signal transduction in the gut tissue, and the gut digesta represented amino acid, carbohydrate, vitamin and cofactor metabolisms, and replication and repair. Co-occurrence network analysis showed the potential relationships and key taxa, such as the highly abundant Arcobacter and Propionigenium, influencing population patterns and taxonomic organization between the gut tissue and digesta. These results demonstrate a trend of microbial community integration, allocation, predicted metabolic roles, and taxonomic co-occurrence patterns in the S. purpuratus gut ecosystem.

Rapid, Experience-Related Changes in the Organization of Children’s Semantic Knowledge

The organization of knowledge according to relations between concepts is crucially important for many cognitive processes, and its emergence during childhood is a key focus of cognitive development research. Prior evidence about the role of learning and experience in the development of knowledge organization primarily comes from studies investigating naturally-occurring group differenes (such as children from rural vs. ubran settings, or children who own a pet vs. children who don’t). However, we know little about whether knowledge organization can be relatively rapidly molded by shorter-term learning experiences (e.g., on a time-scale of days vs. months and years). The present study investigated whether learning experiences can drive rapid, measurable changes in knowledge organization in children by investigating the effects of a week-long Zoo summer camp (compared to a control school-based camp) on the degree to which 4- to 9-year-old children’s knowledge about animals was organized according to taxonomic relations. Although there were no differences in taxonomic organization between the Zoo and the school-based camp at pre-test, only children who participated in the Zoo camp showed increases in taxonomic organization at post-test. These findings provide novel evidence that experiences can drive rapid changes in knowledge organization.