Taxonomic Biodiversity Research Articles

Biodiversity in agricultural landscapes: Grassy field margins and semi-natural fragments both foster spider diversity and body size

Agricultural intensification is one of the most important drivers of biodiversity loss. To preserve taxonomic diversity in agricultural landscapes, there is an increasing need for refuge areas within agroecosystems, but best practices for providing such sites are debated. Here, we compared the taxonomic diversity and trait composition of spiders, being important terrestrial predators, among cereal fields, grassy field margins, set aside fields sown with wildflowers, and semi-natural sites within an agricultural landscape in western Germany. Spider taxonomic diversity was similarly high in all non-crop habitats, indicating a surprisingly high value of field margins and set-aside fields. Cereal fields, in contrast, were dominated by a few, mainly euryecious species. Moreover, community mean body size was smallest on cereal fields but highest on semi-natural sites, suggesting that spider body size may serve as a valuable indicator of the level of anthropogenic disturbance. Spider communities differed partly among non-crop habitats, stressing the need for combining different conservation measures to maximize taxonomic biodiversity and trait composition. These should also include remnants of natural vegetation, which were especially important for large and red list species and therefore for reaching the aims of nature conservation.

Status of aquatic and riparian biodiversity in artificial lake ecosystems with and without management for recreational fisheries: Implications for conservation

Abstract Humanity is facing a biodiversity crisis, with freshwater‐associated biodiversity in a particularly dire state. Novel ecosystems created through human use of mineral resources, such as gravel pit lakes, can provide substitute habitats for the conservation of freshwater and riparian biodiversity. Many of these artificial ecosystems are subject to a high intensity of recreational use, however, which may limit their biodiversity potential. The species richness of several taxa (plants, amphibians, dragonflies, damselflies, waterfowl, and songbirds) was assessed and a range of taxonomic biodiversity metrics were compared between gravel pit lakes managed for recreational fisheries (n = 16) and unmanaged reference lakes (n = 10), controlling for non‐fishing‐related environmental variation. The average species richness of all the taxa examined was similar among lakes in both lake types and no substantial differences in species composition were found when examining the pooled species inventory. Similarly, there were no differences between lake types in the presence of rare species and in the Simpson diversity index across all of the taxa assessed. Variation in species richness among lakes was correlated with woody habitat, lake morphology (surface area and steepness), and land use, but was not correlated with the presence of recreational fisheries. Thus, non‐fishing‐related environmental variables had stronger effects on local species presence than recreational fisheries management or the presence of recreational anglers. Collectively, no evidence was found that anglers and recreational fisheries management constrain the development of aquatic and riparian biodiversity in gravel pit lakes in the study region; however, the conservation of species diversity in gravel pit lakes could benefit from an increasing reliance on habitat enhancement activities.

Metagenomic Analysis Reveals Bacterial and Fungal Diversity and Their Bioremediation Potential From Sediments of River Ganga and Yamuna in India.

In this study, we report the presence of a microbial community of bioremediation potential in terms of relative abundance and taxonomic biodiversity in sediment samples of river Ganga and Yamuna, India at nine different sites. Metagenomic libraries were constructed using TruSeq Nano DNA Library Prep Kit and sequenced on NextSeq 500 by Illumina Next Generation Sequencing (NGS) technology. Bioremediation bacteria belong to 45 genera with 92 species and fungi belong to 13 genera with 24 species have been classified using Kaiju taxonomical classification. The study revealed that Proteobacteria was the most dominant bacterial flora, followed by Actinobacteria, Firmicutes, and Deinococcus–Thermus. PCA analysis revealed that bioremediation bacteria viz. Streptomyces bikiniensis, Rhodococcus qingshengii, Bacillus aerophilus, Pseudomonas veronii, etc., were more dominant in highly polluted river stretch as compared to less polluted river stretch. Similarly, the relative abundance of bioremediation fungi viz. Phanerochaete chrysosporium and Rhizopus oryzae, etc., were significantly correlated with the polluted Kanpur stretch of river Ganga. Several protein domains, which play a pivotal role in bioremediation in the polluted environments, including urea ABC transporter, UrtA, UrtD, UrtE, zinc/cadmium/mercury/lead-transporting ATPase, etc., were identified using protein domain analysis. The protein domains involved in pesticide biodegradation viz. P450, short-chain dehydrogenases/reductases (SDR), etc., were also discovered in river sediment metagenomics data. This is the first report on the richness of bioremediation microbial communities in the Ganga and Yamuna riverine ecosystems, highlighting their importance in aquatic pollution management.

Ultraconserved element bait set for trypanosomatida target enrichment and phylogenetics

Lack of knowledge of taxonomic biodiversity and reliable genetic markers in Trypanosomatidae limit our understanding of their phylogenetic relationships. Ultraconserved elements (UCEs) have improved phylogenetic analyses and inferences in many vertebrate and invertebrate taxa. However, it is unknown whether protozoans have these markers, their abundance, and if these could be reliably used for phylogenetics. In this study I design a target enrichment bait set for UCE loci for this group. In silico testing showed good loci recovery rates across 63 taxa and produced consistent, highly supported phylogenetic trees. This bait set adds a new resource of useful genetic markers for Trypanosomatidae phylogenetics.

Biodiversity Loss Threatens the Current Functional Similarity of Beta Diversity in Benthic Diatom Communities

The global biodiversity loss has increased the need to understand the effects of decreasing diversity, but our knowledge on how species loss will affect the functioning of communities and ecosystems is still very limited. Here, the levels of taxonomic and functional beta diversity and the effect of species loss on functional beta diversity were investigated in an estuary that provides a naturally steep environmental gradient. The study was conducted using diatoms that are among the most important microorganisms in all aquatic ecosystems and globally account for 40% of marine primary production. Along the estuary, the taxonomic beta diversity of diatom communities was high (Bray-Curtis taxonomic similarity 0.044) and strongly controlled by the environment, particularly wind exposure, salinity, and temperature. In contrast, the functional beta diversity was low (Bray-Curtis functional similarity 0.658) and much less controlled by the environment. Thus, the diatom communities stayed functionally almost similar despite large changes in species composition and environment. This may indicate that, through high taxonomic diversity and redundancy in functions, microorganisms provide an insurance effect against environmental change. However, when studying the effect of decreasing species richness on functional similarity of communities, simulated species loss to 45% of the current species richness decreased functional similarity significantly. This suggests that decreasing species richness may increase variability and reduce the stability and resilience of communities. These results highlight the importance of high taxonomic biodiversity for the stable functioning of benthic communities.

An integrative DNA barcoding framework of ladybird beetles (Coleoptera: Coccinellidae)

Even though ladybirds are well known as economically important biological control agents, an integrative framework of DNA barcoding research was not available for the family so far. We designed and present a set of efficient mini-barcoding primers to recover full DNA barcoding sequences for Coccinellidae, even for specimens collected 40 years ago. Based on these mini-barcoding primers, we obtained 104 full DNA barcode sequences for 104 species of Coccinellidae, in which 101 barcodes were newly reported for the first time. We also downloaded 870 COI barcode sequences (658 bp) from GenBank and BOLD database, belonging to 108 species within 46 genera, to assess the optimum genetic distance threshold and compare four methods of species delimitation (GMYC, bPTP, BIN and ABGD) to determine the most accurate approach for the family. The results suggested the existence of a ‘barcode gap’ and that 3% is likely an appropriate genetic distance threshold to delimit species of Coccinellidae using DNA barcodes. Species delimitation analyses confirm ABGD as an accurate and efficient approach, more suitable than the other three methods. Our research provides an integrative framework for DNA barcoding and descriptions of new taxa in Coccinellidae. Our results enrich DNA barcoding public reference libraries, including data for Chinese coccinellids. This will facilitate taxonomic identification and biodiversity monitoring of ladybirds using metabarcoding.

Inventario florístico y vegetación del cráter de la Alberca de Teremendo, Michoacán, México

Antecedentes y Objetivos: El cráter de la Alberca de Teremendo de los Reyes, municipio Morelia, es una de las tres albercas volcánicas que existen en Michoacán, México. Actualmente, cuenta únicamente con investigaciones enfocadas al estudio de la calidad del agua y las algas, pero carece de un inventario florístico. Los objetivos de este estudio fueron elaborar una lista de la flora vascular y describir su vegetación. Métodos: Se realizaron 27 recorridos en campo entre octubre 2013 y septiembre 2015, realizando recolectas de material vegetal registrando el hábitat, vegetación y forma biológica de las especies. Se describió la vegetación respecto a su composición, estructura y localización. Se calculó el índice de biodiversidad taxonómica para definir la riqueza de especies por hectárea en comparación con otros estudios regionales. Resultados clave: Se registraron 316 especies de plantas y 12 taxa infraespecíficos, pertenecientes a 228 géneros y 85 familias. La familia mejor representada fue Asteraceae con 39 especies (12.3% del total); a nivel genérico fue Euphorbia con siete especies (2.2%); herbáceas dominan con 235 taxones (74.1%). La vegetación que se describe corresponde a una comunidad vegetal de matorral subtropical, la cual es la mejor representada por la superficie que abarca con aproximadamente 57.3 ha, asociada con elementos de bosque tropical caducifolio, vegetación acuática y subacuática, pastizal y plantas arvenses. Conclusiones: La zona de estudio cuenta con 3.8% de las especies registradas para el estado y 2% de las registradas al municipio. Tiene la mayor afinidad genérica y específica (63.9 y 38.8%, respectivamente) con el cerro del Quinceo. La Alberca de Teremendo destaca florísticamente, ya que en una superficie de extensión limitada (108 ha), alberga una vasta flora con 67.6 especies por ha. Tres especies están en la NOM-059-SEMARNAT-2010: una en la categoría de Amenazada (Erythrina americana) y dos Sujetas a protección especial (Gentiana spathacea y Cedrela odorata).

Marine diatom assemblages of the Nosy Be Island coasts, NW Madagascar: species composition and biodiversity using molecular and morphological taxonomy

Madagascar is an isolated oceanic island characterized by high degrees of endemism at all taxonomic levels. The waters surrounding Madagascar are still poorly studied for benthic marine diatom assemblages. The aim of our study was to analyse the taxonomic biodiversity and molecular phylogeny of the diatom assemblages of the Nosy Be archipelago in terms of their ubiquity/rarity. A total of 65 samples from 14 sampling sites were collected from the Nosy Be and Nosy Tanikely islands in June/July 2014. Diatom identification, based on light and electron microscopic examination, revealed 332 diatom taxa. From those, ∼90 strains were isolated and successfully cultured. So far, DNA has been extracted and one chloroplast gene (rbcL) sequenced from 21 strains in order to reconstruct their single gene phylogeny. Taxa selected for sequencing and the preliminary phylogeny are from genera considered common benthic and planktonic forms in the marine littoral: Bellerochea, Melosira, Paralia, Triceratium, Navicula, Hippodonta, Auricula, Nitzschia, Cocconeis, and some araphids. For each site, Shannon and Simpson biodiversity indices were calculated. Diatom assemblages of Nosy Be were characterized by high biodiversity. The most abundant species was Cocconeis scutellum. Whereas some of the cultured taxa seem to represent cosmopolitan or zonal forms: e.g., Bellerochea malleus, Triceratium dubium, Melosira lineata, Paralia crawfordii, or Nitzschia inconspicua, most of the taxa isolated in culture and sequenced have not been observed in earlier works based on use of molecular markers. The dominant taxa were generally those with broad geographic distribution with global/Indo-Pacific affinities. Amongst all 332 taxa, only 35% have been identified to the species level. Many of the taxa identified to the generic level may turn out to represent taxa new to science after further SEM examination and DNA sequencing.

Role of benthic habitat structure and riverine connectivity in controlling the spatial distribution and ecology of estuarine fish

Estuaries are among the most productive ecosystems per unit area, but this productivity is unevenly distributed across a complex mosaic of habitats. Identifying the qualities of different habitats that influence the composition and productivity of biotic communities is fundamental to understanding the dynamics of these ecosystems. We combined field surveys, hydrological modelling and stable isotope analysis to understand the roles of habitat, hydrological connectivity, salinity and temperature in determining assemblage composition, species abundance and trophic ecology of an estuarine fish community. Hydrodynamics, vegetation matrices of macroalgae and seagrass and the presence of epiphytes on vegetation explained spatial patterns in taxonomic biodiversity, multivariate assemblage structure and the occurrence of juvenile black bream Acanthopagrus butcheri, a species that possesses ecological traits common tomany demersal estuarine fish species. Juvenile bream abundance was related to vegetation composition (particularly epiphyte presence), supporting the hypothesis that juvenile habitats that provided resources or conditions that ex - tended beyond just structure conferredmore ecological advantages. This was further evidenced by stable isotope-based estimates of basal resource contributions of epiphytes. Our findings suggest that hydrodynamic connectivity with riverine water masses acts as a coarse determinant for estuarine fish communities at large spatial scales. At smaller scales, habitat-level associations influence local abundances and the identity and importance of specific trophic resources. Coupling hydro - dynamic modellingwith natural biomarkers provides a powerful approach for assessing the spatial context of habitat use that can help resource managers prioritize monitoring and habitat preservation efforts for coastal fish communities in a changing global environment.

Development of a DNA Barcoding Protocol for Fungal Specimens from the E.C. Smith Herbarium (ACAD)

Many field-collected fungal specimens are maintained in herbaria worldwide. These specimens contain an untapped wealth of taxonomic and ecological fungal biodiversity information. However, DNA can be difficult to obtain from preserved specimens. We present a DNA barcoding protocol specifically for preserved fungal specimens (ascomycetes and basidiomycetes). The E.C. Smith Herbarium at Acadia University houses 20,000 fungal specimens representative of northeastern North America. We achieved a DNA barcoding success rate of 18% from pre-1980 specimens (n = 39) using a kit-based DNA extraction protocol and sequencing of the full internal transcribed spacer (ITS) region of ribosomal DNA. This result surpassed success rates of previous protocols. We also explored the use of mini-barcodes from the ITS1 region only. Mini-barcodes (n = 13) demonstrated a 92% success rate in post-1980 specimens compared to full barcodes (46% success rate, n = 13) while retaining all the identification power of full barcodes in the examined specimens. Our approach will enable herbarium collections to be used more efficiently to populate DNA sequence databases such as GenBank. This approach will expand the number of reference DNA barcode sequences from vouchered fungal specimens within publicly available databases.

Molecular characterization of six widespread avian haemoproteids, with description of three new Haemoproteus species

Species of Haemoproteus (Haemosporida, Haemoproteidae) are widespread and often prevalent blood parasites of birds all over the word. They are particularly diverse in tropical countries. Due to limited knowledge of life cycles, these pathogens usually have been considered relatively benign and were neglected in veterinary medicine and bird management. However, recent molecular studies provided evidence that Haemoproteus parasites might cause severe diseases if they infect non–adapted (wrong) avian hosts due to marked damage of organs by exo-erythrocytic stages (megalomeronts). Additionally, high Haemoproteus infections are lethal to blood-sucking insects. Molecular markers are essential for reliable detection and species identification both at tissue stages in vertebrates and sporogonic stages in arthropods however, remain insufficiently developed for wildlife haemosporidian parasites. This study combined PCR-based and microscopic approaches and reported cytochrome b gene (cytb) and apicoplast gene (clpc) markers for characterization of six widespread species of haemoproteids parasitizing common birds wintering in tropics and subtropics of the Old World. Three new Haemoproteus species were described using morphological and molecular markers. Molecular characterization of haemoproteids parasitizing falcons was developed. Morphological and phylogenetic characterization of Haemoproteus tinnunculi (cytb lineage hFALSUB01), H. brachiatus (hLK03), H. parabelopolskyi (hSYAT1), H. homogeneae n. sp. (hSYAT16), H. homopicae n. sp. (hGAGLA07) and H. homominutus n. sp. (hCUKI1) was performed and provides clues for infections diagnostics. This study adds three species to the group of morphologically readily distinct Haemoproteus parasites, which differ in few base pairs (< 1%) in their partial cytb sequences, indicating that low genetic difference in such sequences often show between-species divergence and should be carefully applied in taxonomic biodiversity studies of haemosporidian parasites. Bayesian phylogenetic analysis identified the position of detected lineages in regard of other Haemoproteus species, suggesting that all reported parasites belong to subgenus Parahaemoproteus and likely are transmitted by Culicoides biting midges. Importance of clpc gene sequences was specified in haemosporidian parasite taxonomy on species levels.

Diversity and distribution patterns of benthic insects in streams of the Aurès arid region (NE Algeria)

AbstractThe objective of the present study was to document the knowledge about the biodiversity of benthic insect communities and their distribution patterns in the semi-arid bioclimatic stage in the streams of the Aurès Region (NE Algeria). The distribution patterns of communities were analyzed in relation to some environmental factors: physicochemical water parameters and global habitat characteristics, including human impact. The taxonomic biodiversity of six sampled streams (wadis) comprises 42 insect taxa, belonging to seven orders and 30 families, of which Coleoptera is the most diverse order (15 taxa), whereas Diptera, Trichoptera and Ephemeroptera dominate in terms of abundance. The human impact, flow velocity and some quality parameters of water (potential of hydrogen, nitrite, concentration of orthophosphates and conductivity) were identified as the most influential environmental variables, which allows the prediction of taxonomic diversity indicators. The classification and regression tree analysis (CART) for benthic insects shows the effect of environmental variables (habitat parameters and human impact in the arid region) on the diversity and distribution of insect orders. The RDA analysis showed that altitude, substrate type, human impact and physicochemical parameters of water (pH, flow velocity, conductivity and total dissolved solids) are the most important predictor variables that play an important role in the distribution patterns of benthic insects.

Guild-level responses of bats to habitat conversion in a lowland Amazonian rainforest: species composition and biodiversity.

Landscape modification represents one of the most severe threats to biodiversity from local to global scales. Conversion of forest to agricultural production generally results in patches of habitat that subdivide or isolate populations, alter the behavior of species, modify interspecific interactions, reduce biodiversity, and compromise ecosystem processes. Moreover, conversion may increase exposure of humans to zoonoses to which they would otherwise rarely be exposed. We evaluated the effects of forest conversion to agriculture, and its subsequent successional dynamics, on bat communities in a region of the Amazon that was predominantly closed-canopy rainforest. Based on a nonmanipulative experiment, we quantified differences in species composition, community structure, and taxonomic biodiversity among closed-canopy forest (bosque), agricultural lands (chacra), and secondary forest (purma) for two phyllostomid guilds (frugivores and gleaning animalivores) during the wet and dry seasons. Responses were complex and guild-specific. For frugivores, species composition (species abundance distributions) differed between all possible pairs of habitats in both wet and dry seasons. For gleaning animalivores, species composition differed between all possible pairs of habitats in the dry season, but no differences characterized the wet season. Ecological structure (rank abundance distributions) differed among habitats in guild-specific and season-specific manners. For frugivores, mean diversity, evenness, and dominance were greater in bosque than in purma; mean dominance was greater in bosque than in chacra, but local rarity was greater in chacra than in bosque, and no differences were manifest between purma and chacra. For gleaning animalivores, mean diversity and evenness were greater in bosque than in purma, but no differences were manifest between chacra and bosque, or between purma and chacra. Such results have important implications for management, conservation, and the epidemiology of zoonotic diseases.La actual modificación del paisaje, a escalas que van de lo local a lo global, es una de las amenazas más severas a la biodiversidad. De manera general, la conversión de bosques a áreas agrícolas produce parches de hábitat que subdividen o aíslan poblaciones, alteran la conducta de las especies, modifican las interacciones interespecíficas, reducen la biodiversidad y comprometen las funciones de los ecosistemas. Más aún, la transformación de estos ambientes puede incrementar la probabilidad de que las poblaciones humanas interactúen con zoonosis con las que de otra manera raramente entrarían en contacto. Evaluamos los efectos de la conversión de hábitat en comunidades de murciélagos en una región de Amazonia en la que la vegetación dominante es un bosque lluvioso de copas cerradas, y en la cual los efectos de la conversión a usos agrícolas sobre la biodiversidad, y la subsecuente dinámica sucesional, son aún poco comprendidos. Por medio de un experimento no-manipulativo, cuantificamos las diferencias en composición de especies, estructura de la comunidad y diversidad taxonómica entre bosque cerrado (bosque), áreas agrícolas (chacra) y bosque secundario (purma) para dos gremios tróficos de murciélagos filostómidos (frugívoros y forrajeadores de sustrato) durante dos temporadas (secas y lluvias). Las respuestas fueron complejas y diferentes para cada gremio. Para los frugívoros, la composición de especies (distribución de las abundancias) fue diferente para todos los posibles pares de hábitats tanto para secas como para lluvias. Para los forrajeadores de sustrato, la composición de especies difirió entre todos los posibles pares de hábitats en la temporada seca, pero no en la de lluvias. La estructura ecológica (distribuciones rango-abundancia) fue también específica para gremios y temporadas. Para los frugívoros, la diversidad promedio, equidad y dominancia fueron mayores en bosque que en purma; la dominancia promedio fue mayor en bosque que en chacra, pero la rareza local fue mayor en chacra que en bosque, y no se encontraron diferencias entre purma y chacra. Para los forrajeadores de sustrato, la diversidad promedio y la dominancia fueron mayores en bosque que en purma, pero no se detectaron diferencias entre chacra y bosque, o entre purma y chacra. Estos resultados tienen importantes implicaciones para el manejo, conservación y epidemiología de zoonosis.

The spatial configuration of taxonomic biodiversity along a tropical elevational gradient: α‐, β‐, and γ‐partitions

AbstractBiodiversity at larger spatial scales (γ) can be driven by within‐site partitions (α), with little variation in composition among locations, or can be driven by among‐site partitions (β) that signal the importance of spatial heterogeneity. For tropical elevational gradients, we determined the (a) extent to which variation in γ is driven by α‐ or β‐partitions; (b) elevational form of the relationship for each partition; and (c) extent to which elevational gradients are molded by zonation in vegetation or by gradual variation in climatic or abiotic characteristics. We sampled terrestrial gastropods along two transects in the Luquillo Mountains. One passed through multiple vegetation zones (tabonuco, palo colorado, and elfin forests), and one passed through only palm forest. We quantified variation in hierarchical partitions (α, β, and γ) of species richness, evenness, diversity, and dominance, as well as in the content and quality of litter. Total gastropod abundance linearly decreased with increasing elevation along both transects, but was consistently higher in palm than in other forest types. The gradual linear decline in γ‐richness was a consequence of opposing patterns with regard to α‐richness (monotonic decrease) and β‐richness (monotonic increase). For evenness, diversity, and dominance, α‐partitions and γ‐partitions evinced mid‐elevational peaks. The spatial organization of gastropod biodiversity did not mirror the zonation of vegetation. Rather, it was molded by: (a) elevational variation in productivity or nutrient characteristics, (b) the interspersion of palm forest within other forest types, and (c) the cloud condensation point acting as a transition between low and high elevation faunas.Abstract in Spanish is available with online material.

First inventory of benthic mollusks associated with the reef ecosystems of Morro de São Paulo on Tinharé Island in northeastern Brazil

Abstract: The reef ecosystems of Morro de São Paulo are located in the Tinharé-Boipeba Environmental Preservation Area which was established in 1992 in the state of Bahia, Brazil. Despite this area has been created more than two decades ago, no study has provided knowledge on the invertebrate biodiversity associated with such reef ecosystems. The present investigation provides the first inventory of benthic mollusks associated with the reef ecosystems of Morro de São Paulo based on the collection of living specimens and fresh empty as well as some worn shells. Mollusks were sampled in January 2015 and August 2016 through intensive searches from the intertidal to shallow subtidal habitats of the reefs on three beaches of Morro de São Paulo. Taxonomic richness and biodiversity indices were analyzed. This rapid assessment of the malacofauna resulted in the determination of 84 species belonging to 44 families of gastropods as well as 13 species belonging to eight families of bivalves and one chiton (total: 98 species). Species richness was numerically dominated by members of the subclass Caenogastropoda. The families with the largest number of species were Ranellidae (5), Muricidae (6) and Marginellidae (7). Conus regius, Cypraecassis testiculus, Lobatus goliath, Strombus pugilis, Tonna galea, Turbinella laevigata and Vasum cassiforme are extremely vulnerable macrospecies in the region due to their commercial importance. Comparisons of the malacofauna composition between the study site and Abrolhos Bank were made from data published for this region. ACE and CHAO 1 estimated 133 mollusk species for the region. Despite the rapid assessment, the number of species discovered in the study area approached 73.6% of the estimated total number. The considerable number of mollusk species found in a relatively small area with insufficient sampling underscores the importance of the reef ecosystems of Morro de São Paulo as a one priority area for conservation on the coast of the state of Bahia, Brazil, for which the species richness of other invertebrate groups is virtually unknown.

Taxonomic and functional facets of the resilience to management of mown subalpine grasslands

AbstractQuestionsSustaining ecosystem services for society in the face of global change is a major challenge. Resilience, an ecosystem's ability to absorb disturbance and return to its initial functioning, is critical for this. We assessed the resilience of mown subalpine grasslands following restoration management. Using a novel multi‐indicator approach, we asked how different taxonomic and functional facets of biodiversity influence resilience mechanisms. We demonstrated this approach for a case study in subalpine grasslands, asking: how resilient are grasslands dominated by Patzkea paniculata and their agronomic services to changing mowing regimes?LocationVillar d'Arène, Hautes‐Alpes, Provence‐Alpes‐Côte d'Azur, France. Boundary area of Ecrins National Park.MethodsA manipulative experiment tested the reciprocal effects of mowing cessation and mowing resumption for 10 years. We analysed floristic composition data following four steps. First, we used the Community Structure Integrity Index (CSII; Jaunatre et al., ) to obtain qualitative and quantitative summaries of taxonomic responses. The second step focused on taxonomic biodiversity using species richness, Simpson and Pielou indices, and responsive species identified in the first step. Third, we analysed functional diversity responses using functional groups and community weighted mean (CWM) of vegetative plant traits. Finally, we quantified ecosystem services impacts by estimating fodder quantity and quality using trait‐based models.ResultsThe mowing manipulation demonstrated the high resilience of P. paniculata grasslands and revealed reversibility of transitions between mown and unmown states. By reducing the abundance of P. paniculata, the resumption of mowing restored forage quality. Supported by a complementary case study on post‐disturbance re‐sowing in hay meadows, this study demonstrates the resilience of mown subalpine grasslands to management change and explores underlying belowground mechanisms of vegetative regeneration and belowground reserves.ConclusionOur novel multi‐indicator approach provides multifaceted mechanistic understanding necessary to anticipate impacts of socio‐ecological changes and to maintain the multiple benefits of mountain grasslands. Addressing the different facets of biodiversity from abundance data that are systematically collected in impact or monitoring assessment, this approach provides a common framework, widely applicable to different types of restoration or management interventions, across regions and biota.

The functional response and resilience in small waterbodies along land-use and environmental gradients.

There is growing recognition of the essential services provided to humanity by functionally intact ecosystems. Freshwater ecosystems are found throughout agricultural and urban landscapes and provide a wide range of ecosystem services, but globally they are also amongst the most vulnerable. In particular, ponds (lentic waters typically less than 2ha), provide natural flood management, sequester carbon and hold significant cultural value. However, to inform their management it is important to understand (1) how functional diversity varies in response to disturbance and (2) the link between biodiversity conservation and ecosystem function. In this study, a meta-analysis of seven separate pond studies from across England and Wales was carried out to explore the effect of urban and agricultural land-use gradients, shading, emergent vegetation, surface area and pH upon groups of functionally similar members of the macroinvertebrate fauna. Functional effect groups were first identified by carrying out a hierarchical cluster analysis using body size, voltinism and feeding habits (18 categories) that are closely related to biogeochemical processes (e.g. nutrient and carbon recycling). Secondly, the influence of the gradients upon effect group membership (functional redundancy-FR) and the breadth of traits available to aid ecosystem recovery (response diversity) was assessed using species counts and functional dispersion (FDis) using 12 response traits. The effect of land-use gradients was unpredictable, whilst there was a negative response in both FR and FDis to shading and positive responses to increases in emergent vegetation cover and surface area. An inconsistent association between FDis and FR suggested that arguments for taxonomic biodiversity conservation to augment ecosystem functioning are too simplistic. Thus, a deeper understanding of the response of functional diversity to disturbance could have greater impact with decision-makers who may relate better to the loss of ecosystem function in response to environmental degradation than species loss alone.

First Metagenomic Survey of the Microbial Diversity in Bioaerosols Emitted in Waste Sorting Plants.

Waste sorting activities are source of occupational bioaerosol exposures that are associated with several health disorders. New analytical tools, based on next-generation sequencing (NGS) technologies, provide powerful methods to assess the microbial composition of bioaerosols. The objectives of the study were (i) to assess the feasibility and the repeatability of NGS-based biodiversity measurements and (ii) to study the microbial biodiversity using NGS in bioaerosols emitted in a waste sorting plant (WSP). Three stationary parallel samples were collected in a sorting cabin using closed-face cassettes equipped with polycarbonate membranes. Bacterial and fungal diversity was assessed by sequencing 16S and 18S rDNA genes using either Illumina sequencing or 454 pyrosequencing methods. At sampling point, airborne bacteria were dominated by Proteobacteria, Firmicutes, and Actinobacteria with prevailing genera assigned to unclassified Enterobacteriaceae, Staphylococcus, Acinetobacter, Leuconostoc, Pseudomonas, and Lactobacillus. Airborne fungi were dominated by Ascomycota with prevailing genera assigned to Penicillium, Aspergillus, Rhizopus, Wallemia, and Hemicarpenteles. The NGS biodiversity measurements revealed a higher biodiversity bioaerosols that previously reported for WSP in studies carried out using culture methods followed by identification of microorganisms. These results provide the first survey about taxonomic biodiversity in bioaerosols from WSPs using high-throughput sequencing.

SeqDB: Biological Collection Management with Integrated DNA Sequence Tracking

Agriculture and Agri-Food Canada (AAFC) is home to a world-class taxonomy program based on Canada’s national agricultural collections for Botany, Mycology and Entomology. These collections contain valuable resources, such as type specimen for authoritative identification using approaches that include phenotyping, DNA barcoding, and whole genome sequencing. These authoritative references allow for accurate identification of the taxonomic biodiversity found in environmental samples in fields such as metagenomics. AAFC’s internally developed web application, termed SeqDB, tracks the complete workflow and provenance chain from source specimen information through DNA extractions, PCR reactions, and sequencing leading to binary DNA sequence files. In the context of Next Generation Sequencing (NGS) of environmental samples, SeqDB tracks sampling metadata, DNA extractions, and library preparation workflow leading to demultiplexed sequence files. SeqDB implements the Taxonomic Databases Working Group (TDWG) Darwin Core standard Wieczorek et al. 2012 for Biodiversity Occurrence Data, as well as the Genome Standards Consortium (GSC) Minimum Information about any (X) Sequences (MIxS) specification Yilmaz et al. 2011. When coupled with the built-in data standards validation system, this has led to the ability to search consistent metadata across multiple studies. Furthermore, the application enables tracking the physical storage of the aforementioned specimens and their derivative molecular extracts using an integrated barcode printing and reading system. All the information is presented using a graphical user interface that features intuitive molecular workflows as well as a RESTful API that facilitates integration with external applications and programmatic access of the data. The success of SeqDB has been due to the close collaboration with scientists and technicians undertaking molecular research involving the national collection, and the centralization of their data sets in an access controlled relational database implementing internationally recognized standards. We will describe the overall system, and some of our lessons learned in building it.

Bacterial Physiological Adaptations to Contrasting Edaphic Conditions Identified Using Landscape Scale Metagenomics.

ABSTRACTEnvironmental factors relating to soil pH are important regulators of bacterial taxonomic biodiversity, yet it remains unclear if such drivers affect community functional potential. To address this, we applied whole-genome metagenomics to eight geographically distributed soils at opposing ends of a landscape soil pH gradient (where “low-pH” is ~pH 4.3 and “high-pH” is ~pH 8.3) and evaluated functional differences with respect to functionally annotated genes. First, differences in taxonomic and functional diversity between the two pH categories were assessed with respect to alpha diversity (mean sample richness) and gamma diversity (total richness pooled for each pH category). Low-pH soils, also exhibiting higher organic matter and moisture, consistently had lower taxonomic alpha and gamma diversity, but this was not apparent in assessments of functional alpha and gamma diversity. However, coherent changes in the relative abundances of annotated genes between low- and high-pH soils were identified; with strong multivariate clustering of samples according to pH independent of geography. Assessment of indicator genes revealed that the acidic organic-rich soils possessed a greater abundance of cation efflux pumps, C and N direct fixation systems, and fermentation pathways, indicating adaptations to both acidity and anaerobiosis. Conversely, high-pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings highlight the distinctive physiological adaptations required for bacteria to survive in soils of various nutrient availability and edaphic conditions and more generally indicate that bacterial functional versatility with respect to functional gene annotations may not be constrained by taxonomy.