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Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions1,2. To provide an integrated view of the spatial and seasonal dynamics of fungi, we implemented a globally distributed standardized aerial sampling of fungal spores3. The vast majority of operational taxonomic units were detected within only one climatic zone, and the spatiotemporal patterns of species richness and community composition were mostly explained by annual mean air temperature. Tropical regions hosted the highest fungal diversity except for lichenized, ericoid mycorrhizal and ectomycorrhizal fungi, which reached their peak diversity in temperate regions. The sensitivity in climatic responses was associated with phylogenetic relatedness, suggesting that large-scale distributions of some fungal groups are partially constrained by their ancestral niche. There was a strong phylogenetic signal in seasonal sensitivity, suggesting that some groups of fungi have retained their ancestral trait of sporulating for only a short period. Overall, our results show that the hyperdiverse kingdom of fungi follows globally highly predictable spatial and temporal dynamics, with seasonality in both species richness and community composition increasing with latitude. Our study reports patterns resembling those described for other major groups of organisms, thus making a major contribution to the long-standing debate on whether organisms with a microbial lifestyle follow the global biodiversity paradigms known for macroorganisms4,5.

Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of their DNA, have been suggested as an efficient and well-calibrated tool for surveying fungal diversity across various environments. Here we present data originating from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world. Each sample represents fungal DNA extracted from 24 m3 of air. We applied a conservative bioinformatics pipeline that filtered out sequences that did not show strong evidence of representing a fungal species. The pipeline yielded 27,954 species-level operational taxonomic units (OTUs). Each OTU is accompanied by a probabilistic taxonomic classification, validated through comparison with expert evaluations. To examine the potential of the data for ecological analyses, we partitioned the variation in species distributions into spatial and seasonal components, showing a strong effect of the annual mean temperature on community composition.

Insects are one of the most species-rich groups on Earth. They comprise much of animal diversity and play vital roles in ecosystems, including pollination, pest control, and decomposition. However, only a fraction of this diversity has been formally described. South Africa is recognised as one of the most biologically diverse countries globally, with an estimated 44 000 insect species. Many crops rely on insect pollinators, including canola, apples, oranges, and sunflowers. A shortage of wild pollinators currently threatens crop yields, yet our knowledge of insect diversity within South Africa is sparse. There are few taxonomic specialists relative to South Africa’s biodiversity, and the methods used for insect identification can be time-consuming and expensive. DNA barcoding provides an important research tool to accelerate insect biodiversity research. In this review, we queried the public DNA barcoding BOLD (Barcode of Life Data System) database for records of “Insecta” within South Africa, and 416 211 published records assigned to 28 239 unique BINs (Barcode Index Numbers) were returned. We identified five taxonomic orders with more BINs than known species in southern Africa (Hymenoptera, Diptera, Thysanoptera, Plecoptera, and Strepsiptera). Most of the barcoded records were derived from Malaise trap sampling in Gauteng, Mpumalanga and Limpopo, while the rest of South Africa remains poorly sampled. We suggest that there is a need for a comprehensive national sampling effort alongside increased investment in taxonomic expertise to generate critical baseline data on insect biodiversity before species are lost to extinction. Significance: Insects provide critical ecosystem services, but our knowledge of insect biodiversity is limited. DNA barcoding can help fill biodiversity knowledge gaps; however, within South Africa, sampling has been uneven. Well-sampled provinces include Gauteng, Mpumalanga and Limpopo, while the Eastern Cape, Free State, KwaZulu-Natal, Northern Cape, North-West and Western Cape remain under-sampled. We argue for a broad national Malaise trapping effort to generate crucial baseline data on insect biodiversity. Without urgent investment in taxonomic expertise and biomonitoring, we risk losing much of our biodiversity before it is even described. [ABSTRACT FROM AUTHOR]

The Meliaceae are broadly distributed worldwide, with about 50 genera and over 1400 species. There are 11 genera in South Africa, with 13 indigenous and three naturalized species. Considering the diversity of the indigenous species of this family in South Africa and the lack of recent studies encompassing these species, a taxonomic revision of the South African indigenous species of Meliaceae is presented here. Phylogenetic analysis, anatomical data, herbarium collections, and online data sources were used in this study. The results confirm the monophyly of Melioideae and Swietenioideae. The incongruence of Turraea previously reported was resolved in this study. Most representative genera of South African Meliaceae were recovered monophyletic with strong support. However, multiple samplings of species and including more markers could provide a better understanding of the relationships among South African species of Meliaceae. The review of the taxonomy of the South African Meliaceae, and especially the study of diagnostic characters and hitherto recorded natural distributions, have value in providing an up-to-date inventory of the indigenous genera and species and an easy means of identifying the taxa. Anatomical characters may be of systematic value to explore higher-level relationships in the family. This study is a contribution to tropical botany and to a more comprehensive database for the Meliaceae. [ABSTRACT FROM AUTHOR]

Plant DNA barcoding serves as an effective approach to building community phylogenies and increasing our understanding of the factors that determine plant community assemblages. The aims of the study were to (i) barcode macrophytes with high estuarine fidelity and (ii) to determine the phylogenetic diversity (PD) of selected South African estuaries for conservation prioritisation. Three DNA barcoding gene regions (rbcLa, matK, and trnH-psbA) were assessed, and community phylogenies were constructed for 270 estuaries. Generally, the matK barcode had the greatest discrimination success rate of 67.4% (parsimony informative sites = 418). Closely related species formed clades that also represent estuarine habitat types. Estuaries with high phylogenetic diversity along the southeast coast were associated with a combination of mangrove and salt marsh habitats. Species richness was strongly and significantly correlated with PD (r = 0.93; p < 0.000). Based on mean pairwise distance (MPD), more temperate estuaries (56) showed significant phylogenetic clustering compared to subtropical estuaries (24) (p < 0.05). Similarly, based on mean nearest taxon distance (MNTD), significant phylogenetic clustering was highest in temperate estuaries (50) compared to subtropical estuaries (12) (p < 0.05). This suggests that the coexistence of plant species in estuaries is structured by both biotic and abiotic interactions. Key words: rbcLa, matK, species discrimination rate, phylogenetic community ecology, conservation phylogenetics. Le codage a barres de l'ADN chez les plantes est une approche utile pour construire des phylogenies de communautes et pour augmenter notre comprehension des facteurs qui determinent la composition des communautes vegetales. Les buts de cette etude etaient : (i) d'effecteur le codage a barres de macrophytes fortement associes aux estuaires et (ii) de determiner la diversite phylogenetique (PD) au sein d'estuaires selectionnes en Afrique du Sud en vue de leur priorisation pour des efforts de conservation. Trois regions d'ADN (rbcLa, matK et trnH-psbA) ont ete comparees et des phylogenies des communautes ont ete produites pour 270 estuaires. En general, la region matK s'est averee la plus utile pour distinguer les echantillons, avec un taux de 67,4% (sites informatifs de la parcimonie = 418). Des especes tres apparentees formaient des clades qui correspondaient egalement a des types d'habitats estuariens. Les estuaires a forte diversite phylogenetique le long de la cote sud-est etaient associes a une combinaison de deux habitats : la mangrove et les marais salants. La richesse en especes etait fortement et significativement correlee avec la PD (r = 0,93; p < 0,000). Sur la base des distances genetiques moyennes, les estuaires plus temperes (56) presentaient un groupement phylogenetique significatif par rapport aux estuaires subtropicaux (24) (p < 0,05). De meme, sur la base de la distance moyenne entre taxons les plus proches, le groupement phylogenetique le plus eleve et significatif (p < 0,05) a ete observe au sein des estuaires temperes (50) par rapport aux estuaires subtropicaux (12). Cela suggere que la presence de certaines especes vegetales dans les estuaires est conditionnee par des interactions a la fois biotiques et abiotiques. [Traduit par la Redaction] Mots-cles : rbcLa, matK, taux de discrimination des especes, ecologie des communautes phylogenetiques, phylogenetique de la conservation., Introduction DNA barcoding is a taxonomic method that involves sequencing a gene region for specimen identification to species (Hebert et al. 2003). In 2009, the Consortium for the Barcode of [...]

Bacteria are essential components of natural environments. They contribute to ecosystem functioning through roles as mutualists and pathogens for larger species, and as key components of food webs and nutrient cycles. Bacterial communities respond to environmental disturbances, and the tracking of these communities across space and time may serve as indicators of ecosystem health in areas of conservation concern. Recent advances in DNA sequencing of environmental samples allow for rapid and culture-free characterization of bacterial communities. Here we conduct the first metabarcoding survey of bacterial diversity in the waterholes of the Kruger National Park, South Africa. We show that eDNA can be amplified from waterholes and find strongly structured microbial communities, likely reflecting local abiotic conditions, animal ecology, and anthropogenic disturbance. Over timescales from days to weeks we find increased turnover in community composition, indicating bacteria may represent host-associated taxa of large vertebrates visiting the waterholes. Through taxonomic annotation we also identify pathogenic taxa, demonstrating the utility of eDNA metabarcoding for surveillance of infectious diseases. These samples serve as a baseline survey of bacterial diversity in the Kruger National Park, and in the future, spatially distinct microbial communities may be used as markers of ecosystem disturbance, or biotic homogenization across the park. Key words: microbiome, conservation, biomonitoring, 16S, watering holes. Les bacteries sont une composante essentielle des environnements naturels. Elles contribuent au bon fonctionnement des ecosystemes en agissant a titre de mutualistes et d'agents pathogenes sur de plus grandes especes et forment une composante cle dans les reseaux trophiques et les cycles de nutriments. Les communautes bacteriennes repondent aux perturbations environnementales et le suivi de ces communautes dans le temps et l'espace peut fournir des indicateurs de la sante des ecosystemes dans des regions qui presentent un interet en matiere de conservation. De recentes avancees en sequencage d'echantillons environnementaux permettent de caracteriser les communautes bacteriennes de maniere rapide et sans avoir recours a la mise en culture. Dans ce travail, les auteurs realisent le premier travail de meta-codage a barres pour caracteriser la diversite bacterienne dans les points d'eau situes dans le Parc National Kruger en Afrique du Sud. Les auteurs montrent qu'il est possible d'amplifier l'ADNe de ces points d'eau et d'y trouver des communautes microbiennes fortement structurees, ce qui reflete vraisemblablement les conditions abiotiques locales, l'ecologie animale et les perturbations anthropogeniques. Sur une echelle de temps allantde quelques jours aquelques semaines, des changements croissants dans la composition des communautes ont ete observes, ce qui suggere que les bacteries appartiennent a des taxons associes aux grands vertebres qui visitent ces points d'eau. Par le biais d'une annotation taxonomique, des taxons pathogenes sont egalement identifies, ce qui demontre l'utilite du meta-codage a barres de l'ADNe pour la biosurveillance de maladies infectieuses. Ces echantillons serviront de reference pour la diversite bacterienne dans le Parc Kruger et, dans le futur, des communautes microbiennes distinctes sur le plan spatial pourront servir de marqueurs de la perturbation de l'ecosysteme ou d'une homogeneisation biotique dans le parc. [Traduit par la Redaction] Mots-cles : microbiome, conservation, biosurveillance, 16S, points d'eau., Introduction Traditional programs that monitor for early signs of ecosystem degradation require baseline data on the distributions and ecology of species in an ecosystem. DNA barcoding uses differences in conserved [...]

Alien invasive species are problematic both economically and ecologically, particularly on islands. As such, understanding how they interact with their environment is necessary to inform invasive species management. Here, we ask the following questions: What are the main functional traits that correlate with invasion success of alien plants on Robben Island? How does phylogenetic structure shape biotic interactions on the island? Using multiple approaches to explore these questions, we found that alien invasive species flower later during the year and for longer period, although flowering phenology was sensitive to alternative starting date. Additionally, we observed that alien invasive species are mostly abiotically pollinated and are generally hermaphroditic whilst their native counterparts rely on biotic pollinators, flower earlier, and are generally dioecious, suggesting that alien invasive and native species use different ecological niches. Furthermore, we found a facilitative interaction between an alien invasive legume and other invasive plants as predicted by the invasional meltdown hypothesis, but this does not influence the phylogenetic structure of plant communities. Finally, phylogenetically diverse set of native species are less receptive to alien invasive species. Collectively, our findings reveal how biotic interactions and phylogenetic relatedness structure alien invasive--native co-existence. Key words: Acacia cyclops, biological invasions, evolutionary history, functional traits, invasional meltdown, niche partition. Les especes envahissantes sont problematiques tant sur le plan economique qu'ecologique, particulierement sur des iles. En tant que tel, il est necessaire de comprendre comment elles interagissent avec leur environnement pour guider leur gestion. Dans ce travail, les auteurs posent les questions suivantes : Quels sont les principaux caracteres fonctionnels qui sont correles avec le potentiel envahissant des especes exotiques sur Robben Island? Comment la structure phylogenetique faconne-t-elle les interactions biotiques sur l'ile? A l'aide d'approches multiples, les auteurs trouvent que les especes exotiques fleurissent plus tard et pendant une plus longue periode, bien que la phenologie de la floraison etait sensible a une date alternative de debut de floraison. De plus, les auteurs observent que les especes envahissantes sont principalement sujettes a une pollinisation abiotique et sont generalement hermaphrodites, tandis que les especes indigenes beneficient de pollinisateurs biotiques, fleurissent plus tot et sont generalement dioiques, ce qui suggere que les especes exotiques et indigenes occupent des niches ecologiques differentes. Aussi, une interaction facultative entre une legumineuse envahissante et d'autres plantes envahissantes, tel que predit sur la base de l'hypothese de l'effondrement des especes indigenes, a ete observee, mais celle-ci n'influence pas la structure phylogenetique des communautes vegetales. Finalement, des communautes de plantes indigenes qui sont diversifiees sur le plan phylogenetique sont moins sujettes a l'envahissement par des especes exotiques. Ensemble, ces resultats revelent comment les interactions biotiques et la parente phylogenetique influencent la coexistence entre especes exotiques et indigenes. [Traduit par la Redaction] Mots-cles : Acacia cyclops, invasions biologiques, histoire evolutive, caracteres fonctionnels, effondrement des especes indigenes., Introduction The stability and productivity of ecosystems, as well as their ability to provide a diverse set of ecological services, correlate with their phylogenetic structure (Cadotte et al. 2008, 2009; [...]

This open-access special issue features 12 full articles representing emerging trends from the international DNA barcoding community. Several articles highlight how DNA-based techniques are elucidating the species diversity, biogeography, and [...]

Aizoaceae is the largest succulent plant family in the world, including in excess of 1800 species. Despite its richness, a large proportion of its taxa are listed as data deficient and as such, has been identified as the top priority for taxonomic research in South Africa. Limitations to accurate taxonomic identification of taxa in the family may be partly attributed to the degree of technical knowledge required to identify taxa in the Aizoaceae. DNA barcoding may provide an alternative method of identification; however, the suitability of commonly used gene regions has not been tested in the family. Here, we analyse variable and parsimony informative characters (PIC), as well as the barcoding gap, in commonly used plastid regions (atpB-rbcL, matK, psbA-trnH, psbJ-petA, rpl16, rps16, trnD-trnT, trnL-trnF, trnQ-rps16, and trnS-trnG) and the nuclear region ITS (for Aizooideae only) across two subfamilies and two expanded clades within the Aizoaceae. The relative percentage of PIC was much greater in subfamilies Aizooideae and Mesembryanthemoideae than in Ruschioideae. Although nrITS had the highest percentage of PIC, barcoding gap analyses identified neither ITS nor any chloroplast region as suitable for barcoding of the family. From the results, it is evident that novel barcoding regions need to be explored within the Aizoaceae.Key words: Aizooideae, barcoding gap, Mesembryanthemoideae, parsimony informative characters, recent radiation, Ruschioideae, variable characters.La famille des Aizoaceae est la plus grande au monde parmi les plantes succulentes et compte plus de 1800 especes. En depit de sa richesse, une grande proportion de ses taxons sont decrits comme presentant une insuffisance de donnees de telle maniere qu'elle a ete identifiee comme la plus grande priorite en recherche taxonomique en Afrique du Sud. Les carences dans l'identification des taxons au sein de cette famille sont en partie attribuables aux importantes connaissances techniques requises pour identifier les taxons chez les Aizoaceae. Le codage a barres de l'ADN pourrait fournir une methode alternative d'identification. Cependant, la pertinence des regions geniques souvent employees en codage a barres n'a pas encore ete examinee chez cette famille. Dans ce travail, les auteurs ont analyse des caracteres variables et des caracteres informatifs de la parcimonie (PIC), de meme que l'ecart entre taxons, au moyen des regions plastidiques communement employees (atpB-rbcL, matK, psbA-trnH, psbJ-petA, rpl16, rps16, trnD-trnT, trnL-trnF, trnQ-rps16 et trnS-trnG) et la region de l'ITS nucleaire (chez les Aizooideae seulement) parmi deux sous-familles ainsi qu'au sein de deux grands clades chez les Aizoaceae. Le pourcentage du PIC etait beaucoup plus grand au sein des sous-familles des Aizooideae et des Mesembryanthemoideae que chez les Ruschioideae. Bien que la region nrlITS presentait le plus fort pourcentage de PIC, une analyse de l'ecart entre les taxons a indique que ni les ITS ni aucune des regions chloroplastiques ne s'averaient utiles pour le codage a barres au sein de cette famille. En fonction de ces resultats, il est evident que de nouvelles regions de codage a barres devront etre explorees chez les Aizoaceae. [Traduit par la Redaction]Mots-cles: Aizooideae, ecart entre les taxons, Mesembryanthemoideae, caracteres informatifs de la parcimonie, radiation recente, Ruschioideae, caracteres variables., IntroductionAizoaceae is the largest succulent plant family in the world (Chesselet et al. 2002) and the largest angiosperm family represented in the arid regions of the Greater Cape Floristic Region [...]

Abstract: Although a standard DNA barcode has been identified for plants, it does not always provide species-level specimen identifications for investigating important ecological questions. In this study, we assessed the [...]

The two special issues--Barcodes to Biomes--mark the one-year anniversary of the 6th International Barcode of Life Conference held in Guelph, Canada. The 6th Conference brought together 601 delegates from 51 [...]