Two decades of climate driving the dynamics of functional and taxonomic diversity of a tropical small mammal community in western Mexico.

PubMed

Mason-Romo, Edgard David; Farías, Ariel A; Ceballos, Gerardo

2017-01-01

Understanding the effects of global climate disruption on biodiversity is important to future conservation efforts. While taxonomic diversity is widely studied, functional diversity of plants, and recently animals, is receiving increasing attention. Most studies of mammals are short-term, focus on temperate habitats, and rely on traits described in the literature rather than generating traits from observations. Unlike previous studies, this long-term field study assessed the factors driving the functional and taxonomic diversity of small-mammal assemblages in dry tropical forests using both traits recorded from literature and a demographic database. We assessed the drivers (abundance and biomass, temperature and rainfall) of taxonomic richness and functional diversity for two rain-driven seasons in two adjacent but distinct forests-upland and lowland (arroyo or riparian) forests. Our analysis found that rainfall, both seasonal and atypical, was the primary factor driving functional and taxonomic diversity of small-mammal assemblages. Functional responses differed between the two types of forests, however, with effects being stronger in the harsher conditions of the upland forests than in the less severe conditions prevailing in the arroyo (riparian) forest. The latter also supports a richer, more diverse, and more stable small-mammal assemblage. These findings highlight the importance of climate to tropical biological diversity, as extreme climate events (hurricanes, droughts and floods) and disruption of rainfall patterns were shown to decrease biodiversity. They also support the need to preserve these habitats, as their high taxonomic diversity and functional redundancy makes them resilient against global climate disruption and local extreme events. Tropical dry forests constitute a potential reservoir for biodiversity and the ecosystem services they provide. Unfortunately, these forests are among the most endangered terrestrial ecosystems because of deforestation and the likely impacts of global climate disruption.

The complex roles of space and environment in structuring functional, taxonomic and phylogenetic beta diversity of frogs in the Atlantic Forest

PubMed Central

Luiz, Amom Mendes; Sawaya, Ricardo J.

2018-01-01

Ecological communities are complex entities that can be maintained and structured by niche-based processes such as environmental conditions, and spatial processes such as dispersal. Thus, diversity patterns may be shaped simultaneously at different spatial scales by very distinct processes. Herein we assess whether and how functional, taxonomic, and phylogenetic beta diversities of frog tadpoles are explained by environmental and/or spatial predictors. We implemented a distance–based redundancy analysis to explore variation in components of beta diversity explained by pure environmental and pure spatial predictors, as well as their interactions, at both fine and broad spatial scales. Our results indicated important but complex roles of spatial and environmental predictors in structuring phylogenetic, taxonomic and functional beta diversities. The pure fine-scales spatial fraction was more important in structuring all beta diversity components, especially to functional and taxonomical spatial turnover. Environmental variables such as canopy cover and vegetation structure were important predictors of all components, but especially to functional and taxonomic beta diversity. We emphasize that distinct factors related to environment and space are affecting distinct components of beta diversity in different ways. Although weaker, phylogenetic beta diversity, which is structured more on biogeographical scales, and thus can be represented by spatially structured processes, was more related to broad spatial processes than other components. However, selected fine-scale spatial predictors denoted negative autocorrelation, which may be revealing the existence of differences in unmeasured habitat variables among samples. Although overall important, local environmental-based processes explained better functional and taxonomic beta diversity, as these diversity components carry an important ecological value. We highlight the importance of assessing different components of diversity patterns at different scales by spatially explicit models in order to improve our understanding of community structure and help to unravel the complex nature of biodiversity. PMID:29672575

Oligonucleotide fingerprinting of rRNA genes for analysis of fungal community composition.

PubMed

Valinsky, Lea; Della Vedova, Gianluca; Jiang, Tao; Borneman, James

2002-12-01

Thorough assessments of fungal diversity are currently hindered by technological limitations. Here we describe a new method for identifying fungi, oligonucleotide fingerprinting of rRNA genes (OFRG). ORFG sorts arrayed rRNA gene (ribosomal DNA [rDNA]) clones into taxonomic clusters through a series of hybridization experiments, each using a single oligonucleotide probe. A simulated annealing algorithm was used to design an OFRG probe set for fungal rDNA. Analysis of 1,536 fungal rDNA clones derived from soil generated 455 clusters. A pairwise sequence analysis showed that clones with average sequence identities of 99.2% were grouped into the same cluster. To examine the accuracy of the taxonomic identities produced by this OFRG experiment, we determined the nucleotide sequences for 117 clones distributed throughout the tree. For all but two of these clones, the taxonomic identities generated by this OFRG experiment were consistent with those generated by a nucleotide sequence analysis. Eighty-eight percent of the clones were affiliated with Ascomycota, while 12% belonged to BASIDIOMYCOTA: A large fraction of the clones were affiliated with the genera Fusarium (404 clones) and Raciborskiomyces (176 clones). Smaller assemblages of clones had high sequence identities to the Alternaria, Ascobolus, Chaetomium, Cryptococcus, and Rhizoctonia clades.

Biodiversity Analysis of Forest Litter Ant Assemblages in the Wayanad Region of Western Ghats Using Taxonomic and Conventional Diversity Measures

PubMed Central

Anu, Anto; Sabu, Thomas K.

2007-01-01

The diversity of litter ant assemblages in evergreen, deciduous and Shola evergreen (Shola) forest vegetation types of the Wayanad region of the Western Ghats was assessed employing conventional and taxonomic diversity indices. Non-dependence on quantitative data and the ability to relate the phylogenetic structure of assemblages with ecological conditions of the habitat, and to ascertain priorities for conservation of habitats, makes non-parametric taxonomic diversity measures, such as variation in taxonomic distinctness Λ+ and average taxonomic distinctness Δ+, highly useful tools for assessment of litter ant biodiversity. Although Δ+ values saturated leading to closer values for the 3 litter ant assemblages, Λ+ proved to be a more dependable index. Evenness in taxonomic spread was high in ant assemblages in deciduous forests and low in evergreen forests compared to the regional master list. Low Λ+ of ant assemblage in deciduous forests indicates that among the 3 forest vegetation types, deciduous forests provided the most favorable habitat conditions for litter ants. Low evenness, as is indicated by Λ+ in evergreen forests, was attributed to the presence of a group of taxonomically closely related ant assemblage more adapted to prevail in moist and wet ecological conditions. PMID:20334594

Asian longhorned beetle complicates the relationship between taxonomic diversity and pest vulnerability in street tree assemblages

EPA Science Inventory

Urban foresters routinely emphasise the importance of taxonomic diversity to reduce the vulnerability of tree assemblages to invasive pests, but it is unclear to what extent diversity reduces vulnerability to polyphagous (i.e. generalist) pests. Drawing on field data from seven c...

Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages

PubMed Central

Aguirre, Luis F.; Montaño-Centellas, Flavia A.; Gavilanez, M. Mercedes; Stevens, Richard D.

2016-01-01

Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional diversity, highlighting the need for examining different dimensions of biodiversity of bats in hyperdiverse ecosystems. PMID:27384441

Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages.

PubMed

Aguirre, Luis F; Montaño-Centellas, Flavia A; Gavilanez, M Mercedes; Stevens, Richard D

2016-01-01

Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional diversity, highlighting the need for examining different dimensions of biodiversity of bats in hyperdiverse ecosystems.

Beta-diversity of ectoparasites at two spatial scales: nested hierarchy, geography and habitat type.

PubMed

Warburton, Elizabeth M; van der Mescht, Luther; Stanko, Michal; Vinarski, Maxim V; Korallo-Vinarskaya, Natalia P; Khokhlova, Irina S; Krasnov, Boris R

2017-06-01

Beta-diversity of biological communities can be decomposed into (a) dissimilarity of communities among units of finer scale within units of broader scale and (b) dissimilarity of communities among units of broader scale. We investigated compositional, phylogenetic/taxonomic and functional beta-diversity of compound communities of fleas and gamasid mites parasitic on small Palearctic mammals in a nested hierarchy at two spatial scales: (a) continental scale (across the Palearctic) and (b) regional scale (across sites within Slovakia). At each scale, we analyzed beta-diversity among smaller units within larger units and among larger units with partitioning based on either geography or ecology. We asked (a) whether compositional, phylogenetic/taxonomic and functional dissimilarities of flea and mite assemblages are scale dependent; (b) how geographical (partitioning of sites according to geographic position) or ecological (partitioning of sites according to habitat type) characteristics affect phylogenetic/taxonomic and functional components of dissimilarity of ectoparasite assemblages and (c) whether assemblages of fleas and gamasid mites differ in their degree of dissimilarity, all else being equal. We found that compositional, phylogenetic/taxonomic, or functional beta-diversity was greater on a continental rather than a regional scale. Compositional and phylogenetic/taxonomic components of beta-diversity were greater among larger units than among smaller units within larger units, whereas functional beta-diversity did not exhibit any consistent trend regarding site partitioning. Geographic partitioning resulted in higher values of beta-diversity of ectoparasites than ecological partitioning. Compositional and phylogenetic components of beta-diversity were higher in fleas than mites but the opposite was true for functional beta-diversity in some, but not all, traits.

Functional Diversity as a New Framework for Understanding the Ecology of an Emerging Generalist Pathogen.

PubMed

Morris, Aaron; Guégan, Jean-François; Benbow, M Eric; Williamson, Heather; Small, Pamela L C; Quaye, Charles; Boakye, Daniel; Merritt, Richard W; Gozlan, Rodolphe E

2016-09-01

Emerging infectious disease outbreaks are increasingly suspected to be a consequence of human pressures exerted on natural ecosystems. Previously, host taxonomic communities have been used as indicators of infectious disease emergence, and the loss of their diversity has been implicated as a driver of increased presence. The mechanistic details in how such pathogen-host systems function, however, may not always be explained by taxonomic variation or loss. Here we used machine learning and methods based on Gower's dissimilarity to quantify metrics of invertebrate functional diversity, in addition to functional groups and their taxonomic diversity at sites endemic and non-endemic for the model generalist pathogen Mycobacterium ulcerans, the causative agent of Buruli ulcer. Changes in these metrics allowed the rapid categorisation of the ecological niche of the mycobacterium's hosts and the ability to relate specific host traits to its presence in aquatic ecosystems. We found that taxonomic diversity of hosts and overall functional diversity loss and evenness had no bearing on the mycobacterium's presence, or whether the site was in an endemic area. These findings, however, provide strong evidence that generalist environmentally persistent bacteria such as M. ulcerans can be associated with specific functional traits rather than taxonomic groups of organisms, increasing our understanding of emerging disease ecology and origin.

Partitioning taxonomic diversity of aquatic insect assemblages ...

EPA Pesticide Factsheets

Biological diversity can be divided into: alpha (α, local), beta (β, difference in assemblage composition among locals), and gamma (γ, total diversity). We assessed the partitioning of taxonomic diversity of Ephemeroptera, Plecoptera and Trichoptera (EPT) and of functional feeding groups (FFG) in Neotropical Savanna (southeastern Brazilian Cerrado) streams. To do so, we considered three diversity components: stream site (α), among stream sites (β1), and among hydrologic units (β2). We also evaluated the association of EPT genera composition with heterogeneity in land use, instream physical habitat structure, and instream water quality variables. The percent of EPT taxonomic α diversity (20.7%) was lower than the β1 and β2 diversities (53.1% and 26.2%, respectively). The EPT FFG α diversity (26.5%) was lower than the β1 diversity (55.8%) and higher than the β2 (17.7%) diversity. The collector-gatherer FFG was predominant and had the greatest β diversity among stream sites (β1, 55.8%). Our findings support the need for implementing regional scale conservation strategies in the Cerrado biome, which has been degraded by anthropogenic activities. Using adaptations of the US EPA’s National Aquatic Resource Survey (NARS) designs and methods, Ferreira and colleagues examined the distribution of taxonomic and functional diversity of aquatic insects among basins, stream sites within basins, and within stream sample reaches. They sampled 160 low-order stre

Functional and Taxonomic Diversity of Stinging Wasps in Brazilian Atlantic Rainforest Areas.

PubMed

Dos Santos, E F; Noll, F B; Brandão, C R F

2014-04-01

Vespoidea are the most functionally diverse superfamily of Hymenoptera. Ecological studies involving this family are primarily based on eusocial groups, including ants and social paper wasps. In the present study, we examine stinging wasp (Vespoidea) faunal diversity in the Atlantic Rain Forest, which is one of the most diverse and threatened ecosystems in the World. Three conservation areas were sampled employing a standardized sample protocol. Families and functional groups of Vespoidea were collected in each area, with the exception ants (Formicidae), and analyzed using diversity analyses, to generate taxonomic diversity and distinctness indices. Results indicated Pompilidae was the most diverse family, and the idiobiont parasitoid type was the most diverse functional group in the three study areas. Núcleo Picinguaba of the Parque Estadual da Serra do Mar was taxonomically and functionally the most diverse and species rich area. Parque Estadual Intervales showed the highest number of dominant species and diversity of koinobiont parasitoids, while the Rebio Sooretama exhibited a decrease in several diversity parameters.

Parasite biodiversity and its determinants in coastal marine teleost fishes of Brazil.

PubMed

Luque, J L; Mouillot, D; Poulin, R

2004-06-01

Recent studies of the forces behind the diversification of parasite assemblages have shed light on many aspects of parasite biodiversity. By using only parasite species richness as their measure of diversity, however, previous investigations have ignored the relatedness among parasite species and the taxonomic structure of the assemblages, which contain much information about their evolutionary origins. Here, we performed a comparative analysis across 50 species of fish from the coast of Brazil; we evaluated the effects of several host traits (body size, social behaviour, feeding habits, preference for benthic vs. pelagic habitats, depth range, and ability to enter brackish waters) on the diversity of their assemblages of metazoan parasites. As measures of diversity, we used parasite species richness, as well as the average taxonomic distinctness of the assemblage and its variance; the latter measures are based on the average taxonomic distance between any two parasite species in an assemblage. Unlike parasite species richness, taxonomic distinctness was unaffected by the number of host individuals examined per species. Fish body length proved to be the main predictor of parasite species richness, even when controlling for the confounding influences of host phylogeny and sampling effort, although it did not correlate with measures of parasite taxonomic distinctness. Predatory fish also had higher parasite species richness than planktivores, but this trend could not be confirmed using phylogenetically independent contrasts between host taxa. The main host feature associated with the taxonomic diversity of parasites was schooling behaviour, with schooling fish having more taxonomically diverse parasite assemblages than those of their non-schooling relatives. When focusing on endoparasite species only, both predatory feeding habits and a broad depth range were associated with the taxonomic distinctness of parasites. Our results suggest that certain host traits (i.e. body size) determine how many parasite species a host can accumulate over evolutionary time, whereas different host features influence the processes causing the taxonomic diversification of parasite assemblages.

taxonomic diversity and pest vulnerability in street tree assemblages

EPA Pesticide Factsheets

Urban foresters routinely emphasise the importance of taxonomic diversity to reduce the vulnerability of tree assemblages to invasive pests, but it is unclear to what extent diversity reduces vulnerability to polyphagous (i.e. generalist) pests. Drawing on field data from seven communities in metropolitan Cincinnati, Ohio, USA, we tested the hypothesis that communities with higher diversity would exhibit lower vulnerability to the polyphagous Asian longhorned beetle, which currently threatens the region. Based on street tree compositions and the beetle??s host preferences, Asian longhorned beetle threatened up to 35.6% of individual street trees and 47.5% of the total basal area across the study area, but we did not see clear connections between taxonomic diversity and beetle vulnerability among study communities. For example, the city of Fairfield was among the least diverse communities but had the lowest proportion of trees vulnerable to Asian longhorned beetle, whereas the city of Wyoming exhibited high diversity and high vulnerability. On the other hand, Forest Park aligned with our original hypothesis, as it was characterised by low diversity and high vulnerability. Our results demonstrate that relatively high taxonomic diversity in street tree assemblages does not necessarily lead to reduced vulnerability to a polyphagous pest. Considering the threats posed by polyphagous pests, selecting a set of relatively pest resistant trees known to perform well in ur

Trends in Taxonomic and Functional Composition of Soil Microbiome Along a Precipitation Gradient in Israel.

PubMed

Tripathi, Binu M; Moroenyane, Itumeleng; Sherman, Chen; Lee, Yoo Kyung; Adams, Jonathan M; Steinberger, Yosef

2017-07-01

The soil microbiome is important for the functioning of terrestrial ecosystems. However, the impacts of climate on taxonomic and functional diversity of soil microbiome are not well understood. A precipitation gradient along regional scale transects may offer a model setting for understanding the effect of climate on the composition and function of the soil microbiome. Here, we compared taxonomic and functional attributes of soil microorganisms in arid, semiarid, Mediterranean, and humid Mediterranean climatic conditions of Israel using shotgun metagenomic sequencing. We hypothesized that there would be a distinct taxonomic and functional soil community for each precipitation zone, with arid environments having lower taxonomic and functional diversity, greater relative abundance of stress response and sporulation-related genes, and lower relative abundance of genes related to nutrient cycling and degradation of complex organic compounds. As hypothesized, our results showed a distinct taxonomic and functional community in each precipitation zone, revealing differences in soil taxonomic and functional selection in the different climates. Although the taxonomic diversity remained similar across all sites, the functional diversity was-as hypothesized-lower in the arid environments, suggesting that functionality is more constrained in "extreme" environments. Also, with increasing aridity, we found a significant increase in genes related to dormancy/sporulation and a decrease in those related to nutrient cycling (genes related to nitrogen, potassium, and sulfur metabolism), respectively. However, relative abundance of genes related to stress response were lower in arid soils. Overall, these results indicate that climatic conditions play an important role in shaping taxonomic and functional attributes of soil microbiome. These findings have important implications for understanding the impacts of climate change (e.g., precipitation change) on structure and function of the soil microbiome.

Two decades of climate driving the dynamics of functional and taxonomic diversity of a tropical small mammal community in western Mexico

PubMed Central

2017-01-01

Understanding the effects of global climate disruption on biodiversity is important to future conservation efforts. While taxonomic diversity is widely studied, functional diversity of plants, and recently animals, is receiving increasing attention. Most studies of mammals are short-term, focus on temperate habitats, and rely on traits described in the literature rather than generating traits from observations. Unlike previous studies, this long-term field study assessed the factors driving the functional and taxonomic diversity of small-mammal assemblages in dry tropical forests using both traits recorded from literature and a demographic database. We assessed the drivers (abundance and biomass, temperature and rainfall) of taxonomic richness and functional diversity for two rain-driven seasons in two adjacent but distinct forests—upland and lowland (arroyo or riparian) forests. Our analysis found that rainfall, both seasonal and atypical, was the primary factor driving functional and taxonomic diversity of small-mammal assemblages. Functional responses differed between the two types of forests, however, with effects being stronger in the harsher conditions of the upland forests than in the less severe conditions prevailing in the arroyo (riparian) forest. The latter also supports a richer, more diverse, and more stable small-mammal assemblage. These findings highlight the importance of climate to tropical biological diversity, as extreme climate events (hurricanes, droughts and floods) and disruption of rainfall patterns were shown to decrease biodiversity. They also support the need to preserve these habitats, as their high taxonomic diversity and functional redundancy makes them resilient against global climate disruption and local extreme events. Tropical dry forests constitute a potential reservoir for biodiversity and the ecosystem services they provide. Unfortunately, these forests are among the most endangered terrestrial ecosystems because of deforestation and the likely impacts of global climate disruption. PMID:29228017

Genus age, provincial area and the taxonomic structure of marine faunas.

PubMed

Harnik, Paul G; Jablonski, David; Krug, Andrew Z; Valentine, James W

2010-11-22

Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf-Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area.

Genus age, provincial area and the taxonomic structure of marine faunas

PubMed Central

Harnik, Paul G.; Jablonski, David; Krug, Andrew Z.; Valentine, James W.

2010-01-01

Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf–Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area. PMID:20534619

Phylogenetic and functional traits of ectomycorrhizal assemblages in top soil from different biogeographic regions and forest types.

PubMed

Pena, Rodica; Lang, Christa; Lohaus, Gertrud; Boch, Steffen; Schall, Peter; Schöning, Ingo; Ammer, Christian; Fischer, Markus; Polle, Andrea

2017-04-01

Ectomycorrhizal (EM) fungal taxonomic, phylogenetic, and trait diversity (exploration types) were analyzed in beech and conifer forests along a north-to-south gradient in three biogeographic regions in Germany. The taxonomic community structures of the ectomycorrhizal assemblages in top soil were influenced by stand density and forest type, by biogeographic environmental factors (soil physical properties, temperature, and precipitation), and by nitrogen forms (amino acids, ammonium, and nitrate). While α-diversity did not differ between forest types, β-diversity increased, leading to higher γ-diversity on the landscape level when both forest types were present. The highest taxonomic diversity of EM was found in forests in cool, moist climate on clay and silty soils and the lowest in the forests in warm, dry climate on sandy soils. In the region with higher taxonomic diversity, phylogenetic clustering was found, but not trait clustering. In the warm region, trait clustering occurred despite neutral phylogenetic effects. These results suggest that different forest types and favorable environmental conditions in forests promote high EM species richness in top soil presumably with both high functional diversity and phylogenetic redundancy, while stressful environmental conditions lead to lower species richness and functional redundancy.

Why are there more arboreal ant species in primary than in secondary tropical forests?

PubMed

Klimes, Petr; Idigel, Cliffson; Rimandai, Maling; Fayle, Tom M; Janda, Milan; Weiblen, George D; Novotny, Vojtech

2012-09-01

1. Species diversity of arboreal arthropods tends to increase during rainforest succession so that primary forest communities comprise more species than those from secondary vegetation, but it is not well understood why. Primary forests differ from secondary forests in a wide array of factors whose relative impacts on arthropod diversity have not yet been quantified. 2. We assessed the effects of succession-related determinants on a keystone ecological group, arboreal ants, by conducting a complete census of 1332 ant nests from all trees with diameter at breast height ≥ 5 cm occurring within two (unreplicated) 0·32-ha plots, one in primary and one in secondary lowland forest in New Guinea. Specifically, we used a novel rarefaction-based approach to match number, size distribution and taxonomic structure of trees in primary forest communities to those in secondary forest and compared the resulting numbers of ant species. 3. In total, we recorded 80 nesting ant species from 389 trees in primary forest but only 42 species from 295 trees in secondary forest. The two habitats did not differ in the mean number of ant species per tree or in the relationship between ant diversity and tree size. However, the between-tree similarity of ant communities was higher in secondary forest than in primary forest, as was the between-tree nest site similarity, suggesting that secondary trees were more uniform in providing nesting microhabitats. 4. Using our rarefaction method, the difference in ant species richness between two forest types was partitioned according to the effects of higher tree density (22·6%), larger tree size (15·5%) and higher taxonomic diversity of trees (14·3%) in primary than in secondary forest. The remaining difference (47·6%) was because of higher beta diversity of ant communities between primary forest trees. In contrast, difference in nest density was explained solely by difference in tree density. 5. Our study shows that reduction in plant taxonomic diversity in secondary forests is not the main driver of the reduction in canopy ant species richness. We suggest that the majority of arboreal species losses in secondary tropical forests are attributable to simpler vegetation structure, combined with lower turnover of nesting microhabitats between trees. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.

Gold bugs and beyond: a review of iridescence and structural colour mechanisms in beetles (Coleoptera)

PubMed Central

Seago, Ainsley E.; Brady, Parrish; Vigneron, Jean-Pol; Schultz, Tom D.

2008-01-01

Members of the order Coleoptera are sometimes referred to as ‘living jewels’, in allusion to the strikingly diverse array of iridescence mechanisms and optical effects that have arisen in beetles. A number of novel and sophisticated reflectance mechanisms have been discovered in recent years, including three-dimensional photonic crystals and quasi-ordered coherent scattering arrays. However, the literature on beetle structural coloration is often redundant and lacks synthesis, with little interchange between the entomological and optical research communities. Here, an overview is provided for all iridescence mechanisms observed in Coleoptera. Types of iridescence are illustrated and classified into three mechanistic groups: multilayer reflectors, three-dimensional photonic crystals and diffraction gratings. Taxonomic and phylogenetic distributions are provided, along with discussion of the putative functions and evolutionary pathways by which iridescence has repeatedly arisen in beetles. PMID:18957361

Biodiversity of free-living marine nematodes in the southern Yellow Sea, China

NASA Astrophysics Data System (ADS)

Liu, Xiaoshou; Xu, Man; Hua, Er; Zhang, Zhinan

2016-02-01

Biodiversity patterns of free-living marine nematodes were studied using specific, taxonomic and phylogenetic diversity measures in the southern Yellow Sea, China. The results showed that the average of Shannon-Wiener diversity index ( H') in the study area was 3.17. The higher values were distributed in the east part of Shandong coastal waters and north part of Jiangsu coastal waters, while the lower values were distributed in the southern Yellow Sea Cold Water Mass (YSCWM). The average of taxonomic diversity ( Δ) was 62.09 in the study region. The higher values were distributed in the transitional areas between the coastal areas and the southern YSCWM, while the lower values were distributed near the north part of Jiangsu coastal waters and the YSCWM. Results of correlation analysis of species diversity and taxonomic diversity showed that some of the two kinds of diversity index were independent, which suggested that combining the two kinds of diversity indices can reflect the ecological characteristics better. A test for 95% probability funnels of average taxonomic distinctness and variation in taxonomic distinctness suggested that Station 8794 (in the YSCWM) was outside of the 95% probability funnels, which may be due to the environmental stress. Results of correlation analysis between marine nematodes biodiversity and environmental variables showed that the sediment characteristics (Mdø and Silt-clay fraction) and phaeophorbide a (Pha- a) were the most important factors to determine the biodiversity patterns of marine nematodes.

Ovarian control and monitoring in amphibians.

PubMed

Calatayud, N E; Stoops, M; Durrant, B S

2018-03-15

Amphibian evolution spans over 350 million years, consequently this taxonomic group displays a wide, complex array of physiological adaptations and their diverse modes of reproduction are a prime example. Reproduction can be affected by taxonomy, geographic and altitudinal distribution, and environmental factors. With some exceptions, amphibians can be categorized into discontinuous (strictly seasonal) and continuous breeders. Temperature and its close association with other proximate and genetic factors control reproduction via a tight relationship with circadian rhythms which drive genetic and hormonal responses to the environment. In recent times, the relationship of proximate factors and reproduction has directly or indirectly lead to the decline of this taxonomic group. Conservationists are tackling the rapid loss of species through a wide range of approaches including captive rescue. However, there is still much to be learned about the mechanisms of reproductive control and its requirements in order to fabricate species-appropriate captive environments that address a variety of reproductive strategies. As with other taxonomic groups, assisted reproductive technologies and other reproductive monitoring tools such as ultrasound, hormone analysis and body condition indices can assist conservationists in optimizing captive husbandry and breeding. In this review we discuss some of the mechanisms of ovarian control and the different tools being used to monitor female reproduction. Copyright © 2018 Elsevier Inc. All rights reserved.

High taxonomic diversity of cultivation-recalcitrant endophytic bacteria in grapevine field shoots, their in vitro introduction, and unsuspected persistence.

PubMed

Thomas, Pious; Sekhar, Aparna C; Shaik, Sadiq Pasha

2017-11-01

Molecular and microscopic analyses reveal enormous non-cultivable endophytic bacteria in grapevine field shoots with functional significance. Diverse bacteria enter tissue cultures through surface-sterilized tissues and survive surreptitiously with varying taxonomic realignments. The study was envisaged to assess the extent of endophytic bacterial association with field shoot tissues of grapevine and the likelihood of introduction of such internally colonizing bacteria in vitro adopting molecular techniques targeting the non-cultivable bacterial community. PowerFood ® -kit derived DNA from surface-sterilized field shoot tips of grapevine Flame Seedless was employed in a preliminary bacterial class-specific PCR screening proving positive for major prokaryotic taxa including Archaea. Taxonomic and functional diversity were analyzed through whole metagenome profiling (WMG) which revealed predominantly phylum Actinobacteria, Proteobacteria, and minor shares of Firmicutes, Bacteroidetes, and Deinococcus-Thermus with varying functional roles ascribable to the whole bacterial community. Field shoot tip tissues and callus derived from stem segments were further employed in 16S rRNA V3-V4 amplicon taxonomic profiling. This revealed elevated taxonomic diversity in field shoots over WMG, predominantly Proteobacteria succeeded by Actinobacteria, Firmicutes, Bacteroidetes, and 15 other phyla including several candidate phyla (135 families, 179 genera). Callus stocks also displayed broad bacterial diversity (16 phyla; 96 families; 141 genera) bearing resemblance to field tissues with Proteobacterial dominance but a reduction in its share, enrichment of Actinobacteria and Firmicutes, disappearance of some field-associated phyla and detection of a few additional taxonomic groups over field community. Similar results were documented during 16S V3-V4 amplicon taxonomic profiling on Thompson Seedless field shoot tip and callus tissues. Video microscopy on tissue homogenates corroborated enormous endophytic bacteria. This study elucidates a vast diversity of cultivation-recalcitrant endophytic bacteria prevailing in grapevine field shoots, their in vitro introduction, and unsuspecting sustenance with possible silent participation in tissue culture processes.

Resource availability controls fungal diversity across a plant diversity gradient

USGS Publications Warehouse

Waldrop, M.P.; Zak, D.R.; Blackwood, C.B.; Curtis, C.D.; Tilman, D.

2006-01-01

Despite decades of research, the ecological determinants of microbial diversity remain poorly understood. Here, we test two alternative hypotheses concerning the factors regulating fungal diversity in soil. The first states that higher levels of plant detritus production increase the supply of limiting resources (i.e. organic substrates) thereby increasing fungal diversity. Alternatively, greater plant diversity increases the range of organic substrates entering soil, thereby increasing the number of niches to be filled by a greater array of heterotrophic fungi. These two hypotheses were simultaneously examined in experimental plant communities consisting of one to 16 species that have been maintained for a decade. We used ribosomal intergenic spacer analysis (RISA), in combination with cloning and sequencing, to quantify fungal community composition and diversity within the experimental plant communities. We used soil microbial biomass as a temporally integrated measure of resource supply. Plant diversity was unrelated to fungal diversity, but fungal diversity was a unimodal function of resource supply. Canonical correspondence analysis (CCA) indicated that plant diversity showed a relationship to fungal community composition, although the occurrence of RISA bands and operational taxonomic units (OTUs) did not differ among the treatments. The relationship between fungal diversity and resource availability parallels similar relationships reported for grasslands, tropical forests, coral reefs, and other biotic communities, strongly suggesting that the same underlying mechanisms determine the diversity of organisms at multiple scales. ?? 2006 Blackwell Publishing Ltd/CNRS.

Disentangling the drivers of taxonomic and phylogenetic beta diversities in disturbed and undisturbed subtropical forests

NASA Astrophysics Data System (ADS)

Liu, Jinliang; Qian, Hong; Jin, Yi; Wu, Chuping; Chen, Jianhua; Yu, Shuquan; Wei, Xinliang; Jin, Xiaofeng; Liu, Jiajia; Yu, Mingjian

2016-10-01

Understanding the relative importance of dispersal limitation and environmental filtering processes in structuring the beta diversities of subtropical forests in human disturbed landscapes is still limited. Here we used taxonomic (TBD) and phylogenetic (PBD), including terminal PBD (PBDt) and basal PBD (PBDb), beta diversity indices to quantify the taxonomic and phylogenetic turnovers at different depths of evolutionary history in disturbed and undisturbed subtropical forests. Multiple linear regression model and distance-based redundancy analysis were used to disentangle the relative importance of environmental and spatial variables. Environmental variables were significantly correlated with TBD and PBDt metrics. Temperature and precipitation were major environmental drivers of beta diversity patterns, which explained 7-27% of the variance in TBD and PBDt, whereas the spatial variables independently explained less than 1% of the variation for all forests. The relative importance of environmental and spatial variables differed between disturbed and undisturbed forests (e.g., when Bray-Curtis was used as a beta diversity metric, environmental variable had a significant effect on beta diversity for disturbed forests but had no effect on undisturbed forests). We conclude that environmental filtering plays a more important role than geographical limitation and disturbance history in driving taxonomic and terminal phylogenetic beta diversity.

Disentangling the drivers of taxonomic and phylogenetic beta diversities in disturbed and undisturbed subtropical forests

PubMed Central

Liu, Jinliang; Qian, Hong; Jin, Yi; Wu, Chuping; Chen, Jianhua; Yu, Shuquan; Wei, Xinliang; Jin, Xiaofeng; Liu, Jiajia; Yu, Mingjian

2016-01-01

Understanding the relative importance of dispersal limitation and environmental filtering processes in structuring the beta diversities of subtropical forests in human disturbed landscapes is still limited. Here we used taxonomic (TBD) and phylogenetic (PBD), including terminal PBD (PBDt) and basal PBD (PBDb), beta diversity indices to quantify the taxonomic and phylogenetic turnovers at different depths of evolutionary history in disturbed and undisturbed subtropical forests. Multiple linear regression model and distance-based redundancy analysis were used to disentangle the relative importance of environmental and spatial variables. Environmental variables were significantly correlated with TBD and PBDt metrics. Temperature and precipitation were major environmental drivers of beta diversity patterns, which explained 7–27% of the variance in TBD and PBDt, whereas the spatial variables independently explained less than 1% of the variation for all forests. The relative importance of environmental and spatial variables differed between disturbed and undisturbed forests (e.g., when Bray-Curtis was used as a beta diversity metric, environmental variable had a significant effect on beta diversity for disturbed forests but had no effect on undisturbed forests). We conclude that environmental filtering plays a more important role than geographical limitation and disturbance history in driving taxonomic and terminal phylogenetic beta diversity. PMID:27775021

Phylogenetic structure of soil bacterial communities predicts ecosystem functioning.

PubMed

Pérez-Valera, Eduardo; Goberna, Marta; Verdú, Miguel

2015-05-01

Quantifying diversity with phylogeny-informed metrics helps understand the effects of diversity on ecosystem functioning (EF). The sign of these effects remains controversial because phylogenetic diversity and taxonomic identity may interactively influence EF. Positive relationships, traditionally attributed to complementarity effects, seem unimportant in natural soil bacterial communities. Negative relationships could be attributed to fitness differences leading to the overrepresentation of few productive clades, a mechanism recently invoked to assemble soil bacteria communities. We tested in two ecosystems contrasting in terms of environmental heterogeneity whether two metrics of phylogenetic community structure, a simpler measure of phylogenetic diversity (NRI) and a more complex metric incorporating taxonomic identity (PCPS), correctly predict microbially mediated EF. We show that the relationship between phylogenetic diversity and EF depends on the taxonomic identity of the main coexisting lineages. Phylogenetic diversity was negatively related to EF in soils where a marked fertility gradient exists and a single and productive clade (Proteobacteria) outcompete other clades in the most fertile plots. However, phylogenetic diversity was unrelated to EF in soils where the fertility gradient is less marked and Proteobacteria coexist with other abundant lineages. Including the taxonomic identity of bacterial lineages in metrics of phylogenetic community structure allows the prediction of EF in both ecosystems. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

COMPARISON OF TAXONOMIC, COLONY MORPHOTYPE AND PCR-RFLP METHODS TO CHARACTERIZE MICROFUNGAL DIVERSITY

EPA Science Inventory

We compared three methods for estimating fungal species diversity in soil samples. A rapid screening method based on gross colony morphological features and color reference standards was compared with traditional fungal taxonomic methods and PCR-RFLP for estimation of ecological ...

Natural revegetation of a semiarid habitat alters taxonomic and functional diversity of soil microbial communities.

PubMed

Guo, Yanqing; Chen, Xiaotian; Wu, Yuanyuan; Zhang, Lu; Cheng, Jimin; Wei, Gehong; Lin, Yanbing

2018-04-18

Revegetation of degraded lands has a profound impact on the maintenance and stability of ecosystem processes. However, the impacts of this land use change on functional diversity of soil microbial communities are poorly understood. Here, using 16S rRNA gene amplicon and shotgun metagenomic sequencing, we compared the taxonomic and functional communities of soil microbiome, and analyzed the effects of plant diversity and soil chemical properties, in a chronosequence of restored ex-farmland that had been naturally revegetated to grassland over periods of 5, 15 and 30years with adjacent farmland, on the Loess Plateau, China. We found that microbial taxonomic diversity was positively correlated with plant diversity and was higher in the revegetated sites. Functional diversity increased significantly in the oldest grassland. Actinobacteria, commonly considered a copiotrophic phylum, was more abundant in the revegetated sites, while Acidobacteria, an oligotrophic phylum, was more abundant in farmland. Furthermore, the structure of taxonomic and functional communities was significantly different between revegetated sites and farmland, and organic matter was the best environmental predictor in determining these microbial communities. Compared with the farmland, revegetation increased the proportion of genes associated with energy metabolism, carbohydrate metabolism and xenobiotics biodegradation and metabolism. Notably, the higher proportion of carbohydrate degradation gene subfamilies in the revegetated sites indicated higher levels of soil nutrient cycling. These results elucidate the significant shifts in belowground microbial taxonomic and functional diversity following vegetation restoration and have implications for ecological restoration programs in arid and semi-arid ecosystems. Copyright © 2018. Published by Elsevier B.V.

Taxonomic distinctness and richness of helminth parasite assemblages of freshwater fishes in Mexican hydrological basins.

PubMed

Quiroz-Martínez, Benjamín; Salgado-Maldonado, Guillermo

2013-01-01

In this paper, we analyse the distributional patterns of adult helminth parasites of freshwater fishes with respect to the main hydrological basins of Mexico. We use the taxonomic distinctness and the variation in taxonomic distinctness to explore patterns of parasite diversity and how these patterns change between zoogeographical regions. We address questions about the factors that determine the variation of observed diversity of helminths between basins. We also investigate patterns of richness, taxonomic distinctness and distance decay of similarity amongst basins. Our analyses suggest that the evolution of the fauna of helminth parasites in Mexico is mostly dominated by independent host colonization events and that intra--host speciation could be a minor factor explaining the origin of this diversity. This paper points out a clear separation between the helminth faunas of northern--nearctic and southern--neotropical components in Mexican continental waters, suggesting the availability of two distinct taxonomic pools of parasites in Mexican drainage basins. Data identifies Mexican drainage basins as unities inhabited by freshwater fishes, hosting a mixture of neotropical and nearctic species, in addition, data confirms neotropical and neartic basins/helminth faunas. The neotropical basins of Mexico are host to a richest and more diversified helminth fauna, including more families, genera and species, compared to the less rich and less diverse helminth fauna in the nearctic basins. The present analysis confirms distance--decay as one of the important factors contributing to the patterns of diversity observed. The hypothesis that helminth diversity could be explained by the ichthyological diversity of the basin received no support from present analysis.

Taxonomic Distinctness and Richness of Helminth Parasite Assemblages of Freshwater Fishes in Mexican Hydrological Basins

PubMed Central

Quiroz-Martínez, Benjamín; Salgado-Maldonado, Guillermo

2013-01-01

In this paper, we analyse the distributional patterns of adult helminth parasites of freshwater fishes with respect to the main hydrological basins of Mexico. We use the taxonomic distinctness and the variation in taxonomic distinctness to explore patterns of parasite diversity and how these patterns change between zoogeographical regions. We address questions about the factors that determine the variation of observed diversity of helminths between basins. We also investigate patterns of richness, taxonomic distinctness and distance decay of similarity amongst basins. Our analyses suggest that the evolution of the fauna of helminth parasites in Mexico is mostly dominated by independent host colonization events and that intra - host speciation could be a minor factor explaining the origin of this diversity. This paper points out a clear separation between the helminth faunas of northern - nearctic and southern - neotropical components in Mexican continental waters, suggesting the availability of two distinct taxonomic pools of parasites in Mexican drainage basins. Data identifies Mexican drainage basins as unities inhabited by freshwater fishes, hosting a mixture of neotropical and nearctic species, in addition, data confirms neotropical and neartic basins/helminth faunas. The neotropical basins of Mexico are host to a richest and more diversified helminth fauna, including more families, genera and species, compared to the less rich and less diverse helminth fauna in the nearctic basins. The present analysis confirms distance - decay as one of the important factors contributing to the patterns of diversity observed. The hypothesis that helminth diversity could be explained by the ichthyological diversity of the basin received no support from present analysis. PMID:24086342

Seasonal comparison of aquatic macroinvertebrate assemblages in a flooded coastal freshwater marsh

USGS Publications Warehouse

Kang, Sung-Ryong; King, Sammy L.

2013-01-01

Marsh flooding and drying may be important factors affecting aquatic macroinvertebrate density and distribution in coastal freshwater marshes. Limited availability of water as a result of drying in emergent marsh may decrease density, taxonomic diversity, and taxa richness. The principal objectives of this study are to characterize the seasonal aquatic macroinvertebrate assemblage in a freshwater emergent marsh and compare aquatic macroinvertebrate species composition, density, and taxonomic diversity to that of freshwater marsh ponds. We hypothesize that 1) freshwater emergent marsh has lower seasonal density and taxonomic diversity compared to that of freshwater marsh ponds; and 2) freshwater emergent marsh has lower taxa richness than freshwater marsh ponds. Seasonal aquatic macroinvertebrate density in freshwater emergent marsh ranged from 0 organisms/m2 (summer 2009) to 91.1 ± 20.53 organisms/m2 (mean ± SE; spring 2009). Density in spring was higher than in all other seasons. Taxonomic diversity did not differ and there were no unique species in the freshwater emergent marsh. Our data only partially support our first hypothesis as aquatic macroinvertebrate density and taxonomic diversity between freshwater emergent marsh and ponds did not differ in spring, fall, and winter but ponds supported higher macroinvertebrate densities than freshwater emergent marsh during summer. However, our data did not support our second hypothesis as taxa richness between freshwater emergent marsh and ponds did not statistically differ.

Genetic diversity, structure, and patterns of differentiation in the genus vitis

USDA-ARS?s Scientific Manuscript database

Vitis (Vitaceae) is a taxonomically complicated genus with ca. 60 taxa divided into two subgenera, Vitis and Muscadinia. We used population genetic approaches to gain insights into the genetic diversity, patterns of evolutionary differentiation and to decipher the taxonomic status of some of the con...

ENSO and anthropogenic impacts on phytoplankton diversity in tropical coastal waters

NASA Astrophysics Data System (ADS)

Doan-Nhu, Hai; Nguyen-Ngoc, Lam; Nguyen, Chi-Thoi

2016-01-01

16-year phytoplankton data were analysed to assess ENSO and anthropogenic impacts on biodiversity and community structure at 3 locations (Nha-Trang and Phan-Thiet Bays and near Phu-Qui Island) in South Centre Viet Nam to understand (1) the primary scales of change in phytoplankton community structure, and traditional and taxonomic diversity indices; (2) the significance of environmental changes and/or climate variability on phytoplankton diversity; and (3) the usefulness of these long-term data for analysing future impacts of anthropogenic and climate changes. Traditional and taxonomic diversity indices were compared and tested in linkage with environmental conditions and ENSO. Nutrient data indicated stronger environmental impacts in Phan-Thiet Bay, milder in Nha-Trang Bay and less noticeable near Phu-Qui Island. There were measurable impacts of both anthropogenic and ENSO on phytoplankton at different locations in various parameters, e.g. species number, diversity and community structures. The lowest diversity was recorded in the most anthropogenically impacted site, Phan-Thiet Bay. Although a stronger impact on phytoplankton was recorded in ENSO year in Phan Thiet Bay, quantitative separation between anthropogenic and ENSO impacts using phytoplankton biodiversity indices was impossible. In the waters with less anthropogenic impacts, ENSO effects on taxonomic diversity was better indicated by negative phytoplankton responses to the ONI index (Nha-Trang Bay) and recovery of phytoplankton after the ENSO events (near Phu-Qui Island). Among the diversity indices, the taxonomic diversity indices (e.g. Δ+ and Λ+) better described impacts of ENSO than the traditional ones.

Insights into assessing water quality using taxonomic distinctness based on a small species pool of biofilm-dwelling ciliate fauna in coastal waters of the Yellow Sea, northern China.

PubMed

Zhang, Wei; Liu, Yuanyuan; Warren, Alan; Xu, Henglong

2014-12-15

The aim of this study is to determine the feasibility of using a small species pool from a raw dataset of biofilm-dwelling ciliates for bioassessment based on taxonomic diversity. Samples were collected monthly at four stations within a gradient of environmental stress in coastal waters of the Yellow Sea, northern China from August 2011 to July 2012. A 33-species subset was identified from the raw 137-species dataset using a multivariate method. The spatial patterns of this subset were significantly correlated with the changes in the nutrients and chemical oxygen demand. The taxonomic diversity indices were significantly correlated with nutrients. The pair-wise indices of average taxonomic distinctness (Δ(+)) and the taxonomic distinctness (Λ(+)) showed a clear departure from the expected taxonomic pattern. These findings suggest that this small ciliate assemblage might be used as an adequate species pool for discriminating water quality status based on taxonomic distinctness in marine ecosystems. Copyright © 2014 Elsevier Ltd. All rights reserved.

The taxonomic distinctness of macroinvertebrate communities of Atlantic Forest streams cannot be predicted by landscape and climate variables, but traditional biodiversity indices can.

PubMed

Roque, F O; Guimarães, E A; Ribeiro, M C; Escarpinati, S C; Suriano, M T; Siqueira, T

2014-11-01

Predicting how anthropogenic activities may influence the various components of biodiversity is essential for finding ways to reduce diversity loss. This challenge involves: a) understanding how environmental factors influence diversity across different spatial scales, and b) developing ways to measure these relationships in a way that is fast, economical, and easy to communicate. In this study, we investigate whether landscape and bioclimatic variables could explain variation in biodiversity indices in macroinvertebrate communities from 39 Atlantic Forest streams. In addition to traditional diversity measures, i.e., species richness, abundance and Shannon index, we used a taxonomic distinctness index that measures the degree of phylogenetic relationship among taxa. The amount of variation in the diversity measures that was explained by environmental and spatial variables was estimated using variation partitioning based on multiple regression. Our study demonstrates that taxonomic distinctness does not respond in the same way as the traditional used in biodiversity studies. We found no evidence that taxonomic distinctness responds predictably to variation in landscape metrics, indicating the need for the incorporation of predictors at multiple scales in this type of study. The lack of congruence between taxonomic distinctness and other indices and its low predictability may be related to the fact that this measure expresses long-term evolutionary adaptation to ecosystem conditions, while the other traditional biodiversity metrics respond to short-term environmental changes.

Effectiveness of protected areas for vertebrates based on taxonomic and phylogenetic diversity.

PubMed

Quan, Qing; Che, Xianli; Wu, Yongjie; Wu, Yuchun; Zhang, Qiang; Zhang, Min; Zou, Fasheng

2018-04-01

Establishing protected areas is the primary goal and tool for preventing irreversible biodiversity loss. However, the effectiveness of protected areas that target specific species has been questioned for some time because targeting key species for conservation may impair the integral regional pool of species diversity and phylogenetic and functional diversity are seldom considered. We assessed the efficacy of protected areas in China for the conservation of phylogenetic diversity based on the ranges and phylogenies of 2279 terrestrial vertebrates. Phylogenetic and taxonomic diversity were strongly and positively correlated, and only 12.1-43.8% of priority conservation areas are currently protected. However, the patterns and coverage of phylogenetic diversity were affected when weighted by species richness. These results indicated that in China, protected areas targeting high species richness protected phylogenetic diversity well overall but failed to do so in some regions with more unique or threatened communities (e.g., coastal areas of eastern China, where severely threatened avian communities were less protected). Our results suggest that the current distribution of protected areas could be improved, although most protected areas protect both taxonomic and phylogenetic diversity. © 2017 Society for Conservation Biology.

Comparison of Sewage and Animal Fecal Microbiomes by using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups

EPA Science Inventory

Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but human and other animal gut microbiota contain an array of other taxonomic groups that might serve as indicators for sources of fecal pollution. High thr...

Taxonomic indexing--extending the role of taxonomy.

PubMed

Patterson, David J; Remsen, David; Marino, William A; Norton, Cathy

2006-06-01

Taxonomic indexing refers to a new array of taxonomically intelligent network services that use nomenclatural principles and elements of expert taxonomic knowledge to manage information about organisms. Taxonomic indexing was introduced to help manage the increasing amounts of digital information about biology. It has been designed to form a near basal layer in a layered cyberinfrastructure that deals with biological information. Taxonomic Indexing accommodates the special problems of using names of organisms to index biological material. It links alternative names for the same entity (reconciliation), and distinguishes between uses of the same name for different entities (disambiguation), and names are placed within an indefinite number of hierarchical schemes. In order to access all information on all organisms, Taxonomic indexing must be able to call on a registry of all names in all forms for all organisms. NameBank has been developed to meet that need. Taxonomic indexing is an area of informatics that overlaps with taxonomy, is dependent on the expert input of taxonomists, and reveals the relevance of the discipline to a wide audience.

Clever birds are lousy: co-variation between avian innovation and the taxonomic richness of their amblyceran lice.

PubMed

Vas, Zoltán; Lefebvre, Louis; Johnson, Kevin P; Reiczigel, Jeno; Rózsa, Lajos

2011-10-01

Lice (Insecta: Phthiraptera) are ectoparasites that reduce host life expectancy and sexual attractiveness. Their taxonomic richness varies considerably among their hosts. Previous studies have already explored some important factors shaping louse diversity. An unexplored potential correlate of louse taxonomic richness is host behavioural flexibility. In this comparative study, we examine the relationship between louse generic richness, innovative capabilities (as a proxy for behavioural flexibility), and brain size while controlling for host species diversity, phylogeny, body size and research effort. Using data for 108 avian families, we found a highly significant positive relationship between host innovative capabilities and the taxonomic richness of amblyceran lice, but a lack of a similar relationship in ischnoceran lice. Host brain size had only a marginal impact on amblyceran diversity and no correlation with ischnoceran diversity. This suggests that the effect in Amblycera is not mediated by metabolic limitations due to the energetic costs of brain size and maintenance, rather directly caused by the ecological differences between hosts with differing cognitive capabilities. We propose four alternative and mutually non-exclusive hypotheses that may explain this phenomenon. Copyright © 2011 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

The importance of taxonomic resolution for additive beta diversity as revealed through DNA barcoding.

PubMed

Bringloe, Trevor T; Cottenie, Karl; Martin, Gillian K; Adamowicz, Sarah J

2016-12-01

Additive diversity partitioning (α, β, and γ) is commonly used to study the distribution of species-level diversity across spatial scales. Here, we first investigate whether published studies of additive diversity partitioning show signs of difficulty attaining species-level resolution due to inherent limitations with morphological identifications. Second, we present a DNA barcoding approach to delineate specimens of stream caddisfly larvae (order Trichoptera) and consider the importance of taxonomic resolution on classical (additive) measures of beta (β) diversity. Caddisfly larvae were sampled using a hierarchical spatial design in two regions (subarctic Churchill, Manitoba, Canada; temperate Pennsylvania, USA) and then additively partitioned according to Barcode Index Numbers (molecular clusters that serve as a proxy for species), genus, and family levels; diversity components were expressed as proportional species turnover. We screened 114 articles of additive diversity partitioning and found that a third reported difficulties with achieving species-level identifications, with a clear taxonomic tendency towards challenges identifying invertebrate taxa. Regarding our own study, caddisfly BINs appeared to show greater subregional turnover (e.g., proportional additive β) compared to genus or family levels. Diversity component studies failing to achieve species resolution due to morphological identifications may therefore be underestimating diversity turnover at larger spatial scales.

Effects of growth form and functional traits on response of woody plants to clearing and fragmentation of subtropical rainforest.

PubMed

Kooyman, R M; Zanne, A E; Gallagher, R V; Cornwell, W; Rossetto, M; O'Connor, P; Parkes, E A; Catterall, C F; Laffan, S W; Lusk, C H

2013-12-01

The conservation implications of large-scale rainforest clearing and fragmentation on the persistence of functional and taxonomic diversity remain poorly understood. If traits represent adaptive strategies of plant species to particular circumstances, the expectation is that the effect of forest clearing and fragmentation will be affected by species functional traits, particularly those related to dispersal. We used species occurrence data for woody plants in 46 rainforest patches across 75,000 ha largely cleared of forest by the early 1900s to determine the combined effects of area reduction, fragmentation, and patch size on the taxonomic structure and functional diversity of subtropical rainforest. We compiled species trait values for leaf area, seed dry mass, wood density, and maximum height and calculated species niche breadths. Taxonomic structure, trait values (means, ranges), and the functional diversity of assemblages of climbing and free-standing plants in remnant patches were quantified. Larger rainforest patches had higher species richness. Species in smaller patches were taxonomically less related than species in larger patches. Free-standing plants had a high percentage of frugivore dispersed seeds; climbers had a high proportion of small wind-dispersed seeds. Connections between the patchy spatial distribution of free-standing species, larger seed sizes, and dispersal syndrome were weak. Assemblages of free-standing plants in patches showed more taxonomic and spatial structuring than climbing plants. Smaller isolated patches retained relatively high functional diversity and similar taxonomic structure to larger tracts of forest despite lower species richness. The response of woody plants to clearing and fragmentation of subtropical rainforest differed between climbers and slow-growing mature-phase forest trees but not between climbers and pioneer trees. Quantifying taxonomic structure and functional diversity provides an improved basis for conservation planning and management by elucidating the effects of forest-area reduction and fragmentation. Efectos de la Forma de Crecimiento y Atributos Funcionales en la Respuesta de Plantas Leñosas al Desmonte y Fragmentación de Bosque Lluvioso Subtropical. © 2013 Society for Conservation Biology.

Natural Products from the Lithistida: A Review of the Literature since 2000

PubMed Central

Winder, Priscilla L.; Pomponi, Shirley A.; Wright, Amy E.

2011-01-01

Lithistid sponges are known to produce a diverse array of compounds ranging from polyketides, cyclic and linear peptides, alkaloids, pigments, lipids, and sterols. A majority of these structurally complex compounds have very potent and interesting biological activities. It has been a decade since a thorough review has been published that summarizes the literature on the natural products reported from this amazing sponge order. This review provides an update on the current taxonomic classification of the Lithistida, describes structures and biological activities of 131 new natural products, and discusses highlights from the total syntheses of 16 compounds from marine sponges of the Order Lithistida providing a compilation of the literature since the last review published in 2002. PMID:22363244

Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity

USGS Publications Warehouse

Strecker, A.L.; Olden, J.D.; Whittier, Joanna B.; Paukert, C.P.

2011-01-01

To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential tradeoffs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity;contemporary threats to biodiversity (including interactions with nonnative species);and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities;however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates multiple and complementary conservation values describing taxonomic, functional, and phylogenetic diversity. ??2011 by the Ecological Society of America.

Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity

USGS Publications Warehouse

Strecker, Angela L.; Olden, Julian D.; Whittier, Joanna B.; Paukert, Craig P.

2011-01-01

To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential trade-offs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity; contemporary threats to biodiversity (including interactions with nonnative species); and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities; however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates multiple and complementary conservation values describing taxonomic, functional, and phylogenetic diversity.

Highly diverse community structure in a remote central Tibetan geothermal spring does not display monotonic variation to thermal stress.

PubMed

Yim, Lau Chui; Hongmei, Jing; Aitchison, Jonathan C; Pointing, Stephen B

2006-07-01

We report an assessment of whole-community diversity for an extremely isolated geothermal location with considerable phylogenetic and phylogeographic novelty. We further demonstrate, using multiple statistical analyses of sequence data, that the response of community diversity is not monotonic to thermal stress along a gradient of 52-83 degrees C. A combination of domain- and division-specific PCR was used to obtain a broad spectrum of community phylotypes, which were resolved by denaturing gradient gel electrophoresis. Among 58 sequences obtained from microbial mats and streamers, some 95% suggest novel archaeal and bacterial diversity at the species level or higher. Moreover, new phylogeographic and thermally defined lineages among the Cyanobacteria, Chloroflexi, Eubacterium and Thermus are identified. Shannon-Wiener diversity estimates suggest that mats at 63 degrees C supported highest diversity, but when alternate models were applied [Average Taxonomic Distinctness (AvTD) and Variation in Taxonomic Distinctness (VarTD)] that also take into account the phylogenetic relationships between phylotypes, it is evident that greatest taxonomic diversity (AvTD) occurred in streamers at 65-70 degrees C, whereas greatest phylogenetic distance between taxa (VarTD) occurred in streamers of 83 degrees C. All models demonstrated that diversity is not related to thermal stress in a linear fashion.

Asian longhorned beetle complicates the relationship ...

EPA Pesticide Factsheets

Urban foresters routinely emphasise the importance of taxonomic diversity to reduce the vulnerability of tree assemblages to invasive pests, but it is unclear to what extent diversity reduces vulnerability to polyphagous (i.e. generalist) pests. Drawing on field data from seven communities in metropolitan Cincinnati, Ohio, USA, we tested the hypothesis that communities with higher diversity would exhibit lower vulnerability to the polyphagous Asian longhorned beetle, which currently threatens the region. Based on street tree compositions and the beetle?s host preferences, Asian longhorned beetle threatened up to 35.6% of individual street trees and 47.5% of the total basal area across the study area, but we did not see clear connections between taxonomic diversity and beetle vulnerability among study communities. For example, the city of Fairfield was among the least diverse communities but had the lowest proportion of trees vulnerable to Asian longhorned beetle, whereas the city of Wyoming exhibited high diversity and high vulnerability. On the other hand, Forest Park aligned with our original hypothesis, as it was characterised by low diversity and high vulnerability. Our results demonstrate that relatively high taxonomic diversity in street tree assemblages does not necessarily lead to reduced vulnerability to a polyphagous pest. Considering the threats posed by polyphagous pests, selecting a set of relatively pest resistant trees known to perform well in urb

Lack of congruence in species diversity indices and community structures of planktonic groups based on local environmental factors.

PubMed

Doi, Hideyuki; Chang, Kwang-Hyeon; Nishibe, Yuichiro; Imai, Hiroyuki; Nakano, Shin-ichi

2013-01-01

The importance of analyzing the determinants of biodiversity and community composition by using multiple trophic levels is well recognized; however, relevant data are lacking. In the present study, we investigated variations in species diversity indices and community structures of the plankton taxonomic groups-zooplankton, rotifers, ciliates, and phytoplankton-under a range of local environmental factors in pond ecosystems. For each planktonic group, we estimated the species diversity index by using linear models and analyzed the community structure by using canonical correspondence analysis. We showed that the species diversity indices and community structures varied among the planktonic groups and according to local environmental factors. The observed lack of congruence among the planktonic groups may have been caused by niche competition between groups with similar trophic guilds or by weak trophic interactions. Our findings highlight the difficulty of predicting total biodiversity within a system, based upon a single taxonomic group. Thus, to conserve the biodiversity of an ecosystem, it is crucial to consider variations in species diversity indices and community structures of different taxonomic groups, under a range of local conditions.

Amazon plant diversity revealed by a taxonomically verified species list.

PubMed

Cardoso, Domingos; Särkinen, Tiina; Alexander, Sara; Amorim, André M; Bittrich, Volker; Celis, Marcela; Daly, Douglas C; Fiaschi, Pedro; Funk, Vicki A; Giacomin, Leandro L; Goldenberg, Renato; Heiden, Gustavo; Iganci, João; Kelloff, Carol L; Knapp, Sandra; Cavalcante de Lima, Haroldo; Machado, Anderson F P; Dos Santos, Rubens Manoel; Mello-Silva, Renato; Michelangeli, Fabián A; Mitchell, John; Moonlight, Peter; de Moraes, Pedro Luís Rodrigues; Mori, Scott A; Nunes, Teonildes Sacramento; Pennington, Terry D; Pirani, José Rubens; Prance, Ghillean T; de Queiroz, Luciano Paganucci; Rapini, Alessandro; Riina, Ricarda; Rincon, Carlos Alberto Vargas; Roque, Nádia; Shimizu, Gustavo; Sobral, Marcos; Stehmann, João Renato; Stevens, Warren D; Taylor, Charlotte M; Trovó, Marcelo; van den Berg, Cássio; van der Werff, Henk; Viana, Pedro Lage; Zartman, Charles E; Forzza, Rafaela Campostrini

2017-10-03

Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests.

Amazon plant diversity revealed by a taxonomically verified species list

PubMed Central

Cardoso, Domingos; Särkinen, Tiina; Alexander, Sara; Amorim, André M.; Bittrich, Volker; Celis, Marcela; Daly, Douglas C.; Fiaschi, Pedro; Funk, Vicki A.; Giacomin, Leandro L.; Heiden, Gustavo; Iganci, João; Kelloff, Carol L.; Knapp, Sandra; Cavalcante de Lima, Haroldo; Machado, Anderson F. P.; dos Santos, Rubens Manoel; Mello-Silva, Renato; Michelangeli, Fabián A.; Mitchell, John; Moonlight, Peter; de Moraes, Pedro Luís Rodrigues; Mori, Scott A.; Nunes, Teonildes Sacramento; Pennington, Terry D.; Pirani, José Rubens; Prance, Ghillean T.; de Queiroz, Luciano Paganucci; Rapini, Alessandro; Rincon, Carlos Alberto Vargas; Roque, Nádia; Shimizu, Gustavo; Sobral, Marcos; Stehmann, João Renato; Stevens, Warren D.; Taylor, Charlotte M.; Trovó, Marcelo; van den Berg, Cássio; van der Werff, Henk; Viana, Pedro Lage; Zartman, Charles E.; Forzza, Rafaela Campostrini

2017-01-01

Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests. PMID:28923966

Response of rocky invertebrate diversity, structure and function to the vertical layering of vegetation

NASA Astrophysics Data System (ADS)

Bustamante, María; Tajadura, Javier; Gorostiaga, José María; Saiz-Salinas, José Ignacio

2014-06-01

Macroalgae comprise a prominent part of the rocky benthos where many invertebrates develop, and are believed to be undergoing severe declines worldwide. In order to investigate how the vegetation structure (crustose, basal and canopy layers) contributes to the diversity, structure and function of benthic invertebrates, a total of 31 subtidal transects were sampled along the northeast Atlantic coast of Spain. Significant positive relationships were found between the canopy layer and faunal abundance, taxonomic diversity and functional group diversity. Canopy forming algae were also related to epiphytic invertebrates, medium size forms, colonial strategy and suspensivores. By contrast, basal algae showed negative relationships with all variables tested except for detritivores. Multivariate multiple regression analyses (DISTLM) point to crustose as well as canopy layers as the best link between seaweeds and invertebrate assemblage structure. A close relationship was found between taxonomic and functional diversities. In general, low levels of taxonomic redundancy were detected for functional groups correlated with vegetation structure. A conceptual model based on the results is proposed, describing distinct stages of invertebrate assemblages in relation to the vertical structure of vegetation.

Glycosides from Marine Sponges (Porifera, Demospongiae): Structures, Taxonomical Distribution, Biological Activities and Biological Roles

PubMed Central

Kalinin, Vladimir I.; Ivanchina, Natalia V.; Krasokhin, Vladimir B.; Makarieva, Tatyana N.; Stonik, Valentin A.

2012-01-01

Literature data about glycosides from sponges (Porifera, Demospongiae) are reviewed. Structural diversity, biological activities, taxonomic distribution and biological functions of these natural products are discussed. PMID:23015769

Microbial Diversity in the Midguts of Field and Lab-Reared Populations of the European Corn Borer Ostrinia nubilalis

PubMed Central

Belda, Eugeni; Pedrola, Laia; Peretó, Juli; Martínez-Blanch, Juan F.; Montagud, Arnau; Navarro, Emilio; Urchueguía, Javier; Ramón, Daniel; Moya, Andrés; Porcar, Manuel

2011-01-01

Background Insects are associated with microorganisms that contribute to the digestion and processing of nutrients. The European Corn Borer (ECB) is a moth present world-wide, causing severe economical damage as a pest on corn and other crops. In the present work, we give a detailed view of the complexity of the microorganisms forming the ECB midgut microbiota with the objective of comparing the biodiversity of the midgut-associated microbiota and explore their potential as a source of genes and enzymes with biotechnological applications. Methodological/Principal Findings A high-throughput sequencing approach has been used to identify bacterial species, genes and metabolic pathways, particularly those involved in plant-matter degradation, in two different ECB populations (field-collected vs. lab-reared population with artificial diet). Analysis of the resulting sequences revealed the massive presence of Staphylococcus warneri and Weissella paramesenteroides in the lab-reared sample. This enabled us to reconstruct both genomes almost completely. Despite the apparently low diversity, 208 different genera were detected in the sample, although most of them at very low frequency. By contrast, the natural population exhibited an even higher taxonomic diversity along with a wider array of cellulolytic enzyme families. However, in spite of the differences in relative abundance of major taxonomic groups, not only did both metagenomes share a similar functional profile but also a similar distribution of non-redundant genes in different functional categories. Conclusions/Significance Our results reveal a highly diverse pool of bacterial species in both O. nubilalis populations, with major differences: The lab-reared sample is rich in gram-positive species (two of which have almost fully sequenced genomes) while the field sample harbors mainly gram-negative species and has a larger set of cellulolytic enzymes. We have found a clear relationship between the diet and the midgut microbiota, which reveals the selection pressure of food on the community of intestinal bacteria. PMID:21738787

Global Diversity of the Placozoa

PubMed Central

Eitel, Michael; Osigus, Hans-Jürgen; DeSalle, Rob; Schierwater, Bernd

2013-01-01

The enigmatic animal phylum Placozoa holds a key position in the metazoan Tree of Life. A simple bauplan makes it appear to be the most basal metazoan known and genetic evidence also points to a position close to the last common metazoan ancestor. Trichoplax adhaerens is the only formally described species in the phylum to date, making the Placozoa the only monotypic phylum in the animal kingdom. However, recent molecular genetic as well as morphological studies have identified a high level of diversity, and hence a potential high level of taxonomic diversity, within this phylum. Different taxa, possibly at different taxonomic levels, are awaiting description. In this review we firstly summarize knowledge on the morphology, phylogenetic position and ecology of the Placozoa. Secondly, we give an overview of placozoan morphological and genetic diversity and finally present an updated distribution of placozoan populations. We conclude that there is great potential and need to erect new taxa and to establish a firm system for this taxonomic tabula rasa. PMID:23565136

Climate warming promotes species diversity, but with greater taxonomic redundancy, in complex environments

PubMed Central

Thakur, Madhav P.; Tilman, David; Purschke, Oliver; Ciobanu, Marcel; Cowles, Jane; Isbell, Forest; Wragg, Peter D.; Eisenhauer, Nico

2017-01-01

Climate warming is predicted to alter species interactions, which could potentially lead to extinction events. However, there is an ongoing debate whether the effects of warming on biodiversity may be moderated by biodiversity itself. We tested warming effects on soil nematodes, one of the most diverse and abundant metazoans in terrestrial ecosystems, along a gradient of environmental complexity created by a gradient of plant species richness. Warming increased nematode species diversity in complex (16-species mixtures) plant communities (by ~36%) but decreased it in simple (monocultures) plant communities (by ~39%) compared to ambient temperature. Further, warming led to higher levels of taxonomic relatedness in nematode communities across all levels of plant species richness. Our results highlight both the need for maintaining species-rich plant communities to help offset detrimental warming effects and the inability of species-rich plant communities to maintain nematode taxonomic distinctness when warming occur. PMID:28740868

Initial nitrogen enrichment conditions determines variations in nitrogen substrate utilization by heterotrophic bacterial isolates.

PubMed

Ghosh, Suchismita; Ayayee, Paul A; Valverde-Barrantes, Oscar J; Blackwood, Christopher B; Royer, Todd V; Leff, Laura G

2017-04-04

The nitrogen (N) cycle consists of complex microbe-mediated transformations driven by a variety of factors, including diversity and concentrations of N compounds. In this study, we examined taxonomic diversity and N substrate utilization by heterotrophic bacteria isolated from streams under complex and simple N-enrichment conditions. Diversity estimates differed among isolates from the enrichments, but no significant composition were detected. Substrate utilization and substrate range of bacterial assemblages differed within and among enrichments types, and not simply between simple and complex N-enrichments. N substrate use patterns differed between isolates from some complex and simple N-enrichments while others were unexpectedly similar. Taxonomic composition of isolates did not differ among enrichments and was unrelated to N use suggesting strong functional redundancy. Ultimately, our results imply that the available N pool influences physiology and selects for bacteria with various abilities that are unrelated to their taxonomic affiliation.

Anaplasma marginale major surface protein 1a: a marker of strain diversity with implications for control of bovine anaplasmosis.

PubMed

Cabezas-Cruz, Alejandro; de la Fuente, José

2015-04-01

Classification of bacteria is challenging due to the lack of a theory-based framework. In addition, the adaptation of bacteria to ecological niches often results in selection of strains with diverse virulence, pathogenicity and transmission characteristics. Bacterial strain diversity presents challenges for taxonomic classification, which in turn impacts the ability to develop accurate diagnostics and effective vaccines. Over the past decade, the worldwide diversity of Anaplasma marginale, an economically important tick-borne pathogen of cattle, has become apparent. The extent of A. marginale strain diversity, formerly underappreciated, has contributed to the challenges of classification which, in turn, likely impacts the design and development of improved vaccines. Notably, the A. marginale surface protein 1a (MSP1a) is a model molecule for these studies because it serves as a marker for strain identity, is both an adhesin necessary for infection of cells and an immuno-reactive protein and is also an indicator of the evolution of strain diversity. Herein, we discuss a molecular taxonomic approach for classification of A. marginale strain diversity. Taxonomic analysis of this important molecule provides the opportunity to understand A. marginale strain diversity as it relates geographic and ecological factors and to the development of effective vaccines for control of bovine anaplasmosis worldwide. Copyright © 2015 Elsevier GmbH. All rights reserved.

Distinct composition signatures of archaeal and bacterial phylotypes in the Wanda Glacier forefield, Antarctic Peninsula.

PubMed

Pessi, Igor S; Osorio-Forero, César; Gálvez, Eric J C; Simões, Felipe L; Simões, Jefferson C; Junca, Howard; Macedo, Alexandre J

2015-01-01

Several studies have shown that microbial communities in Antarctic environments are highly diverse. However, considering that the Antarctic Peninsula is among the regions with the fastest warming rates, and that regional climate change has been linked to an increase in the mean rate of glacier retreat, the microbial diversity in Antarctic soil is still poorly understood. In this study, we analysed more than 40 000 sequences of the V5-V6 hypervariable region of the 16S rRNA gene obtained by 454 pyrosequencing from four soil samples from the Wanda Glacier forefield, King George Island, Antarctic Peninsula. Phylotype diversity and richness were surprisingly high, and taxonomic assignment of sequences revealed that communities are dominated by Proteobacteria, Bacteroidetes and Euryarchaeota, with a high frequency of archaeal and bacterial phylotypes unclassified at the genus level and without cultured representative strains, representing a distinct microbial community signature. Several phylotypes were related to marine microorganisms, indicating the importance of the marine environment as a source of colonizers for this recently deglaciated environment. Finally, dominant phylotypes were related to different microorganisms possessing a large array of metabolic strategies, indicating that early successional communities in Antarctic glacier forefield can be also functionally diverse. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

North Andean origin and diversification of the largest ithomiine butterfly genus

PubMed Central

Lisa De-Silva, Donna; Mota, Luísa L.; Chazot, Nicolas; Mallarino, Ricardo; Silva-Brandão, Karina L.; Piñerez, Luz Miryam Gómez; Freitas, André V.L.; Lamas, Gerardo; Joron, Mathieu; Mallet, James; Giraldo, Carlos E.; Uribe, Sandra; Särkinen, Tiina; Knapp, Sandra; Jiggins, Chris D.; Willmott, Keith R.; Elias, Marianne

2017-01-01

The Neotropics harbour the most diverse flora and fauna on Earth. The Andes are a major centre of diversification and source of diversity for adjacent areas in plants and vertebrates, but studies on insects remain scarce, even though they constitute the largest fraction of terrestrial biodiversity. Here, we combine molecular and morphological characters to generate a dated phylogeny of the butterfly genus Pteronymia (Nymphalidae: Danainae), which we use to infer spatial, elevational and temporal diversification patterns. We first propose six taxonomic changes that raise the generic species total to 53, making Pteronymia the most diverse genus of the tribe Ithomiini. Our biogeographic reconstruction shows that Pteronymia originated in the Northern Andes, where it diversified extensively. Some lineages colonized lowlands and adjacent montane areas, but diversification in those areas remained scarce. The recent colonization of lowland areas was reflected by an increase in the rate of evolution of species’ elevational ranges towards present. By contrast, speciation rate decelerated with time, with no extinction. The geological history of the Andes and adjacent regions have likely contributed to Pteronymia diversification by providing compartmentalized habitats and an array of biotic and abiotic conditions, and by limiting dispersal between some areas while promoting interchange across others. PMID:28387233

Biodiversity hot spot on a hot spot: novel extremophile diversity in Hawaiian fumaroles.

PubMed

Wall, Kate; Cornell, Jennifer; Bizzoco, Richard W; Kelley, Scott T

2015-01-06

Fumaroles (steam vents) are the most common, yet least understood, microbial habitat in terrestrial geothermal settings. Long believed too extreme for life, recent advances in sample collection and DNA extraction methods have found that fumarole deposits and subsurface waters harbor a considerable diversity of viable microbes. In this study, we applied culture-independent molecular methods to explore fumarole deposit microbial assemblages in 15 different fumaroles in four geographic locations on the Big Island of Hawai'i. Just over half of the vents yielded sufficient high-quality DNA for the construction of 16S ribosomal RNA gene sequence clone libraries. The bacterial clone libraries contained sequences belonging to 11 recognized bacterial divisions and seven other division-level phylogenetic groups. Archaeal sequences were less numerous, but similarly diverse. The taxonomic composition among fumarole deposits was highly heterogeneous. Phylogenetic analysis found cloned fumarole sequences were related to microbes identified from a broad array of globally distributed ecotypes, including hot springs, terrestrial soils, and industrial waste sites. Our results suggest that fumarole deposits function as an "extremophile collector" and may be a hot spot of novel extremophile biodiversity. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

North Andean origin and diversification of the largest ithomiine butterfly genus

NASA Astrophysics Data System (ADS)

Lisa de-Silva, Donna; Mota, Luísa L.; Chazot, Nicolas; Mallarino, Ricardo; Silva-Brandão, Karina L.; Piñerez, Luz Miryam Gómez; Freitas, André V. L.; Lamas, Gerardo; Joron, Mathieu; Mallet, James; Giraldo, Carlos E.; Uribe, Sandra; Särkinen, Tiina; Knapp, Sandra; Jiggins, Chris D.; Willmott, Keith R.; Elias, Marianne

2017-04-01

The Neotropics harbour the most diverse flora and fauna on Earth. The Andes are a major centre of diversification and source of diversity for adjacent areas in plants and vertebrates, but studies on insects remain scarce, even though they constitute the largest fraction of terrestrial biodiversity. Here, we combine molecular and morphological characters to generate a dated phylogeny of the butterfly genus Pteronymia (Nymphalidae: Danainae), which we use to infer spatial, elevational and temporal diversification patterns. We first propose six taxonomic changes that raise the generic species total to 53, making Pteronymia the most diverse genus of the tribe Ithomiini. Our biogeographic reconstruction shows that Pteronymia originated in the Northern Andes, where it diversified extensively. Some lineages colonized lowlands and adjacent montane areas, but diversification in those areas remained scarce. The recent colonization of lowland areas was reflected by an increase in the rate of evolution of species’ elevational ranges towards present. By contrast, speciation rate decelerated with time, with no extinction. The geological history of the Andes and adjacent regions have likely contributed to Pteronymia diversification by providing compartmentalized habitats and an array of biotic and abiotic conditions, and by limiting dispersal between some areas while promoting interchange across others.

Biodiversity hot spot on a hot spot: novel extremophile diversity in Hawaiian fumaroles

PubMed Central

Wall, Kate; Cornell, Jennifer; Bizzoco, Richard W; Kelley, Scott T

2015-01-01

Fumaroles (steam vents) are the most common, yet least understood, microbial habitat in terrestrial geothermal settings. Long believed too extreme for life, recent advances in sample collection and DNA extraction methods have found that fumarole deposits and subsurface waters harbor a considerable diversity of viable microbes. In this study, we applied culture-independent molecular methods to explore fumarole deposit microbial assemblages in 15 different fumaroles in four geographic locations on the Big Island of Hawai'i. Just over half of the vents yielded sufficient high-quality DNA for the construction of 16S ribosomal RNA gene sequence clone libraries. The bacterial clone libraries contained sequences belonging to 11 recognized bacterial divisions and seven other division-level phylogenetic groups. Archaeal sequences were less numerous, but similarly diverse. The taxonomic composition among fumarole deposits was highly heterogeneous. Phylogenetic analysis found cloned fumarole sequences were related to microbes identified from a broad array of globally distributed ecotypes, including hot springs, terrestrial soils, and industrial waste sites. Our results suggest that fumarole deposits function as an “extremophile collector” and may be a hot spot of novel extremophile biodiversity. PMID:25565172

Degradation in landscape matrix has diverse impacts on diversity in protected areas

PubMed Central

Brotons, Lluís; Rajasärkkä, Ari; Tornberg, Risto

2017-01-01

Introduction A main goal of protected areas is to maintain species diversity and the integrity of biological assemblages. Intensifying land use in the matrix surrounding protected areas creates a challenge for biodiversity conservation. Earlier studies have mainly focused on taxonomic diversity within protected areas. However, functional and especially phylogenetic diversities are less studied phenomena, especially with respect to the impacts of the matrix that surrounds protected areas. Phylogenetic diversity refers to the range of evolutionary lineages, the maintenance of which ensures that future evolutionary potential is safeguarded. Functional diversity refers to the range of ecological roles that members of a community perform. For ecosystem functioning and long-term resilience, they are at least as important as taxonomic diversity. Aim We studied how the characteristics of protected areas and land use intensity in the surrounding matrix affect the diversity of bird communities in protected boreal forests. We used line-transect count and land-cover data from 91 forest reserves in Northern Finland, and land-cover data from buffer zones surrounding these reserves. We studied if habitat diversity and productivity inside protected areas, and intensity of forest management in the matrix have consistent effects on taxonomic, functional and phylogenetic diversities, and community specialization. Results We found that habitat diversity and productivity inside protected areas have strong effects on all diversity metrics, but matrix effects were inconsistent. The proportion of old forest in the matrix, reflecting low intensity forest management, had positive effects on community specialization. Interestingly, functional diversity increased with increasing logging intensity in the matrix. Conclusions Our results indicate that boreal forest reserves are not able to maintain their species composition and abundances if embedded in a severely degraded matrix. Our study also highlights the importance of focusing on different aspects of biodiversity. PMID:28950017

MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution

PubMed Central

Boeuf, Dominique; Audic, Stéphane; Brillet-Guéguen, Loraine; Caron, Christophe; Jeanthon, Christian

2015-01-01

Microbial rhodopsins are a diverse group of photoactive transmembrane proteins found in all three domains of life and in viruses. Today, microbial rhodopsin research is a flourishing research field in which new understandings of rhodopsin diversity, function and evolution are contributing to broader microbiological and molecular knowledge. Here, we describe MicRhoDE, a comprehensive, high-quality and freely accessible database that facilitates analysis of the diversity and evolution of microbial rhodopsins. Rhodopsin sequences isolated from a vast array of marine and terrestrial environments were manually collected and curated. To each rhodopsin sequence are associated related metadata, including predicted spectral tuning of the protein, putative activity and function, taxonomy for sequences that can be linked to a 16S rRNA gene, sampling date and location, and supporting literature. The database currently covers 7857 aligned sequences from more than 450 environmental samples or organisms. Based on a robust phylogenetic analysis, we introduce an operational classification system with multiple phylogenetic levels ranging from superclusters to species-level operational taxonomic units. An integrated pipeline for online sequence alignment and phylogenetic tree construction is also provided. With a user-friendly interface and integrated online bioinformatics tools, this unique resource should be highly valuable for upcoming studies of the biogeography, diversity, distribution and evolution of microbial rhodopsins. Database URL: http://micrhode.sb-roscoff.fr. PMID:26286928

MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution.

PubMed

Boeuf, Dominique; Audic, Stéphane; Brillet-Guéguen, Loraine; Caron, Christophe; Jeanthon, Christian

2015-01-01

Microbial rhodopsins are a diverse group of photoactive transmembrane proteins found in all three domains of life and in viruses. Today, microbial rhodopsin research is a flourishing research field in which new understandings of rhodopsin diversity, function and evolution are contributing to broader microbiological and molecular knowledge. Here, we describe MicRhoDE, a comprehensive, high-quality and freely accessible database that facilitates analysis of the diversity and evolution of microbial rhodopsins. Rhodopsin sequences isolated from a vast array of marine and terrestrial environments were manually collected and curated. To each rhodopsin sequence are associated related metadata, including predicted spectral tuning of the protein, putative activity and function, taxonomy for sequences that can be linked to a 16S rRNA gene, sampling date and location, and supporting literature. The database currently covers 7857 aligned sequences from more than 450 environmental samples or organisms. Based on a robust phylogenetic analysis, we introduce an operational classification system with multiple phylogenetic levels ranging from superclusters to species-level operational taxonomic units. An integrated pipeline for online sequence alignment and phylogenetic tree construction is also provided. With a user-friendly interface and integrated online bioinformatics tools, this unique resource should be highly valuable for upcoming studies of the biogeography, diversity, distribution and evolution of microbial rhodopsins. Database URL: http://micrhode.sb-roscoff.fr. © The Author(s) 2015. Published by Oxford University Press.

MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.

PubMed

Blank, Carrine E; Cui, Hong; Moore, Lisa R; Walls, Ramona L

2016-01-01

MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The ontology was built to support the ongoing development of a natural language processing algorithm, MicroPIE (or, Microbial Phenomics Information Extractor). During the MicroPIE design process, we realized there was a need for a prokaryotic ontology which would capture the evolutionary diversity of phenotypes and metabolic processes across the tree of life, capture the diversity of synonyms and information contained in the taxonomic literature, and relate microbiological entities and processes to terms in a large number of other ontologies, most particularly the Gene Ontology (GO), the Phenotypic Quality Ontology (PATO), and the Chemical Entities of Biological Interest (ChEBI). We thus constructed MicrO to be rich in logical axioms and synonyms gathered from the taxonomic literature. MicrO currently has ~14550 classes (~2550 of which are new, the remainder being microbiologically-relevant classes imported from other ontologies), connected by ~24,130 logical axioms (5,446 of which are new), and is available at (http://purl.obolibrary.org/obo/MicrO.owl) and on the project website at https://github.com/carrineblank/MicrO. MicrO has been integrated into the OBO Foundry Library (http://www.obofoundry.org/ontology/micro.html), so that other ontologies can borrow and re-use classes. Term requests and user feedback can be made using MicrO's Issue Tracker in GitHub. We designed MicrO such that it can support the ongoing and future development of algorithms that can leverage the controlled vocabulary and logical inference power provided by the ontology. By connecting microbial classes with large numbers of chemical entities, material entities, biological processes, molecular functions, and qualities using a dense array of logical axioms, we intend MicrO to be a powerful new tool to increase the computing power of bioinformatics tools such as the automated text mining of prokaryotic taxonomic descriptions using natural language processing. We also intend MicrO to support the development of new bioinformatics tools that aim to develop new connections between microbial phenotypes and genotypes (i.e., the gene content in genomes). Future ontology development will include incorporation of pathogenic phenotypes and prokaryotic habitats.

Concordant Biogeographic Patterns among Multiple Taxonomic Groups in the Mexican Freshwater Biota

PubMed Central

Quiroz-Martínez, Benjamín; Álvarez, Fernando; Espinosa, Héctor; Salgado-Maldonado, Guillermo

2014-01-01

In this paper we analyse the degree of concordance in species richness and taxonomic distinctness (diversity) patterns among different freshwater taxonomic groups in order to test three long held patterns described in Mexican freshwater biogeography: 1. The aquatic biota of Mexico includes two distinct faunas, a rich Neotropical component in the south and a south-eastern region and a less rich Nearctic component towards central and northern latitudes of the country. 2. A hotspot of species richness and diversity has been recorded in the Usumacinta, including the Yucatan Peninsula. 3. The presence of two distinct biotas in Mexico, an eastern one distributed along the Gulf of Mexico slope, and a western one associated to the Pacific versant. We use species richness and taxonomic distinctness to explore patterns of diversity and how these patterns change between zoogeographical regions. This paper points out a clear separation between Neotropical and Nearctic drainage basins but also between eastern (Gulf of Mexico) and western (Pacific) drainage basins. Present data gives additional empirical support from freshwater biota for three long held beliefs regarding distributional patterns of the Mexican biota. The neotropical basins of Mexico are generally host to a richest and more diversified fauna, that includes more families, genera and species, compared to the less rich and less diverse fauna in the nearctic basins. PMID:25136979

Barcoding snakeheads (Teleostei, Channidae) revisited: Discovering greater species diversity and resolving perpetuated taxonomic confusions

PubMed Central

Conte-Grand, Cecilia; Britz, Ralf; Dahanukar, Neelesh; Raghavan, Rajeev; Pethiyagoda, Rohan; Tan, Heok Hui; Hadiaty, Renny K.; Yaakob, Norsham S.

2017-01-01

Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group with those previously reported revealed several inconsistencies that prompted us to expand and improve on previous studies. By generating 343 novel snakehead coxI sequences and combining them with an additional 434 coxI sequences from GenBank we highlight several problems with previous efforts towards the assembly of a snakehead reference barcode library. We found that 16.3% of the channid coxI sequences deposited in GenBank are based on misidentifications. With the inclusion of our own data we were, however, able to solve these cases of perpetuated taxonomic confusion. Different species delimitation approaches we employed (BIN, GMYC, and PTP) were congruent in suggesting a potentially much higher species diversity within snakeheads than currently recognized. In total, 90 BINs were recovered and within a total of 15 currently recognized species multiple BINs were identified. This higher species diversity is mostly due to either the incorporation of undescribed, narrow range, endemics from the Eastern Himalaya biodiversity hotspot or the incorporation of several widespread species characterized by deep genetic splits between geographically well-defined lineages. In the latter case, over-lumping in the past has deflated the actual species numbers. Further integrative approaches are clearly needed for providing a better taxonomic understanding of snakehead diversity, new species descriptions and taxonomic revisions of the group. PMID:28931084

Similarity in volatile communities leads to increased herbivory and greater tropical forest diversity.

PubMed

Massad, Tara J; Martins de Moraes, Marcílio; Philbin, Casey; Oliveira, Celso; Cebrian Torrejon, Gerardo; Fumiko Yamaguchi, Lydia; Jeffrey, Christopher S; Dyer, Lee A; Richards, Lora A; Kato, Massuo J

2017-07-01

A longstanding paradigm in ecology is that there are positive associations between herbivore diversity, specialization, and plant species diversity, with a focus on taxonomic diversity. However, phytochemical diversity is also an informative metric, as insect herbivores interact with host plants not as taxonomic entities, but as sources of nutrients, primary metabolites, and mixtures of attractant and repellant chemicals. The present research examines herbivore responses to phytochemical diversity measured as volatile similarity in the tropical genus Piper. We quantified associations between naturally occurring volatile variation and herbivory by specialist and generalist insects. Intraspecific similarity of volatile compounds across individuals was associated with greater overall herbivory. A structural equation model supported the hypothesis that plot level volatile similarity caused greater herbivory by generalists, but not specialists, which led to increased understory plant richness. These results demonstrate that using volatiles as a functional diversity metric is informative for understanding tropical forest diversity and indicate that generalist herbivores contribute to the maintenance of diversity. © 2017 by the Ecological Society of America.

Intensive agriculture reduces soil biodiversity across Europe.

PubMed

Tsiafouli, Maria A; Thébault, Elisa; Sgardelis, Stefanos P; de Ruiter, Peter C; van der Putten, Wim H; Birkhofer, Klaus; Hemerik, Lia; de Vries, Franciska T; Bardgett, Richard D; Brady, Mark Vincent; Bjornlund, Lisa; Jørgensen, Helene Bracht; Christensen, Sören; Hertefeldt, Tina D'; Hotes, Stefan; Gera Hol, W H; Frouz, Jan; Liiri, Mira; Mortimer, Simon R; Setälä, Heikki; Tzanopoulos, Joseph; Uteseny, Karoline; Pižl, Václav; Stary, Josef; Wolters, Volkmar; Hedlund, Katarina

2015-02-01

Soil biodiversity plays a key role in regulating the processes that underpin the delivery of ecosystem goods and services in terrestrial ecosystems. Agricultural intensification is known to change the diversity of individual groups of soil biota, but less is known about how intensification affects biodiversity of the soil food web as a whole, and whether or not these effects may be generalized across regions. We examined biodiversity in soil food webs from grasslands, extensive, and intensive rotations in four agricultural regions across Europe: in Sweden, the UK, the Czech Republic and Greece. Effects of land-use intensity were quantified based on structure and diversity among functional groups in the soil food web, as well as on community-weighted mean body mass of soil fauna. We also elucidate land-use intensity effects on diversity of taxonomic units within taxonomic groups of soil fauna. We found that between regions soil food web diversity measures were variable, but that increasing land-use intensity caused highly consistent responses. In particular, land-use intensification reduced the complexity in the soil food webs, as well as the community-weighted mean body mass of soil fauna. In all regions across Europe, species richness of earthworms, Collembolans, and oribatid mites was negatively affected by increased land-use intensity. The taxonomic distinctness, which is a measure of taxonomic relatedness of species in a community that is independent of species richness, was also reduced by land-use intensification. We conclude that intensive agriculture reduces soil biodiversity, making soil food webs less diverse and composed of smaller bodied organisms. Land-use intensification results in fewer functional groups of soil biota with fewer and taxonomically more closely related species. We discuss how these changes in soil biodiversity due to land-use intensification may threaten the functioning of soil in agricultural production systems. © 2014 John Wiley & Sons Ltd.

Shifts in taxonomic and functional microbial diversity with agriculture: How fragile is the Brazilian Cerrado?

PubMed

Souza, Renata Carolini; Mendes, Iêda Carvalho; Reis-Junior, Fábio Bueno; Carvalho, Fabíola Marques; Nogueira, Marco Antonio; Vasconcelos, Ana Tereza Ribeiro; Vicente, Vânia Aparecida; Hungria, Mariangela

2016-03-16

The Cerrado--an edaphic type of savannah--comprises the second largest biome of the Brazilian territory and is the main area for grain production in the country, but information about the impact of land conversion to agriculture on microbial diversity is still scarce. We used a shotgun metagenomic approach to compare undisturbed (native) soil and soils cropped for 23 years with soybean/maize under conservation tillage--"no-till" (NT)--and conventional tillage (CT) systems in the Cerrado biome. Soil management and fertilizer inputs with the introduction of agriculture improved chemical properties, but decreased soil macroporosity and microbial biomass of carbon and nitrogen. Principal coordinates analyses confirmed different taxonomic and functional profiles for each treatment. There was predominance of the Bacteria domain, especially the phylum Proteobacteria, with higher numbers of sequences in the NT and CT treatments; Archaea and Viruses also had lower numbers of sequences in the undisturbed soil. Within the Alphaproteobacteria, there was dominance of Rhizobiales and of the genus Bradyrhizobium in the NT and CT systems, attributed to massive inoculation of soybean, and also of Burkholderiales. In contrast, Rhizobium, Azospirillum, Xanthomonas, Pseudomonas and Acidobacterium predominated in the native Cerrado. More Eukaryota, especially of the phylum Ascomycota were detected in the NT. The functional analysis revealed lower numbers of sequences in the five dominant categories for the CT system, whereas the undisturbed Cerrado presented higher abundance. High impact of agriculture in taxonomic and functional microbial diversity in the biome Cerrado was confirmed. Functional diversity was not necessarily associated with taxonomic diversity, as the less conservationist treatment (CT) presented increased taxonomic sequences and reduced functional profiles, indicating a strategy to try to maintain soil functioning by favoring taxa that are probably not the most efficient for some functions. Our results highlight that underneath the rustic appearance of the Cerrado vegetation there is a fragile soil microbial community.

Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.

PubMed

Rudney, Joel D; Jagtap, Pratik D; Reilly, Cavan S; Chen, Ruoqiong; Markowski, Todd W; Higgins, LeeAnn; Johnson, James E; Griffin, Timothy J

2015-12-19

The etiology of dental caries is multifactorial, but frequent consumption of free sugars, notably sucrose, appears to be a major factor driving the supragingival microbiota in the direction of dysbiosis. Recent 16S rRNA-based studies indicated that caries-associated communities were less diverse than healthy supragingival plaque but still displayed considerable taxonomic diversity between individuals. Metagenomic studies likewise have found that healthy oral sites from different people were broadly similar with respect to gene function, even though there was an extensive individual variation in their taxonomic profiles. That pattern may also extend to dysbiotic communities. In that case, shifts in community-wide protein relative abundance might provide better biomarkers of dysbiosis that can be achieved through taxonomy alone. In this study, we used a paired oral microcosm biofilm model of dental caries to investigate differences in community composition and protein relative abundance in the presence and absence of sucrose. This approach provided large quantities of protein, which facilitated deep metaproteomic analysis. Community composition was evaluated using 16S rRNA sequencing and metaproteomic approaches. Although taxonomic diversity was reduced by sucrose pulsing, considerable inter-subject variation in community composition remained. By contrast, functional analysis using the SEED ontology found that sucrose induced changes in protein relative abundance patterns for pathways involving glycolysis, lactate production, aciduricity, and ammonia/glutamate metabolism that were conserved across taxonomically diverse dysbiotic oral microcosm biofilm communities. Our findings support the concept of using function-based changes in protein relative abundance as indicators of dysbiosis. Our microcosm model cannot replicate all aspects of the oral environment, but the deep level of metaproteomic analysis it allows makes it suitable for discovering which proteins are most consistently abundant during dysbiosis. It then may be possible to define biomarkers that could be used to detect at-risk tooth surfaces before the development of overt carious lesions.

Phylogenetically diverse macrophyte community promotes species diversity of mobile epi-benthic invertebrates

NASA Astrophysics Data System (ADS)

Nakamoto, Kenta; Hayakawa, Jun; Kawamura, Tomohiko; Kodama, Masafumi; Yamada, Hideaki; Kitagawa, Takashi; Watanabe, Yoshiro

2018-07-01

Various aspects of plant diversity such as species diversity and phylogenetic diversity enhance the species diversity of associated animals in terrestrial systems. In marine systems, however, the effects of macrophyte diversity on the species diversity of associated animals have received little attention. Here, we sampled in a subtropical seagrass-seaweed mixed bed to elucidate the effect of the macrophyte phylogenetic diversity based on the taxonomic relatedness as well as the macrophyte species diversity on species diversity of mobile epi-benthic invertebrates. Using regression analyses for each macrophyte parameter as well as multiple regression analyses, we found that the macrophyte phylogenetic diversity (taxonomic diversity index: Delta) positively influenced the invertebrate species richness and diversity index (H‧). Although the macrophyte species richness and H‧ also positively influenced the invertebrate species richness, the best fit model for invertebrate species richness did not include them, suggesting that the macrophyte species diversity indirectly influenced invertebrate species diversity. Possible explanations of the effects of macrophyte Delta on the invertebrate species diversity were the niche complementarity effect and the selection effect. This is the first study which demonstrates that macrophyte phylogenetic diversity has a strong effect on the species diversity of mobile epi-benthic invertebrates.

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

PubMed

Fierer, Noah; Leff, Jonathan W; Adams, Byron J; Nielsen, Uffe N; Bates, Scott Thomas; Lauber, Christian L; Owens, Sarah; Gilbert, Jack A; Wall, Diana H; Caporaso, J Gregory

2012-12-26

For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.

DNA Barcoding the Medusozoa using mtCOI

NASA Astrophysics Data System (ADS)

Ortman, Brian D.; Bucklin, Ann; Pagès, Francesc; Youngbluth, Marsh

2010-12-01

The Medusozoa are a clade within the Cnidaria comprising the classes Hydrozoa, Scyphozoa, and Cubozoa. Identification of medusozoan species is challenging, even for taxonomic experts, due to their fragile forms and complex, morphologically-distinct life history stages. In this study 231 sequences for a portion of the mitochondrial Cytochrome Oxidase I (mtCOI) gene were obtained from 95 species of Medusozoans including; 84 hydrozoans (61 siphonophores, eight anthomedusae, four leptomedusae, seven trachymedusae, and four narcomedusae), 10 scyphozoans (three coronatae, four semaeostomae, two rhizostomae, and one stauromedusae), and one cubozoan. This region of mtCOI has been used as a DNA barcode (i.e., a molecular character for species recognition and discrimination) for a diverse array of taxa, including some Cnidaria. Kimura 2-parameter (K2P) genetic distances between sequence variants within species ranged from 0 to 0.057 (mean 0.013). Within the 13 genera for which multiple species were available, K2P distance between congeneric species ranged from 0.056 to 0.381. A cluster diagram generated by Neighbor Joining (NJ) using K2P distances reliably clustered all barcodes of the same species with ≥99% bootstrap support, ensuring accurate identification of species. Intra- and inter-specific variation of the mtCOI gene for the Medusozoa are appropriate for this gene to be used as a DNA barcode for species-level identification, but not for phylogenetic analysis or taxonomic classification of unknown sequences at higher taxonomic levels. This study provides a set of molecular tools that can be used to address questions of speciation, biodiversity, life-history, and population boundaries in the Medusozoa.

Taxonomic and functional distinctness of the fish assemblages in three coastal environments (bays, coastal lagoons and oceanic beaches) in Southeastern Brazil.

PubMed

Azevedo, Márcia Cristina Costa; Gomes-Gonçalves, Rafaela de Sousa; Mattos, Tailan Moretti; Uehara, Wagner; Guedes, Gustavo Henrique Soares; Araújo, Francisco Gerson

2017-08-01

Several species of marine fish use different coastal systems especially during their early development. However, these habitats are jeopardized by anthropogenic influences threatening the success of fish populations, and urgent measures are needed to priorize areas to protect their sustainability. We applied taxonomic (Δ+) and functional (X+) distinctiveness indices that represent taxonomic composition and functional roles to assess biodiversity of three different costal systems: bays, coastal lagoons and oceanic beaches. We hypothesized that difference in habitat characteristics, especially in the more dynamism and habitat homogeneity of oceanic beaches compared with more habitat diversity and sheltered conditions of bays and coastal lagoons results in differences in fish richness and taxonomic and functional diversity. The main premise is that communities phylogenetically and functionally more distinct have more interest in conservation policies. Significant differences (P < 0.004) were found in the species richness, Δ+ and X+ among the three systems according to PERMANOVA. Fish richness was higher in bays compared with the coastal lagoons and oceanic beaches. Higher Δ+ was found for the coastal lagoons compared with the bays and oceanic beaches, with the bays having some values below the confidence limit. Similar patterns were found for X+, although all values were within the confidence limits for the bays, suggesting that the absence of some taxa does not interfere in functional diversity. The hypothesis that taxonomic and functional structure of fish assemblages differ among the three systems was accepted and we suggest that coastal lagoons should be priorized in conservation programs because they support more taxonomic and functional distinctiveness. Copyright © 2017 Elsevier Ltd. All rights reserved.

Taxonomic and thematic organisation of proper name conceptual knowledge.

PubMed

Crutch, Sebastian J; Warrington, Elizabeth K

2011-01-01

We report the investigation of the organisation of proper names in two aphasic patients (NBC and FBI). The performance of both patients on spoken word to written word matching tasks was inconsistent, affected by presentation rate and semantic relatedness of the competing responses, all hallmarks of a refractory semantic access dysphasia. In a series of experiments we explored the semantic relatedness effects within their proper name vocabulary, including brand names and person names. First we demonstrated the interaction between very fine grain organisation and personal experience, with one patient with a special interest in the cinema demonstrating higher error rates when identifying the names of actors working in a similar film genre (e.g., action movies: Arnold Schwarzenegger, Bruce Willis, Sylvester Stallone, Mel Gibson) than those working in different genres (e.g., Arnold Schwarzenegger, Gregory Peck, Robin Williams, Gene Kelly). Second we compared directly two potential principles of semantic organisation - taxonomic and thematic. Furthermore we considered these principles of organisation in the context of the individuals' personal knowledge base. We selected topics matching the interests and experience of each patient, namely cinema and literature (NBC) and naval history (FBI). The stimulus items were arranged in taxonomic arrays (e.g., Jane Austen, Emily Bronte, Agatha Christie), thematic arrays (e.g., Jane Austen, Pride and Prejudice, Mr Darcy), and unrelated arrays (e.g., Jane Austen, Wuthering Heights, Hercule Poirot). We documented that different patterns of taxonomic and thematic organisation were constrained by whether the individual has limited knowledge, moderate knowledge or detailed knowledge of a particular vocabulary. It is suggested that moderate proper name knowledge is primarily organised by taxonomy whereas extensive experience results in a more detailed knowledge base in which theme is a powerful organising principle.

Taxonomic and Thematic Organisation of Proper Name Conceptual Knowledge

PubMed Central

Crutch, Sebastian J.; Warrington, Elizabeth K.

2011-01-01

We report the investigation of the organisation of proper names in two aphasic patients (NBC and FBI). The performance of both patients on spoken word to written word matching tasks was inconsistent, affected by presentation rate and semantic relatedness of the competing responses, all hallmarks of a refractory semantic access dysphasia. In a series of experiments we explored the semantic relatedness effects within their proper name vocabulary, including brand names and person names. First we demonstrated the interaction between very fine grain organisation and personal experience, with one patient with a special interest in the cinema demonstrating higher error rates when identifying the names of actors working in a similar film genre (e.g. action movies: Arnold Schwarzenegger, Bruce Willis, Sylvester Stallone, Mel Gibson) than those working in different genres (e.g. Arnold Schwarzenegger, Gregory Peck, Robin Williams, Gene Kelly). Second we compared directly two potential principles of semantic organisation – taxonomic and thematic. Furthermore we considered these principles of organisation in the context of the individuals' personal knowledge base. We selected topics matching the interests and experience of each patient, namely cinema and literature (NBC) and naval history (FBI). The stimulus items were arranged in taxonomic arrays (e.g. Jane Austen, Emily Bronte, Agatha Christie), thematic arrays (e.g. Jane Austen, Pride and Prejudice, Mr Darcy), and unrelated arrays (e.g. Jane Austen, Wuthering Heights, Hercule Poirot). We documented that different patterns of taxonomic and thematic organisation were constrained by whether the individual has limited knowledge, moderate knowledge or detailed knowledge of a particular vocabulary. It is suggested that moderate proper name knowledge is primarily organised by taxonomy whereas extensive experience results in a more detailed knowledge base in which theme is a powerful organising principle. PMID:22063815

Macrobenthic diversity in protected, disturbed, and newly formed intertidal wetlands of a subtropical estuary in China.

PubMed

Lv, Weiwei; Ma, Chang-An; Huang, Youhui; Yang, Yang; Yu, Ji; Zhang, Mingqing; Zhao, Yunlong

2014-12-15

In this study, intertidal macrobenthic diversity in protected, disturbed, and newly formed wetlands of Yangtze estuary was assessed using PRIMER 5.2 based on species diversity and species relatedness. We observed high diversity in nature reserves and low diversity in adjacent disturbed and newly formed wetlands. These diversity data were then integrated with historical data to detect the variation in macrobenthic diversity over the past two decades. The integrated data indicated that the intertidal macrobenthic diversity sharply decreased in heavy reclamation tidal flats whereas markedly increased in non-disturbed nature reserve and newly formed wetland. Benthic health was observed with the departure degree of average taxonomic distinctness (Δ(+)) and variation in taxonomic distinctness (Λ(+)) from the simulated 95% confidence funnel. All the habitats were subjected to different levels of human interference, except Jiuduansha and Beigangbeisha. The degradation of intertidal wetland in Yangtze estuary was mainly attributed to land reclamation, overgrazing, and overfishing. Copyright © 2014 Elsevier Ltd. All rights reserved.

Life in Oligotropic Desert Environments: Contrasting Taxonomic and Functional Diversity of Two Microbial Mats with Metagenomics

NASA Astrophysics Data System (ADS)

Bonilla-Rosso, G.; Peimbert, M.; Olmedo, G.; Alcaraz, L. D.; Eguiarte, L. E.; Souza, V.

2010-04-01

The metagenomic analysis of two microbial mats from the oligotrophic waters in the Cuatrociéngas basin reveals large differences both at taxonomic and functional level. These are explained in terms of environmental stability and nutrient availability.

Classification of malignant and benign lung nodules using taxonomic diversity index and phylogenetic distance.

PubMed

de Sousa Costa, Robherson Wector; da Silva, Giovanni Lucca França; de Carvalho Filho, Antonio Oseas; Silva, Aristófanes Corrêa; de Paiva, Anselmo Cardoso; Gattass, Marcelo

2018-05-23

Lung cancer presents the highest cause of death among patients around the world, in addition of being one of the smallest survival rates after diagnosis. Therefore, this study proposes a methodology for diagnosis of lung nodules in benign and malignant tumors based on image processing and pattern recognition techniques. Mean phylogenetic distance (MPD) and taxonomic diversity index (Δ) were used as texture descriptors. Finally, the genetic algorithm in conjunction with the support vector machine were applied to select the best training model. The proposed methodology was tested on computed tomography (CT) images from the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI), with the best sensitivity of 93.42%, specificity of 91.21%, accuracy of 91.81%, and area under the ROC curve of 0.94. The results demonstrate the promising performance of texture extraction techniques using mean phylogenetic distance and taxonomic diversity index combined with phylogenetic trees. Graphical Abstract Stages of the proposed methodology.

Avian Species and Functional Diversity in Agricultural Landscapes: Does Landscape Heterogeneity Matter?

PubMed Central

2017-01-01

While the positive relationship between avian diversity and habitat heterogeneity is widely accepted, it is primarily based on observed species richness without accounting for imperfect detection. Other facets of diversity such as functional diversity are also rarely explored. We investigated the avian diversity-landscape heterogeneity relationship in agricultural landscapes by considering two aspects of diversity: taxonomic diversity (species richness) estimated from a multi-species dynamic occupancy model, and functional diversity (functional evenness [FEve] and divergence [FDiv]) based on traits of occurring species. We also assessed how agricultural lands enrolled in a conservation program managed on behalf of declining early successional bird species (hereafter CP38 fields, an agri-environment scheme) influenced avian diversity. We analyzed breeding bird data collected at CP38 fields in Mississippi, USA, during 2010–2012, and two principal components of environmental variables: a gradient of heterogeneity (Shannon’s landscape diversity index) and of the amount of CP38 fields (percent cover of CP38 fields; CP38). FEve did not show significant responses to environmental variables, whereas FDiv responded positively to heterogeneity and negatively to CP38. However, most FDiv values did not significantly differ from random expectations along an environmental gradient. When there was a significant difference, FDiv was lower than that expected. Unlike functional diversity, species richness showed a clear pattern. Species richness increased with increasing landscape heterogeneity but decreased with increasing amounts of CP38 fields. Only one species responded negatively to heterogeneity and positively to CP38. Our results suggest that the relationships between avian diversity and landscape heterogeneity may vary depending on the aspect of diversity considered: strong positive effects of heterogeneity on taxonomic diversity, but weakly positive or non-significant effects on functional diversity. Our results also indicate that effectiveness of CP38 in conserving avian diversity, particularly, taxonomic diversity, could be limited without the consideration of landscape heterogeneity. PMID:28125653

Avian Species and Functional Diversity in Agricultural Landscapes: Does Landscape Heterogeneity Matter?

PubMed

Lee, Myung-Bok; Martin, James A

2017-01-01

While the positive relationship between avian diversity and habitat heterogeneity is widely accepted, it is primarily based on observed species richness without accounting for imperfect detection. Other facets of diversity such as functional diversity are also rarely explored. We investigated the avian diversity-landscape heterogeneity relationship in agricultural landscapes by considering two aspects of diversity: taxonomic diversity (species richness) estimated from a multi-species dynamic occupancy model, and functional diversity (functional evenness [FEve] and divergence [FDiv]) based on traits of occurring species. We also assessed how agricultural lands enrolled in a conservation program managed on behalf of declining early successional bird species (hereafter CP38 fields, an agri-environment scheme) influenced avian diversity. We analyzed breeding bird data collected at CP38 fields in Mississippi, USA, during 2010-2012, and two principal components of environmental variables: a gradient of heterogeneity (Shannon's landscape diversity index) and of the amount of CP38 fields (percent cover of CP38 fields; CP38). FEve did not show significant responses to environmental variables, whereas FDiv responded positively to heterogeneity and negatively to CP38. However, most FDiv values did not significantly differ from random expectations along an environmental gradient. When there was a significant difference, FDiv was lower than that expected. Unlike functional diversity, species richness showed a clear pattern. Species richness increased with increasing landscape heterogeneity but decreased with increasing amounts of CP38 fields. Only one species responded negatively to heterogeneity and positively to CP38. Our results suggest that the relationships between avian diversity and landscape heterogeneity may vary depending on the aspect of diversity considered: strong positive effects of heterogeneity on taxonomic diversity, but weakly positive or non-significant effects on functional diversity. Our results also indicate that effectiveness of CP38 in conserving avian diversity, particularly, taxonomic diversity, could be limited without the consideration of landscape heterogeneity.

Contrasting changes in the abundance and diversity of North American bird assemblages from 1971 to 2010.

PubMed

Schipper, Aafke M; Belmaker, Jonathan; de Miranda, Murilo Dantas; Navarro, Laetitia M; Böhning-Gaese, Katrin; Costello, Mark J; Dornelas, Maria; Foppen, Ruud; Hortal, Joaquín; Huijbregts, Mark A J; Martín-López, Berta; Pettorelli, Nathalie; Queiroz, Cibele; Rossberg, Axel G; Santini, Luca; Schiffers, Katja; Steinmann, Zoran J N; Visconti, Piero; Rondinini, Carlo; Pereira, Henrique M

2016-12-01

Although it is generally recognized that global biodiversity is declining, few studies have examined long-term changes in multiple biodiversity dimensions simultaneously. In this study, we quantified and compared temporal changes in the abundance, taxonomic diversity, functional diversity, and phylogenetic diversity of bird assemblages, using roadside monitoring data of the North American Breeding Bird Survey from 1971 to 2010. We calculated 12 abundance and diversity metrics based on 5-year average abundances of 519 species for each of 768 monitoring routes. We did this for all bird species together as well as for four subgroups based on breeding habitat affinity (grassland, woodland, wetland, and shrubland breeders). The majority of the biodiversity metrics increased or remained constant over the study period, whereas the overall abundance of birds showed a pronounced decrease, primarily driven by declines of the most abundant species. These results highlight how stable or even increasing metrics of taxonomic, functional, or phylogenetic diversity may occur in parallel with substantial losses of individuals. We further found that patterns of change differed among the species subgroups, with both abundance and diversity increasing for woodland birds and decreasing for grassland breeders. The contrasting changes between abundance and diversity and among the breeding habitat groups underscore the relevance of a multifaceted approach to measuring biodiversity change. Our findings further stress the importance of monitoring the overall abundance of individuals in addition to metrics of taxonomic, functional, or phylogenetic diversity, thus confirming the importance of population abundance as an essential biodiversity variable. © 2016 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Faster the better: a reliable technique to sample anopluran lice in large hosts.

PubMed

Leonardi, María Soledad

2014-06-01

Among Anoplura, the family Echinophthiriidae includes those species that infest mainly the pinnipeds. Working with large hosts implies methodological considerations as the time spent in the sampling, and the way in that the animal is restrained. Previous works on echinophthiriids combined a diverse array of analyses including field counts of lice and in vitro observations. To collect lice, the authors used forceps, and each louse was collected individually. This implied a long manipulation time, i.e., ≈60 min and the need to physically and/or chemically immobilize the animal. The present work described and discussed for the first a sample technique that minimized the manipulation time and also avoiding the use of anesthesia. This methodology implied combing the host's pelage with a fine-tooth plastic comb, as used in the treatment of human pediculosis, and keeping the comb with the lice retained in a Ziploc® bag with ethanol. This technique was used successfully in studies of population dynamic, habitat selection, and transmission pattern, being a reliable methodology. Lice are collected entirely and are in a good condition to prepare them for mounting for studying under light or scanning electron microscopy. Moreover, the use of the plastic comb protects from damaging taxonomically important structures as spines being also recommended to reach taxonomic or morphological goals.

Genetic calibration of species diversity among North America's freshwater fishes.

PubMed

April, Julien; Mayden, Richard L; Hanner, Robert H; Bernatchez, Louis

2011-06-28

Freshwater ecosystems are being heavily exploited and degraded by human activities all over the world, including in North America, where fishes and fisheries are strongly affected. Despite centuries of taxonomic inquiry, problems inherent to species identification continue to hamper the conservation of North American freshwater fishes. Indeed, nearly 10% of species diversity is thought to remain undescribed. To provide an independent calibration of taxonomic uncertainty and to establish a more accessible molecular identification key for its application, we generated a standard reference library of mtDNA sequences (DNA barcodes) derived from expert-identified museum specimens for 752 North American freshwater fish species. This study demonstrates that 90% of known species can be delineated using barcodes. Moreover, it reveals numerous genetic discontinuities indicative of independently evolving lineages within described species, which points to the presence of morphologically cryptic diversity. From the 752 species analyzed, our survey flagged 138 named species that represent as many as 347 candidate species, which suggests a 28% increase in species diversity. In contrast, several species of parasitic and nonparasitic lampreys lack such discontinuity and may represent alternative life history strategies within single species. Therefore, it appears that the current North American freshwater fish taxonomy at the species level significantly conceals diversity in some groups, although artificially creating diversity in others. In addition to providing an easily accessible digital identification system, this study identifies 151 fish species for which taxonomic revision is required.

Simulated tri-trophic networks reveal complex relationships between species diversity and interaction diversity

PubMed Central

Lumpkin, Will; Hurtado, Paul J.; Dyer, Lee A.

2018-01-01

Most of earth’s biodiversity is comprised of interactions among species, yet it is unclear what causes variation in interaction diversity across space and time. We define interaction diversity as the richness and relative abundance of interactions linking species together at scales from localized, measurable webs to entire ecosystems. Large-scale patterns suggest that two basic components of interaction diversity differ substantially and predictably between different ecosystems: overall taxonomic diversity and host specificity of consumers. Understanding how these factors influence interaction diversity, and quantifying the causes and effects of variation in interaction diversity are important goals for community ecology. While previous studies have examined the effects of sampling bias and consumer specialization on determining patterns of ecological networks, these studies were restricted to two trophic levels and did not incorporate realistic variation in species diversity and consumer diet breadth. Here, we developed a food web model to generate tri-trophic ecological networks, and evaluated specific hypotheses about how the diversity of trophic interactions and species diversity are related under different scenarios of species richness, taxonomic abundance, and consumer diet breadth. We investigated the accumulation of species and interactions and found that interactions accumulate more quickly; thus, the accumulation of novel interactions may require less sampling effort than sampling species in order to get reliable estimates of either type of diversity. Mean consumer diet breadth influenced the correlation between species and interaction diversity significantly more than variation in both species richness and taxonomic abundance. However, this effect of diet breadth on interaction diversity is conditional on the number of observed interactions included in the models. The results presented here will help develop realistic predictions of the relationships between consumer diet breadth, interaction diversity, and species diversity within multi-trophic communities, which is critical for the conservation of biodiversity in this period of accelerated global change. PMID:29579077

Simulated tri-trophic networks reveal complex relationships between species diversity and interaction diversity.

PubMed

Pardikes, Nicholas A; Lumpkin, Will; Hurtado, Paul J; Dyer, Lee A

2018-01-01

Most of earth's biodiversity is comprised of interactions among species, yet it is unclear what causes variation in interaction diversity across space and time. We define interaction diversity as the richness and relative abundance of interactions linking species together at scales from localized, measurable webs to entire ecosystems. Large-scale patterns suggest that two basic components of interaction diversity differ substantially and predictably between different ecosystems: overall taxonomic diversity and host specificity of consumers. Understanding how these factors influence interaction diversity, and quantifying the causes and effects of variation in interaction diversity are important goals for community ecology. While previous studies have examined the effects of sampling bias and consumer specialization on determining patterns of ecological networks, these studies were restricted to two trophic levels and did not incorporate realistic variation in species diversity and consumer diet breadth. Here, we developed a food web model to generate tri-trophic ecological networks, and evaluated specific hypotheses about how the diversity of trophic interactions and species diversity are related under different scenarios of species richness, taxonomic abundance, and consumer diet breadth. We investigated the accumulation of species and interactions and found that interactions accumulate more quickly; thus, the accumulation of novel interactions may require less sampling effort than sampling species in order to get reliable estimates of either type of diversity. Mean consumer diet breadth influenced the correlation between species and interaction diversity significantly more than variation in both species richness and taxonomic abundance. However, this effect of diet breadth on interaction diversity is conditional on the number of observed interactions included in the models. The results presented here will help develop realistic predictions of the relationships between consumer diet breadth, interaction diversity, and species diversity within multi-trophic communities, which is critical for the conservation of biodiversity in this period of accelerated global change.

Niche partitioning and biogeography of high light adapted Prochlorococcus across taxonomic ranks in the North Pacific

PubMed Central

Larkin, Alyse A; Blinebry, Sara K; Howes, Caroline; Lin, Yajuan; Loftus, Sarah E; Schmaus, Carrie A; Zinser, Erik R; Johnson, Zackary I

2016-01-01

The distribution of major clades of Prochlorococcus tracks light, temperature and other environmental variables; yet, the drivers of genomic diversity within these ecotypes and the net effect on biodiversity of the larger community are poorly understood. We examined high light (HL) adapted Prochlorococcus communities across spatial and temporal environmental gradients in the Pacific Ocean to determine the ecological drivers of population structure and diversity across taxonomic ranks. We show that the Prochlorococcus community has the highest diversity at low latitudes, but seasonality driven by temperature, day length and nutrients adds complexity. At finer taxonomic resolution, some ‘sub-ecotype' clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Intriguingly, biogeographies of the HL-I sub-ecotypes are driven by unique combinations of environmental traits, rather than through trait hierarchy, while the HL-II sub-ecotypes appear ecologically similar, thus demonstrating differences among these dominant HL ecotypes. Examining biodiversity across taxonomic ranks reveals high-resolution dynamics of Prochlorococcus evolution and ecology that are masked at phylogenetically coarse resolution. Spatial and seasonal trends of Prochlorococcus communities suggest that the future ocean may be comprised of different populations, with implications for ecosystem structure and function. PMID:26800235

Marasas’ et al. 1984 toxigenic fusarium species: identity and mycotoxicology revisted

USDA-ARS?s Scientific Manuscript database

Fusarium ranks one of the world’s most economically destructive and taxonomically challenging genera of mycotoxigenic plant pathogens. This is reflected, in part, by the numerous efforts to catalog its taxonomic diversity and mycotoxin potential over the past half century. Given the significant thre...

EFFECTS OF NONINDIGENOUS SPECIES ON THE TAXONOMIC DIVERSITY OF ESTUARINE ASSEMBLAGES

EPA Science Inventory

The effects of the few numerically dominant invasive species on benthic community abundance patterns has been documented in a number of estuaries. What is less appreciated is that the entire suite of nonindigenous species may alter the taxonomic composition of a community or biog...

Patterns of variation in diversity of the Mississippi river microbiome over 1,300 kilometers

PubMed Central

Payne, Jason T.; Millar, Justin J.; Jackson, Colin R.

2017-01-01

We examined the downriver patterns of variation in taxonomic diversity of the Mississippi River bacterioplankton microbiome along 1,300 river kilometers, or approximately one third the total length of the river. The study section included portions of the Upper, Middle, and Lower Mississippi River, confluences with five tributaries draining distinct sub-basins, river cities, and extended stretches without major inputs to the Mississippi. The composition and proportional abundance of dominant bacterial phyla was distinct for free-living and particle-associated cells, and constant along the entire reach, except for a substantial but transient disturbance near the city of Memphis, Tennessee. At a finer scale of taxonomic resolution (operational taxonomic units, OTUs), however, there were notable patterns in downriver variation in bacterial community alpha diversity (richness within a site) and beta diversity (variation in composition among sites). There was a strong and steady increase downriver in alpha diversity of OTUs on suspended particles, suggesting an increase in particle niche heterogeneity, and/or particle colonization. Relatively large shifts in beta diversity of free-living and particle-associated communities occurred following major tributary confluences and transiently at Memphis, while in long stretches between these points diversity typically varied more gradually. We conclude that the Mississippi River possesses a bacterioplankton microbiome distinct in diversity from other large river microbiomes in the Mississippi River Basin, that at major river confluences or urban point sources its OTU diversity may shift abruptly and substantially, presumably by immigration of distinct external microbiomes, but that where environmental conditions are more stable along the downriver gradient, microbiome diversity tends to vary gradually, presumably by a process of successional change in community composition. PMID:28350888

METHODS OF EXPLORING METABOLIC STRUCTURE AND TAXONOMIC DIVERSITY RELATIONSHIPS BETWEEN BACTERIOPLANKTON AND PHYTOPLANKTON IN SALT MARSH TIDAL CREEKS

EPA Science Inventory

Bacterial metabolic diversity and phytoplankton community diversity were examined in eight shallow tidal creeks over a two-year period (1997-1998) within North Inlet estuary, South Carolina. The BIOLOG 96-well microplate method was used to assess metabolic diversity of bacteria, ...

Rates of species accumulation and taxonomic diversification during phototrophic biofilm development are controlled by both nutrient supply and current velocity.

PubMed

Larson, Chad A; Passy, Sophia I

2013-03-01

The accumulation of new and taxonomically diverse species is a marked feature of community development, but the role of the environment in this process is not well understood. To address this problem, we subjected periphyton in laboratory streams to low (10-cm · s(-1)), high (30-cm · s(-1)), and variable (9- to 32-cm · s(-1)) current velocity and low- versus high-nutrient inputs. We examined how current velocity and resource supply constrained (i) the rates of species accumulation, a measure of temporal beta-diversity, and (ii) the rates of diversification of higher taxonomic categories, defined here as the rate of higher taxon richness increase with the increase of species richness. Temporal biofilm dynamics were controlled by a strong nutrient-current interaction. Nutrients accelerated the rates of accumulation of new species, when flow velocity was not too stressful. Species were more taxonomically diverse under variable than under low-flow conditions, indicating that flow heterogeneity increased the niche diversity in the high-nutrient treatments. Conversely, the lower diversification rates under high- than under low-nutrient conditions at low velocity are explained with finer resource partitioning among species, belonging to a limited number of related genera. The overall low rates of diversification in high-current treatments suggest that the ability to withstand current stress was conserved within closely related species. Temporal heterogeneity of disturbance has been shown to promote species richness, but here we further demonstrate that it also affects two other components of biodiversity, i.e., temporal beta-diversity and diversification rate. Therefore, management efforts for preserving the inherent temporal heterogeneity of natural ecosystems will have detectable positive effects on biodiversity.

Temporal changes in taxonomic and functional diversity of fish assemblages downstream from mountaintop mining

USGS Publications Warehouse

Hitt, Nathaniel P.; Chambers, Douglas B.

2014-01-01

Mountaintop mining (MTM) affects chemical, physical, and hydrological properties of receiving streams, but the long-term consequences for fish-assemblage structure and function are poorly understood. We sampled stream fish assemblages using electrofishing techniques in MTM exposure sites and reference sites within the Guyandotte River basin, USA, during 2010–2011. We calculated indices of taxonomic diversity (species richness, abundance, Shannon diversity) and functional diversity (functional richness, functional evenness, functional divergence) to compare exposure and reference assemblages between seasons (spring and autumn) and across years (1999–2011). We based temporal comparisons on 2 sites that were sampled during 1999–2001 by Stauffer and Ferreri (2002). Exposure assemblages had lower taxonomic and functional diversity than reference assemblages or simulated assemblages that accounted for random variation. Differences in taxonomic composition between reference and exposure assemblages were associated with conductivity and aqueous Se concentrations. Exposure assemblages had fewer species, lower abundances, and less biomass than reference assemblages across years and seasons. Green Sunfish (Lepomis cyanellus) and Creek Chub (Semotilus atromaculatus) became numerically dominant in exposure assemblages over time because of their persistence and losses of other taxa. In contrast, species richness increased over time in reference assemblages, a result that may indicate recovery from drought. Mean individual biomass increased as fish density decreased and most obligate invertivores were apparently extirpated at MTM exposure sites. Effects of MTM were not related to physical-habitat conditions but were associated with water-quality variables, which may limit quality and availability of benthic macroinvertebrate prey. Simulations revealed effects of MTM that could not be attributed to random variation in fish assemblage structure.

Rates of Species Accumulation and Taxonomic Diversification during Phototrophic Biofilm Development Are Controlled by both Nutrient Supply and Current Velocity

PubMed Central

2013-01-01

The accumulation of new and taxonomically diverse species is a marked feature of community development, but the role of the environment in this process is not well understood. To address this problem, we subjected periphyton in laboratory streams to low (10-cm · s−1), high (30-cm · s−1), and variable (9- to 32-cm · s−1) current velocity and low- versus high-nutrient inputs. We examined how current velocity and resource supply constrained (i) the rates of species accumulation, a measure of temporal beta-diversity, and (ii) the rates of diversification of higher taxonomic categories, defined here as the rate of higher taxon richness increase with the increase of species richness. Temporal biofilm dynamics were controlled by a strong nutrient-current interaction. Nutrients accelerated the rates of accumulation of new species, when flow velocity was not too stressful. Species were more taxonomically diverse under variable than under low-flow conditions, indicating that flow heterogeneity increased the niche diversity in the high-nutrient treatments. Conversely, the lower diversification rates under high- than under low-nutrient conditions at low velocity are explained with finer resource partitioning among species, belonging to a limited number of related genera. The overall low rates of diversification in high-current treatments suggest that the ability to withstand current stress was conserved within closely related species. Temporal heterogeneity of disturbance has been shown to promote species richness, but here we further demonstrate that it also affects two other components of biodiversity, i.e., temporal beta-diversity and diversification rate. Therefore, management efforts for preserving the inherent temporal heterogeneity of natural ecosystems will have detectable positive effects on biodiversity. PMID:23335757

Bird diversity and dissimilarity show contrasting patterns along heavy metal pollution gradients in the Urals, Russia.

PubMed

Belskii, Eugen A; Mikryukov, Vladimir S

2018-05-07

The effects of industrial pollution on bird diversity have been widely studied using traditional diversity measures, which assume all species to be equivalent. We compared species richness and Shannon index with distance-based measures of taxonomic, functional, and phylogenetic diversity (the abundance-weighted mean nearest taxon distances), which describe within-community dissimilarity at terminal branches. Analysis of dissimilarity can shed light on the processes underlying community assembly, i.e., environmental filtering decreases dissimilarity whereas competitive exclusion increases it. In the 2-year study near Karabash and Revda copper smelters in Russia, point counts of nesting birds and habitat descriptions were taken at 10 sites (40 plots) along each pollution gradient. The abundance and diversity of birds showed good repeatability in both regions. The total density of birds, number of species per plot, and Shannon diversity decreased at high toxic load in both regions. The taxonomic, functional, and phylogenetic nearest taxon distances showed the same pattern within regions. Species dissimilarity within communities increased with pollution in Karabash (due to loss of functionally similar species), but did not change in Revda (due to mass replacement of forest species by species of open habitats). Pollution-induced changes in bird communities near Karabash were greater due to the stronger deterioration of the forest ecosystems and less favorable natural conditions (more arid climate, lower diversity and vitality of the tree stand and understorey) compared to Revda. This study emphasizes the need for a multi-level approach to the analysis of bird communities using traditional indices of diversity, functional, taxonomic, or phylogenetic distances between species and environmental variables.

Mapping Biodiversity and Setting Conservation Priorities for SE Queensland’s Rainforests Using DNA Barcoding

PubMed Central

Shapcott, Alison; Forster, Paul I.; Guymer, Gordon P.; McDonald, William J. F.; Faith, Daniel P.; Erickson, David; Kress, W. John

2015-01-01

Australian rainforests have been fragmented due to past climatic changes and more recently landscape change as a result of clearing for agriculture and urban spread. The subtropical rainforests of South Eastern Queensland are significantly more fragmented than the tropical World Heritage listed northern rainforests and are subject to much greater human population pressures. The Australian rainforest flora is relatively taxonomically rich at the family level, but less so at the species level. Current methods to assess biodiversity based on species numbers fail to adequately capture this richness at higher taxonomic levels. We developed a DNA barcode library for the SE Queensland rainforest flora to support a methodology for biodiversity assessment that incorporates both taxonomic diversity and phylogenetic relationships. We placed our SE Queensland phylogeny based on a three marker DNA barcode within a larger international rainforest barcode library and used this to calculate phylogenetic diversity (PD). We compared phylo- diversity measures, species composition and richness and ecosystem diversity of the SE Queensland rainforest estate to identify which bio subregions contain the greatest rainforest biodiversity, subregion relationships and their level of protection. We identified areas of highest conservation priority. Diversity was not correlated with rainforest area in SE Queensland subregions but PD was correlated with both the percent of the subregion occupied by rainforest and the diversity of regional ecosystems (RE) present. The patterns of species diversity and phylogenetic diversity suggest a strong influence of historical biogeography. Some subregions contain significantly more PD than expected by chance, consistent with the concept of refugia, while others were significantly phylogenetically clustered, consistent with recent range expansions. PMID:25803607

Mapping biodiversity and setting conservation priorities for SE Queensland's rainforests using DNA barcoding.

PubMed

Shapcott, Alison; Forster, Paul I; Guymer, Gordon P; McDonald, William J F; Faith, Daniel P; Erickson, David; Kress, W John

2015-01-01

Australian rainforests have been fragmented due to past climatic changes and more recently landscape change as a result of clearing for agriculture and urban spread. The subtropical rainforests of South Eastern Queensland are significantly more fragmented than the tropical World Heritage listed northern rainforests and are subject to much greater human population pressures. The Australian rainforest flora is relatively taxonomically rich at the family level, but less so at the species level. Current methods to assess biodiversity based on species numbers fail to adequately capture this richness at higher taxonomic levels. We developed a DNA barcode library for the SE Queensland rainforest flora to support a methodology for biodiversity assessment that incorporates both taxonomic diversity and phylogenetic relationships. We placed our SE Queensland phylogeny based on a three marker DNA barcode within a larger international rainforest barcode library and used this to calculate phylogenetic diversity (PD). We compared phylo- diversity measures, species composition and richness and ecosystem diversity of the SE Queensland rainforest estate to identify which bio subregions contain the greatest rainforest biodiversity, subregion relationships and their level of protection. We identified areas of highest conservation priority. Diversity was not correlated with rainforest area in SE Queensland subregions but PD was correlated with both the percent of the subregion occupied by rainforest and the diversity of regional ecosystems (RE) present. The patterns of species diversity and phylogenetic diversity suggest a strong influence of historical biogeography. Some subregions contain significantly more PD than expected by chance, consistent with the concept of refugia, while others were significantly phylogenetically clustered, consistent with recent range expansions.

Soft Coral Sarcophyton (Cnidaria: Anthozoa: Octocorallia) Species Diversity and Chemotypes

PubMed Central

Aratake, Satoe; Tomura, Tomohiko; Saitoh, Seikoh; Yokokura, Ryouma; Kawanishi, Yuichi; Shinjo, Ryuichi; Reimer, James Davis; Tanaka, Junichi; Maekawa, Hideaki

2012-01-01

Research on the soft coral genus Sarcophyton extends over a wide range of fields, including marine natural products and the isolation of a number of cembranoid diterpenes. However, it is still unknown how soft corals produce this diverse array of metabolites, and the relationship between soft coral diversity and cembranoid diterpene production is not clear. In order to understand this relationship, we examined Sarcophyton specimens from Okinawa, Japan, by utilizing three methods: morphological examination of sclerites, chemotype identification, and phylogenetic examination of both Sarcophyton (utilizing mitochondrial protein-coding genes MutS homolog: msh1) and their endosymbiotic Symbiodinium spp. (utilizing nuclear internal transcribed spacer of ribosomal DNA: ITS- rDNA). Chemotypes, molecular phylogenetic clades, and sclerites of Sarcophyton trocheliophorum specimens formed a clear and distinct group, but the relationships between chemotypes, molecular phylogenetic clade types and sclerites of the most common species, Sarcophyton glaucum, was not clear. S. glaucum was divided into four clades. A characteristic chemotype was observed within one phylogenetic clade of S. glaucum. Identities of symbiotic algae Symbiodinium spp. had no apparent relation to chemotypes of Sarcophyton spp. This study demonstrates that the complex results observed for S. glaucum are due to the incomplete and complex taxonomy of this species group. Our novel method of identification should help contribute to classification and taxonomic reassessment of this diverse soft coral genus. PMID:22272344

Soft coral Sarcophyton (Cnidaria: Anthozoa: Octocorallia) species diversity and chemotypes.

PubMed

Aratake, Satoe; Tomura, Tomohiko; Saitoh, Seikoh; Yokokura, Ryouma; Kawanishi, Yuichi; Shinjo, Ryuichi; Reimer, James Davis; Tanaka, Junichi; Maekawa, Hideaki

2012-01-01

Research on the soft coral genus Sarcophyton extends over a wide range of fields, including marine natural products and the isolation of a number of cembranoid diterpenes. However, it is still unknown how soft corals produce this diverse array of metabolites, and the relationship between soft coral diversity and cembranoid diterpene production is not clear. In order to understand this relationship, we examined Sarcophyton specimens from Okinawa, Japan, by utilizing three methods: morphological examination of sclerites, chemotype identification, and phylogenetic examination of both Sarcophyton (utilizing mitochondrial protein-coding genes MutS homolog: msh1) and their endosymbiotic Symbiodinium spp. (utilizing nuclear internal transcribed spacer of ribosomal DNA: ITS- rDNA). Chemotypes, molecular phylogenetic clades, and sclerites of Sarcophyton trocheliophorum specimens formed a clear and distinct group, but the relationships between chemotypes, molecular phylogenetic clade types and sclerites of the most common species, Sarcophyton glaucum, was not clear. S. glaucum was divided into four clades. A characteristic chemotype was observed within one phylogenetic clade of S. glaucum. Identities of symbiotic algae Symbiodinium spp. had no apparent relation to chemotypes of Sarcophyton spp. This study demonstrates that the complex results observed for S. glaucum are due to the incomplete and complex taxonomy of this species group. Our novel method of identification should help contribute to classification and taxonomic reassessment of this diverse soft coral genus.

Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hodkinson, Brendan P; Gottel, Neil R; Schadt, Christopher Warren

2011-01-01

Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli. For this study, comparative analyses were conducted on lichen-associated bacterial communities to test for effects of photobiont-types (i.e. green algal vs. cyanobacterial), mycobiont-types and large-scale spatial distances (from tropical to arctic latitudes). Amplicons of the 16S (SSU) rRNA gene were examined using both Sanger sequencing of cloned fragments and barcoded pyrosequencing. Rhizobiales is typically the most abundant andmore » taxonomically diverse order in lichen microbiomes; however, overall bacterial diversity in lichens is shown to be much higher than previously reported. Members of Acidobacteriaceae, Acetobacteraceae, Brucellaceae and sequence group LAR1 are the most commonly found groups across the phylogenetically and geographically broad array of lichens examined here. Major bacterial community trends are significantly correlated with differences in large-scale geography, photobiont-type and mycobiont-type. The lichen as a microcosm represents a structured, unique microbial habitat with greater ecological complexity and bacterial diversity than previously appreciated and can serve as a model system for studying larger ecological and evolutionary principles.« less

Comparative phylogeography and demographic history of the wood lemming (Myopus schisticolor): implications for late Quaternary history of the taiga species in Eurasia.

PubMed

Fedorov, V B; Goropashnaya, A V; Boeskorov, G G; Cook, J A

2008-01-01

The association between demographic history, genealogy and geographical distribution of mitochondrial DNA cytochrome b haplotypes was studied in the wood lemming (Myopus schisticolor), a species that is closely associated with the boreal forest of the Eurasian taiga zone from Scandinavia to the Pacific coast. Except for a major phylogeographic discontinuity (0.9% nucleotide divergence) in southeastern Siberia, only shallow regional genetic structure was detected across northern Eurasia. Genetic signs of demographic expansions imply that successive range contractions and expansions on different spatial scales represented the primary historical events that shaped geographical patterns of genetic variation. Comparison of phylogeographic structure across a taxonomically diverse array of other species that are ecologically associated with the taiga forest revealed similar patterns and identified two general aspects. First, the major south-north phylogeographic discontinuity observed in five out of six species studied in southeastern Siberia and the Far East implies vicariant separation in two different refugial areas. The limited distribution range of the southeastern lineages provides no evidence of the importance of the putative southeastern refugial area for postglacial colonization of northern Eurasia by boreal forest species. Second, the lack of phylogeographic structure associated with significant reciprocal monophyly and genetic signatures of demographic expansion in all nine boreal forest animal species studied to date across most of northern Eurasia imply contraction of each species to a single refugial area during the late Pleistocene followed by range expansion on a continental scale. Similar phylogeographic patterns observed in this taxonomically diverse set of organisms with different life histories and dispersal potentials reflect the historical dynamics of their shared environment, the taiga forest in northern Eurasia.

Rare alluvial sands of El Monte Valley, California (San Diego County), support high herpetofaunal species richness and diversity, despite severe habitat disturbance

USGS Publications Warehouse

Richmond, Jonathan Q.; Rochester, Carlton J.; Smith, Nathan W.; Nordland, Jeffrey A.; Fisher, Robert N.

2016-01-01

We characterized the species richness, diversity, and distribution of amphibians and reptiles inhabiting El Monte Valley, a heavily disturbed, alluvium-filled basin within the lower San Diego River in Lakeside, California. This rare habitat type in coastal southern California is designated as a critical sand resource by the state of California and is currently under consideration for a large-scale sand mining operation with subsequent habitat restoration. We conducted field surveys from June 2015 to May 2016 using drift fence lines with funnel traps, coverboard arrays, walking transects, and road driving. We recorded 1,208 total captures, revealing high species richness and diversity, but with marked unevenness in species' abundances. Snakes were the most species-rich taxonomic group (13 species representing 11 genera), followed by lizards (11 species representing 9 genera). After the southern Pacific rattlesnake (Crotalus oreganus helleri), the California glossy snake (Arizona elegans occidentalis) was the second most frequently detected snake species (n = 23 captures). Amphibian species richness was limited to only three species in three genera. Despite the relatively limited 12-month sampling period, a longstanding drought, and severe habitat disturbance, our study demonstrates that El Monte Valley harbors a rich herpetofauna that includes many sensitive species.

Against the naming of fungi.

PubMed

Money, Nicholas P

2013-01-01

The use of molecular bar-coding and consensus on nomenclatural practices has encouraged optimism about the future of fungal taxonomy and systematics. There are, however, profound deficiencies in our understanding of fungal diversity and broader problems with the taxonomic enterprise that deserve greater attention. For 250 years mycologists have tried to reconcile fungal diversity with the Linnean fantasy of a divine order throughout nature that included unambiguous species. This effort has failed and today's taxonomy rests on an unstable philosophical foundation. Rather than persisting with the present endeavour, it may be more fruitful to abandon the notion of fungal species pending further basic research. In the meantime, mycologists should consider tagging collections with digital codes and assigning these operational taxonomic units to higher taxonomic ranks whose objective reality is corroborated by strong phylogenetic evidence. Copyright © 2013 The Author. Published by Elsevier Ltd.. All rights reserved.

Biodiversity of the Deep-Sea Continental Margin Bordering the Gulf of Maine (NW Atlantic): Relationships among Sub-Regions and to Shelf Systems

PubMed Central

Kelly, Noreen E.; Shea, Elizabeth K.; Metaxas, Anna; Haedrich, Richard L.; Auster, Peter J.

2010-01-01

Background In contrast to the well-studied continental shelf region of the Gulf of Maine, fundamental questions regarding the diversity, distribution, and abundance of species living in deep-sea habitats along the adjacent continental margin remain unanswered. Lack of such knowledge precludes a greater understanding of the Gulf of Maine ecosystem and limits development of alternatives for conservation and management. Methodology/Principal Findings We use data from the published literature, unpublished studies, museum records and online sources, to: (1) assess the current state of knowledge of species diversity in the deep-sea habitats adjacent to the Gulf of Maine (39–43°N, 63–71°W, 150–3000 m depth); (2) compare patterns of taxonomic diversity and distribution of megafaunal and macrofaunal species among six distinct sub-regions and to the continental shelf; and (3) estimate the amount of unknown diversity in the region. Known diversity for the deep-sea region is 1,671 species; most are narrowly distributed and known to occur within only one sub-region. The number of species varies by sub-region and is directly related to sampling effort occurring within each. Fishes, corals, decapod crustaceans, molluscs, and echinoderms are relatively well known, while most other taxonomic groups are poorly known. Taxonomic diversity decreases with increasing distance from the continental shelf and with changes in benthic topography. Low similarity in faunal composition suggests the deep-sea region harbours faunal communities distinct from those of the continental shelf. Non-parametric estimators of species richness suggest a minimum of 50% of the deep-sea species inventory remains to be discovered. Conclusions/Significance The current state of knowledge of biodiversity in this deep-sea region is rudimentary. Our ability to answer questions is hampered by a lack of sufficient data for many taxonomic groups, which is constrained by sampling biases, life-history characteristics of target species, and the lack of trained taxonomists. PMID:21124960

Stochastic and deterministic processes regulate spatio-temporal variation in seed bank diversity

Treesearch

Alejandro A. Royo; Todd E. Ristau

2013-01-01

Seed banks often serve as reservoirs of taxonomic and genetic diversity that buffer plant populations and influence post-disturbance vegetation trajectories; yet evaluating their importance requires understanding how their composition varies within and across spatial and temporal scales (α- and β-diversity). Shifts in seed bank diversity are strongly...

Taxonomic and Functional Diversity of Soil and Hypolithic Microbial Communities in Miers Valley, McMurdo Dry Valleys, Antarctica.

PubMed

Wei, Sean T S; Lacap-Bugler, Donnabella C; Lau, Maggie C Y; Caruso, Tancredi; Rao, Subramanya; de Los Rios, Asunción; Archer, Stephen K; Chiu, Jill M Y; Higgins, Colleen; Van Nostrand, Joy D; Zhou, Jizhong; Hopkins, David W; Pointing, Stephen B

2016-01-01

The McMurdo Dry Valleys of Antarctica are an extreme polar desert. Mineral soils support subsurface microbial communities and translucent rocks support development of hypolithic communities on ventral surfaces in soil contact. Despite significant research attention, relatively little is known about taxonomic and functional diversity or their inter-relationships. Here we report a combined diversity and functional interrogation for soil and hypoliths of the Miers Valley in the McMurdo Dry Valleys of Antarctica. The study employed 16S rRNA fingerprinting and high throughput sequencing combined with the GeoChip functional microarray. The soil community was revealed as a highly diverse reservoir of bacterial diversity dominated by actinobacteria. Hypolithic communities were less diverse and dominated by cyanobacteria. Major differences in putative functionality were that soil communities displayed greater diversity in stress tolerance and recalcitrant substrate utilization pathways, whilst hypolithic communities supported greater diversity of nutrient limitation adaptation pathways. A relatively high level of functional redundancy in both soil and hypoliths may indicate adaptation of these communities to fluctuating environmental conditions.

Complex depth-related patterns in taxonomic and functional diversity of polychaetes in the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Carvalho, Russell; Wei, Chih-Lin; Rowe, Gilbert; Schulze, Anja

2013-10-01

Patterns of taxonomic and functional diversity in polychaete assemblages were examined in the deep northern Gulf of Mexico, including the first analysis of polychaete feeding guild distribution. An analysis of samples from a total of 51 stations located along 7 transects plus additional nearby sites, indicated that density decreased exponentially with depth, with the central locations having higher densities than the eastern and western regions. Alpha diversity was also highest at the central stations associated with the Mississippi trough. The samples can be grouped into three significant clusters based on thirty percent similarity of species composition. BIO-ENV indicated depth, sediment particle size, and export POC were most important variables explaining distributions. The diversity of polychaete feeding guilds was high in the Mississippi trough, upper and mid-slope regions but declined to a few guilds on the Sigsbee abyssal plain. Combining feeding guild analysis with traditional analysis of species diversity contributes to a clearer understanding of trophic diversity in deep-sea benthic assemblages.

Impacts of environmental factors on the whole microbial communities in the rhizosphere of a metal-tolerant plant: Elsholtzia haichowensis Sun.

PubMed

Deng, Songqiang; Ke, Tan; Li, Longtai; Cai, Shenwen; Zhou, Yuyue; Liu, Yue; Guo, Limin; Chen, Lanzhou; Zhang, Dayi

2018-06-01

Rhizospheric microbes play important roles in plant growth and heavy metals (HMs) transformation, possessing great potential for the successful phytoremediation of environmental pollutants. In the present study, the rhizosphere of Elsholtzia haichowensis Sun was comprehensively studied to uncover the influence of environmental factors (EFs) on the whole microbial communities including bacteria, fungi and archaea, via quantitative polymerase chain reaction (qPCR) and high-throughput sequencing. By analyzing molecular ecological network and multivariate regression trees (MRT), we evaluated the distinct impacts of 37 EFs on soil microbial community. Of them, soil pH, HMs, soil texture and nitrogen were identified as the most influencing factors, and their roles varied across different domains. Soil pH was the main environmental variable on archaeal and bacterial community but not fungi, explaining 25.7%, 46.5% and 40.7% variation of bacterial taxonomic composition, archaeal taxonomic composition and a-diversity, respectively. HMs showed important roles in driving the whole microbial community and explained the major variation in different domains. Nitrogen (NH 4 -N, NO 3 -N, NO 2 -N and TN) explained 47.3% variation of microbial population composition and 15.9% of archaeal taxonomic composition, demonstrating its influence in structuring the rhizospheric microbiome, particularly archaeal and bacterial community. Soil texture accounted for 10.2% variation of population composition, 28.9% of fungal taxonomic composition, 19.2% of fungal a-diversity and 7.8% of archaeal a-diversity. Rhizosphere only showed strong impacts on fungi and bacteria, accounting for 14.7% and 4.9% variation of fungal taxonomic composition and bacterial a-diversity. Spatial distance had stronger influence on bacteria and archaea than fungi, but not as significant as other EFs. For the first time, our study provides a complete insight into key influential EFs on rhizospheric microbes and how their roles vary across microbial domains, giving a hand for understanding the construction of microbial communities in rhizosphere. Copyright © 2017 Elsevier Ltd. All rights reserved.

Systematic and Evolutionary Insights Derived from mtDNA COI Barcode Diversity in the Decapoda (Crustacea: Malacostraca)

PubMed Central

Matzen da Silva, Joana; Creer, Simon; dos Santos, Antonina; Costa, Ana C.; Cunha, Marina R.; Costa, Filipe O.; Carvalho, Gary R.

2011-01-01

Background Decapods are the most recognizable of all crustaceans and comprise a dominant group of benthic invertebrates of the continental shelf and slope, including many species of economic importance. Of the 17635 morphologically described Decapoda species, only 5.4% are represented by COI barcode region sequences. It therefore remains a challenge to compile regional databases that identify and analyse the extent and patterns of decapod diversity throughout the world. Methodology/Principal Findings We contributed 101 decapod species from the North East Atlantic, the Gulf of Cadiz and the Mediterranean Sea, of which 81 species represent novel COI records. Within the newly-generated dataset, 3.6% of the species barcodes conflicted with the assigned morphological taxonomic identification, highlighting both the apparent taxonomic ambiguity among certain groups, and the need for an accelerated and independent taxonomic approach. Using the combined COI barcode projects from the Barcode of Life Database, we provide the most comprehensive COI data set so far examined for the Order (1572 sequences of 528 species, 213 genera, and 67 families). Patterns within families show a general predicted molecular hierarchy, but the scale of divergence at each taxonomic level appears to vary extensively between families. The range values of mean K2P distance observed were: within species 0.285% to 1.375%, within genus 6.376% to 20.924% and within family 11.392% to 25.617%. Nucleotide composition varied greatly across decapods, ranging from 30.8 % to 49.4 % GC content. Conclusions/Significance Decapod biological diversity was quantified by identifying putative cryptic species allowing a rapid assessment of taxon diversity in groups that have until now received limited morphological and systematic examination. We highlight taxonomic groups or species with unusual nucleotide composition or evolutionary rates. Such data are relevant to strategies for conservation of existing decapod biodiversity, as well as elucidating the mechanisms and constraints shaping the patterns observed. PMID:21589909

Visualisation and graph-theoretic analysis of a large-scale protein structural interactome

PubMed Central

Bolser, Dan; Dafas, Panos; Harrington, Richard; Park, Jong; Schroeder, Michael

2003-01-01

Background Large-scale protein interaction maps provide a new, global perspective with which to analyse protein function. PSIMAP, the Protein Structural Interactome Map, is a database of all the structurally observed interactions between superfamilies of protein domains with known three-dimensional structure in the PDB. PSIMAP incorporates both functional and evolutionary information into a single network. Results We present a global analysis of PSIMAP using several distinct network measures relating to centrality, interactivity, fault-tolerance, and taxonomic diversity. We found the following results: Centrality: we show that the center and barycenter of PSIMAP do not coincide, and that the superfamilies forming the barycenter relate to very general functions, while those constituting the center relate to enzymatic activity. Interactivity: we identify the P-loop and immunoglobulin superfamilies as the most highly interactive. We successfully use connectivity and cluster index, which characterise the connectivity of a superfamily's neighbourhood, to discover superfamilies of complex I and II. This is particularly significant as the structure of complex I is not yet solved. Taxonomic diversity: we found that highly interactive superfamilies are in general taxonomically very diverse and are thus amongst the oldest. Fault-tolerance: we found that the network is very robust as for the majority of superfamilies removal from the network will not break up the network. Conclusions Overall, we can single out the P-loop containing nucleotide triphosphate hydrolases superfamily as it is the most highly connected and has the highest taxonomic diversity. In addition, this superfamily has the highest interaction rank, is the barycenter of the network (it has the shortest average path to every other superfamily in the network), and is an articulation vertex, whose removal will disconnect the network. More generally, we conclude that the graph-theoretic and taxonomic analysis of PSIMAP is an important step towards the understanding of protein function and could be an important tool for tracing the evolution of life at the molecular level. PMID:14531933

Genetic calibration of species diversity among North America's freshwater fishes

PubMed Central

April, Julien; Mayden, Richard L.; Hanner, Robert H.; Bernatchez, Louis

2011-01-01

Freshwater ecosystems are being heavily exploited and degraded by human activities all over the world, including in North America, where fishes and fisheries are strongly affected. Despite centuries of taxonomic inquiry, problems inherent to species identification continue to hamper the conservation of North American freshwater fishes. Indeed, nearly 10% of species diversity is thought to remain undescribed. To provide an independent calibration of taxonomic uncertainty and to establish a more accessible molecular identification key for its application, we generated a standard reference library of mtDNA sequences (DNA barcodes) derived from expert-identified museum specimens for 752 North American freshwater fish species. This study demonstrates that 90% of known species can be delineated using barcodes. Moreover, it reveals numerous genetic discontinuities indicative of independently evolving lineages within described species, which points to the presence of morphologically cryptic diversity. From the 752 species analyzed, our survey flagged 138 named species that represent as many as 347 candidate species, which suggests a 28% increase in species diversity. In contrast, several species of parasitic and nonparasitic lampreys lack such discontinuity and may represent alternative life history strategies within single species. Therefore, it appears that the current North American freshwater fish taxonomy at the species level significantly conceals diversity in some groups, although artificially creating diversity in others. In addition to providing an easily accessible digital identification system, this study identifies 151 fish species for which taxonomic revision is required. PMID:21670289

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data

USDA-ARS?s Scientific Manuscript database

Community composition data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alt...

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.

PubMed

Rodriguez-R, Luis M; Gunturu, Santosh; Harvey, William T; Rosselló-Mora, Ramon; Tiedje, James M; Cole, James R; Konstantinidis, Konstantinos T

2018-06-14

The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introduced the Microbial Genomes Atlas (MiGA), a webserver that allows the classification of an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well as comparisons to other related genomes including uncultivated ones, based on the genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI) concepts. MiGA integrates best practices in sequence quality trimming and assembly and allows input to be raw reads or assemblies from isolate genomes, single-cell sequences, and metagenome-assembled genomes (MAGs). Further, MiGA can take as input hundreds of closely related genomes of the same or closely related species (a so-called 'Clade Project') to assess their gene content diversity and evolutionary relationships, and calculate important clade properties such as the pangenome and core gene sets. Therefore, MiGA is expected to facilitate a range of genome-based taxonomic and diversity studies, and quality assessment across environmental and clinical settings. MiGA is available at http://microbial-genomes.org/.

Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China.

PubMed

Huang, Qiuyuan; Briggs, Brandon R; Dong, Hailiang; Jiang, Hongchen; Wu, Geng; Edwardson, Christian; De Vlaminck, Iwijn; Quake, Stephen

2014-01-01

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change.

Taxonomic and Functional Diversity Provides Insight into Microbial Pathways and Stress Responses in the Saline Qinghai Lake, China

PubMed Central

Dong, Hailiang; Jiang, Hongchen; Wu, Geng; Edwardson, Christian; De Vlaminck, Iwijn; Quake, Stephen

2014-01-01

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change. PMID:25365331

[Taxonomic theory for non-classical systematics].

PubMed

Pavlinov, I Ia

2012-01-01

Outlined briefly are basic principles of construing general taxonomic theory for biological systematics considered in the context of non-classical scientific paradigm. The necessity of such kind of theory is substantiated, and some key points of its elaboration are exposed: its interpretation as a framework concept for the partial taxonomic theories in various schools of systematics; elaboration of idea of cognitive situation including three interrelated components, namely subject, object, and epistemic ones; its construing as a content-wisely interpreted quasi-axiomatics, with strong structuring of its conceptual space including demarcation between axioms and inferring rules; its construing as a "conceptual pyramid" of concepts of various levels of generality; inclusion of a basic model into definition of the taxonomic system (classification) regulating its content. Two problems are indicated as fundamental: definition of taxonomic diversity as a subject domain for the systematics as a whole; definition of onto-epistemological status of taxonomic system (classification) in general and of taxa in particular.

Biodiversity-ecosystem functioning relationships in a long-term non-weeded field experiment.

PubMed

Veen, Ciska G F; van der Putten, Wim H; Bezemer, T Martijn

2018-05-30

Many grassland biodiversity experiments show a positive relationship between biodiversity and ecosystem functioning, however, in most these experiments plant communities are established by sowing and natural colonization is prevented by selective weeding of non-sown species. During ecosystem restoration, for example on abandoned fields, plant communities start on bare soil, and diversity is often manipulated in a single sowing event. How such initial plant diversity manipulations influence plant biodiversity development and ecosystem functioning is not well understood. We examined how relationships between taxonomic and functional diversity, biomass production and stability develop over 16 years in non-weeded plots sown with 15 species, 4 species, or that were not sown. We found that sown plant communities become functionally similar to unsown, naturally colonized plant communities. However, initial sowing treatments had long-lasting effects on species composition and taxonomic diversity. We found only few relationships between biomass production, or stability in biomass production, and functional or taxonomic diversity, and the ones we observed were negative. In addition, the cover of dominant plant species was positively related to biomass production and stability. We conclude that effects of introducing plant species at the start of secondary succession can persist for a long time, and that in secondary succession communities with natural plant species dynamics diversity-functioning relationships can be weak or negative. Moreover, our findings indicate that in systems where natural colonization of species is allowed effects of plant dominance may underlie diversity-functioning relationships. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus

Treesearch

Daniel L. Lindner; Mark T. Banik

2011-01-01

Regions of rDNA are commonly used to infer phylogenetic relationships among fungal species and as DNA barcodes for identification. These regions occur in large tandem arrays, and concerted evolution is believed to reduce intragenomic variation among copies within these arrays, although some variation still might exist. Phylogenetic studies typically use consensus...

Utility of Classical α-Taxonomy for Biodiversity of Aquatic Nematodes

PubMed Central

Decraemer, Wilfrida; Backeljau, Thierry

2015-01-01

“Classical α-taxonomy” has different interpretations. Therefore, within the framework of an integrated taxonomic approach it is not relevant to divide taxonomy in different components, each being allocated a different weight of importance. Preferably, taxonomy should be seen in a holistic way, including the act of delimiting and describing taxa, based on different features and available methods, and taxonomy can not be interpreted without looking at evolutionary relationships. The concept of diversity itself is quite diverse as is the measure of diversity. Taxonomic descriptions of free-living aquatic nematodes are very valuable as they provide basic phenotypic information that is necessary for the functional ecological, behavioral, and evolutionary interpretation of data gathered from molecular analyses and of the organism as a whole. In general, molecular taxonomic analyses have the advantage of being much faster and of being able to deal with a larger number of specimens but also possess the important advantage of dealing with a huge amount of features compared to the morphology-based approach. However, just as morphological studies, molecular analyses deal only with partial of an organism. PMID:25861112

Integrating DNA barcode data and taxonomic practice: determination, discovery, and description.

PubMed

Goldstein, Paul Z; DeSalle, Rob

2011-02-01

DNA barcodes, like traditional sources of taxonomic information, are potentially powerful heuristics in the identification of described species but require mindful analytical interpretation. The role of DNA barcoding in generating hypotheses of new taxa in need of formal taxonomic treatment is discussed, and it is emphasized that the recursive process of character evaluation is both necessary and best served by understanding the empirical mechanics of the discovery process. These undertakings carry enormous ramifications not only for the translation of DNA sequence data into taxonomic information but also for our comprehension of the magnitude of species diversity and its disappearance. This paper examines the potential strengths and pitfalls of integrating DNA sequence data, specifically in the form of DNA barcodes as they are currently generated and analyzed, with taxonomic practice.

Taxonomic and Functional Responses to Fire and Post-Fire Management of a Mediterranean Hymenoptera Community

NASA Astrophysics Data System (ADS)

Mateos, Eduardo; Santos, Xavier; Pujade-Villar, Juli

2011-11-01

Fire is one of the commonest disturbances worldwide, transforming habitat structure and affecting ecosystem functioning. Understanding how species respond to such environmental disturbances is a major conservation goal that should be monitored using functionally and taxonomically diverse groups such as Hymenoptera. In this respect, we have analyzed the taxonomic and functional response to fire and post-fire management of a Hymenoptera community from a Mediterranean protected area. Thus, Hymenoptera were sampled at fifteen sites located in three burnt areas submitted to different post-fire practices, as well as at five sites located in peripheral unburnt pine forest. A total of 4882 specimens belonging to 33 families, which were classified into six feeding groups according to their dietary preferences, were collected. ANOVA and Redundancy Analyses showed a taxonomic and functional response to fire as all burnt areas had more Hymenoptera families, different community composition and higher numbers of parasitoids than the unburnt area. Taxonomic differences were also found between burnt areas in terms of the response of Hymenoptera to post-fire management. In general the number of parasitoids was positively correlated to the number of potential host arthropods. Parasitoids are recognized to be sensitive to habitat changes, thus highlighting their value for monitoring the functional responses of organisms to habitat disturbance. The taxonomic and functional responses of Hymenoptera suggest that some pine-forest fires can enhance habitat heterogeneity and arthropod diversity, hence increasing interspecific interactions such as those established by parasitoids and their hosts.

Taxonomic and functional responses to fire and post-fire management of a Mediterranean hymenoptera community.

PubMed

Mateos, Eduardo; Santos, Xavier; Pujade-Villar, Juli

2011-11-01

Fire is one of the commonest disturbances worldwide, transforming habitat structure and affecting ecosystem functioning. Understanding how species respond to such environmental disturbances is a major conservation goal that should be monitored using functionally and taxonomically diverse groups such as Hymenoptera. In this respect, we have analyzed the taxonomic and functional response to fire and post-fire management of a Hymenoptera community from a Mediterranean protected area. Thus, Hymenoptera were sampled at fifteen sites located in three burnt areas submitted to different post-fire practices, as well as at five sites located in peripheral unburnt pine forest. A total of 4882 specimens belonging to 33 families, which were classified into six feeding groups according to their dietary preferences, were collected. ANOVA and Redundancy Analyses showed a taxonomic and functional response to fire as all burnt areas had more Hymenoptera families, different community composition and higher numbers of parasitoids than the unburnt area. Taxonomic differences were also found between burnt areas in terms of the response of Hymenoptera to post-fire management. In general the number of parasitoids was positively correlated to the number of potential host arthropods. Parasitoids are recognized to be sensitive to habitat changes, thus highlighting their value for monitoring the functional responses of organisms to habitat disturbance. The taxonomic and functional responses of Hymenoptera suggest that some pine-forest fires can enhance habitat heterogeneity and arthropod diversity, hence increasing interspecific interactions such as those established by parasitoids and their hosts.

Habitat connectivity and local conditions shape taxonomic and functional diversity of arthropods on green roofs.

PubMed

Braaker, Sonja; Obrist, Martin Karl; Ghazoul, Jaboury; Moretti, Marco

2017-05-01

Increasing development of urban environments creates high pressure on green spaces with potential negative impacts on biodiversity and ecosystem services. There is growing evidence that green roofs - rooftops covered with vegetation - can contribute mitigate the loss of urban green spaces by providing new habitats for numerous arthropod species. Whether green roofs can contribute to enhance taxonomic and functional diversity and increase connectivity across urbanized areas remains, however, largely unknown. Furthermore, only limited information is available on how environmental conditions shape green roof arthropod communities. We investigated the community composition of arthropods (Apidae, Curculionidae, Araneae and Carabidae) on 40 green roofs and 40 green sites at ground level in the city of Zurich, Switzerland. We assessed how the site's environmental variables (such as area, height, vegetation, substrate and connectivity among sites) affect species richness and functional diversity using generalized linear models. We used an extension of co-inertia analysis (RLQ) and fourth-corner analysis to highlight the mechanism underlying community assemblages across taxonomic groups on green roof and ground communities. Species richness was higher at ground-level sites, while no difference in functional diversity was found between green roofs and ground sites. Green roof arthropod diversity increased with higher connectivity and plant species richness, irrespective of substrate depth, height and area of green roofs. The species trait analysis reviewed the mechanisms related to the environmental predictors that shape the species assemblages of the different taxa at ground and roof sites. Our study shows the important contribution of green roofs in maintaining high functional diversity of arthropod communities across different taxonomic groups, despite their lower species richness compared with ground sites. Species communities on green roofs revealed to be characterized by specific trait assemblages. The study also provides details on the environmental conditions that influence arthropod diversity and gives new perspectives on how the design of green roofs can be improved to increase their ecological value. Furthermore, the study highlights the importance of integrating green roofs in planning policies which aim to enhance urban habitat connectivity. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Large variability of bathypelagic microbial eukaryotic communities across the world's oceans.

PubMed

Pernice, Massimo C; Giner, Caterina R; Logares, Ramiro; Perera-Bel, Júlia; Acinas, Silvia G; Duarte, Carlos M; Gasol, Josep M; Massana, Ramon

2016-04-01

In this work, we study the diversity of bathypelagic microbial eukaryotes (0.8-20 μm) in the global ocean. Seawater samples from 3000 to 4000 m depth from 27 stations in the Atlantic, Pacific and Indian Oceans were analyzed by pyrosequencing the V4 region of the 18S ribosomal DNA. The relative abundance of the most abundant operational taxonomic units agreed with the results of a parallel metagenomic analysis, suggesting limited PCR biases in the tag approach. Although rarefaction curves for single stations were seldom saturated, the global analysis of all sequences together suggested an adequate recovery of bathypelagic diversity. Community composition presented a large variability among samples, which was poorly explained by linear geographic distance. In fact, the similarity between communities was better explained by water mass composition (26% of the variability) and the ratio in cell abundance between prokaryotes and microbial eukaryotes (21%). Deep diversity appeared dominated by four taxonomic groups (Collodaria, Chrysophytes, Basidiomycota and MALV-II) appearing in different proportions in each sample. Novel diversity amounted to 1% of the pyrotags and was lower than expected. Our study represents an essential step in the investigation of bathypelagic microbial eukaryotes, indicating dominating taxonomic groups and suggesting idiosyncratic assemblages in distinct oceanic regions.

A polyphasic taxonomic approach in isolated strains of Cyanobacteria from thermal springs of Greece.

PubMed

Bravakos, Panos; Kotoulas, Georgios; Skaraki, Katerina; Pantazidou, Adriani; Economou-Amilli, Athena

2016-05-01

Strains of Cyanobacteria isolated from mats of 9 thermal springs of Greece have been studied for their taxonomic evaluation. A polyphasic taxonomic approach was employed which included: morphological observations by light microscopy and scanning electron microscopy, maximum parsimony, maximum likelihood and Bayesian analysis of 16S rDNA sequences, secondary structural comparisons of 16S-23S rRNA Internal Transcribed Spacer sequences, and finally environmental data. The 17 cyanobacterial isolates formed a diverse group that contained filamentous, coccoid and heterocytous strains. These included representatives of the polyphyletic genera of Synechococcus and Phormidium, and the orders Oscillatoriales, Spirulinales, Chroococcales and Nostocales. After analysis, at least 6 new taxa at the genus level provide new evidence in the taxonomy of Cyanobacteria and highlight the abundant diversity of thermal spring environments with many potential endemic species or ecotypes. Copyright © 2016 Elsevier Inc. All rights reserved.

Early Homo and the role of the genus in paleoanthropology.

PubMed

Villmoare, Brian

2018-01-01

The history of the discovery of early fossils attributed to the genus Homo has been contentious, with scholars disagreeing over the generic assignment of fossils proposed as members of our genus. In this manuscript I review the history of discovery and debate over early Homo and evaluate the various taxonomic hypotheses for the genus. To get a sense of how hominin taxonomy compares to taxonomic practice outside paleoanthropology, I compare the diversity of Homo to genera in other vertebrate clades. Finally, I propose a taxonomic model that hews closely to current models for hominin phylogeny and is consistent with taxonomic practice across evolutionary biology. © 2018 American Association of Physical Anthropologists.

Urbanization alters the functional composition, but not taxonomic diversity, of the soil nematode community

Treesearch

Mitchell A. Pavao-Zuckerman; David C. Coleman

2007-01-01

We evaluated the response of riparian forest soil nematode community structure to the physico-chemical environment associated with urban land use. Soils were sampled seasonally between December 2000 and October 2002 along an urban-rural transect in Asheville, North Carolina. We characterized the taxonomic (to genus) and functional composition (trophic groups) of the...

Body mass evolution and diversification within horses (family Equidae).

PubMed

Shoemaker, Lauren; Clauset, Aaron

2014-02-01

Horses (family Equidae) are a classic example of adaptive radiation, exhibiting a nearly 60-fold increase in maximum body mass and a peak taxonomic diversity of nearly 100 species across four continents. Such patterns are commonly attributed to niche competition, in which increased taxonomic diversity drives increased size disparity. However, neutral processes, such as macroevolutionary 'diffusion', can produce similar increases in disparity without increased diversity. Using a comprehensive database of Equidae species size estimates and a common mathematical framework, we measure the contributions of diversity-driven and diffusion-driven mechanisms for increased disparity during the Equidae radiation. We find that more than 90% of changes in size disparity are attributable to diffusion alone. These results clarify the role of species competition in body size evolution, indicate that morphological disparity and species diversity may be only weakly coupled in general, and demonstrate that large species may evolve from neutral macroevolutionary diffusion processes alone. © 2013 John Wiley & Sons Ltd/CNRS.

Large-scale spatio-temporal monitoring highlights hotspots of demersal fish diversity in the Mediterranean Sea

NASA Astrophysics Data System (ADS)

Granger, Victoria; Fromentin, Jean-Marc; Bez, Nicolas; Relini, Giulio; Meynard, Christine N.; Gaertner, Jean-Claude; Maiorano, Porzia; Garcia Ruiz, Cristina; Follesa, Cristina; Gristina, Michele; Peristeraki, Panagiota; Brind'Amour, Anik; Carbonara, Pierluigi; Charilaou, Charis; Esteban, Antonio; Jadaud, Angélique; Joksimovic, Aleksandar; Kallianiotis, Argyris; Kolitari, Jerina; Manfredi, Chiara; Massuti, Enric; Mifsud, Roberta; Quetglas, Antoni; Refes, Wahid; Sbrana, Mario; Vrgoc, Nedo; Spedicato, Maria Teresa; Mérigot, Bastien

2015-01-01

Increasing human pressures and global environmental change may severely affect the diversity of species assemblages and associated ecosystem services. Despite the recent interest in phylogenetic and functional diversity, our knowledge on large spatio-temporal patterns of demersal fish diversity sampled by trawling remains still incomplete, notably in the Mediterranean Sea, one of the most threatened marine regions of the world. We investigated large spatio-temporal diversity patterns by analysing a dataset of 19,886 hauls from 10 to 800 m depth performed annually during the last two decades by standardised scientific bottom trawl field surveys across the Mediterranean Sea, within the MEDITS program. A multi-component (eight diversity indices) and multi-scale (local assemblages, biogeographic regions to basins) approach indicates that only the two most traditional components (species richness and evenness) were sufficient to reflect patterns in taxonomic, phylogenetic or functional richness and divergence. We also put into question the use of widely computed indices that allow comparing directly taxonomic, phylogenetic and functional diversity within a unique mathematical framework. In addition, demersal fish assemblages sampled by trawl do not follow a continuous decreasing longitudinal/latitudinal diversity gradients (spatial effects explained up to 70.6% of deviance in regression tree and generalised linear models), for any of the indices and spatial scales analysed. Indeed, at both local and regional scales species richness was relatively high in the Iberian region, Malta, the Eastern Ionian and Aegean seas, meanwhile the Adriatic Sea and Cyprus showed a relatively low level. In contrast, evenness as well as taxonomic, phylogenetic and functional divergences did not show regional hotspots. All studied diversity components remained stable over the last two decades. Overall, our results highlight the need to use complementary diversity indices through different spatial scales when developing conservation strategies and defining delimitations for protected areas.

Global taxonomic diversity of living reptiles.

PubMed

Pincheira-Donoso, Daniel; Bauer, Aaron M; Meiri, Shai; Uetz, Peter

2013-01-01

Reptiles are one of the most ecologically and evolutionarily remarkable groups of living organisms, having successfully colonized most of the planet, including the oceans and some of the harshest and more environmentally unstable ecosystems on earth. Here, based on a complete dataset of all the world's diversity of living reptiles, we analyse lineage taxonomic richness both within and among clades, at different levels of the phylogenetic hierarchy. We also analyse the historical tendencies in the descriptions of new reptile species from Linnaeus to March 2012. Although (non-avian) reptiles are the second most species-rich group of amniotes after birds, most of their diversity (96.3%) is concentrated in squamates (59% lizards, 35% snakes, and 2% amphisbaenians). In strong contrast, turtles (3.4%), crocodilians (0.3%), and tuataras (0.01%) are far less diverse. In terms of species discoveries, most turtles and crocodilians were described early, while descriptions of lizards, snakes and amphisbaenians are multimodal with respect to time. Lizard descriptions, in particular, have reached unprecedented levels during the last decade. Finally, despite such remarkably asymmetric distributions of reptile taxonomic diversity among groups, we found that the distributions of lineage richness are consistently right-skewed, with most clades (monophyletic families and genera) containing few lineages (monophyletic genera and species, respectively), while only a few have radiated greatly (notably the families Colubridae and Scincidae, and the lizard genera Anolis and Liolaemus). Therefore, such consistency in the frequency distribution of richness among clades and among phylogenetic levels suggests that the nature of reptile biodiversity is fundamentally fractal (i.e., it is scale invariant). We then compared current reptile diversity with the global reptile diversity and taxonomy known in 1980. Despite substantial differences in the taxonomies (relative to 2012), the patterns of lineage richness remain qualitatively identical, hence reinforcing our conclusions about the fractal nature of reptile biodiversity.

Diversity of the soil biota in burned areas of southern taiga forests (Tver oblast)

NASA Astrophysics Data System (ADS)

Gongalsky, K. B.; Zaitsev, A. S.; Korobushkin, D. I.; Saifutdinov, R. A.; Yazrikova, T. E.; Benediktova, A. I.; Gorbunova, A. Yu.; Gorshkova, I. A.; Butenko, K. O.; Kosina, N. V.; Lapygina, E. V.; Kuznetsova, D. M.; Rakhleeva, A. A.; Shakhab, S. V.

2016-03-01

Relations between soil biota diversity and its contribution to the performance of some ecosystem functions were assessed based on the results obtained in undisturbed and burned spruce forests near the Central Forest Nature Biosphere Reserve (Tver oblast). In August 2014, in two 4-year-old burned areas, abiotic parameters of the soils, indicators of the state of the microbial communities, the number, taxonomic diversity, and the abundance of the main groups of soil invertebrates (testate amoebae, nematodes, enchytraeids, mites, collembolans, and the mesofauna as a whole) were determined. In the soils of the burned areas, higher CO2, CH4, and N2O emissions were observed. The number of bacterial cells remained similar, and the total length of active mycelium was not significantly different. All this implies a certain intensification of biogenic processes promoting the mobilization of carbon and nitrogen after fire. The number of most of the groups of soil animals was lower (not always significantly) in the burned area than that in the soils of the undisturbed forests. The changes in the taxonomic diversity were specific for each taxon studied. Overall, the diversity of invertebrates was related to the litter thickness. However, the high taxonomic diversity of soil fauna did not always correspond to the active functioning of the ecosystem. Thus, for some taxa, a quite close correlation was found, for instance, between the total number of species (of testate amoebae in particular) and the berry crop, as well as between the soil mesofauna population and the dead wood stock. The total diversity of the investigated taxa included in the detrital trophic web was the most reliable indicator of the carbon stock in the burned areas.

Spatio-temporal variation of fish taxonomic composition in a South-East Asian flood-pulse system.

PubMed

Kong, Heng; Chevalier, Mathieu; Laffaille, Pascal; Lek, Sovan

2017-01-01

The Tonle Sap Lake (TSL) is a flood-pulse system. It is the largest natural lake in South-East Asia and constitutes one of the largest fisheries over the world, supporting the livelihood of million peoples. Nonetheless, the Mekong River Basin is changing rapidly due to accelerating water infrastructure development (hydropower, irrigation, flood control, and water supply) and climate change, bringing considerable modifications to the annual flood-pulse of the TSL. Such modifications are expected to have strong impacts on fish biodiversity and abundance. This paper aims to characterize the spatio-temporal variations of fish taxonomic composition and to highlights the underlying determinants of these variations. For this purpose, we used data collected from a community catch monitoring program conducted at six sites during 141 weeks, covering two full hydrological cycles. For each week, we estimated beta diversity as the total variance of the site-by-species community matrix and partitioned it into Local Contribution to Beta Diversity (LCBD) and Species Contribution to Beta Diversity (SCBD). We then performed multiple linear regressions to determine whether species richness, species abundances and water level explained the temporal variation in the contribution of site and species to beta diversity. Our results indicate strong temporal variation of beta diversity due to differential contributions of sites and species to the spatial variation of fish taxonomic composition. We further found that the direction, the shape and the relative effect of species richness, abundances and water level on temporal variation in LCBD and SCBD values greatly varied among sites, thus suggesting spatial variation in the processes leading to temporal variation in community composition. Overall, our results suggest that fish taxonomic composition is not homogeneously distributed over space and time and is likely to be impacted in the future if the flood-pulse dynamic of the system is altered by human activities.

High-throughput Methods Redefine the Rumen Microbiome and Its Relationship with Nutrition and Metabolism

PubMed Central

McCann, Joshua C.; Wickersham, Tryon A.; Loor, Juan J.

2014-01-01

Diversity in the forestomach microbiome is one of the key features of ruminant animals. The diverse microbial community adapts to a wide array of dietary feedstuffs and management strategies. Understanding rumen microbiome composition, adaptation, and function has global implications ranging from climatology to applied animal production. Classical knowledge of rumen microbiology was based on anaerobic, culture-dependent methods. Next-generation sequencing and other molecular techniques have uncovered novel features of the rumen microbiome. For instance, pyrosequencing of the 16S ribosomal RNA gene has revealed the taxonomic identity of bacteria and archaea to the genus level, and when complemented with barcoding adds multiple samples to a single run. Whole genome shotgun sequencing generates true metagenomic sequences to predict the functional capability of a microbiome, and can also be used to construct genomes of isolated organisms. Integration of high-throughput data describing the rumen microbiome with classic fermentation and animal performance parameters has produced meaningful advances and opened additional areas for study. In this review, we highlight recent studies of the rumen microbiome in the context of cattle production focusing on nutrition, rumen development, animal efficiency, and microbial function. PMID:24940050

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

PubMed Central

Lee, On On; Wang, Yong; Yang, Jiangke; Lafi, Feras F; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

2011-01-01

Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored. PMID:21085196

Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape

PubMed Central

Zimmerman, Naupaka B.; Vitousek, Peter M.

2012-01-01

We surveyed endophytic fungal communities in leaves of a single tree species (Metrosideros polymorpha) across wide environmental gradients (500–5,500 mm of rain/y; 10–22 °C mean annual temperature) spanning short geographic distances on Mauna Loa Volcano, Hawai’i. Using barcoded amplicon pyrosequencing at 13 sites (10 trees/site; 10 leaves/tree), we found very high levels of diversity within sites (a mean of 551 ± 134 taxonomic units per site). However, among-site diversity contributed even more than did within-site diversity to the overall richness of more than 4,200 taxonomic units observed in M. polymorpha, and this among-site variation in endophyte community composition correlated strongly with temperature and rainfall. These results are consistent with suggestions that foliar endophytic fungi are hyperdiverse. They further suggest that microbial diversity may be even greater than has been assumed and that broad-scale environmental controls such as temperature and rainfall can structure eukaryotic microbial diversity. Appropriately constrained study systems across strong environmental gradients present a useful means to understand the environmental factors that structure the diversity of microbial communities. PMID:22837398

Microbial biodiversity in arable soils is affected by agricultural practices

NASA Astrophysics Data System (ADS)

Wolińska, Agnieszka; Górniak, Dorota; Zielenkiewicz, Urszula; Goryluk-Salmonowicz, Agata; Kuźniar, Agnieszka; Stępniewska, Zofia; Błaszczyk, Mieczysław

2017-04-01

The aim of the study was to examine the differences in microbial community structure as a result of agricultural practices. Sixteen samples of cultivated and the same number of non-cultivated soils were selected. Gel bands were identified using the GelCompar software to create the presence-absence matrix, where each band represented a bacterial operational taxonomic unit. The data were used for principal-component analysis and additionally, the Shannon- Weaver index of general diversity, Simpson index of dominance and Simpson index of diversity were calculated. Denaturing gradient gel electrophoresis profiles clearly indicated differentiation of tested samples into two clusters: cultivated and non-cultivated soils. Greater numbers of dominant operational taxonomic units (65) in non-cultivated soils were noted compared to cultivated soils (47 operational taxonomic units). This implies that there was a reduction of dominant bacterial operational taxonomic units by nearly 30% in cultivated soils. Simpson dominance index expressing the number of species weighted by their abundance amounted to 1.22 in cultivated soils, whereas a 3-fold higher value (3.38) was observed in non-cultivated soils. Land-use practices seemed to be a important factors affected on biodiversity, because more than soil type determined the clustering into groups.

Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient

PubMed Central

Cheaib, Bachar; Le Boulch, Malo; Mercier, Pierre-Luc; Derome, Nicolas

2018-01-01

Adaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD). Our results highlight three adaptive signatures. First, a signature of taxon—function decoupling was detected in the microbial communities of moderately and highly polluted lakes. Second, parallel shifts in taxonomic composition occurred between polluted and unpolluted lakes. Third, variation in the abundance of functional modules suggested a gradual deterioration of ecosystem services (i.e., photosynthesis) and secondary metabolism in highly polluted lakes. Overall, changes in the abundance of taxa, function, and more importantly the polymetallic resistance genes such as copA, copB, czcA, cadR, cCusA, were correlated with trace metal content (mainly Cadmium) and acidity. Our findings highlight the impact of polymetallic pollution gradient at the lowest trophic levels. PMID:29774016

Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient.

PubMed

Cheaib, Bachar; Le Boulch, Malo; Mercier, Pierre-Luc; Derome, Nicolas

2018-01-01

Adaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD). Our results highlight three adaptive signatures. First, a signature of taxon-function decoupling was detected in the microbial communities of moderately and highly polluted lakes. Second, parallel shifts in taxonomic composition occurred between polluted and unpolluted lakes. Third, variation in the abundance of functional modules suggested a gradual deterioration of ecosystem services (i.e., photosynthesis) and secondary metabolism in highly polluted lakes. Overall, changes in the abundance of taxa, function, and more importantly the polymetallic resistance genes such as copA, copB, czcA, cadR, cCusA , were correlated with trace metal content (mainly Cadmium) and acidity. Our findings highlight the impact of polymetallic pollution gradient at the lowest trophic levels.

Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases.

PubMed

De Palma, Adriana; Abrahamczyk, Stefan; Aizen, Marcelo A; Albrecht, Matthias; Basset, Yves; Bates, Adam; Blake, Robin J; Boutin, Céline; Bugter, Rob; Connop, Stuart; Cruz-López, Leopoldo; Cunningham, Saul A; Darvill, Ben; Diekötter, Tim; Dorn, Silvia; Downing, Nicola; Entling, Martin H; Farwig, Nina; Felicioli, Antonio; Fonte, Steven J; Fowler, Robert; Franzén, Markus; Goulson, Dave; Grass, Ingo; Hanley, Mick E; Hendrix, Stephen D; Herrmann, Farina; Herzog, Felix; Holzschuh, Andrea; Jauker, Birgit; Kessler, Michael; Knight, M E; Kruess, Andreas; Lavelle, Patrick; Le Féon, Violette; Lentini, Pia; Malone, Louise A; Marshall, Jon; Pachón, Eliana Martínez; McFrederick, Quinn S; Morales, Carolina L; Mudri-Stojnic, Sonja; Nates-Parra, Guiomar; Nilsson, Sven G; Öckinger, Erik; Osgathorpe, Lynne; Parra-H, Alejandro; Peres, Carlos A; Persson, Anna S; Petanidou, Theodora; Poveda, Katja; Power, Eileen F; Quaranta, Marino; Quintero, Carolina; Rader, Romina; Richards, Miriam H; Roulston, T'ai; Rousseau, Laurent; Sadler, Jonathan P; Samnegård, Ulrika; Schellhorn, Nancy A; Schüepp, Christof; Schweiger, Oliver; Smith-Pardo, Allan H; Steffan-Dewenter, Ingolf; Stout, Jane C; Tonietto, Rebecca K; Tscharntke, Teja; Tylianakis, Jason M; Verboven, Hans A F; Vergara, Carlos H; Verhulst, Jort; Westphal, Catrin; Yoon, Hyung Joo; Purvis, Andy

2016-08-11

Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.

Application of an indicator based on taxonomic relatedness of ciliated protozoan assemblages for marine environmental assessment.

PubMed

Xu, Henglong; Jiang, Yong; Al-Rasheid, Khaled A S; Al-Farraj, Saleh A; Song, Weibo

2011-08-01

Ciliated protozoa play important roles in aquatic ecosystems especially regarding their functions in micro-food web and have many advantages in environmental assessment compared with most other eukaryotic organisms. The aims of this study were focused on analyzing the application of an indicator based on taxonomic relatedness of ciliated protozoan assemblages for marine environmental assessment. The spatial taxonomic patterns and diversity measures in response to physical-chemical variables were studied based on data from samples collected during 1-year cycle in the semi-enclosed Jiaozhou Bay, northern China. The spatial patterns of ciliate communities were significantly correlated with the changes of environmental status. The taxonomic distinctness (Δ*) and the average taxonomic distinctness (Δ+) were significantly negatively correlated with the changes of nutrients (e.g., nitrate nitrogen and soluble active phosphate; P<0.05). Pairwise indices of Δ+ and the variation in taxonomic distinctness (Λ+) showed a decreasing trend of departure from the expected taxonomic breadth in response to the eutrophication stress and anthropogenic impact. The taxonomic relatedness (especially the pairwise Δ+ and Λ+) indices of ciliate communities are robust as an indicator with scientifically operational value in marine environmental assessment.

Effects of loss of lateral hydrological connectivity on fish functional diversity.

PubMed

Liu, Xueqin; Wang, Hongzhu

2018-05-26

Loss of lateral hydrological connectivity (LHC) is a major cause of biodiversity decline in river floodplains, yet little is known about its effects on aquatic functional diversity in these ecosystems. We quantified functional alpha and beta diversity of fish assemblages in Yangtze River floodplain lakes, and explored their responses to loss of LHC using generalized linear mixed models. Functional richness was much lower in river disconnected lakes where functional evenness and divergence were higher. LHC was the most important factor shaping fish diversity patterns in this region. The predicted reduction due to loss of LHC was higher in functional richness (0.47-0.82) than in taxonomic richness (0.32) of all species assemblages in contrast to non-migratory species assemblages. It seemed that functional strategies were highly unevenly distributed between migratory and non-migratory fishes in the floodplain. Taxonomic beta diversity was much higher than functional beta diversity. The former was contributed mainly by spatial turnover component (73.6-83.8%) suggesting that dissimilarity among fish assemblages was largely induced by species replacement, while the latter was induced by nestedness-resultant component (70.7-86.0%) indicating a stronger role of function loss without replacement. Both taxonomic and functional beta diversity were higher in disconnected lakes, where they were significantly correlated with fishing activity and water quality. Our study determined for the first time the effects of loss of LHC on fish functional diversity in large river floodplains. We highlight the serious decline of fish functional richness in a large floodplain, and functional diversity remained highly vulnerable to loss of LHC even in such a species rich ecosystem. Our results provide important implications regarding biodiversity conservation and LHC restoration in large river floodplains. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa.

PubMed

Corbelli, Julian Martin; Zurita, Gustavo Andres; Filloy, Julieta; Galvis, Juan Pablo; Vespa, Natalia Isabel; Bellocq, Isabel

2015-01-01

The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD), functional (FBD) and phylogenetic (PBD) facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools) and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants) from two contrasting biomes (subtropical forest and grassland) and land uses (tree plantations and cropfields) in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland), and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation.

Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa

PubMed Central

Corbelli, Julian Martin; Zurita, Gustavo Andres; Filloy, Julieta; Galvis, Juan Pablo; Vespa, Natalia Isabel; Bellocq, Isabel

2015-01-01

The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD), functional (FBD) and phylogenetic (PBD) facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools) and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants) from two contrasting biomes (subtropical forest and grassland) and land uses (tree plantations and cropfields) in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland), and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation. PMID:25978319

Ionizing radiation and taxonomic, functional and evolutionary diversity of bird communities.

PubMed

Morelli, Federico; Benedetti, Yanina; Mousseau, Timothy A; Møller, Anders Pape

2018-08-15

Ionizing radiation from nuclear accidents at Chernobyl, Fukushima and elsewhere has reduced the abundance, species richness and diversity of ecosystems. Here we analyzed the taxonomic, functional and evolutionary diversity of bird communities in forested areas around Chernobyl. Species richness decreased with increasing radiation, mainly in 2007. Functional richness, but not functional evenness and divergence, decreased with increasing level of ionizing radiation. Evolutionary distinctiveness of bird communities was higher in areas with higher levels of ionizing radiation. Regression tree models revealed that species richness was higher in bird communities in areas with radiation levels lower than 0.7 μSv/h. In contrast, when radiation levels were higher than 16.67 μSv/h, bird species richness reached a minimum. Functional richness was affected by two variables: Forest cover and radiation level. Higher functional richness was found in bird communities in areas with forest cover lower than 50%. In the areas with forest cover higher than 50%, the functional richness was lower when radiation level was higher than 0.91 μSv/h. Finally, the average evolutionary distinctiveness of bird communities was higher in areas with forest cover exceeding 50%. These findings imply that level of ionizing radiation interacted with forest cover to affect species richness and its component parts, i.e. taxonomic, functional, and evolutionary diversity. Copyright © 2018 Elsevier Ltd. All rights reserved.

Fungal Community Shifts in Structure and Function across a Boreal Forest Fire Chronosequence

PubMed Central

Santalahti, Minna; Pumpanen, Jukka; Köster, Kajar; Berninger, Frank; Raffaello, Tommaso; Jumpponen, Ari; Asiegbu, Fred O.; Heinonsalo, Jussi

2015-01-01

Forest fires are a common natural disturbance in forested ecosystems and have a large impact on the microbial communities in forest soils. The response of soil fungal communities to forest fire is poorly documented. Here, we investigated fungal community structure and function across a 152-year boreal forest fire chronosequence using high-throughput sequencing of the internal transcribed spacer 2 (ITS2) region and a functional gene array (GeoChip). Our results demonstrate that the boreal forest soil fungal community was most diverse soon after a fire disturbance and declined over time. The differences in the fungal communities were explained by changes in the abundance of basidiomycetes and ascomycetes. Ectomycorrhizal (ECM) fungi contributed to the increase in basidiomycete abundance over time, with the operational taxonomic units (OTUs) representing the genera Cortinarius and Piloderma dominating in abundance. Hierarchical cluster analysis by using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting differences in the potential to maintain essential biogeochemical soil processes. The site with the greatest biological diversity had also the most diverse genes. The genes involved in organic matter degradation in the mature forest, in which ECM fungi were the most abundant, were as common in the youngest site, in which saprotrophic fungi had a relatively higher abundance. This study provides insight into the impact of fire disturbance on soil fungal community dynamics. PMID:26341215

Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain.

PubMed

Shen, Congcong; Shi, Yu; Ni, Yingying; Deng, Ye; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong; Chu, Haiyan

2016-01-01

The elevational and latitudinal diversity patterns of microbial taxa have attracted great attention in the past decade. Recently, the distribution of functional attributes has been in the spotlight. Here, we report a study profiling soil microbial communities along an elevation gradient (500-2200 m) on Changbai Mountain. Using a comprehensive functional gene microarray (GeoChip 5.0), we found that microbial functional gene richness exhibited a dramatic increase at the treeline ecotone, but the bacterial taxonomic and phylogenetic diversity based on 16S rRNA gene sequencing did not exhibit such a similar trend. However, the β-diversity (compositional dissimilarity among sites) pattern for both bacterial taxa and functional genes was similar, showing significant elevational distance-decay patterns which presented increased dissimilarity with elevation. The bacterial taxonomic diversity/structure was strongly influenced by soil pH, while the functional gene diversity/structure was significantly correlated with soil dissolved organic carbon (DOC). This finding highlights that soil DOC may be a good predictor in determining the elevational distribution of microbial functional genes. The finding of significant shifts in functional gene diversity at the treeline ecotone could also provide valuable information for predicting the responses of microbial functions to climate change.

Diversity and stability in Mississippi stream fish assemblages

Treesearch

Jocob F. Schaefer; Scott R. Clark; Melvin L. Jr. Warren

2012-01-01

Positive correlations between diversity and stability have been reported for a number of ecosystems and are thought to be caused by a stabilizing effect of differential species’ responses to environmental perturbation. Empirical field studies in which investigators tested for diversity–stability relationships are lacking for some taxonomic groups and typically have not...

Effects of pulsed nutrient inputs on phytoplankton assemblage structure and blooms in an enclosed coastal area

NASA Astrophysics Data System (ADS)

Spatharis, Sofie; Tsirtsis, George; Danielidis, Daniel B.; Chi, Thang Do; Mouillot, David

2007-07-01

The response of phytoplankton assemblage structure to terrestrial nutrient inputs was examined for the Gulf of Kalloni in the Northern Aegean Sea, a productive semi-enclosed coastal marine ecosystem. The study was focused on a typical annual cycle, and emphasis was placed on the comparative analysis between blooms developing after significant nutrient inputs from the watershed, and naturally occurring blooms. Baseline information was collected on a monthly basis from a network of stations located in the oligotrophic open sea and the interior and more productive part of the embayment. Intensive sampling was also carried out along a gradient in the vicinity of a river which was the most important source of freshwater and nutrient input for the Gulf. Phytoplankton assemblage structure was analyzed from 188 samples using diversity indices (Shannon and Average Taxonomic Distinctness), multivariate plotting methods (NMDS), multivariate statistics (PERMANOVA), and canonical correspondence analysis (CCA). Three characteristic assemblages were recognized: (1) an autumn assemblage developed under nutrient depleted conditions, having low diversity due to the dominance of two small diatoms, (2) a winter bloom of the potentially toxic species Pseudo-nitzschia calliantha occurring immediately after a nutrient peak and characterized by very low diversity, and (3) a naturally occurring early summer bloom of centric diatoms with relatively high diversity. The results of the study support the view that moderate nutrient inputs may have a beneficial effect on the functioning of coastal ecosystems, stimulating the taxonomic diversity through the growth of different taxonomic groups and taxa. On the other hand, a sudden pulse of high nutrient concentrations may greatly affect the natural succession of organisms, have a negative effect on the diversity through the dominance of a single species, and can increase the possibility of a harmful algal bloom development.

How Many Kinds of Birds Are There and Why Does It Matter?

PubMed

Barrowclough, George F; Cracraft, Joel; Klicka, John; Zink, Robert M

2016-01-01

Estimates of global species diversity have varied widely, primarily based on variation in the numbers derived from different inventory methods of arthropods and other small invertebrates. Within vertebrates, current diversity metrics for fishes, amphibians, and reptiles are known to be poor estimators, whereas those for birds and mammals are often assumed to be relatively well established. We show that avian evolutionary diversity is significantly underestimated due to a taxonomic tradition not found in most other taxonomic groups. Using a sample of 200 species taken from a list of 9159 biological species determined primarily by morphological criteria, we applied a diagnostic, evolutionary species concept to a morphological and distributional data set that resulted in an estimate of 18,043 species of birds worldwide, with a 95% confidence interval of 15,845 to 20,470. In a second, independent analysis, we examined intraspecific genetic data from 437 traditional avian species, finding an average of 2.4 evolutionary units per species, which can be considered proxies for phylogenetic species. Comparing recent lists of species to that used in this study (based primarily on morphology) revealed that taxonomic changes in the past 25 years have led to an increase of only 9%, well below what our results predict. Therefore, our molecular and morphological results suggest that the current taxonomy of birds understimates avian species diversity by at least a factor of two. We suggest that a revised taxonomy that better captures avian species diversity will enhance the quantification and analysis of global patterns of diversity and distribution, as well as provide a more appropriate framework for understanding the evolutionary history of birds.

The generalizability of the Youth Self-Report syndrome structure in 23 societies.

PubMed

Ivanova, Masha Y; Achenbach, Thomas M; Rescorla, Leslie A; Dumenci, Levent; Almqvist, Fredrik; Bilenberg, Niels; Bird, Hector; Broberg, Anders G; Dobrean, Anca; Döpfner, Manfred; Erol, Nese; Forns, Maria; Hannesdottir, Helga; Kanbayashi, Yasuko; Lambert, Michael C; Leung, Patrick; Minaei, Asghar; Mulatu, Mesfin S; Novik, Torunn; Oh, Kyung Ja; Roussos, Alexandra; Sawyer, Michael; Simsek, Zeynep; Steinhausen, Hans-Christoph; Weintraub, Sheila; Winkler Metzke, Christa; Wolanczyk, Tomasz; Zilber, Nelly; Zukauskiene, Rita; Verhulst, Frank C

2007-10-01

As a basis for theories of psychopathology, clinical psychology and related disciplines need sound taxonomies that are generalizable across diverse populations. To test the generalizability of a statistically derived 8-syndrome taxonomic model for youth psychopathology, confirmatory factor analyses (CFAs) were performed on the Youth Self-Report (T. M. Achenbach & L. A. Rescorla, 2001) completed by 30,243 youths 11-18 years old from 23 societies. The 8-syndrome taxonomic model met criteria for good fit to the data from each society. This was consistent with findings for the parent-completed Child Behavior Checklist (Achenbach & Rescorla, 2001) and the teacher-completed Teacher's Report Form (Achenbach & Rescorla, 2001) from many societies. Separate CFAs by gender and age group supported the 8-syndrome model for boys and girls and for younger and older youths within individual societies. The findings provide initial support for the taxonomic generalizability of the 8-syndrome model across very diverse societies, both genders, and 2 age groups. (PsycINFO Database Record (c) 2007 APA, all rights reserved).

Phylogenetic-based nomenclatural proposals for Ophiocordycipitaceae (Hypocreales) with new combinations in Tolypocladium.

PubMed

Quandt, C Alisha; Kepler, Ryan M; Gams, Walter; Araújo, João P M; Ban, Sayaka; Evans, Harry C; Hughes, David; Humber, Richard; Hywel-Jones, Nigel; Li, Zengzhi; Luangsa-Ard, J Jennifer; Rehner, Stephen A; Sanjuan, Tatiana; Sato, Hiroki; Shrestha, Bhushan; Sung, Gi-Ho; Yao, Yi-Jian; Zare, Rasoul; Spatafora, Joseph W

2014-06-01

Ophiocordycipitaceae is a diverse family comprising ecologically, economically, medicinally, and culturally important fungi. The family was recognized due to the polyphyly of the genus Cordyceps and the broad diversity of the mostly arthropod-pathogenic lineages of Hypocreales. The other two cordyceps-like families, Cordycipitaceae and Clavicipitaceae, will be revised taxonomically elsewhere. Historically, many species were placed in Cordyceps, but other genera have been described in this family as well, including several based on anamorphic features. Currently there are 24 generic names in use across both asexual and sexual life stages for species of Ophiocordycipitaceae. To reflect changes in Art. 59 in the International Code of Nomenclature for algae, fungi, and plants (ICN), we propose to protect and to suppress names within Ophiocordycipitaceae, and to present taxonomic revisions in the genus Tolypocladium, based on rigorous and extensively sampled molecular phylogenetic analyses. When approaching this task, we considered the principles of priority, monophyly, minimizing taxonomic revisions, and the practical utility of these fungi within the wider biological research community.

Patterns and Variation in Benthic Biodiversity in a Large Marine Ecosystem.

PubMed

Piacenza, Susan E; Barner, Allison K; Benkwitt, Cassandra E; Boersma, Kate S; Cerny-Chipman, Elizabeth B; Ingeman, Kurt E; Kindinger, Tye L; Lee, Jonathan D; Lindsley, Amy J; Reimer, Jessica N; Rowe, Jennifer C; Shen, Chenchen; Thompson, Kevin A; Thurman, Lindsey L; Heppell, Selina S

2015-01-01

While there is a persistent inverse relationship between latitude and species diversity across many taxa and ecosystems, deviations from this norm offer an opportunity to understand the conditions that contribute to large-scale diversity patterns. Marine systems, in particular, provide such an opportunity, as marine diversity does not always follow a strict latitudinal gradient, perhaps because several hypothesized drivers of the latitudinal diversity gradient are uncorrelated in marine systems. We used a large scale public monitoring dataset collected over an eight year period to examine benthic marine faunal biodiversity patterns for the continental shelf (55-183 m depth) and slope habitats (184-1280 m depth) off the US West Coast (47°20'N-32°40'N). We specifically asked whether marine biodiversity followed a strict latitudinal gradient, and if these latitudinal patterns varied across depth, in different benthic substrates, and over ecological time scales. Further, we subdivided our study area into three smaller regions to test whether coast-wide patterns of biodiversity held at regional scales, where local oceanographic processes tend to influence community structure and function. Overall, we found complex patterns of biodiversity on both the coast-wide and regional scales that differed by taxonomic group. Importantly, marine biodiversity was not always highest at low latitudes. We found that latitude, depth, substrate, and year were all important descriptors of fish and invertebrate diversity. Invertebrate richness and taxonomic diversity were highest at high latitudes and in deeper waters. Fish richness also increased with latitude, but exhibited a hump-shaped relationship with depth, increasing with depth up to the continental shelf break, ~200 m depth, and then decreasing in deeper waters. We found relationships between fish taxonomic and functional diversity and latitude, depth, substrate, and time at the regional scale, but not at the coast-wide scale, suggesting that coast-wide patterns can obscure important correlates at smaller scales. Our study provides insight into complex diversity patterns of the deep water soft substrate benthic ecosystems off the US West Coast.

Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

PubMed Central

Knief, Claudia

2015-01-01

Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing “unknown methanotrophic bacteria.” This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities. PMID:26696968

Macroinvertebrate Taxonomic and Functional Trait Compositions within Lotic Habitats Affected By River Restoration Practices

NASA Astrophysics Data System (ADS)

White, J. C.; Hill, M. J.; Bickerton, M. A.; Wood, P. J.

2017-09-01

The widespread degradation of lotic ecosystems has prompted extensive river restoration efforts globally, but many studies have reported modest ecological responses to rehabilitation practices. The functional properties of biotic communities are rarely examined within post-project appraisals, which would provide more ecological information underpinning ecosystem responses to restoration practices and potentially pinpoint project limitations. This study examines macroinvertebrate community responses to three projects which aimed to physically restore channel morphologies. Taxonomic and functional trait compositions supported by widely occurring lotic habitats (biotopes) were examined across paired restored and non-restored (control) reaches. The multivariate location (average community composition) of taxonomic and functional trait compositions differed marginally between control and restored reaches. However, changes in the amount of multivariate dispersion were more robust and indicated greater ecological heterogeneity within restored reaches, particularly when considering functional trait compositions. Organic biotopes (macrophyte stands and macroalgae) occurred widely across all study sites and supported a high alpha (within-habitat) taxonomic diversity compared to mineralogical biotopes (sand and gravel patches), which were characteristic of restored reaches. However, mineralogical biotopes possessed a higher beta (between-habitat) functional diversity, although this was less pronounced for taxonomic compositions. This study demonstrates that examining the functional and structural properties of taxa across distinct biotopes can provide a greater understanding of biotic responses to river restoration works. Such information could be used to better understand the ecological implications of rehabilitation practices and guide more effective management strategies.

Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams

PubMed Central

Ren, Ze; Wang, Fang; Qu, Xiaodong; Elser, James J.; Liu, Yang; Chu, Limin

2017-01-01

Understanding microbial communities in terms of taxon and function is essential to decipher the biogeochemical cycling in aquatic ecosystems. Lakes and their input streams are highly linked. However, the differences between microbial assemblages in streams and lakes are still unclear. In this study, we conducted an intensive field sampling of microbial communities from lake water and stream biofilms in the Qinghai Lake watershed, the largest lake in China. We determined bacterial communities using high-throughput 16S rRNA gene sequencing and predicted functional profiles using PICRUSt to determine the taxonomic and functional differences between microbial communities in stream biofilms and lake water. The results showed that stream biofilms and lake water harbored distinct microbial communities. The microbial communities were different taxonomically and functionally between stream and lake. Moreover, streams biofilms had a microbial network with higher connectivity and modularity than lake water. Functional beta diversity was strongly correlated with taxonomic beta diversity in both the stream and lake microbial communities. Lake microbial assemblages displayed greater predicted metabolic potentials of many metabolism pathways while the microbial assemblages in stream biofilms were more abundant in xenobiotic biodegradation and metabolism and lipid metabolism. Furthermore, lake microbial assemblages had stronger predicted metabolic potentials in amino acid metabolism, carbon fixation, and photosynthesis while stream microbial assemblages were higher in carbohydrate metabolism, oxidative phosphorylation, and nitrogen metabolism. This study adds to our knowledge of stream-lake linkages from the functional and taxonomic composition of microbial assemblages. PMID:29213266

More than just orphans: are taxonomically-restricted genes important in evolution?

PubMed

Khalturin, Konstantin; Hemmrich, Georg; Fraune, Sebastian; Augustin, René; Bosch, Thomas C G

2009-09-01

Comparative genome analyses indicate that every taxonomic group so far studied contains 10-20% of genes that lack recognizable homologs in other species. Do such 'orphan' or 'taxonomically-restricted' genes comprise spurious, non-functional ORFs, or does their presence reflect important evolutionary processes? Recent studies in basal metazoans such as Nematostella, Acropora and Hydra have shed light on the function of these genes, and now indicate that they are involved in important species-specific adaptive processes. Here we focus on evidence from Hydra suggesting that taxonomically-restricted genes play a role in the creation of phylum-specific novelties such as cnidocytes, in the generation of morphological diversity, and in the innate defence system. We propose that taxon-specific genes drive morphological specification, enabling organisms to adapt to changing conditions.

Long-term organic-inorganic fertilization ensures great soil productivity and bacterial diversity after natural-to-agricultural ecosystem conversion.

PubMed

Xun, Weibing; Xu, Zhihui; Li, Wei; Ren, Yi; Huang, Ting; Ran, Wei; Wang, Boren; Shen, Qirong; Zhang, Ruifu

2016-09-01

Natural ecosystems comprise the planet's wild plant and animal resources, but large tracts of land have been converted to agroecosystems to support the demand for agricultural products. This conversion limits the number of plant species and decreases the soil biological diversity. Here we used high-throughput 16S rRNA gene sequencing to evaluate the responses of soil bacterial communities in long-term converted and fertilized red soils (a type of Ferralic Cambisol). We observed that soil bacterial diversity was strongly affected by different types of fertilization management. Oligotrophic bacterial taxa demonstrated large relative abundances in chemically fertilized soil, whereas copiotrophic bacterial taxa were found in large relative abundances in organically fertilized and fallow management soils. Only organic-inorganic fertilization exhibited the same local taxonomic and phylogenetic diversity as that of a natural ecosystem. However, the independent use of organic or inorganic fertilizer reduced local taxonomic and phylogenetic diversity and caused biotic homogenization. This study demonstrated that the homogenization of bacterial communities caused by natural-to-agricultural ecosystem conversion can be mitigated by employing rational organic-inorganic fertilization management.

AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees.

PubMed

Zhou, Chan; Mao, Fenglou; Yin, Yanbin; Huang, Jinling; Gogarten, Johann Peter; Xu, Ying

2014-01-01

A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php.

AST: An Automated Sequence-Sampling Method for Improving the Taxonomic Diversity of Gene Phylogenetic Trees

PubMed Central

Zhou, Chan; Mao, Fenglou; Yin, Yanbin; Huang, Jinling; Gogarten, Johann Peter; Xu, Ying

2014-01-01

A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php. PMID:24892935

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat.

PubMed

Harris, J Kirk; Caporaso, J Gregory; Walker, Jeffrey J; Spear, John R; Gold, Nicholas J; Robertson, Charles E; Hugenholtz, Philip; Goodrich, Julia; McDonald, Daniel; Knights, Dan; Marshall, Paul; Tufo, Henry; Knight, Rob; Pace, Norman R

2013-01-01

The microbial mats of Guerrero Negro (GN), Baja California Sur, Mexico historically were considered a simple environment, dominated by cyanobacteria and sulfate-reducing bacteria. Culture-independent rRNA community profiling instead revealed these microbial mats as among the most phylogenetically diverse environments known. A preliminary molecular survey of the GN mat based on only ∼1500 small subunit rRNA gene sequences discovered several new phylum-level groups in the bacterial phylogenetic domain and many previously undetected lower-level taxa. We determined an additional ∼119,000 nearly full-length sequences and 28,000 >200 nucleotide 454 reads from a 10-layer depth profile of the GN mat. With this unprecedented coverage of long sequences from one environment, we confirm the mat is phylogenetically stratified, presumably corresponding to light and geochemical gradients throughout the depth of the mat. Previous shotgun metagenomic data from the same depth profile show the same stratified pattern and suggest that metagenome properties may be predictable from rRNA gene sequences. We verify previously identified novel lineages and identify new phylogenetic diversity at lower taxonomic levels, for example, thousands of operational taxonomic units at the family-genus levels differ considerably from known sequences. The new sequences populate parts of the bacterial phylogenetic tree that previously were poorly described, but indicate that any comprehensive survey of GN diversity has only begun. Finally, we show that taxonomic conclusions are generally congruent between Sanger and 454 sequencing technologies, with the taxonomic resolution achieved dependent on the abundance of reference sequences in the relevant region of the rRNA tree of life.

Diversity surveys and evolutionary relationships of aoxB genes in aerobic arsenite-oxidizing bacteria.

PubMed

Quéméneur, Marianne; Heinrich-Salmeron, Audrey; Muller, Daniel; Lièvremont, Didier; Jauzein, Michel; Bertin, Philippe N; Garrido, Francis; Joulian, Catherine

2008-07-01

A new primer set was designed to specifically amplify ca. 1,100 bp of aoxB genes encoding the As(III) oxidase catalytic subunit from taxonomically diverse aerobic As(III)-oxidizing bacteria. Comparative analysis of AoxB protein sequences showed variable conservation levels and highlighted the conservation of essential amino acids and structural motifs. AoxB phylogeny of pure strains showed well-discriminated taxonomic groups and was similar to 16S rRNA phylogeny. Alphaproteobacteria-, Betaproteobacteria-, and Gammaproteobacteria-related sequences were retrieved from environmental surveys, demonstrating their prevalence in mesophilic As-contaminated soils. Our study underlines the usefulness of the aoxB gene as a functional marker of aerobic As(III) oxidizers.

Forest-to-pasture conversion increases the diversity of the phylum Verrucomicrobia in Amazon rainforest soils.

PubMed

Ranjan, Kshitij; Paula, Fabiana S; Mueller, Rebecca C; Jesus, Ederson da C; Cenciani, Karina; Bohannan, Brendan J M; Nüsslein, Klaus; Rodrigues, Jorge L M

2015-01-01

The Amazon rainforest is well known for its rich plant and animal diversity, but its bacterial diversity is virtually unexplored. Due to ongoing and widespread deforestation followed by conversion to agriculture, there is an urgent need to quantify the soil biological diversity within this tropical ecosystem. Given the abundance of the phylum Verrucomicrobia in soils, we targeted this group to examine its response to forest-to-pasture conversion. Both taxonomic and phylogenetic diversities were higher for pasture in comparison to primary and secondary forests. The community composition of Verrucomicrobia in pasture soils was significantly different from those of forests, with a 11.6% increase in the number of sequences belonging to subphylum 3 and a proportional decrease in sequences belonging to the class Spartobacteria. Based on 99% operational taxonomic unit identity, 40% of the sequences have not been detected in previous studies, underscoring the limited knowledge regarding the diversity of microorganisms in tropical ecosystems. The abundance of Verrucomicrobia, measured with quantitative PCR, was strongly correlated with soil C content (r = 0.80, P = 0.0016), indicating their importance in metabolizing plant-derived carbon compounds in soils.

Forest-to-pasture conversion increases the diversity of the phylum Verrucomicrobia in Amazon rainforest soils

PubMed Central

Ranjan, Kshitij; Paula, Fabiana S.; Mueller, Rebecca C.; Jesus, Ederson da C.; Cenciani, Karina; Bohannan, Brendan J. M.; Nüsslein, Klaus; Rodrigues, Jorge L. M.

2015-01-01

The Amazon rainforest is well known for its rich plant and animal diversity, but its bacterial diversity is virtually unexplored. Due to ongoing and widespread deforestation followed by conversion to agriculture, there is an urgent need to quantify the soil biological diversity within this tropical ecosystem. Given the abundance of the phylum Verrucomicrobia in soils, we targeted this group to examine its response to forest-to-pasture conversion. Both taxonomic and phylogenetic diversities were higher for pasture in comparison to primary and secondary forests. The community composition of Verrucomicrobia in pasture soils was significantly different from those of forests, with a 11.6% increase in the number of sequences belonging to subphylum 3 and a proportional decrease in sequences belonging to the class Spartobacteria. Based on 99% operational taxonomic unit identity, 40% of the sequences have not been detected in previous studies, underscoring the limited knowledge regarding the diversity of microorganisms in tropical ecosystems. The abundance of Verrucomicrobia, measured with quantitative PCR, was strongly correlated with soil C content (r = 0.80, P = 0.0016), indicating their importance in metabolizing plant-derived carbon compounds in soils. PMID:26284056

The potential role of habitat-forming seaweeds in modeling benthic ecosystem properties

NASA Astrophysics Data System (ADS)

Bustamante, María; Tajadura, Javier; Díez, Isabel; Saiz-Salinas, José Ignacio

2017-12-01

Canopy-forming seaweeds provide specific habitats with key ecological properties and are facing severe declines worldwide with unforeseeable consequences for ecosystem processes. Investigating the loss of such natural habitats in order to develop management strategies for conservation is a major challenge in marine ecological research. This study investigated the shallow rocky bottoms of the southern Bay of Biscay at two sampling times with a view to identifying the effect of canopy seaweed availability on the taxonomic and functional properties of invertebrate multivariate structure, abundance, density, diversity and evenness. The multivariate taxonomic and functional structure of assemblages changed significantly according to canopy availability in terms of taxa and functional groups abundance, but no substantial change was observed in composition. Biogenic habitat simplification resulted in a decrease in total invertebrate abundance and in taxonomic and functional density and diversity, whilst no effects were observed in taxonomic and functional evenness. Loss of canopy involved an impoverishment of the whole community particularly for epiphytic colonial sessile suspension-feeders, but it also extended to non-epiphytic forms. Our results emphasize the importance of canopy decline as a major driver of changes in benthic ecosystem properties and highlight that biogenic space provided by canopy is a limiting resource for the development of rocky subtidal invertebrates.

Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases

PubMed Central

De Palma, Adriana; Abrahamczyk, Stefan; Aizen, Marcelo A.; Albrecht, Matthias; Basset, Yves; Bates, Adam; Blake, Robin J.; Boutin, Céline; Bugter, Rob; Connop, Stuart; Cruz-López, Leopoldo; Cunningham, Saul A.; Darvill, Ben; Diekötter, Tim; Dorn, Silvia; Downing, Nicola; Entling, Martin H.; Farwig, Nina; Felicioli, Antonio; Fonte, Steven J.; Fowler, Robert; Franzén, Markus; Goulson, Dave; Grass, Ingo; Hanley, Mick E.; Hendrix, Stephen D.; Herrmann, Farina; Herzog, Felix; Holzschuh, Andrea; Jauker, Birgit; Kessler, Michael; Knight, M. E.; Kruess, Andreas; Lavelle, Patrick; Le Féon, Violette; Lentini, Pia; Malone, Louise A.; Marshall, Jon; Pachón, Eliana Martínez; McFrederick, Quinn S.; Morales, Carolina L.; Mudri-Stojnic, Sonja; Nates-Parra, Guiomar; Nilsson, Sven G.; Öckinger, Erik; Osgathorpe, Lynne; Parra-H, Alejandro; Peres, Carlos A.; Persson, Anna S.; Petanidou, Theodora; Poveda, Katja; Power, Eileen F.; Quaranta, Marino; Quintero, Carolina; Rader, Romina; Richards, Miriam H.; Roulston, T’ai; Rousseau, Laurent; Sadler, Jonathan P.; Samnegård, Ulrika; Schellhorn, Nancy A.; Schüepp, Christof; Schweiger, Oliver; Smith-Pardo, Allan H.; Steffan-Dewenter, Ingolf; Stout, Jane C.; Tonietto, Rebecca K.; Tscharntke, Teja; Tylianakis, Jason M.; Verboven, Hans A. F.; Vergara, Carlos H.; Verhulst, Jort; Westphal, Catrin; Yoon, Hyung Joo; Purvis, Andy

2016-01-01

Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises. PMID:27509831

Karst tiankengs as refugia for indigenous tree flora amidst a degraded landscape in southwestern China.

PubMed

Su, Yuqiao; Tang, Qiming; Mo, Fuyan; Xue, Yuegui

2017-06-26

We conducted floristic and community analyses to compare the floristic composition, forest structure, taxonomic richness, and species diversity between two tiankeng (large doline, or sinkhole) habitats and two outside-tiankeng habitats of forest fragments in a degraded karst area in southwestern China. We found remarkably higher taxonomic richness in the tiankeng habitats than in the outside-tiankeng habitats at the species, generic, and familial levels. The inside-tiankeng habitats had higher floristic diversity but lower dominance. The remarkably higher uniqueness at all taxonomic levels and the much larger tree size in the two tiankeng habitats than in the outside-tiankeng habitats demonstrated the old-growth and isolated nature of the tiankeng flora. Plot-scale species richness, Shannon-Wiener index, Pielou's evenness, and Berger-Parker dominance significantly differed across habitats. Heterogeneity in floristic composition at the species, generic, and familial levels was extremely significant across habitats. In pairwise comparisons, except for the Chuandong Tiankeng-Shenmu Tiankeng pair, all the pairs showed significant between-habitat heterogeneity in floristic composition. Our results suggest that as oases amidst the degraded karst landscape, tiankengs serve as modern refugia that preserve old-growth forest communities with their rich floristic diversity, and can provide a model for habitat conservation and forest restoration in that area.

Epidermal and dermal integumentary structures of ankylosaurian dinosaurs.

PubMed

Arbour, Victoria M; Burns, Michael E; Bell, Phil R; Currie, Philip J

2014-01-01

Ankylosaurian dinosaurs are most notable for their abundant and morphologically diverse osteoderms, which would have given them a spiky appearance in life. Isolated osteoderms are relatively common and provide important information about the structure of the ankylosaur dermis, but fossilized impressions of the soft-tissue epidermis of ankylosaurs are rare. Nevertheless, well-preserved integument exists on several ankylosaur fossils that shows osteoderms were covered by a single epidermal scale, but one or many millimeter-sized ossicles may be present under polygonal, basement epidermal scales. Evidence for the taxonomic utility of ankylosaurid epidermal scale architecture is presented for the first time. This study builds on previous osteological work that argues for a greater diversity of ankylosaurids in the Dinosaur Park Formation of Alberta than has been traditionally recognized and adds to the hypothesis that epidermal skin impressions are taxonomically relevant across diverse dinosaur clades. Copyright © 2013 Wiley Periodicals, Inc.

[Phylogenetic diversity of microorganisms associated with the deep-water sponge Baikalospongia intermedia].

PubMed

Kalyzhnaya, O V; Itskovich, V B

2014-07-01

The diversity of bacteria associated with deep-water sponge Baikalospongia intermedia was evaluated by sequence analysis of 16S rRNA genes from two sponge samples collected in Lake Baikal from depths of 550 and 1204 m. A total of 64 operational taxonomic units, belonging to nine bacterial phyla, Proteobacteria (classes Alphaproteobacteria,. Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria), Actinobacteria, Planctomycetes, Cloroflexi, Verrucomicrobia, Acidobacteria, Chlorobi, and Nitrospirae, including candidate phylum WS5, were identified. Phylogenetic analysis showed that the examined communities contained phylotypes exhibiting homology to uncultured bacteria from different lake ecosystems, freshwater sediments, soil and geological formations. Moreover, a number of phylotypes were relative to psychrophilic, methane-oxidizing, sulfate-reducing bacteria, and to microorganisms resistant to the influence of heavy metals. It seems likely that the unusual habitation conditions of deep-water sponges contribute to the taxonomic diversity of associated bacteria and have an influence on the presence of functionally important microorganisms in bacterial communities.

Taxonomic and functional diversity increase the aesthetic value of coralligenous reefs

PubMed Central

Tribot, Anne-Sophie; Mouquet, Nicolas; Villéger, Sébastien; Raymond, Michel; Hoff, Fabrice; Boissery, Pierre; Holon, Florian; Deter, Julie

2016-01-01

The aesthetic value of landscapes contributes to human well-being. However, studies which have investigated the link between biodiversity and ecosystem services have not taken aesthetic value into account. In this study we evaluated how the aesthetics of coralligenous reefs, a key marine ecosystem in the Mediterranean, is perceived by the general public and how aesthetic preferences are related to biodiversity facets (taxonomic, phylogenetic and functional diversities). We performed both biodiversity measures and online-surveys of aesthetic perception on photographic quadrats sampled along the French Mediterranean coast. Our results show that species richness and functional richness have a significant positive effect on aesthetic value. Most of the ecological literature, exploring the relationship between biodiversity and ecosystem functioning and service has focused so far on ‘economical’ aspects of biodiversity (provision or regulation). Our results illustrate that cultural facets, such as ‘beauty’, should also be central in our motivations to preserve ecological diversity. PMID:27677850

Variations of soil microbial community structures beneath broadleaved forest trees in temperate and subtropical climate zones

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Sihang; Zhang, Yuguang; Cong, Jing

Global warming has shifted climate zones poleward or upward. Furthermore, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate). Although plant species richness decreased with latitudes, the microbial taxonomic α-diversity increased with latitudes, concomitant with increases in soil total and available nitrogen and phosphorus contents. Phylogenetic NRImore » (Net Relatedness Index) values increased from 0.718 in temperate zone (WLM) to 1.042 in subtropical zone (SNJ), showing a shift from over dispersion to clustering likely caused by environmental filtering such as low pH and nutrients. Similarly, taxonomybased association networks of subtropical forest samples were larger and tighter, suggesting clustering. In contrast, functional α-diversity was similar among three forests, but functional gene networks of the FNM forest significantly (P < 0.050) differed from the others. A significant correlation (R = 0.616, P < 0.001) between taxonomic and functional β-diversity was observed only in the FNM forest, suggesting low functional redundancy at the border of climate zones. Using a strategy of space-fortime substitution, we predict that poleward climate range shift will lead to decreased microbial taxonomic α-diversities in broadleaved forest.« less

Variations of soil microbial community structures beneath broadleaved forest trees in temperate and subtropical climate zones

DOE PAGES

Yang, Sihang; Zhang, Yuguang; Cong, Jing; ...

2017-02-10

Global warming has shifted climate zones poleward or upward. Furthermore, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate). Although plant species richness decreased with latitudes, the microbial taxonomic α-diversity increased with latitudes, concomitant with increases in soil total and available nitrogen and phosphorus contents. Phylogenetic NRImore » (Net Relatedness Index) values increased from 0.718 in temperate zone (WLM) to 1.042 in subtropical zone (SNJ), showing a shift from over dispersion to clustering likely caused by environmental filtering such as low pH and nutrients. Similarly, taxonomybased association networks of subtropical forest samples were larger and tighter, suggesting clustering. In contrast, functional α-diversity was similar among three forests, but functional gene networks of the FNM forest significantly (P < 0.050) differed from the others. A significant correlation (R = 0.616, P < 0.001) between taxonomic and functional β-diversity was observed only in the FNM forest, suggesting low functional redundancy at the border of climate zones. Using a strategy of space-fortime substitution, we predict that poleward climate range shift will lead to decreased microbial taxonomic α-diversities in broadleaved forest.« less

Multiple metrics of diversity have different effects on temperate forest functioning over succession.

PubMed

Yuan, Zuoqiang; Wang, Shaopeng; Gazol, Antonio; Mellard, Jarad; Lin, Fei; Ye, Ji; Hao, Zhanqing; Wang, Xugao; Loreau, Michel

2016-12-01

Biodiversity can be measured by taxonomic, phylogenetic, and functional diversity. How ecosystem functioning depends on these measures of diversity can vary from site to site and depends on successional stage. Here, we measured taxonomic, phylogenetic, and functional diversity, and examined their relationship with biomass in two successional stages of the broad-leaved Korean pine forest in northeastern China. Functional diversity was calculated from six plant traits, and aboveground biomass (AGB) and coarse woody productivity (CWP) were estimated using data from three forest censuses (10 years) in two large fully mapped forest plots (25 and 5 ha). 11 of the 12 regressions between biomass variables (AGB and CWP) and indices of diversity showed significant positive relationships, especially those with phylogenetic diversity. The mean tree diversity-biomass regressions increased from 0.11 in secondary forest to 0.31 in old-growth forest, implying a stronger biodiversity effect in more mature forest. Multi-model selection results showed that models including species richness, phylogenetic diversity, and single functional traits explained more variation in forest biomass than other candidate models. The models with a single functional trait, i.e., leaf area in secondary forest and wood density in mature forest, provided better explanations for forest biomass than models that combined all six functional traits. This finding may reflect different strategies in growth and resource acquisition in secondary and old-growth forests.

Global mammal beta diversity shows parallel assemblage structure in similar but isolated environments

PubMed Central

Graham, Catherine H.; Brooks, Thomas M.; Rondinini, Carlo; Hedges, S. Blair; Davidson, Ana D.; Costa, Gabriel C.

2016-01-01

The taxonomic, phylogenetic and trait dimensions of beta diversity each provide us unique insights into the importance of historical isolation and environmental conditions in shaping global diversity. These three dimensions should, in general, be positively correlated. However, if similar environmental conditions filter species with similar trait values, then assemblages located in similar environmental conditions, but separated by large dispersal barriers, may show high taxonomic, high phylogenetic, but low trait beta diversity. Conversely, we expect lower phylogenetic diversity, but higher trait biodiversity among assemblages that are connected but are in differing environmental conditions. We calculated all pairwise comparisons of approximately 110 × 110 km grid cells across the globe for more than 5000 mammal species (approx. 70 million comparisons). We considered realms as units representing geographical distance and historical isolation and biomes as units with similar environmental conditions. While beta diversity dimensions were generally correlated, we highlight geographical regions of decoupling among beta diversity dimensions. Our analysis shows that assemblages from tropical forests in different realms had low trait dissimilarity while phylogenetic beta diversity was significantly higher than expected, suggesting potential convergent evolution. Low trait beta diversity was surprisingly not found between isolated deserts, despite harsh environmental conditions. Overall, our results provide evidence for parallel assemblage structure of mammal assemblages driven by environmental conditions at a global scale. PMID:27559061

Global Taxonomic Diversity of Living Reptiles

PubMed Central

Pincheira-Donoso, Daniel; Bauer, Aaron M.; Meiri, Shai; Uetz, Peter

2013-01-01

Reptiles are one of the most ecologically and evolutionarily remarkable groups of living organisms, having successfully colonized most of the planet, including the oceans and some of the harshest and more environmentally unstable ecosystems on earth. Here, based on a complete dataset of all the world’s diversity of living reptiles, we analyse lineage taxonomic richness both within and among clades, at different levels of the phylogenetic hierarchy. We also analyse the historical tendencies in the descriptions of new reptile species from Linnaeus to March 2012. Although (non-avian) reptiles are the second most species-rich group of amniotes after birds, most of their diversity (96.3%) is concentrated in squamates (59% lizards, 35% snakes, and 2% amphisbaenians). In strong contrast, turtles (3.4%), crocodilians (0.3%), and tuataras (0.01%) are far less diverse. In terms of species discoveries, most turtles and crocodilians were described early, while descriptions of lizards, snakes and amphisbaenians are multimodal with respect to time. Lizard descriptions, in particular, have reached unprecedented levels during the last decade. Finally, despite such remarkably asymmetric distributions of reptile taxonomic diversity among groups, we found that the distributions of lineage richness are consistently right-skewed, with most clades (monophyletic families and genera) containing few lineages (monophyletic genera and species, respectively), while only a few have radiated greatly (notably the families Colubridae and Scincidae, and the lizard genera Anolis and Liolaemus). Therefore, such consistency in the frequency distribution of richness among clades and among phylogenetic levels suggests that the nature of reptile biodiversity is fundamentally fractal (i.e., it is scale invariant). We then compared current reptile diversity with the global reptile diversity and taxonomy known in 1980. Despite substantial differences in the taxonomies (relative to 2012), the patterns of lineage richness remain qualitatively identical, hence reinforcing our conclusions about the fractal nature of reptile biodiversity. PMID:23544091

Surface ocean metabarcoding confirms limited diversity in planktonic foraminifera but reveals unknown hyper-abundant lineages.

PubMed

Morard, Raphaël; Garet-Delmas, Marie-José; Mahé, Frédéric; Romac, Sarah; Poulain, Julie; Kucera, Michal; de Vargas, Colomban

2018-02-07

Since the advent of DNA metabarcoding surveys, the planktonic realm is considered a treasure trove of diversity, inhabited by a small number of abundant taxa, and a hugely diverse and taxonomically uncharacterized consortium of rare species. Here we assess if the apparent underestimation of plankton diversity applies universally. We target planktonic foraminifera, a group of protists whose known morphological diversity is limited, taxonomically resolved and linked to ribosomal DNA barcodes. We generated a pyrosequencing dataset of ~100,000 partial 18S rRNA foraminiferal sequences from 32 size fractioned photic-zone plankton samples collected at 8 stations in the Indian and Atlantic Oceans during the Tara Oceans expedition (2009-2012). We identified 69 genetic types belonging to 41 morphotaxa in our metabarcoding dataset. The diversity saturated at local and regional scale as well as in the three size fractions and the two depths sampled indicating that the diversity of foraminifera is modest and finite. The large majority of the newly discovered lineages occur in the small size fraction, neglected by classical taxonomy. These unknown lineages dominate the bulk [>0.8 µm] size fraction, implying that a considerable part of the planktonic foraminifera community biomass has its origin in unknown lineages.

Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain

PubMed Central

Shen, Congcong; Shi, Yu; Ni, Yingying; Deng, Ye; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Chu, Haiyan

2016-01-01

The elevational and latitudinal diversity patterns of microbial taxa have attracted great attention in the past decade. Recently, the distribution of functional attributes has been in the spotlight. Here, we report a study profiling soil microbial communities along an elevation gradient (500–2200 m) on Changbai Mountain. Using a comprehensive functional gene microarray (GeoChip 5.0), we found that microbial functional gene richness exhibited a dramatic increase at the treeline ecotone, but the bacterial taxonomic and phylogenetic diversity based on 16S rRNA gene sequencing did not exhibit such a similar trend. However, the β-diversity (compositional dissimilarity among sites) pattern for both bacterial taxa and functional genes was similar, showing significant elevational distance-decay patterns which presented increased dissimilarity with elevation. The bacterial taxonomic diversity/structure was strongly influenced by soil pH, while the functional gene diversity/structure was significantly correlated with soil dissolved organic carbon (DOC). This finding highlights that soil DOC may be a good predictor in determining the elevational distribution of microbial functional genes. The finding of significant shifts in functional gene diversity at the treeline ecotone could also provide valuable information for predicting the responses of microbial functions to climate change. PMID:27524983

Anticancer Drugs from Marine Flora: An Overview

PubMed Central

Sithranga Boopathy, N.; Kathiresan, K.

2010-01-01

Marine floras, such as bacteria, actinobacteria, cyanobacteria, fungi, microalgae, seaweeds, mangroves, and other halophytes are extremely important oceanic resources, constituting over 90% of the oceanic biomass. They are taxonomically diverse, largely productive, biologically active, and chemically unique offering a great scope for discovery of new anticancer drugs. The marine floras are rich in medicinally potent chemicals predominantly belonging to polyphenols and sulphated polysaccharides. The chemicals have displayed an array of pharmacological properties especially antioxidant, immunostimulatory, and antitumour activities. The phytochemicals possibly activate macrophages, induce apoptosis, and prevent oxidative damage of DNA, thereby controlling carcinogenesis. In spite of vast resources enriched with chemicals, the marine floras are largely unexplored for anticancer lead compounds. Hence, this paper reviews the works so far conducted on this aspect with a view to provide a baseline information for promoting the marine flora-based anticancer research in the present context of increasing cancer incidence, deprived of the cheaper, safer, and potent medicines to challenge the dreadful human disease. PMID:21461373

Diversity of Lactobacilli in the Oral Cavities of Young Women with Dental Caries

PubMed Central

Caufield, P.W.; Li, Y.; Dasanayake, A.; Saxena, D.

2009-01-01

For nearly a century, lactobacilli (LB) in the oral cavity have been generally associated with dental caries. Here, we characterized the LB isolated from the saliva of 6 women with active caries using genetic-based taxonomical identification methods. From each subject, 30 isolates growing on Rogosa medium and presumed to be LB were analyzed. Of the 180 isolates, 176 were further characterized by biotyping, DNA melting points, DNA chromosomal fingerprinting, genotyping, and phylogenetic cluster assessment. We found a total of 30 unique genotypes of LB in the saliva of caries-active women, with each woman harboring between 2 and 8 distinct genotypes. Although Lactobacillus vaginalis, Lactobacillus fermentum, and Lactobacillus salivarius were found in 4 of 6 of the subjects, results from other studies using comparable methods show an entirely different array of LB associated with caries. These collective observations lead us to surmise that LB associated with dental caries are likely exogenous and opportunistic colonizers, arising from food or other reservoirs outside the oral cavity. PMID:17167253

The faster-X effect: integrating theory and data.

PubMed

Meisel, Richard P; Connallon, Tim

2013-09-01

Population genetics theory predicts that X (or Z) chromosomes could play disproportionate roles in speciation and evolutionary divergence, and recent genome-wide analyses have identified situations in which X or Z-linked divergence exceeds that on the autosomes (the so-called 'faster-X effect'). Here, we summarize the current state of both the theory and data surrounding the study of faster-X evolution. Our survey indicates that the faster-X effect is pervasive across a taxonomically diverse array of evolutionary lineages. These patterns could be informative of the dominance or recessivity of beneficial mutations and the nature of genetic variation acted upon by natural selection. We also identify several aspects of disagreement between these empirical results and the population genetic models used to interpret them. However, there are clearly delineated aspects of the problem for which additional modeling and collection of genomic data will address these discrepancies and provide novel insights into the population genetics of adaptation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Anticancer drugs from marine flora: an overview.

PubMed

Sithranga Boopathy, N; Kathiresan, K

2010-01-01

Marine floras, such as bacteria, actinobacteria, cyanobacteria, fungi, microalgae, seaweeds, mangroves, and other halophytes are extremely important oceanic resources, constituting over 90% of the oceanic biomass. They are taxonomically diverse, largely productive, biologically active, and chemically unique offering a great scope for discovery of new anticancer drugs. The marine floras are rich in medicinally potent chemicals predominantly belonging to polyphenols and sulphated polysaccharides. The chemicals have displayed an array of pharmacological properties especially antioxidant, immunostimulatory, and antitumour activities. The phytochemicals possibly activate macrophages, induce apoptosis, and prevent oxidative damage of DNA, thereby controlling carcinogenesis. In spite of vast resources enriched with chemicals, the marine floras are largely unexplored for anticancer lead compounds. Hence, this paper reviews the works so far conducted on this aspect with a view to provide a baseline information for promoting the marine flora-based anticancer research in the present context of increasing cancer incidence, deprived of the cheaper, safer, and potent medicines to challenge the dreadful human disease.

Global diversity and distribution of macrofungi

Treesearch

Gregory M. Mueller; John P. Schmit; Patrick R. Leacock; Bart Buyck; Joaquin Cifuentes; Dennis E. Desjardin; Roy E. Halling; Kurt Hjortstam; Teresa Iturriaga; Karl-Henrik Larsson; D. Jean Lodge; Tom W. May; David Minter; Mario Rajchenberg; Scott A. Redhead; Leif Ryvarden; James M. Trappe; Roy Watling; Qiuxin Wu

2007-01-01

Data on macrofungal diversity and distribution patterns were compiled for major geographical regions of the world. Macrofungi are defined here to include ascomycetes and basidiomycetes with large, easily observed spore-bearing structures that form above or below ground. Each coauthor either provided data on a particular taxonomic group of macrofungi or information on...

Taxonomic review of and natural history notes on the genus Ecclisister Reichensperger (Coleoptera: Histeridae: Haeteriinae)

USDA-ARS?s Scientific Manuscript database

A great diversity of arthropods is symbiotically associated with army ant colonies. Despite the efforts of several generations of researchers to survey army ant symbiont diversity, many species still await scientific discovery. Moreover, the taxonomy of many army-ant associated groups remains unsett...

Parallel changes of taxonomic interaction networks in lacustrine bacterial communities induced by a polymetallic perturbation

PubMed Central

Laplante, Karine; Sébastien, Boutin; Derome, Nicolas

2013-01-01

Heavy metals released by anthropogenic activities such as mining trigger profound changes to bacterial communities. In this study we used 16S SSU rRNA gene high-throughput sequencing to characterize the impact of a polymetallic perturbation and other environmental parameters on taxonomic networks within five lacustrine bacterial communities from sites located near Rouyn-Noranda, Quebec, Canada. The results showed that community equilibrium was disturbed in terms of both diversity and structure. Moreover, heavy metals, especially cadmium combined with water acidity, induced parallel changes among sites via the selection of resistant OTUs (Operational Taxonomic Unit) and taxonomic dominance perturbations favoring the Alphaproteobacteria. Furthermore, under a similar selective pressure, covariation trends between phyla revealed conservation and parallelism within interphylum interactions. Our study sheds light on the importance of analyzing communities not only from a phylogenetic perspective but also including a quantitative approach to provide significant insights into the evolutionary forces that shape the dynamic of the taxonomic interaction networks in bacterial communities. PMID:23789031

(GTG)5-PCR reference framework for acetic acid bacteria.

PubMed

Papalexandratou, Zoi; Cleenwerck, Ilse; De Vos, Paul; De Vuyst, Luc

2009-11-01

One hundred and fifty-eight strains of acetic acid bacteria (AAB) were subjected to (GTG)(5)-PCR fingerprinting to construct a reference framework for their rapid classification and identification. Most of them clustered according to their respective taxonomic designation; others had to be reclassified based on polyphasic data. This study shows the usefulness of the method to determine the taxonomic and phylogenetic relationships among AAB and to study the AAB diversity of complex ecosystems.

Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s “species minimum” concept

PubMed Central

Kristoffersen, Jon B.; Oulas, Anastasis; De Troch, Marleen; Arvanitidis, Christos

2017-01-01

Several models have been developed for the description of diversity in estuaries and other brackish habitats, with the most recognized being Remane’s Artenminimum (“species minimum”) concept. It was developed for the Baltic Sea, one of the world’s largest semi-enclosed brackish water body with a unique permanent salinity gradient, and it argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum (5 to 8 psu). The aim of the present study was to investigate the relationship between salinity and sediment microbial diversity at a freshwater-marine transect in Amvrakikos Gulf (Ionian Sea, Western Greece) and assess whether species composition and community function follow a generalized concept such as Remane’s. DNA was extracted from sediment samples from six stations along the aforementioned transect and sequenced for the 16S rRNA gene using high-throughput sequencing. The metabolic functions of the OTUs were predicted and the most abundant metabolic pathways were extracted. Key abiotic variables, i.e., salinity, temperature, chlorophyll-a and oxygen concentration etc., were measured and their relation with diversity and functional patterns was explored. Microbial communities were found to differ in the three habitats examined (river, lagoon and sea) with certain taxonomic groups being more abundant in the freshwater and less in the marine environment, and vice versa. Salinity was the environmental factor with the highest correlation to the microbial community pattern, while oxygen concentration was highly correlated to the metabolic functional pattern. The total number of OTUs showed a negative relationship with increasing salinity, thus the sediment microbial OTUs in this study area do not follow Remane’s concept. PMID:29043106

[Taxonomic and functional diversity of the bycatch fishes community of trawl fishing from Northern Gulf of California, Mexico].

PubMed

Herrera-Valdivia, Eloísa; López-Martínez, Juana; Castillo Vargasmachuca, Sergio; García-Juárez, Rosa

2016-06-01

The Northern Gulf of California (NGC) is a mega diverse area of high endemism with major economic interest because of the multi-specific fisheries developed, mainly shrimp. There is a lack of recent studies on bycatch fish assemblages, so during the fishing seasons from 2009-2010 and 2010-2011, on board 13 shrimp boats, 14 commercial fishing trips were performed from 5 m - 90 m in depth with a total of 119 catches. The 119 catches were analyzed to assess fish community structure using taxonomic diversity indices to detect changes in the community following the taxonomic distinctness average Δ+ and the diversity index Δ* (TAXDEST of the PRIMER v6 program). To confirm the structure of functional groups, we considered similarities of ecologic and morphologic traits among species. The results showed that the indices Δ+ and Δ* were within the expected average and confidence intervals at 95%, finding significant differences between the indices. The analyses showed a well-structured community because of the great variety of forms and functions of the species within the community. In the community of the functional groups, reproduction was the ecological attribute that contributed the most to their structure. The community structure was represented by intermediate trophic levels (3-3.9), preferably primary and secondary carnivores within the trophic categories of predators of benthic ichthyo-fauna that belong to demersal species of soft bottoms and mostly fusiform body. To conclude, the NGC showed high functional redundancy according to the estimated functional groups, thus the ecosystem was considered stable and with great diversity. This type of studies should be followed using fishing and environmental effort due to the great biological and ecologic importance in the area.

Calibrating snakehead diversity with DNA barcodes: expanding taxonomic coverage to enable identification of potential and established invasive species.

PubMed

Serrao, Natasha R; Steinke, Dirk; Hanner, Robert H

2014-01-01

Detecting and documenting the occurrence of invasive species outside their native range requires tools to support their identification. This can be challenging for taxa with diverse life stages and/or problematic or unresolved morphological taxonomies. DNA barcoding provides a potent method for identifying invasive species, as it allows for species identification at all life stages, including fragmentary remains. It also provides an efficient interim taxonomic framework for quantifying cryptic genetic diversity by parsing barcode sequences into discontinuous haplogroup clusters (typical of reproductively isolated species) and labelling them with unique alphanumeric identifiers. Snakehead fishes are a diverse group of opportunistic predators endemic to Asia and Africa that may potentially pose significant threats as aquatic invasive species. At least three snakehead species (Channa argus, C. maculata, and C. marulius) are thought to have entered North America through the aquarium and live-food fish markets, and have established populations, yet their origins remain unclear. The objectives of this study were to assemble a library of DNA barcode sequences derived from expert identified reference specimens in order to determine the identity and aid invasion pathway analysis of the non-indigenous species found in North America using DNA barcodes. Sequences were obtained from 121 tissue samples representing 25 species and combined with public records from GenBank for a total of 36 putative species, which then partitioned into 49 discrete haplogroups. Multiple divergent clusters were observed within C. gachua, C. marulius, C. punctata and C. striata suggesting the potential presence of cryptic species diversity within these lineages. Our findings demonstrate that DNA barcoding is a valuable tool for species identification in challenging and under-studied taxonomic groups such as snakeheads, and provides a useful framework for inferring invasion pathway analysis.

Diversity Surveys and Evolutionary Relationships of aoxB Genes in Aerobic Arsenite-Oxidizing Bacteria▿ †

PubMed Central

Quéméneur, Marianne; Heinrich-Salmeron, Audrey; Muller, Daniel; Lièvremont, Didier; Jauzein, Michel; Bertin, Philippe N.; Garrido, Francis; Joulian, Catherine

2008-01-01

A new primer set was designed to specifically amplify ca. 1,100 bp of aoxB genes encoding the As(III) oxidase catalytic subunit from taxonomically diverse aerobic As(III)-oxidizing bacteria. Comparative analysis of AoxB protein sequences showed variable conservation levels and highlighted the conservation of essential amino acids and structural motifs. AoxB phylogeny of pure strains showed well-discriminated taxonomic groups and was similar to 16S rRNA phylogeny. Alphaproteobacteria-, Betaproteobacteria-, and Gammaproteobacteria-related sequences were retrieved from environmental surveys, demonstrating their prevalence in mesophilic As-contaminated soils. Our study underlines the usefulness of the aoxB gene as a functional marker of aerobic As(III) oxidizers. PMID:18502920

Functional & phylogenetic diversity of copepod communities

NASA Astrophysics Data System (ADS)

Benedetti, F.; Ayata, S. D.; Blanco-Bercial, L.; Cornils, A.; Guilhaumon, F.

2016-02-01

The diversity of natural communities is classically estimated through species identification (taxonomic diversity) but can also be estimated from the ecological functions performed by the species (functional diversity), or from the phylogenetic relationships among them (phylogenetic diversity). Estimating functional diversity requires the definition of specific functional traits, i.e., phenotypic characteristics that impact fitness and are relevant to ecosystem functioning. Estimating phylogenetic diversity requires the description of phylogenetic relationships, for instance by using molecular tools. In the present study, we focused on the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. First, we implemented a specific trait database for the most commonly-sampled and abundant copepod species of the Mediterranean Sea. Our database includes 191 species, described by seven traits encompassing diverse ecological functions: minimal and maximal body length, trophic group, feeding type, spawning strategy, diel vertical migration and vertical habitat. Clustering analysis in the functional trait space revealed that Mediterranean copepods can be gathered into groups that have different ecological roles. Second, we reconstructed a phylogenetic tree using the available sequences of 18S rRNA. Our tree included 154 of the analyzed Mediterranean copepod species. We used these two datasets to describe the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. The replacement component (turn-over) and the species richness difference component (nestedness) of the beta diversity indices were identified. Finally, by comparing various and complementary aspects of plankton diversity (taxonomic, functional, and phylogenetic diversity) we were able to gain a better understanding of the relationships among the zooplankton community, biodiversity, ecosystem function, and environmental forcing.

Cyanobacterial diversity and halotolerance in a variable hypersaline environment.

PubMed

Kirkwood, Andrea E; Buchheim, Julie A; Buchheim, Mark A; Henley, William J

2008-04-01

The Great Salt Plains (GSP) in north-central Oklahoma, USA is an expansive salt flat (approximately 65 km(2)) that is part of the federally protected Salt Plains National Wildlife Refuge. The GSP serves as an ideal environment to study the microbial diversity of a terrestrial, hypersaline system that experiences wide fluctuations in freshwater influx and diel temperature. Our study assessed cyanobacterial diversity at the GSP by focusing on the taxonomic and physiological diversity of GSP isolates, and the 16S rRNA phylogenetic diversity of isolates and environmental clones from three sites (north, central, and south). Taxonomic diversity of isolates was limited to a few genera (mostly Phormidium and Geitlerinema), but physiological diversity based on halotolerance ranges was strikingly more diverse, even between strains of the same phylotype. The phylogenetic tree revealed diversity that spanned a number of cyanobacterial lineages, although diversity at each site was dominated by only a few phylotypes. Unlike other hypersaline systems, a number of environmental clones from the GSP were members of the heterocystous lineage. Although a number of cyanobacterial isolates were close matches with prevalent environmental clones, it is not certain if these clones reflect the same halotolerance ranges of their matching isolates. This caveat is based on the notable disparities we found between strains of the same phylotype and their inherent halotolerance. Our findings support the hypothesis that variable or poikilotrophic environments promote diversification, and in particular, select for variation in ecotype more than phylotype.

Relating appendicular skeletal variation of sigmodontine rodents to locomotion modes in a phylogenetic context.

PubMed

Carvalho Coutinho, Ludmilla; Alves de Oliveira, João

2017-10-01

Sigmodontinae rodents constitute the second-largest subfamily among mammals. Alongside the taxonomic diversity, they are also ecologically diverse, exhibiting a wide array of locomotion modes, with semifossorial, terrestrial, semiaquatic, scansorial, arboreal, and saltatorial forms. To understand the ecomorphologic aspects that allow these rodents to display such locomotion diversity, we analyzed 35 qualitative characters of the appendicular skeleton (humerus, ulna, radius, scapula, femur, tibia, ilium, ischium and pubis) in 795 specimens belonging to 64 species, 34 genera and 10 tribes, representing all locomotion modes assigned to this subfamily. We performed a statistical analysis based upon the coefficient of trait differentiation to test the congruence of character states and the different locomotion modes. We also mapped characters states in a molecular phylogeny in order to reconstruct ancestral states and to evaluate how appendicular characters evolved within main lineages of Sigmodontinae radiation under a phylogenetic framework. The statistical analyses revealed six characters related to specific locomotion modes, except terrestrial. The mapping and parsimony ancestral states reconstruction identified two characters with phylogenetical signal and eight characters that are exclusively or more frequently recorded in certain modes of locomotion, four of them also detected by the statistical analysis. Notwithstanding the documented morphological variation, few changes characterize the transition to each of the locomotion modes, at least regarding the appendicular skeleton. This finding corroborates previous results that showed that sigmodontines exhibit an all-purpose appendicular morphology that allows them to use and explore a great variety of habitats. © 2017 Anatomical Society.

Phylogenetic diversity measures based on Hill numbers.

PubMed

Chao, Anne; Chiu, Chun-Huo; Jost, Lou

2010-11-27

We propose a parametric class of phylogenetic diversity (PD) measures that are sensitive to both species abundance and species taxonomic or phylogenetic distances. This work extends the conventional parametric species-neutral approach (based on 'effective number of species' or Hill numbers) to take into account species relatedness, and also generalizes the traditional phylogenetic approach (based on 'total phylogenetic length') to incorporate species abundances. The proposed measure quantifies 'the mean effective number of species' over any time interval of interest, or the 'effective number of maximally distinct lineages' over that time interval. The product of the measure and the interval length quantifies the 'branch diversity' of the phylogenetic tree during that interval. The new measures generalize and unify many existing measures and lead to a natural definition of taxonomic diversity as a special case. The replication principle (or doubling property), an important requirement for species-neutral diversity, is generalized to PD. The widely used Rao's quadratic entropy and the phylogenetic entropy do not satisfy this essential property, but a simple transformation converts each to our measures, which do satisfy the property. The proposed approach is applied to forest data for interpreting the effects of thinning.

Functional diversity response to hardwood forest management varies across taxa and spatial scales.

PubMed

Murray, Bryan D; Holland, Jeffrey D; Summerville, Keith S; Dunning, John B; Saunders, Michael R; Jenkins, Michael A

2017-06-01

Contemporary forest management offers a trade-off between the potential positive effects of habitat heterogeneity on biodiversity, and the potential harm to mature forest communities caused by habitat loss and perforation of the forest canopy. While the response of taxonomic diversity to forest management has received a great deal of scrutiny, the response of functional diversity is largely unexplored. However, functional diversity may represent a more direct link between biodiversity and ecosystem function. To examine how forest management affects diversity at multiple spatial scales, we analyzed a long-term data set that captured changes in taxonomic and functional diversity of moths (Lepidoptera), longhorned beetles (Coleoptera: Cerambycidae), and breeding birds in response to contemporary silvicultural systems in oak-hickory hardwood forests. We used these data sets to address the following questions: how do even- and uneven-aged silvicultural systems affect taxonomic and functional diversity at the scale of managed landscapes compared to the individual harvested and unharvested forest patches that comprise the landscapes, and how do these silvicultural systems affect the functional similarity of assemblages at the scale of managed landscapes and patches? Due to increased heterogeneity within landscapes, we expected even-aged silviculture to increase and uneven-aged silviculture to decrease functional diversity at the landscape level regardless of impacts at the patch level. Functional diversity responses were taxon-specific with respect to the direction of change and time since harvest. Responses were also consistent across patch and landscape levels within each taxon. Moth assemblage species richness, functional richness, and functional divergence were negatively affected by harvesting, with stronger effects resulting from uneven-aged than even-aged management. Longhorned beetle assemblages exhibited a peak in species richness two years after harvesting, while functional diversity metrics did not differ between harvested and unharvested patches and managed landscapes. The species and functional richness of breeding bird assemblages increased in response to harvesting with more persistent effects in uneven- than in even-aged managed landscapes. For moth and bird assemblages, species turnover was driven by species with more extreme trait combinations. Our study highlights the variability of multi-taxon functional diversity in response to forest management across multiple spatial scales. © 2017 by the Ecological Society of America.

A Unified Taxonomic Approach to the Laboratory Assessment of Visionic Devices

DTIC Science & Technology

2006-09-01

the ratification stage with member nations. Marasco and Task 4 presented a large array of tests applicable to image intensification-based visionic...aircraft.” In print. 4. Marasco , P. L., and Task, H. L. 1999. “Optical characterization of wide field-of-view night vision devices,” in

The assembly of ecological communities inferred from taxonomic and functional composition

Treesearch

Eric R. Sokol; E.F. Benfield; Lisa K. Belden; H. Maurice. Valett

2011-01-01

Among-site variation in metacommunities (beta diversity) is typically correlated with the distance separating the sites (spatial lag). This distance decay in similarity pattern has been linked to both niche-based and dispersal-based community assembly hypotheses. Here we show that beta diversity patterns in community composition, when supplemented with functional-trait...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Mengmeng; Liu, Shanshan; Wang, Feng

We report that soil transplant serves as a proxy to simulate climate changes. Recently, we have shown that southward transplant of black soil and northward transplant of red soil altered soil microbial communities and biogeochemical variables. However, fundamental differences in soil types have prevented direct comparison between southward and northward transplants. To tackle it, herein we report an analysis of microbial communities of Cambisol soil in an agriculture field after 4 years of adaptation to southward and northward soil transplants over large transects. Analysis of bare fallow soils revealed concurrent increase in microbial functional diversity and coarse-scale taxonomic diversity atmore » both transplanted sites, as detected by GeoChip 3.0 and DGGE, respectively. Furthermore, a correlation between microbial functional diversity and taxonomic diversity was detected, which was masked in maize cropped soils. Mean annual temperature, soil moisture, and nitrate (NO 3¯-N) showed strong correlations with microbial communities. In addition, abundances of ammonium-oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO 3¯-N contents, suggesting that microbial responses to soil transplant could alter microbe-mediated biogeochemical cycle at the ecosystem level.« less

Arctic plant diversity in the Early Eocene greenhouse

PubMed Central

Harrington, Guy J.; Eberle, Jaelyn; Le-Page, Ben A.; Dawson, Mary; Hutchison, J. Howard

2012-01-01

For the majority of the Early Caenozoic, a remarkable expanse of humid, mesothermal to temperate forests spread across Northern Polar regions that now contain specialized plant and animal communities adapted to life in extreme environments. Little is known on the taxonomic diversity of Arctic floras during greenhouse periods of the Caenozoic. We show for the first time that plant richness in the globally warm Early Eocene (approx. 55–52 Myr) in the Canadian High Arctic (76° N) is comparable with that approximately 3500 km further south at mid-latitudes in the US western interior (44–47° N). Arctic Eocene pollen floras are most comparable in richness with today's forests in the southeastern United States, some 5000 km further south of the Arctic. Nearly half of the Eocene, Arctic plant taxa are endemic and the richness of pollen floras implies significant patchiness to the vegetation type and clear regional richness of angiosperms. The reduced latitudinal diversity gradient in Early Eocene North American plant species demonstrates that extreme photoperiod in the Arctic did not limit taxonomic diversity of plants. PMID:22072610

Modelling alpha-diversities of coastal lagoon fish assemblages from the Mediterranean Sea

NASA Astrophysics Data System (ADS)

Riera, R.; Tuset, V. M.; Betancur-R, R.; Lombarte, A.; Marcos, C.; Pérez-Ruzafa, A.

2018-07-01

Coastal lagoons are marine ecosystems spread worldwide with high ecological value; however, they are increasingly becoming deteriorated as a result of anthropogenic activity. Their conservation requires a better understanding of the biodiversity factors that may help identifying priority areas. The present study is focused on 37 Mediterranean coastal lagoons and we use predictive modelling approaches based on Generalized Linear Model (GLM) analysis to investigate variables (geomorphological, environmental, trophic or biogeographic) that may predict variations in alpha-diversity. It included taxonomic diversity, average taxonomic distinctness, and phylogenetic and functional diversity. Two GLM models by index were built depending on available variables for lagoons: in the model 1 all lagoons were used, and in the model 2 only 23. All alpha-diversity indices showed variability between lagoons associated to exogenous factors considered. The biogeographic region strongly conditioned most of models, being the first variable introduced in the models. The salinity and chlorophyll a concentration played a secondary role for the models 1 and 2, respectively. In general, the highest values of alpha-diversities were found in northwestern Mediterranean (Balearic Sea, Alborán Sea and Gulf of Lion), hence they might be considered "hotspots" at the Mediterranean scale and should have a special status for their protection.

Current Taxonomical Situation of Streptococcus suis

PubMed Central

Okura, Masatoshi; Osaki, Makoto; Nomoto, Ryohei; Arai, Sakura; Osawa, Ro; Sekizaki, Tsutomu; Takamatsu, Daisuke

2016-01-01

Streptococcus suis, a major porcine pathogen and an important zoonotic agent, is considered to be composed of phenotypically and genetically diverse strains. However, recent studies reported several “S. suis-like strains” that were identified as S. suis by commonly used methods for the identification of this bacterium, but were regarded as distinct species from S. suis according to the standards of several taxonomic analyses. Furthermore, it has been suggested that some S. suis-like strains can be assigned to several novel species. In this review, we discuss the current taxonomical situation of S. suis with a focus on (1) the classification history of the taxon of S. suis; (2) S. suis-like strains revealed by taxonomic analyses; (3) methods for detecting and identifying this species, including a novel method that can distinguish S. suis isolates from S. suis-like strains; and (4) current topics on the reclassification of S. suis-like strains. PMID:27348006

Current Taxonomical Situation of Streptococcus suis.

PubMed

Okura, Masatoshi; Osaki, Makoto; Nomoto, Ryohei; Arai, Sakura; Osawa, Ro; Sekizaki, Tsutomu; Takamatsu, Daisuke

2016-06-24

Streptococcus suis, a major porcine pathogen and an important zoonotic agent, is considered to be composed of phenotypically and genetically diverse strains. However, recent studies reported several "S. suis-like strains" that were identified as S. suis by commonly used methods for the identification of this bacterium, but were regarded as distinct species from S. suis according to the standards of several taxonomic analyses. Furthermore, it has been suggested that some S. suis-like strains can be assigned to several novel species. In this review, we discuss the current taxonomical situation of S. suis with a focus on (1) the classification history of the taxon of S. suis; (2) S. suis-like strains revealed by taxonomic analyses; (3) methods for detecting and identifying this species, including a novel method that can distinguish S. suis isolates from S. suis-like strains; and (4) current topics on the reclassification of S. suis-like strains.

Assessment of variations in taxonomic diversity, forest structure, and aboveground biomass using remote sensing along an altitudinal gradient in tropical montane forest of Costa Rica

NASA Astrophysics Data System (ADS)

Robinson, C. M.; Saatchi, S. S.; Clark, D.; Fricker, G. A.; Wolf, J.; Gillespie, T. W.; Rovzar, C. M.; Andelman, S.

2012-12-01

This research sought to understand how alpha and beta diversity of plants vary and relate to the three-dimensional vegetation structure and aboveground biomass along environmental gradients in the tropical montane forests of Braulio Carrillo National Park in Costa Rica. There is growing evidence that ecosystem structure plays an important role in defining patterns of species diversity and along with abiotic factors (climate and edaphic) control the phenotypic and functional variations across landscapes. It is well documented that strong subdivisions at local and regional scales are found mainly on geologic or climate gradients. These general determinants of biodiversity are best demonstrated in regions with natural gradients such as tropical montane forests. Altitudinal gradients provide a landscape scale changes through variations in topography, climate, and edaphic conditions on which we tested several theoretical and biological hypotheses regarding drivers of biodiversity. The study was performed by using forest inventory and botanical data from nine 1-ha plots ranging from 100 m to 2800 m above sea level and remote sensing data from airborne lidar and radar sensors to quantify variations in forest structure. In this study we report on the effectiveness of relating patterns of tree taxonomic alpha diversity to three-dimensional structure of a tropical montane forest using lidar and radar observations of forest structure and biomass. We assessed alpha and beta diversity at the species, genus, and family levels utilizing datasets provided by the Terrestrial Ecology Assessment and Monitoring (TEAM) Network. Through the comparison to active remote sensing imagery, our results show that there is a strong relationship between forest 3D-structure, and alpha and beta diversity controlled by variations in abiotic factors along the altitudinal gradient. Using spatial analysis with the aid of remote sensing data, we find distinct patterns along the environmental gradients defining species turnover and changes in functional diversity. The study will provide novel approaches to use detailed spatial information from remote sensing data to study relations between functional and taxonomic dimensions of diversity.

Patterns and Variation in Benthic Biodiversity in a Large Marine Ecosystem

PubMed Central

Lee, Jonathan D.

2015-01-01

While there is a persistent inverse relationship between latitude and species diversity across many taxa and ecosystems, deviations from this norm offer an opportunity to understand the conditions that contribute to large-scale diversity patterns. Marine systems, in particular, provide such an opportunity, as marine diversity does not always follow a strict latitudinal gradient, perhaps because several hypothesized drivers of the latitudinal diversity gradient are uncorrelated in marine systems. We used a large scale public monitoring dataset collected over an eight year period to examine benthic marine faunal biodiversity patterns for the continental shelf (55–183 m depth) and slope habitats (184–1280 m depth) off the US West Coast (47°20′N—32°40′N). We specifically asked whether marine biodiversity followed a strict latitudinal gradient, and if these latitudinal patterns varied across depth, in different benthic substrates, and over ecological time scales. Further, we subdivided our study area into three smaller regions to test whether coast-wide patterns of biodiversity held at regional scales, where local oceanographic processes tend to influence community structure and function. Overall, we found complex patterns of biodiversity on both the coast-wide and regional scales that differed by taxonomic group. Importantly, marine biodiversity was not always highest at low latitudes. We found that latitude, depth, substrate, and year were all important descriptors of fish and invertebrate diversity. Invertebrate richness and taxonomic diversity were highest at high latitudes and in deeper waters. Fish richness also increased with latitude, but exhibited a hump-shaped relationship with depth, increasing with depth up to the continental shelf break, ~200 m depth, and then decreasing in deeper waters. We found relationships between fish taxonomic and functional diversity and latitude, depth, substrate, and time at the regional scale, but not at the coast-wide scale, suggesting that coast-wide patterns can obscure important correlates at smaller scales. Our study provides insight into complex diversity patterns of the deep water soft substrate benthic ecosystems off the US West Coast. PMID:26308521

Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession.

PubMed

Ortiz-Álvarez, Rüdiger; Fierer, Noah; de Los Ríos, Asunción; Casamayor, Emilio O; Barberán, Albert

2018-02-20

Ecologists have long studied primary succession, the changes that occur in biological communities after initial colonization of an environment. Most of this work has focused on succession in plant communities, laying the conceptual foundation for much of what we currently know about community assembly patterns over time. Because of their prevalence and importance in ecosystems, an increasing number of studies have focused on microbial community dynamics during succession. Here, we conducted a meta-analysis of bacterial primary succession patterns across a range of distinct habitats, including the infant gut, plant surfaces, soil chronosequences, and aquatic environments, to determine whether consistent changes in bacterial diversity, community composition, and functional traits are evident over the course of succession. Although these distinct habitats harbor unique bacterial communities, we were able to identify patterns in community assembly that were shared across habitat types. We found an increase in taxonomic and functional diversity with time while the taxonomic composition and functional profiles of communities became less variable (lower beta diversity) in late successional stages. In addition, we found consistent decreases in the rRNA operon copy number and in the high-efficient phosphate assimilation process (Pst system) suggesting that reductions in resource availability during succession select for taxa adapted to low-resource conditions. Together, these results highlight that, like many plant communities, microbial communities also exhibit predictable patterns during primary succession.

Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs.

PubMed

Dupont, A Ö C; Griffiths, R I; Bell, T; Bass, D

2016-06-01

A recent large-scale assessment of bacterial communities across a range of UK soil types showed that bacterial community structure was strongly determined by soil pH. We analysed a data set of eukaryotic 454 sequencing 18S rDNA from the surveyed samples and showed significant differences in eukaryotic assemblages according to pH class, mostly between low pH and higher pH soils. Soil eukaryote communities (per sample) differed most at the taxonomic rank approximating to order level. Taxonomies assigned with the Protist Ribosomal Reference and the Silva 119 databases were taxonomically inconsistent, mostly due to differing 18S annotations, although general structure and composition according to pH were coherent. A relatively small number of lineages, mostly putative parasitic protists and fungi, drive most differences between pH classes, with weaker contributions from bacterivores and autotrophs. Overall, soil parasites included a large diversity of alveolates, in particular apicomplexans. Phylogenetic analysis of alveolate lineages demonstrates a large diversity of unknown gregarines, novel perkinsids, coccidians, colpodellids and uncharacterized alveolates. Other novel and/or divergent lineages were revealed across the eukaryote tree of life. Our study provides an in-depth taxonomic evaluation of micro-eukaryotic diversity, and reveals novel lineages and insights into their relationships with environmental variables across soil gradients. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Human-Induced Landscape Changes Homogenize Atlantic Forest Bird Assemblages through Nested Species Loss

PubMed Central

Villegas Vallejos, Marcelo Alejandro; Padial, André Andrian; Vitule, Jean Ricardo Simões

2016-01-01

The increasing number of quantitative assessments of homogenization using citizen science data is particularly important in the Neotropics, given its high biodiversity and ecological peculiarity, and whose communities may react differently to landscape changes. We looked for evidence of taxonomic homogenization in terrestrial birds by investigating patterns of beta diversity along a gradient of human-altered landscapes (HAL), trying to identify species associated with this process. We analyzed bird data from 87 sites sampled in a citizen science program in the south Brazilian Atlantic Forest. Regional-scale taxonomic homogenization was assessed by comparing beta diversity among sites in different HALs (natural, rural or urban landscapes) accounting for variation derived from geographical distance and zoogeographical affinities by georeferencing sites and determining their position in a phytogeographical domain. Beta diversity was calculated by multivariate dispersion and by testing compositional changes due to turnover and nestedness among HALs and phytogeographical domains. Finally, we assessed which species were typical for each group using indicator species analysis. Bird homogenization was indicated by decreases in beta diversity following landscape changes. Beta diversity of rural sites was roughly half that of natural habitats, while urban sites held less than 10% of the natural areas’ beta diversity. Species composition analysis revealed that the turnover component was important in differentiating sites depending on HAL and phytogeography; the nestedness component was important among HALs, where directional species loss is maintained even considering effects of sampling effort. A similar result was obtained among phytogeographical domains, indicating nested-pattern dissimilarity among compositions of overlapping communities. As expected, a few native generalists and non-native urban specialists were characteristic of rural and urban sites. We generated strong evidence that taxonomic homogenization occurs in the south Brazilian Atlantic Forest as a result of a directional and nested species loss, with the resultant assemblages composed of few disturbance-tolerant birds. PMID:26840957

Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis.

PubMed

Luo, Gang; Fotidis, Ioannis A; Angelidaki, Irini

2016-01-01

Biogas production is a very complex process due to the high complexity in diversity and interactions of the microorganisms mediating it, and only limited and diffuse knowledge exists about the variation of taxonomic and functional patterns of microbiomes across different biogas reactors, and their relationships with the metabolic patterns. The present study used metagenomic sequencing and radioisotopic analysis to assess the taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors operated under various conditions treating either sludge or manure. The results from metagenomic analysis showed that the dominant methanogenic pathway revealed by radioisotopic analysis was not always correlated with the taxonomic and functional compositions. It was found by radioisotopic experiments that the aceticlastic methanogenic pathway was dominant, while metagenomics analysis showed higher relative abundance of hydrogenotrophic methanogens. Principal coordinates analysis showed the sludge-based samples were clearly distinct from the manure-based samples for both taxonomic and functional patterns, and canonical correspondence analysis showed that the both temperature and free ammonia were crucial environmental variables shaping the taxonomic and functional patterns. The study further the overall patterns of functional genes were strongly correlated with overall patterns of taxonomic composition across different biogas reactors. The discrepancy between the metabolic patterns determined by metagenomic analysis and metabolic pathways determined by radioisotopic analysis was found. Besides, a clear correlation between taxonomic and functional patterns was demonstrated for biogas reactors, and also the environmental factors that shaping both taxonomic and functional genes patterns were identified.

Partitioning of functional and taxonomic diversity in surface-associated microbial communities.

PubMed

Roth-Schulze, Alexandra J; Zozaya-Valdés, Enrique; Steinberg, Peter D; Thomas, Torsten

2016-12-01

Surfaces, including those submerged in the marine environment, are subjected to constant interactions and colonisation by surrounding microorganisms. The principles that determine the assembly of those epibiotic communities are however poorly understood. In this study, we employed a hierarchical design to assess the functionality and diversity of microbial communities on different types of host surfaces (e.g. macroalgae, seagrasses). We found that taxonomic diversity was unique to each type of host, but that the majority of functions (> 95%) could be found in any given surface community, suggesting a high degree of functional redundancy. However, some community functions were enriched on certain surfaces and were related to host-specific properties (e.g. the degradation of specific polysaccharides). Together these observations support a model, whereby communities on surfaces are assembled from guilds of microorganisms with a functionality that is partitioned into general properties for a surface-associated life-style, but also specific features that mediate host-specificity. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Modeling microbial community structure and functional diversity across time and space.

PubMed

Larsen, Peter E; Gibbons, Sean M; Gilbert, Jack A

2012-07-01

Microbial communities exhibit exquisitely complex structure. Many aspects of this complexity, from the number of species to the total number of interactions, are currently very difficult to examine directly. However, extraordinary efforts are being made to make these systems accessible to scientific investigation. While recent advances in high-throughput sequencing technologies have improved accessibility to the taxonomic and functional diversity of complex communities, monitoring the dynamics of these systems over time and space - using appropriate experimental design - is still expensive. Fortunately, modeling can be used as a lens to focus low-resolution observations of community dynamics to enable mathematical abstractions of functional and taxonomic dynamics across space and time. Here, we review the approaches for modeling bacterial diversity at both the very large and the very small scales at which microbial systems interact with their environments. We show that modeling can help to connect biogeochemical processes to specific microbial metabolic pathways. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Complex within complex: integrative taxonomy reveals hidden diversity in Cicadetta brevipennis (Hemiptera: Cicadidae) and unexpected relationships with a song divergent relative

USDA-ARS?s Scientific Manuscript database

Multiple sources of data in combination are essential for species delimitation and classification of difficult taxonomic groups. Here we investigate a cicada taxon with unusual cryptic diversity and we attempt to resolve seemingly contradictory data sets. Cicada songs act as species-specific premati...

Genetic diversity and conservation of Mexican forest trees

Treesearch

C. Wehenkel; S. Mariscal-Lucero; J.P. Jaramillo-Correa; C.A. López-Sánchez; J.J. Vargas Hernández; C. Sáenz-Romero

2017-01-01

Over the last 200 years, humans have impacted the genetic diversity of forest trees. Because of widespread deforestation and over-exploitation, about 9,000 tree species are listed worldwide as threatened with extinction, including more than half of the ~600 known conifer taxa. A comprehensive review of the floristic-taxonomic literature compiled a list of 4,331...

Increased anthropogenic disturbance and aridity reduce phylogenetic and functional diversity of ant communities in Caatinga dry forest.

PubMed

Arnan, Xavier; Arcoverde, Gabriela B; Pie, Marcio R; Ribeiro-Neto, José D; Leal, Inara R

2018-08-01

Anthropogenic disturbance and climate change are major threats to biodiversity. The Brazilian Caatinga is the world's largest and most diverse type of seasonally dry tropical forest. It is also one of the most threatened, but remains poorly studied. Here, we analyzed the individual and combined effects of anthropogenic disturbance (three types: livestock grazing, wood extraction, and miscellaneous use of forest resources) and increasing aridity on taxonomic, phylogenetic and functional ant diversity in the Caatinga. We found no aridity and disturbance effects on taxonomic diversity. In spite of this, functional diversity, and to a lesser extent phylogenetic diversity, decreased with increased levels of disturbance and aridity. These effects depended on disturbance type: livestock grazing and miscellaneous resource use, but not wood extraction, deterministically filtered both components of diversity. Interestingly, disturbance and aridity interacted to shape biodiversity responses. While aridity sometimes intensified the negative effects of disturbance, the greatest declines in biodiversity were in the wettest areas. Our results imply that anthropogenic disturbance and aridity interact in complex ways to endanger biodiversity in seasonally dry tropical forests. Given global climate change, neotropical semi-arid areas are habitats of concern, and our findings suggest Caatinga conservation policies must prioritize protection of the wettest areas, where biodiversity loss stands to be the greatest. Given the major ecological relevance of ants, declines in both ant phylogenetic and functional diversity might have downstream effects on ecosystem processes, insect populations, and plant populations. Copyright © 2018 Elsevier B.V. All rights reserved.

Tracking Spatial and Temporal Changes in Microbial Metabolic Potential and Gene Expression Patterns Across Geochemical Gradients at Axial Seamount

NASA Astrophysics Data System (ADS)

Fortunato, C. S.; Butterfield, D. A.; Larson, B.; Algar, C. K.; Huber, J. A.

2016-12-01

Microbial communities living both near and within the subseafloor are important players in the biogeochemical cycling of the deep ocean. To better understand the metabolic and gene expression patterns of these understudied communities, we collected low-temperature diffuse fluids for metagenomic, metatranscriptomic, and geochemical analyses from Axial Seamount, an active submarine volcano off the coast of Oregon, USA in 2013-2015. In April of 2015 Axial Seamount erupted along its north rift, five months before the 2015 samples were collected. This study thus provides both spatial and temporal analysis of subseafloor microbial communities pre and post eruption. The time series for this study focused on three vents at the south end of the caldera: Anemone, Marker 33, and Marker 113. Chemistry data shows that at each vent there are different geochemical conditions and thus a potentially different microbial metabolic profile. Anemone has the most oxidizing conditions and the highest abundance and expression of sulfur oxidation genes, attributed to both SUP05 and Epsilonproteobacteria. The most reducing conditions were observed at Marker 113, the site with the lowest oxygen concentration and where methanogenesis was the dominant metabolism, with 18.5% of all annotated transcripts attributed to methanogenesis. Although individual vents were metabolically distinct, there was very little variation in the overall taxonomic and metabolic profiles of each vent across years, even after the 2015 eruption. A diffuse fluid sample taken from the North Rift Zone post eruption showed similar community taxonomy to both Anemone and Marker 33; analyses of the metabolic potential and gene expression at this site is ongoing and will act as a comparison between the communities of the time series vents and those that were closer to the eruption site. Together, these chemical and `omic datasets reveal a dynamic microbial community at each vent, taxonomically diverse and involved in a wide array of biogeochemical transformations. Results are being used to model the functional dynamics and fluxes of vent communities to more closely link microbiological productivity at hydrothermal systems to deep-sea biogeochemical processes and will be also used to inform future projects using instrumentation on the cabled array at Axial Seamount.

Mitigation of Ricin Contamination in Soils: Sorption and Degradation

DTIC Science & Technology

2003-07-01

Table 2. Castor impacts on fungal taxonomic diversity: Total activity Dominate fungi Castor field: Fusarium (several species) Lower species...richness Cotton field: Trichoderma Fusarium Sterile dark Higher species richness

Contrasting changes in taxonomic vs. functional diversity of tropical fish communities after habitat degradation.

PubMed

Villéger, Sébastien; Ramos Miranda, Julia; Flores Hernández, Domingo; Mouillot, David

2010-09-01

Human activities have strong impacts on ecosystem functioning through their effect on abiotic factors and on biodiversity. There is also growing evidence that species functional traits link changes in species composition and shifts in ecosystem processes. Hence, it appears to be of utmost importance to quantify modifications in the functional structure of species communities after human disturbance in addition to changes in taxonomic structure. Despite this fact, there is still little consensus on the actual impacts of human-mediated habitat alteration on the components of biodiversity, which include species functional traits. Therefore, we studied changes in taxonomic diversity (richness and evenness), in functional diversity, and in functional specialization of estuarine fish communities facing drastic environmental and habitat alterations. The Terminos Lagoon (Gulf of Mexico) is a tropical estuary of primary concern for its biodiversity, its habitats, and its resource supply, which have been severely impacted by human activities. Fish communities were sampled in four zones of the Terminos Lagoon 18 years apart (1980 and 1998). Two functions performed by fish (food acquisition and locomotion) were studied through the measurement of 16 functional traits. Functional diversity of fish communities was quantified using three independent components: richness, evenness, and divergence. Additionally, we measured the degree of functional specialization in fish communities. We used a null model to compare the functional and the taxonomic structure of fish communities between 1980 and 1998. Among the four largest zones studied, three did not show strong functional changes. In the northern part of the lagoon, we found an increase in fish richness but a significant decrease of functional divergence and functional specialization. We explain this result by a decline of specialized species (i.e., those with particular combinations of traits), while newly occurring species are redundant with those already present. The species that decreased in abundance have functional traits linked to seagrass habitats that regressed consecutively to increasing eutrophication. The paradox found in our study highlights the need for a multifaceted approach in the assessment of biodiversity changes in communities under pressure.

Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity.

PubMed

Buckley, Hannah L; Rafat, Arash; Ridden, Johnathon D; Cruickshank, Robert H; Ridgway, Hayley J; Paterson, Adrian M

2014-01-01

The role of species' interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran's eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners' genetic variation. Different lichen taxa showed some variation in their phylogenetic congruence and spatial genetic patterns and where greater sample replication was used, the amount of variation explained by partner genetic variation increased. Our results suggest that the phylogenetic congruence pattern, at least at small spatial scales, is likely due to reciprocal co-adaptation or co-dispersal. However, the detection of these patterns varies among different lichen taxa, across spatial scales and with different levels of sample replication. This work provides insight into the complexities faced in determining how evolutionary and ecological processes may interact to generate diversity in symbiotic association patterns at the population and community levels. Further, it highlights the critical importance of considering sample replication, taxonomic diversity and spatial scale in designing studies of co-diversification.

Piglet nasal microbiota at weaning may influence the development of Glässer's disease during the rearing period.

PubMed

Correa-Fiz, Florencia; Fraile, Lorenzo; Aragon, Virginia

2016-05-26

The microbiota, the ensemble of microorganisms on a particular body site, has been extensively studied during the last few years, and demonstrated to influence the development of many diseases. However, these studies focused mainly on the human digestive system, while the populations in the respiratory tract have been poorly assessed, especially in pigs. The nasal mucosa of piglets is colonized by an array of bacteria, many of which are unknown. Among the early colonizers, Haemophilus parasuis also has clinical importance, since it is also the etiological agent of Glässer's disease. This disease produces economical losses in all the countries with pig production, and the factors influencing its development are not totally understood. Hence, the purpose of this work was to characterize the nasal microbiota composition of piglets, and its possible role in Glässer's disease development. Seven farms from Spain (4 with Glässer's disease and 3 control farms without any respiratory disease) and three farms from UK (all control farms) were studied. Ten piglets from each farm were sampled at 3-4 weeks of age before weaning. The total DNA extracted from nasal swabs was used to amplify the 16S RNA gene for sequencing in Illumina MiSeq. Sequencing data was quality filtered and analyzed using QIIME software. The diversity of the nasal microbiota was low in comparison with other body sites, showing a maximum number of operational taxonomic units (OTUs) per pig of 1,603, clustered in five phyla. Significant differences were found at various taxonomical levels, when the microbiota was compared regarding the farm health status. Healthy status was associated to higher species richness and diversity, and UK farms demonstrated the highest diversity. The composition of the nasal microbiota of healthy piglets was uncovered and different phylotypes were shown to be significantly altered in animals depending on the clinical status of the farm of origin. Several OTUs at genus level were identified over-represented in piglets from control farms, indicating their potential as probiotics. Although we provide relevant data, fully metagenomic approaches could give light on the genes and metabolic pathways involved in the roles of the nasal microbiota to prevent respiratory diseases.

The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates

PubMed Central

Gimmler, Anna; Korn, Ralf; de Vargas, Colomban; Audic, Stéphane; Stoeck, Thorsten

2016-01-01

Illumina reads of the SSU-rDNA-V9 region obtained from the circumglobal Tara Oceans expedition allow the investigation of protistan plankton diversity patterns on a global scale. We analyzed 6,137,350 V9-amplicons from ocean surface waters and the deep chlorophyll maximum, which were taxonomically assigned to the phylum Ciliophora. For open ocean samples global planktonic ciliate diversity is relatively low (ca. 1,300 observed and predicted ciliate OTUs). We found that 17% of all detected ciliate OTUs occurred in all oceanic regions under study. On average, local ciliate OTU richness represented 27% of the global ciliate OTU richness, indicating that a large proportion of ciliates is widely distributed. Yet, more than half of these OTUs shared <90% sequence similarity with reference sequences of described ciliates. While alpha-diversity measures (richness and exp(Shannon H)) are hardly affected by contemporary environmental conditions, species (OTU) turnover and community similarity (β-diversity) across taxonomic groups showed strong correlation to environmental parameters. Logistic regression models predicted significant correlations between the occurrence of specific ciliate genera and individual nutrients, the oceanic carbonate system and temperature. Planktonic ciliates displayed distinct vertical distributions relative to chlorophyll a. In contrast, the Tara Oceans dataset did not reveal any evidence that latitude is structuring ciliate communities. PMID:27633177

Latitudinal variation in nematode diversity and ecological roles along the Chinese coast.

PubMed

Wu, Jihua; Chen, Huili; Zhang, Youzheng

2016-11-01

To test changes in the phylogenetic relatedness, niche breadth, and life-history strategies of nematodes along a latitudinal gradient. Sixteen wetland locations along the Pacific coast of China, from 20°N to 40°N. Linear regression was used to relate nematode phylogenetic relatedness (average taxonomic distinctness (AvTD) and average phylogenetic diversity [AvPD]), life-history group (based on " c - p " colonizer-persister group classification), and dietary specificity (based on guild classification of feeding selectivity) to latitude. Wetland nematode taxonomic diversity (richness and Shannon diversity indices) decreased with increasing latitude along the Chinese coast. Phylogenetic diversity indices (AvTD and AvPD) significantly increased with increasing latitude. This indicates that at lower latitudes, species within the nematode community were more closely related. With increasing latitude, the nematode relative richness and abundance decreased for selective deposit feeders but increased for nonselective deposit feeders. The proportion of general opportunists decreased with increasing latitude, but persisters showed the opposite trend. The annual temperature range and the pH of sediments were more important than vegetation type in structuring nematode communities. Nematode niche breadth was narrower at lower latitudes with respect to dietary specificity. Higher latitudes with a more variable climate favor r over K life-history strategists. Nematode communities at lower latitudes contained more closely related species.

Disentangling the role of management, vegetation structure, and plant quality for Orthoptera in lowland meadows.

PubMed

Schirmel, Jens; Gerlach, Rebekka; Buhk, Constanze

2017-08-17

Seminatural grasslands provide habitats for various species and are important for biodiversity conservation. The understanding of the diverse responses of species and traits to different grassland management methods is therefore urgently needed. We disentangled the role of grassland management (fertilization and irrigation), vegetation structure (biomass, sward height) and plant quality (protein and fiber content) for Orthoptera communities in lowland hay meadows in Germany. We found vegetation structure to be the most important environmental category in explaining community structure of Orthoptera (species richness, total individuals, functional diversity and species composition). Intensively used meadows (fertilized, irrigated, high plant biomass) were characterized by assemblages with few species, low functional diversity, and low conservation value. Thereby, the relatively moderate fertilizer inputs in our study system of up to ∼75 kg N/ha/year reduced functional diversity of Orthoptera, while this negative effect of fertilization was not detectable when solely considering taxonomic aspects. We found strong support for a prominent role of plant quality in shaping Orthoptera communities and especially the trait composition. Our findings demonstrate the usefulness of considering both taxonomic and functional components (functional diversity) in biodiversity research and we suggest a stronger involvement of plant quality measures in Orthoptera studies. © 2017 Institute of Zoology, Chinese Academy of Sciences.

A Higher Level Classification of All Living Organisms

PubMed Central

Ruggiero, Michael A.; Gordon, Dennis P.; Orrell, Thomas M.; Bailly, Nicolas; Bourgoin, Thierry; Brusca, Richard C.; Cavalier-Smith, Thomas; Guiry, Michael D.; Kirk, Paul M.

2015-01-01

We present a consensus classification of life to embrace the more than 1.6 million species already provided by more than 3,000 taxonomists’ expert opinions in a unified and coherent, hierarchically ranked system known as the Catalogue of Life (CoL). The intent of this collaborative effort is to provide a hierarchical classification serving not only the needs of the CoL’s database providers but also the diverse public-domain user community, most of whom are familiar with the Linnaean conceptual system of ordering taxon relationships. This classification is neither phylogenetic nor evolutionary but instead represents a consensus view that accommodates taxonomic choices and practical compromises among diverse expert opinions, public usages, and conflicting evidence about the boundaries between taxa and the ranks of major taxa, including kingdoms. Certain key issues, some not fully resolved, are addressed in particular. Beyond its immediate use as a management tool for the CoL and ITIS (Integrated Taxonomic Information System), it is immediately valuable as a reference for taxonomic and biodiversity research, as a tool for societal communication, and as a classificatory “backbone” for biodiversity databases, museum collections, libraries, and textbooks. Such a modern comprehensive hierarchy has not previously existed at this level of specificity. PMID:25923521

Cryptic diversity in the Azorean beetle genus Tarphius Erichson, 1845 (Coleoptera: Zopheridae): An integrative taxonomic approach with description of four new species.

PubMed

Borges, Paulo A V; Amorim, Isabel R; Terzopoulou, Sofia; Rigal, François; Emerson, Brent C; Serrano, Artur R M

2017-02-23

Recent findings based on molecular data support the occurrence in the Azores of several independently evolving lineages of the beetle genus Tarphius Erichson, 1845 (Coleoptera: Zopheridae Solier, 1834) and higher species richness masked by cryptic diversity, needing formal taxonomic description. All Tarphius from the Azores are revised using an integrative taxonomic approach, using evidence from morphology, morphometrics and molecular data to delimit species. Our results reveal that Azorean Tarphius comprise at least five phyletic lineages, two of which share a similar morphology, despite being divergent at the molecular level. A total of four new species are described grouped into two complexes: i) two new species in the "complex tornvalli" with the new taxa Tarphius relictus sp. nov. (Terceira) and Tarphius furtadoi sp. nov. (São Jorge, Faial and Pico) and; ii) two new species in the "complex azoricus-wollastoni-depressus" with the new taxa Tarphius gabrielae sp. nov. (Pico) and Tarphius floresensis sp. nov. (Flores). Descriptions, photographs of holotypes and morphological details, and remarks on diagnostic features comparing similar species are presented. Additional information on the distribution and conservation status of the 12 described species in the archipelago is also provided.

Taxonomic and functional patterns of macrobenthic communities on a high-Arctic shelf: A case study from the Laptev Sea

NASA Astrophysics Data System (ADS)

Kokarev, V. N.; Vedenin, A. A.; Basin, A. B.; Azovsky, A. I.

2017-11-01

The studies of functional structure of high-Arctic Ecosystems are scarce. We used data on benthic macrofauna from 500-km latitudinal transect in the eastern Laptev Sea, from the Lena delta to the continental shelf break, to describe spatial patterns in species composition, taxonomic and functional structure in relation to environmental factors. Both taxonomy-based approach and Biological Trait analysis yielded similar results and showed general depth-related gradient in benthic diversity and composition. This congruence between taxonomical and functional dimensions of community organization suggests that the same environmental factors (primarily riverine input and regime of sedimentation) have similar effect on both community structure and functioning. BTA also revealed a distinct functional structure of stations situated at the Eastern Lena valley, with dominance of motile, burrowing sub-surface deposit-feeders and absence of sedentary tube-dwelling forms. The overall spatial distribution of benthic assemblages corresponds well to that described there in preceding decades, evidencing the long-term stability of bottom ecosystem. Strong linear relationship between species and traits diversity, however, indicates low functional redundancy, which potentially makes the ecosystem susceptible to a species loss or structural shifts.

Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing

PubMed Central

Mehetre, Gajanan T.; Paranjpe, Aditi; Dastager, Syed G.

2016-01-01

Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche. PMID:26950332

Structural and functional responses of plant communities to climate change-mediated alterations in the hydrology of riparian areas in temperate Europe.

PubMed

Baattrup-Pedersen, Annette; Garssen, Annemarie; Göthe, Emma; Hoffmann, Carl Christian; Oddershede, Andrea; Riis, Tenna; van Bodegom, Peter M; Larsen, Søren E; Soons, Merel

2018-04-01

The hydrology of riparian areas changes rapidly these years because of climate change-mediated alterations in precipitation patterns. In this study, we used a large-scale in situ experimental approach to explore effects of drought and flooding on plant taxonomic diversity and functional trait composition in riparian areas in temperate Europe. We found significant effects of flooding and drought in all study areas, the effects being most pronounced under flooded conditions. In near-stream areas, taxonomic diversity initially declined in response to both drought and flooding (although not significantly so in all years) and remained stable under drought conditions, whereas the decline continued under flooded conditions. For most traits, we found clear indications that the functional diversity also declined under flooded conditions, particularly in near-stream areas, indicating that fewer strategies succeeded under flooded conditions. Consistent changes in community mean trait values were also identified, but fewer than expected. This can have several, not mutually exclusive, explanations. First, different adaptive strategies may coexist in a community. Second, intraspecific variability was not considered for any of the traits. For example, many species can elongate shoots and petioles that enable them to survive shallow, prolonged flooding but such abilities will not be captured when applying mean trait values. Third, we only followed the communities for 3 years. Flooding excludes species intolerant of the altered hydrology, whereas the establishment of new species relies on time-dependent processes, for instance the dispersal and establishment of species within the areas. We expect that altered precipitation patterns will have profound consequences for riparian vegetation in temperate Europe. Riparian areas will experience loss of taxonomic and functional diversity and, over time, possibly also alterations in community trait responses that may have cascading effects on ecosystem functioning.

Sloth hair as a novel source of fungi with potent anti-parasitic, anti-cancer and anti-bacterial bioactivity.

PubMed

Higginbotham, Sarah; Wong, Weng Ruh; Linington, Roger G; Spadafora, Carmenza; Iturrado, Liliana; Arnold, A Elizabeth

2014-01-01

The extraordinary biological diversity of tropical forests harbors a rich chemical diversity with enormous potential as a source of novel bioactive compounds. Of particular interest are new environments for microbial discovery. Sloths--arboreal mammals commonly found in the lowland forests of Panama--carry a wide variety of micro- and macro-organisms on their coarse outer hair. Here we report for the first time the isolation of diverse and bioactive strains of fungi from sloth hair, and their taxonomic placement. Eighty-four isolates of fungi were obtained in culture from the surface of hair that was collected from living three-toed sloths (Bradypus variegatus, Bradypodidae) in Soberanía National Park, Republic of Panama. Phylogenetic analyses revealed a diverse group of Ascomycota belonging to 28 distinct operational taxonomic units (OTUs), several of which are divergent from previously known taxa. Seventy-four isolates were cultivated in liquid broth and crude extracts were tested for bioactivity in vitro. We found a broad range of activities against strains of the parasites that cause malaria (Plasmodium falciparum) and Chagas disease (Trypanosoma cruzi), and against the human breast cancer cell line MCF-7. Fifty fungal extracts were tested for antibacterial activity in a new antibiotic profile screen called BioMAP; of these, 20 were active against at least one bacterial strain, and one had an unusual pattern of bioactivity against Gram-negative bacteria that suggests a potentially new mode of action. Together our results reveal the importance of exploring novel environments for bioactive fungi, and demonstrate for the first time the taxonomic composition and bioactivity of fungi from sloth hair.

Sloth Hair as a Novel Source of Fungi with Potent Anti-Parasitic, Anti-Cancer and Anti-Bacterial Bioactivity

PubMed Central

Higginbotham, Sarah; Wong, Weng Ruh; Linington, Roger G.; Spadafora, Carmenza; Iturrado, Liliana; Arnold, A. Elizabeth

2014-01-01

The extraordinary biological diversity of tropical forests harbors a rich chemical diversity with enormous potential as a source of novel bioactive compounds. Of particular interest are new environments for microbial discovery. Sloths – arboreal mammals commonly found in the lowland forests of Panama – carry a wide variety of micro- and macro-organisms on their coarse outer hair. Here we report for the first time the isolation of diverse and bioactive strains of fungi from sloth hair, and their taxonomic placement. Eighty-four isolates of fungi were obtained in culture from the surface of hair that was collected from living three-toed sloths (Bradypus variegatus, Bradypodidae) in Soberanía National Park, Republic of Panama. Phylogenetic analyses revealed a diverse group of Ascomycota belonging to 28 distinct operational taxonomic units (OTUs), several of which are divergent from previously known taxa. Seventy-four isolates were cultivated in liquid broth and crude extracts were tested for bioactivity in vitro. We found a broad range of activities against strains of the parasites that cause malaria (Plasmodium falciparum) and Chagas disease (Trypanosoma cruzi), and against the human breast cancer cell line MCF-7. Fifty fungal extracts were tested for antibacterial activity in a new antibiotic profile screen called BioMAP; of these, 20 were active against at least one bacterial strain, and one had an unusual pattern of bioactivity against Gram-negative bacteria that suggests a potentially new mode of action. Together our results reveal the importance of exploring novel environments for bioactive fungi, and demonstrate for the first time the taxonomic composition and bioactivity of fungi from sloth hair. PMID:24454729

Taxonomic and phylogenetic diversity of vascular plants at Ma'anling volcano urban park in tropical Haikou, China: Reponses to soil properties.

PubMed

Cheng, Xia-Lan; Yuan, Lang-Xing; Nizamani, Mir Mohammad; Zhu, Zhi-Xin; Friedman, Cynthia Ross; Wang, Hua-Feng

2018-01-01

Anthropogenic processes and socio-economic factors play important roles in shaping plant diversity in urban parks. To investigate how plant diversity of Ma' anling urban volcano park in Hainan Province, China respond to these factors, we carried out a field investigation on the taxonomic and phylogenetic diversity of vascular plants and soil properties in this area. We found 284 species of vascular plants belonging to 88 families and 241 genera, which included 194 native species, 23 invasive species, 31 naturalized species, 40 cultivars, and 4 rare / endangered plant species. Tree composition and richness significantly varied between different vegetation formations (plantation, secondary forest, and abandoned land). Plant species richness and community composition were significantly affected by elevation (El), soil water content (WC), total soil nitrogen (TN) and soil organic matter (SOM). There were significant diversity differences between plantations and abandoned lands, but not between the plantations and secondary forests. The flora in the study site was tropical in nature, characterized by pantropic distributions. Compared to adjacent areas, floristic composition in the study site was most similar to that of Guangdong, followed by that of Vietnam. Our study revealed the diversity patterns of volcanic plants and provided the basis for future planning of plant conservation, such as preserving plant species, maintaining plant habitats, and coordinating plant management in this region.

Environmental and taxonomic bacterial diversity of anaerobic uranium(IV) bio-oxidation.

PubMed

Weber, Karrie A; Thrash, J Cameron; Van Trump, J Ian; Achenbach, Laurie A; Coates, John D

2011-07-01

Microorganisms in diverse terrestrial surface and subsurface environments can anaerobically catalyze the oxidative dissolution of uraninite. While a limited quantity (∼5 to 12 μmol liter(-1)) of uranium is oxidatively dissolved in pure culture studies, the metabolism is coupled to electron transport, providing the potential of uraninite to support indigenous microbial populations and to solubilize uranium.

Metagenomic Evaluation of Bacterial and Archaeal Diversity in the Geothermal Hot Springs of Manikaran, India

PubMed Central

Pathak, Ashish; Green, Stefan J.; Joshi, Amit; Chauhan, Ashvini

2015-01-01

Bacterial and archaeal diversity in geothermal spring water were investigated using 16S rRNA gene amplicon metagenomic sequencing. This revealed the dominance of Firmicutes, Aquificae, and the Deinococcus-Thermus group in this thermophilic environment. A number of sequences remained taxonomically unresolved, indicating the presence of potentially novel microbes in this unique habitat. PMID:25700403

Microbial responses to southward and northward Cambisol soil transplant

DOE PAGES

Wang, Mengmeng; Liu, Shanshan; Wang, Feng; ...

2015-10-26

We report that soil transplant serves as a proxy to simulate climate changes. Recently, we have shown that southward transplant of black soil and northward transplant of red soil altered soil microbial communities and biogeochemical variables. However, fundamental differences in soil types have prevented direct comparison between southward and northward transplants. To tackle it, herein we report an analysis of microbial communities of Cambisol soil in an agriculture field after 4 years of adaptation to southward and northward soil transplants over large transects. Analysis of bare fallow soils revealed concurrent increase in microbial functional diversity and coarse-scale taxonomic diversity atmore » both transplanted sites, as detected by GeoChip 3.0 and DGGE, respectively. Furthermore, a correlation between microbial functional diversity and taxonomic diversity was detected, which was masked in maize cropped soils. Mean annual temperature, soil moisture, and nitrate (NO 3¯-N) showed strong correlations with microbial communities. In addition, abundances of ammonium-oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO 3¯-N contents, suggesting that microbial responses to soil transplant could alter microbe-mediated biogeochemical cycle at the ecosystem level.« less

Utility of DNA barcoding for rapid and accurate assessment of bat diversity in Malaysia in the absence of formally described species.

PubMed

Wilson, J-J; Sing, K-W; Halim, M R A; Ramli, R; Hashim, R; Sofian-Azirun, M

2014-02-19

Bats are important flagship species for biodiversity research; however, diversity in Southeast Asia is considerably underestimated in the current checklists and field guides. Incorporation of DNA barcoding into surveys has revealed numerous species-level taxa overlooked by conventional methods. Inclusion of these taxa in inventories provides a more informative record of diversity, but is problematic as these species lack formal description. We investigated how frequently documented, but undescribed, bat taxa are encountered in Peninsular Malaysia. We discuss whether a barcode library provides a means of recognizing and recording these taxa across biodiversity inventories. Tissue was sampled from bats trapped at Pasir Raja, Dungun Terengganu, Peninsular Malaysia. The DNA was extracted and the COI barcode region amplified and sequenced. We identified 9 species-level taxa within our samples, based on analysis of the DNA barcodes. Six specimens matched to four previously documented taxa considered candidate species but currently lacking formal taxonomic status. This study confirms the high diversity of bats within Peninsular Malaysia (9 species in 13 samples) and demonstrates how DNA barcoding allows for inventory and documentation of known taxa lacking formal taxonomic status.

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

PubMed Central

Tedersoo, Leho; Bahram, Mohammad; Cajthaml, Tomáš; Põlme, Sergei; Hiiesalu, Indrek; Anslan, Sten; Harend, Helery; Buegger, Franz; Pritsch, Karin; Koricheva, Julia; Abarenkov, Kessy

2016-01-01

Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se. PMID:26172210

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent.

PubMed

Tedersoo, Leho; Bahram, Mohammad; Cajthaml, Tomáš; Põlme, Sergei; Hiiesalu, Indrek; Anslan, Sten; Harend, Helery; Buegger, Franz; Pritsch, Karin; Koricheva, Julia; Abarenkov, Kessy

2016-02-01

Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se.

Size-fractionated diversity of eukaryotic microbial communities in the Eastern Tropical North Pacific oxygen minimum zone.

PubMed

Duret, Manon T; Pachiadaki, Maria G; Stewart, Frank J; Sarode, Neha; Christaki, Urania; Monchy, Sébastien; Srivastava, Ankita; Edgcomb, Virginia P

2015-05-01

Oxygen minimum zones (OMZs) caused by water column stratification appear to expand in parts of the world's ocean, with consequences for marine biogeochemical cycles. OMZ formation is often fueled by high surface primary production, and sinking organic particles can be hotspots of interactions and activity within microbial communities. This study investigated the diversity of OMZ protist communities in two biomass size fractions (>30 and 30-1.6 μm filters) from the world's largest permanent OMZ in the Eastern Tropical North Pacific. Diversity was quantified via Illumina MiSeq sequencing of V4 region of 18S SSU rRNA genes in samples spanning oxygen gradients at two stations. Alveolata and Rhizaria dominated the two size fractions at both sites along the oxygen gradient. Community composition at finer taxonomic levels was partially shaped by oxygen concentration, as communities associated with versus anoxic waters shared only ∼32% of operational taxonomic unit (OTU) (97% sequence identity) composition. Overall, only 9.7% of total OTUs were recovered at both stations and under all oxygen conditions sampled, implying structuring of the eukaryotic community in this area. Size-fractionated communities exhibited different taxonomical features (e.g. Syndiniales Group I in the 1.6-30 μm fraction) that could be explained by the microniches created on the surface-originated sinking particles. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers

USDA-ARS?s Scientific Manuscript database

Carrot is one of the most economically important vegetables worldwide, however, genetic and genomic resources supporting carrot breeding remain limited. We developed a Diversity Arrays Technology (DArT) platform for wild and cultivated carrot and used it to investigate genetic diversity and to devel...

Are hotspots always hotspots? The relationship between diversity, resource and ecosystem functions in the Arctic.

PubMed

Link, Heike; Piepenburg, Dieter; Archambault, Philippe

2013-01-01

The diversity-ecosystem function relationship is an important topic in ecology but has not received much attention in Arctic environments, and has rarely been tested for its stability in time. We studied the temporal variability of benthic ecosystem functioning at hotspots (sites with high benthic boundary fluxes) and coldspots (sites with lower fluxes) across two years in the Canadian Arctic. Benthic remineralisation function was measured as fluxes of oxygen, silicic acid, phosphate, nitrate and nitrite at the sediment-water interface. In addition we determined sediment pigment concentration and taxonomic and functional macrobenthic diversity. To separate temporal from spatial variability, we sampled the same nine sites from the Mackenzie Shelf to Baffin Bay during the same season (summer or fall) in 2008 and 2009. We observed that temporal variability of benthic remineralisation function at hotspots is higher than at coldspots and that taxonomic and functional macrobenthic diversity did not change significantly between years. Temporal variability of food availability (i.e., sediment surface pigment concentration) seemed higher at coldspot than at hotspot areas. Sediment chlorophyll a (Chl a) concentration, taxonomic richness, total abundance, water depth and abundance of the largest gallery-burrowing polychaete Lumbrineristetraura together explained 42% of the total variation in fluxes. Food supply proxies (i.e., sediment Chl a and depth) split hot- from coldspot stations and explained variation on the axis of temporal variability, and macrofaunal community parameters explained variation mostly along the axis separating eastern from western sites with hot- or coldspot regimes. We conclude that variability in benthic remineralisation function, food supply and diversity will react to climate change on different time scales, and that their interactive effects may hide the detection of progressive change, particularly at hotspots. Time-series of benthic functions and its related parameters should be conducted at both hot- and coldspots to produce reliable predictive models.

Next-Generation Sequencing Reveals Significant Bacterial Diversity of Botrytized Wine

PubMed Central

Bokulich, Nicholas A.; Joseph, C. M. Lucy; Allen, Greg; Benson, Andrew K.; Mills, David A.

2012-01-01

While wine fermentation has long been known to involve complex microbial communities, the composition and role of bacteria other than a select set of lactic acid bacteria (LAB) has often been assumed either negligible or detrimental. This study served as a pilot study for using barcoded amplicon next-generation sequencing to profile bacterial community structure in wines and grape musts, comparing the taxonomic depth achieved by sequencing two different domains of prokaryotic 16S rDNA (V4 and V5). This study was designed to serve two goals: 1) to empirically determine the most taxonomically informative 16S rDNA target region for barcoded amplicon sequencing of wine, comparing V4 and V5 domains of bacterial 16S rDNA to terminal restriction fragment length polymorphism (TRFLP) of LAB communities; and 2) to explore the bacterial communities of wine fermentation to better understand the biodiversity of wine at a depth previously unattainable using other techniques. Analysis of amplicons from the V4 and V5 provided similar views of the bacterial communities of botrytized wine fermentations, revealing a broad diversity of low-abundance taxa not traditionally associated with wine, as well as atypical LAB communities initially detected by TRFLP. The V4 domain was determined as the more suitable read for wine ecology studies, as it provided greater taxonomic depth for profiling LAB communities. In addition, targeted enrichment was used to isolate two species of Alphaproteobacteria from a finished fermentation. Significant differences in diversity between inoculated and uninoculated samples suggest that Saccharomyces inoculation exerts selective pressure on bacterial diversity in these fermentations, most notably suppressing abundance of acetic acid bacteria. These results determine the bacterial diversity of botrytized wines to be far higher than previously realized, providing further insight into the fermentation dynamics of these wines, and demonstrate the utility of next-generation sequencing for wine ecology studies. PMID:22563494

Independent colonization and extensive cryptic speciation of freshwater amphipods in the isolated groundwater springs of Australia's Great Artesian Basin.

PubMed

Murphy, Nicholas P; Adams, Mark; Austin, Andrew D

2009-01-01

The groundwater-dependent springs of the Great Artesian Basin (GAB) in arid inland Australia represent a unique and threatened ecosystem. These incredibly isolated springs support a diverse array of endemic flora and fauna. One of the common faunal groups in the GAB springs is the freshwater amphipods of the family Chiltoniidae. The morphological conservatism and taxonomic uncertainty associated with these amphipods has ensured their true biodiversity, phylogeographical history and evolutionary affinities have remained unknown. We have used mitochondrial DNA and allozyme data to unravel a complicated history of isolation, extinction and dispersal among spring amphipod populations across the GAB. The results provide evidence for multiple independent colonizations in the GAB springs, particularly within the Lake Eyre group of springs. The inclusion of a group of Western Australian (WA) stygobitic amphipods from populations up to 1500 km away found surprising evidence for a shared evolutionary history between stygobitic and GAB spring amphipods. Approximate dating of the diversity found between major clades suggests the majority of lineages originated in the late Miocene, around the time of the aridification of inland Australia. The large number of independent lineages and the close connection between GAB spring and WA stygobitic amphipods suggest that a significantly rich amphipod fauna existed in the much wetter environment that once existed in inland Australia. The results also provide evidence for a gross underestimation of the species diversity within the springs, with 12 putative species identified, a conclusion with significant implications for the ongoing conservation of the GAB springs.

How could discharge management affect Florida spring fish assemblage structure?

PubMed

Work, Kirsten; Codner, Keneil; Gibbs, Melissa

2017-08-01

Freshwater bodies are increasingly affected by reductions in water quantity and quality and by invasions of exotic species. To protect water quantity and maintain the ecological integrity of many water bodies in central Florida, a program of adopting Minimum Flows and Levels (MFLs) has begun for both lentic and lotic waters. The purpose of this study was to determine whether there were relationships between discharge and stage, water quality, and biological parameters for Volusia Blue Spring, a first magnitude spring (discharge > 380,000 m 3 day -1 or 100 mgd) for which an MFL program was adopted in 2006. Over the course of fourteen years, we assessed fish density and diversity weekly, monthly, or seasonally with seine and snorkel counts. We evaluated annual changes in the assemblages for relationships with water quantity and quality. Low discharge and dissolved oxygen combined with high stage and conductivity produced a fish population with a lower density and diversity in 2014 than in previous years. Densities of fish taxonomic/functional groups also were low in 2014 and measures of water quantity were significant predictors of fish assemblage structure. As a result of the strong relationships between variation in discharge and an array of chemical and biological characteristics of the spring, we conclude that maintaining the historical discharge rate is important for preserving the ecological integrity of Volusia Blue Spring. Copyright © 2017 Elsevier Ltd. All rights reserved.

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.

PubMed

Jiang, Yue; Xiong, Xuejian; Danska, Jayne; Parkinson, John

2016-01-12

Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composition and active biochemical functions of a complex microbial community. However, the lack of established reference genomes, computational tools and pipelines make analysis and interpretation of these datasets challenging. Systematic studies that compare data across microbiomes are needed to demonstrate the ability of such pipelines to deliver biologically meaningful insights on microbiome function. Here, we apply a standardized analytical pipeline to perform a comparative analysis of metatranscriptomic data from diverse microbial communities derived from mouse large intestine, cow rumen, kimchi culture, deep-sea thermal vent and permafrost. Sequence similarity searches allowed annotation of 19 to 76% of putative messenger RNA (mRNA) reads, with the highest frequency in the kimchi dataset due to its relatively low complexity and availability of closely related reference genomes. Metatranscriptomic datasets exhibited distinct taxonomic and functional signatures. From a metabolic perspective, we identified a common core of enzymes involved in amino acid, energy and nucleotide metabolism and also identified microbiome-specific pathways such as phosphonate metabolism (deep sea) and glycan degradation pathways (cow rumen). Integrating taxonomic and functional annotations within a novel visualization framework revealed the contribution of different taxa to metabolic pathways, allowing the identification of taxa that contribute unique functions. The application of a single, standard pipeline confirms that the rich taxonomic and functional diversity observed across microbiomes is not simply an artefact of different analysis pipelines but instead reflects distinct environmental influences. At the same time, our findings show how microbiome complexity and availability of reference genomes can impact comprehensive annotation of metatranscriptomes. Consequently, beyond the application of standardized pipelines, additional caution must be taken when interpreting their output and performing downstream, microbiome-specific, analyses. The pipeline used in these analyses along with a tutorial has been made freely available for download from our project website: http://www.compsysbio.org/microbiome .

Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing.

PubMed

Mehetre, Gajanan T; Paranjpe, Aditi; Dastager, Syed G; Dharne, Mahesh S

2016-02-25

Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche. Copyright © 2016 Mehetre et al.

Beta

USDA-ARS?s Scientific Manuscript database

This chapter covers the use of wild beets in sugar beet improvement, including the basic botany of the species, its distribution; geographical locations of genetic diversity; morphology; cytology and karyotype; genome size; taxonomic position; agricultural status (model plant/weeds/invasive species/...

A phylogenetic perspective on species diversity, β-diversity and biogeography for the microbial world.

PubMed

Barberán, Albert; Casamayor, Emilio O

2014-12-01

There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high-altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High-altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies. © 2014 John Wiley & Sons Ltd.

Convergent Diversity and Trait Composition in Temporary Streams and Ponds

DTIC Science & Technology

2016-05-19

of aquatic invertebrate diversity. We used invertebrate assemblage data from seven arid- land streams in southeastern Arizona, United States...collected over 2 yr and nine temperate woodland ponds in Ontario, Canada collected over 2 yr. Our results showed that although invertebrate assemblages...from streams and ponds differ taxonomically, hydroperi- od had similar influence on invertebrate trait structure regardless of biogeographic and habitat

The diversity and biogeography of the Coleoptera of Churchill: insights from DNA barcoding

PubMed Central

2013-01-01

Background Coleoptera is the most diverse order of insects (>300,000 described species), but its richness diminishes at increasing latitudes (e.g., ca. 7400 species recorded in Canada), particularly of phytophagous and detritivorous species. However, incomplete sampling of northern habitats and a lack of taxonomic study of some families limits our understanding of biodiversity patterns in the Coleoptera. We conducted an intensive biodiversity survey from 2006–2010 at Churchill, Manitoba, Canada in order to quantify beetle species diversity in this model region, and to prepare a barcode library of beetles for sub-arctic biodiversity and ecological research. We employed DNA barcoding to provide estimates of provisional species diversity, including for families currently lacking taxonomic expertise, and to examine the guild structure, habitat distribution, and biogeography of beetles in the Churchill region. Results We obtained DNA barcodes from 3203 specimens representing 302 species or provisional species (the latter quantitatively defined on the basis of Molecular Operational Taxonomic Units, MOTUs) in 31 families of Coleoptera. Of the 184 taxa identified to the level of a Linnaean species name, 170 (92.4%) corresponded to a single MOTU, four (2.2%) represented closely related sibling species pairs within a single MOTU, and ten (5.4%) were divided into two or more MOTUs suggestive of cryptic species. The most diverse families were the Dytiscidae (63 spp.), Staphylinidae (54 spp.), and Carabidae (52 spp.), although the accumulation curve for Staphylinidae suggests that considerable additional diversity remains to be sampled in this family. Most of the species present are predatory, with phytophagous, mycophagous, and saprophagous guilds being represented by fewer species. Most named species of Carabidae and Dytiscidae showed a significant bias toward open habitats (wet or dry). Forest habitats, particularly dry boreal forest, although limited in extent in the region, were undersampled. Conclusions We present an updated species list for this region as well as a species-level DNA barcode reference library. This resource will facilitate future work, such as biomonitoring and the study of the ecology and distribution of larvae. PMID:24164967

Mosquito Species (Diptera: Culicidae) Diversity from Ovitraps in a Mesoamerican Tropical Rainforest.

PubMed

Chaverri, Luis Guillermo; Dillenbeck, Claire; Lewis, Devon; Rivera, Cindy; Romero, Luis Mario; Chaves, Luis Fernando

2018-05-04

Mosquito sampling using efficient traps that can assess species diversity and/or presence of dominant vectors is important for understanding the entomological risk of mosquito-borne disease transmission. Here, we present results from a survey of mosquito species sampled with ovitraps in a neotropical rainforest of Costa Rica. We found the method to be an efficient sampling tool. With a total sampling effort of 29 traps, we collected 157 fourth-instar larvae and three pupae belonging to eight mosquito taxonomic units (seven species and individuals from a homogenous taxonomic unit identified to the genus level). In our samples, we found two medically important species, Sabethes chloropterus (Humboldt) and Trichoprosopon digitatum (Rondani). The former is a proven vector of Yellow Fever in sylvatic environments and the later has been found infected with several arboviruses. We also found that mosquito species abundance and diversity increased with canopy cover and in environments where leaf litter dominated the ground cover. Finally, our results suggest that ovitraps have a great potential for systematic sampling in longitudinal and cross-sectional ecological "semi-field" studies in neotropical settings.

Development of archetypes for non-ranking classification and comparison of European National Health Technology Assessment systems.

PubMed

Allen, Nicola; Pichler, Franz; Wang, Tina; Patel, Sundip; Salek, Sam

2013-12-01

European countries are increasingly utilising health technology assessment (HTA) to inform reimbursement decision-making. However, the current European HTA environment is very diverse, and projects are already underway to initiate a more efficient and aligned HTA practice within Europe. This study aims to identify a non-ranking method for classifying the diversity of European HTA agencies process and the organisational architecture of the national regulatory review to reimbursement systems. Using a previously developed mapping methodology, this research created process maps to describe national processes for regulatory review to reimbursement for 33 European jurisdictions. These process maps enabled the creation of 2 HTA taxonomic sets. The confluence of the two taxonomic sets was subsequently cross-referenced to identify 10 HTA archetype groups. HTA is a young, rapidly evolving field and it can be argued that optimal practices for performing HTA are yet to emerge. Therefore, a non-ranking classification approach could objectively characterise and compare the diversity observed in the current European HTA environment. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Skeletal Morphology of Opius dissitus and Biosteres carbonarius (Hymenoptera: Braconidae), with a Discussion of Terminology

PubMed Central

Karlsson, Dave; Ronquist, Fredrik

2012-01-01

The Braconidae, a family of parasitic wasps, constitute a major taxonomic challenge with an estimated diversity of 40,000 to 120,000 species worldwide, only 18,000 of which have been described to date. The skeletal morphology of braconids is still not adequately understood and the terminology is partly idiosyncratic, despite the fact that anatomical features form the basis for most taxonomic work on the group. To help address this problem, we describe the external skeletal morphology of Opius dissitus Muesebeck 1963 and Biosteres carbonarius Nees 1834, two diverse representatives of one of the least known and most diverse braconid subfamilies, the Opiinae. We review the terminology used to describe skeletal features in the Ichneumonoidea in general and the Opiinae in particular, and identify a list of recommend terms, which are linked to the online Hymenoptera Anatomy Ontology. The morphology of the studied species is illustrated with SEM-micrographs, photos and line drawings. Based on the examined species, we discuss intraspecific and interspecific morphological variation in the Opiinae and point out character complexes that merit further study. PMID:22558068

Skeletal morphology of Opius dissitus and Biosteres carbonarius (Hymenoptera: Braconidae), with a discussion of terminology.

PubMed

Karlsson, Dave; Ronquist, Fredrik

2012-01-01

The Braconidae, a family of parasitic wasps, constitute a major taxonomic challenge with an estimated diversity of 40,000 to 120,000 species worldwide, only 18,000 of which have been described to date. The skeletal morphology of braconids is still not adequately understood and the terminology is partly idiosyncratic, despite the fact that anatomical features form the basis for most taxonomic work on the group. To help address this problem, we describe the external skeletal morphology of Opius dissitus Muesebeck 1963 and Biosteres carbonarius Nees 1834, two diverse representatives of one of the least known and most diverse braconid subfamilies, the Opiinae. We review the terminology used to describe skeletal features in the Ichneumonoidea in general and the Opiinae in particular, and identify a list of recommend terms, which are linked to the online Hymenoptera Anatomy Ontology. The morphology of the studied species is illustrated with SEM-micrographs, photos and line drawings. Based on the examined species, we discuss intraspecific and interspecific morphological variation in the Opiinae and point out character complexes that merit further study.

Characterization of Bacterial Communities Associated with the Tyrian Purple Producing Gland in a Marine Gastropod

PubMed Central

Ngangbam, Ajit Kumar; Baten, Abdul; Waters, Daniel L. E.; Whalan, Steve; Benkendorff, Kirsten

2015-01-01

Dicathais orbita is a marine mollusc recognised for the production of anticancer compounds that are precursors to Tyrian purple. This study aimed to assess the diversity and identity of bacteria associated with the Tyrian purple producing hypobranchial gland, in comparison with foot tissue, using a high-throughput sequencing approach. Taxonomic and phylogenetic analysis of variable region V1-V3 of 16S rRNA bacterial gene amplicons in QIIME and MEGAN were carried out. This analysis revealed a highly diverse bacterial assemblage associated with the hypobranchial gland and foot tissues of D. orbita. The dominant bacterial phylum in the 16S rRNA bacterial profiling data set was Proteobacteria followed by Bacteroidetes, Tenericutes and Spirochaetes. In comparison to the foot, the hypobranchial gland had significantly lower bacterial diversity and a different community composition, based on taxonomic assignment at the genus level. A higher abundance of indole producing Vibrio spp. and the presence of bacteria with brominating capabilities in the hypobranchial gland suggest bacteria have a potential role in biosynthesis of Tyrian purple in D. orbita. PMID:26488885

Checklist of the flower flies of Ecuador (Diptera, Syrphidae).

PubMed

Marín-Armijos, Diego; Quezada-Ríos, Noelia; Soto-Armijos, Carolina; Mengual, Ximo

2017-01-01

Syrphidae is one of the most speciose families of true flies, with more than 6,100 described species and worldwide distribution. They are important for humans acting as crucial pollinators, biological control agents, decomposers, and bioindicators. One third of its diversity is found in the Neotropical Region, but the taxonomic knowledge for this region is incomplete. Thus, taxonomic revisions and species checklists of Syrphidae in the Neotropics are the highest priority for biodiversity studies. Therefore, we present the first checklist of Syrphidae for Ecuador based on literature records, and provide as well the original reference for the first time species citations for the country. A total of 201 species were recorded for Ecuador, with more than 600 records from 24 provinces and 237 localities. Tungurahua, Pastaza, and Galápagos were the best sampled provinces. Although the reported Ecuadorian syrphid fauna only comprises 11.2 % of the described Neotropical species, Ecuador has the third highest flower fly diversity density after Costa Rica and Suriname. These data indicate the high species diversity for this country in such small geographic area.

Checklist of the flower flies of Ecuador (Diptera, Syrphidae)

PubMed Central

Marín-Armijos, Diego; Quezada-Ríos, Noelia; Soto-Armijos, Carolina; Mengual, Ximo

2017-01-01

Abstract Syrphidae is one of the most speciose families of true flies, with more than 6,100 described species and worldwide distribution. They are important for humans acting as crucial pollinators, biological control agents, decomposers, and bioindicators. One third of its diversity is found in the Neotropical Region, but the taxonomic knowledge for this region is incomplete. Thus, taxonomic revisions and species checklists of Syrphidae in the Neotropics are the highest priority for biodiversity studies. Therefore, we present the first checklist of Syrphidae for Ecuador based on literature records, and provide as well the original reference for the first time species citations for the country. A total of 201 species were recorded for Ecuador, with more than 600 records from 24 provinces and 237 localities. Tungurahua, Pastaza, and Galápagos were the best sampled provinces. Although the reported Ecuadorian syrphid fauna only comprises 11.2 % of the described Neotropical species, Ecuador has the third highest flower fly diversity density after Costa Rica and Suriname. These data indicate the high species diversity for this country in such small geographic area. PMID:29200924

Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats

NASA Astrophysics Data System (ADS)

Comeau, André M.; Vincent, Warwick F.; Bernier, Louis; Lovejoy, Connie

2016-07-01

In aquatic environments, fungal communities remain little studied despite their taxonomic and functional diversity. To extend the ecological coverage of this group, we conducted an in-depth analysis of fungal sequences within our collection of 3.6 million V4 18S rRNA pyrosequences originating from 319 individual marine (including sea-ice) and freshwater samples from libraries generated within diverse projects studying Arctic and temperate biomes in the past decade. Among the ~1.7 million post-filtered reads of highest taxonomic and phylogenetic quality, 23,263 fungal sequences were identified. The overall mean proportion was 1.35%, but with large variability; for example, from 0.01 to 59% of total sequences for Arctic seawater samples. Almost all sample types were dominated by Chytridiomycota-like sequences, followed by moderate-to-minor contributions of Ascomycota, Cryptomycota and Basidiomycota. Species and/or strain richness was high, with many novel sequences and high niche separation. The affinity of the most common reads to phytoplankton parasites suggests that aquatic fungi deserve renewed attention for their role in algal succession and carbon cycling.

Taxonomic and nontaxonomic responses to ecological changes in an urban lowland stream through the use of Chironomidae (Diptera) larvae.

PubMed

Cortelezzi, A; Paggi, A C; Rodríguez, M; Capítulo, A Rodrigues

2011-03-01

Biotic descriptors--both taxonomic (diversity indices, species richness, and indicator species) and nontaxonomic (biomass, oxygen consumption/production, and anatomical deformities)--are useful tools for measuring a stream's ecological condition. Nontaxonomic parameters detect critical effects not reflected taxonomically. We analyzed changes in Chironomidae populations as taxonomic parameters and mentum deformities as a nontaxonomic parameter for evaluating a South-American-plains stream (Argentina). We performed samplings seasonally (March, June, September, and December; 2005) and physical and chemical measurements at three sampling sites of the stream (DC1 at river source, through DC3 downstream). The specimens collected in sediment and vegetation were analyzed to investigate mouth deformities in Chironomidae larvae. We identified a total of 9 taxa from Chironomidae and Orthocladiinae subfamilies. Shannon's diversity index for Chironomidae decreased from 1.6 bits ind⁻¹ (DC1) to 0.3 bits ind⁻¹ (DC3). The total density of the Chironomidae exhibited a great increase in abundance at site DC3, especially that of Chironomus calligraphus. Chironomidae taxonomic composition also changed among the three sites despite their spatial proximity: C. calligraphus, Goeldichironomus holoprasinus, Parachironomus longistilus, and Polypedilum were present at all three; Corynoneura and Paratanytarsu at DC1 only; Cricotopus at DC1 and DC3; Apedilum elachistus notably at DC2 and DC3; and Parametriocnemus only at DC2. C. calligraphus individuals from DC1 showed no mentum deformities; only 2 from DC2 exhibited mouth-structure alterations; while specimens from DC3 presented the most abnormalities, especially during autumn and late winter. Type-II deformities (supernumerary teeth and gaps) were the most common. Anatomical deformities are sublethal effects representing an early alert to chemically caused environmental degradation. Mentum deformities in benthic-Chironomidae larvae constitute an effective biological-surveillance tool for detecting adverse conditions in sediments and evaluating sediment-quality-criteria compliance. Taxonomic (community composition) and nontaxonomic (condition of larval mouth parts) descriptors, used together, can indicate a stream's ecological state. Copyright © 2011 Elsevier B.V. All rights reserved.

Genomic evolution of the ascomycetous yeasts

USDA-ARS?s Scientific Manuscript database

Yeasts are important for industrial and biotechnological processes and show remarkable metabolic and phylogenetic diversity despite morphological similarities. We have sequenced the genomes of 16 ascomycete yeasts of taxonomic and industrial importance including members of Saccharomycotina and Taphr...

Diversity of culturable filamentous Ascomycetes in the eastern South Pacific Ocean off Chile.

PubMed

Vera, Jeanett; Gutiérrez, Marcelo H; Palfner, Götz; Pantoja, Silvio

2017-08-01

Our study reports the diversity of culturable mycoplankton in the eastern South Pacific Ocean off Chile to contribute with novel knowledge on taxonomy of filamentous fungi isolated from distinct physicochemical and biological marine environments. We characterized spatial distribution of isolates, evaluated their viability and assessed the influence of organic substrate availability on fungal development. Thirty-nine Operational Taxonomic Units were identified from 99 fungal strains isolated from coastal and oceanic waters by using Automatic Barcode Gap Discovery. All Operational Taxonomic Units belonged to phylum Ascomycota and orders Eurotiales, Dothideales, Sordariales and Hypocreales, mainly Penicillium sp. (82%); 11 sequences did not match existing species in GenBank, suggesting occurrence of novel fungal taxa. Our results suggest that fungal communities in the South Pacific Ocean off Chile appear to thrive in a wide range of environmental conditions in the ocean and that substrate availability may be a factor influencing fungal viability in the ocean.

Revealing the Hyperdiverse Mite Fauna of Subarctic Canada through DNA Barcoding

PubMed Central

Young, Monica R.; Behan-Pelletier, Valerie M.; Hebert, Paul D. N.

2012-01-01

Although mites are one of the most abundant and diverse groups of arthropods, they are rarely targeted for detailed biodiversity surveys due to taxonomic constraints. We address this gap through DNA barcoding, evaluating acarine diversity at Churchill, Manitoba, a site on the tundra-taiga transition. Barcode analysis of 6279 specimens revealed nearly 900 presumptive species of mites with high species turnover between substrates and between forested and non-forested sites. Accumulation curves have not reached an asymptote for any of the three mite orders investigated, and estimates suggest that more than 1200 species of Acari occur at this locality. The coupling of DNA barcode results with taxonomic assignments revealed that Trombidiformes compose 49% of the fauna, a larger fraction than expected based on prior studies. This investigation demonstrates the efficacy of DNA barcoding in facilitating biodiversity assessments of hyperdiverse taxa. PMID:23133656

Unveiling fungal zooflagellates as members of freshwater picoeukaryotes: evidence from a molecular diversity study in a deep meromictic lake.

PubMed

Lefèvre, Emilie; Bardot, Corinne; Noël, Christophe; Carrias, Jean-François; Viscogliosi, Eric; Amblard, Christian; Sime-Ngando, Télesphore

2007-01-01

This study presents an original 18S rRNA PCR survey of the freshwater picoeukaryote community, and was designed to detect unidentified heterotrophic picoflagellates (size range 0.6-5 microm) which are prevalent throughout the year within the heterotrophic flagellate assemblage in Lake Pavin. Four clone libraries were constructed from samples collected in two contrasting zones in the lake. Computerized statistic tools have suggested that sequence retrieval was representative of the in situ picoplankton diversity. The two sampling zones exhibited similar diversity patterns but shared only about 5% of the operational taxonomic units (OTUs). Phylogenetic analysis clustered our sequences into three taxonomic groups: Alveolates (30% of OTUs), Fungi (23%) and Cercozoa (19%). Fungi thus substantially contributed to the detected diversity, as was additionally supported by direct microscopic observations of fungal zoospores and sporangia. A large fraction of the sequences belonged to parasites, including Alveolate sequences affiliated to the genus Perkinsus known as zooparasites, and chytrids that include host-specific parasitic fungi of various freshwater phytoplankton species, primarily diatoms. Phylogenetic analysis revealed five novel clades that probably include typical freshwater environmental sequences. Overall, from the unsuspected fungal diversity unveiled, we think that fungal zooflagellates have been misidentified as phagotrophic nanoflagellates in previous studies. This is in agreement with a recent experimental demonstration that zoospore-producing fungi and parasitic activity may play an important role in aquatic food webs.

Mineral Ecology: Surface Specific Colonization and Geochemical Drivers of Biofilm Accumulation, Composition, and Phylogeny

PubMed Central

Jones, Aaron A.; Bennett, Philip C.

2017-01-01

This study tests the hypothesis that surface composition influences microbial community structure and growth of biofilms. We used laboratory biofilm reactors (inoculated with a diverse subsurface community) to explore the phylogenetic and taxonomic variability in microbial communities as a function of surface type (carbonate, silicate, aluminosilicate), media pH, and carbon and phosphate availability. Using high-throughput pyrosequencing, we found that surface type significantly controlled ~70–90% of the variance in phylogenetic diversity regardless of environmental pressures. Consistent patterns also emerged in the taxonomy of specific guilds (sulfur-oxidizers/reducers, Gram-positives, acidophiles) due to variations in media chemistry. Media phosphate availability was a key property associated with variation in phylogeny and taxonomy of whole reactors and was negatively correlated with biofilm accumulation and α-diversity (species richness and evenness). However, mineral-bound phosphate limitations were correlated with less biofilm. Carbon added to the media was correlated with a significant increase in biofilm accumulation and overall α-diversity. Additionally, planktonic communities were phylogenetically distant from those in biofilms. All treatments harbored structurally (taxonomically and phylogenetically) distinct microbial communities. Selective advantages within each treatment encouraged growth and revealed the presence of hundreds of additional operational taxonomix units (OTU), representing distinct consortiums of microorganisms. Ultimately, these results provide evidence that mineral/rock composition significantly influences microbial community structure, diversity, membership, phylogenetic variability, and biofilm growth in subsurface communities. PMID:28400754

Conservation Action Based on Threatened Species Capture Taxonomic and Phylogenetic Richness in Breeding and Wintering Populations of Central Asian Birds

PubMed Central

Schweizer, Manuel; Ayé, Raffael; Kashkarov, Roman; Roth, Tobias

2014-01-01

Although phylogenetic diversity has been suggested to be relevant from a conservation point of view, its role is still limited in applied nature conservation. Recently, the practice of investing conservation resources based on threatened species was identified as a reason for the slow integration of phylogenetic diversity in nature conservation planning. One of the main arguments is based on the observation that threatened species are not evenly distributed over the phylogenetic tree. However this argument seems to dismiss the fact that conservation action is a spatially explicit process, and even if threatened species are not evenly distributed over the phylogenetic tree, the occurrence of threatened species could still indicate areas with above average phylogenetic diversity and consequently could protect phylogenetic diversity. Here we aim to study the selection of important bird areas in Central Asia, which were nominated largely based on the presence of threatened bird species. We show that although threatened species occurring in Central Asia do not capture phylogenetically more distinct species than expected by chance, the current spatially explicit conservation approach of selecting important bird areas covers above average taxonomic and phylogenetic diversity of breeding and wintering birds. We conclude that the spatially explicit processes of conservation actions need to be considered in the current discussion of whether new prioritization methods are needed to complement conservation action based on threatened species. PMID:25337861

The importance of accounting for imperfect detection when estimating functional and phylogenetic community structure.

PubMed

Si, Xingfeng; Cadotte, Marc W; Zhao, Yuhao; Zhou, Haonan; Zeng, Di; Li, Jiaqi; Jin, Tinghao; Ren, Peng; Wang, Yanping; Ding, Ping; Tingley, Morgan W

2018-06-26

Incorporating imperfect detection when estimating species richness has become commonplace in the past decade. However, the question of how imperfect detection of species affects estimates of functional and phylogenetic community structure remains untested. We used long-term counts of breeding bird species that were detected at least once on islands in a land-bridge island system, and employed multi-species occupancy models to assess the effects of imperfect detection of species on estimates of bird diversity and community structure by incorporating species traits and phylogenies. Our results showed that taxonomic, functional, and phylogenetic diversity were all underestimated significantly as a result of species' imperfect detection, with taxonomic diversity showing the greatest bias. The functional and phylogenetic structure calculated from observed communities were both more clustered than those from the detection-corrected communities due to missed distinct species. The discrepancy between observed and estimated diversity differed according to the measure of biodiversity employed. Our study demonstrates the importance of accounting for species' imperfect detection in biodiversity studies, especially for functional and phylogenetic community ecology, and when attempting to infer community assembly processes. With datasets that allow for detection-corrected community structure, we can better estimate diversity and infer the underlying mechanisms that structure community assembly, and thus make reliable management decisions for the conservation of biodiversity. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

A metagenome for lacustrine Cladophora (Cladophorales) reveals remarkable diversity of eukaryotic epibionts and genes relevant to materials cycling.

PubMed

Graham, Linda E; Knack, Jennifer J; Graham, Melissa E; Graham, James M; Zulkifly, Shahrizim

2015-06-01

Periphyton dominated by the cellulose-rich filamentous green alga Cladophora forms conspicuous growths along rocky marine and freshwater shorelines worldwide, providing habitat for diverse epibionts. Bacterial epibionts have been inferred to display diverse functions of biogeochemical significance: N-fixation and other redox reactions, phosphorus accumulation, and organic degradation. Here, we report taxonomic diversity of eukaryotic and prokaryotic epibionts and diversity of genes associated with materials cycling in a Cladophora metagenome sampled from Lake Mendota, Dane Co., WI, USA, during the growing season of 2012. A total of 1,060 distinct 16S, 173 18S, and 351 28S rRNA operational taxonomic units, from which >220 genera or species of bacteria (~60), protists (~80), fungi (6), and microscopic metazoa (~80), were distinguished with the use of reference databases. We inferred the presence of several algal taxa generally associated with marine systems and detected Jaoa, a freshwater periphytic ulvophyte previously thought endemic to China. We identified six distinct nifH gene sequences marking nitrogen fixation, >25 bacterial and eukaryotic cellulases relevant to sedimentary C-cycling and technological applications, and genes encoding enzymes in aerobic and anaerobic pathways for vitamin B12 biosynthesis. These results emphasize the importance of Cladophora in providing habitat for microscopic metazoa, fungi, protists, and bacteria that are often inconspicuous, yet play important roles in ecosystem biogeochemistry. © 2015 Phycological Society of America.

Body Size Diversity and Frequency Distributions of Neotropical Cichlid Fishes (Cichliformes: Cichlidae: Cichlinae)

PubMed Central

Steele, Sarah E.; López-Fernández, Hernán

2014-01-01

Body size is an important correlate of life history, ecology and distribution of species. Despite this, very little is known about body size evolution in fishes, particularly freshwater fishes of the Neotropics where species and body size diversity are relatively high. Phylogenetic history and body size data were used to explore body size frequency distributions in Neotropical cichlids, a broadly distributed and ecologically diverse group of fishes that is highly representative of body size diversity in Neotropical freshwater fishes. We test for divergence, phylogenetic autocorrelation and among-clade partitioning of body size space. Neotropical cichlids show low phylogenetic autocorrelation and divergence within and among taxonomic levels. Three distinct regions of body size space were identified from body size frequency distributions at various taxonomic levels corresponding to subclades of the most diverse tribe, Geophagini. These regions suggest that lineages may be evolving towards particular size optima that may be tied to specific ecological roles. The diversification of Geophagini appears to constrain the evolution of body size among other Neotropical cichlid lineages; non-Geophagini clades show lower species-richness in body size regions shared with Geophagini. Neotropical cichlid genera show less divergence and extreme body size than expected within and among tribes. Body size divergence among species may instead be present or linked to ecology at the community assembly scale. PMID:25180970

Sensitive and substrate-specific detection of metabolically active microorganisms in natural microbial consortia using community isotope arrays.

PubMed

Tourlousse, Dieter M; Kurisu, Futoshi; Tobino, Tomohiro; Furumai, Hiroaki

2013-05-01

The goal of this study was to develop and validate a novel fosmid-clone-based metagenome isotope array approach - termed the community isotope array (CIArray) - for sensitive detection and identification of microorganisms assimilating a radiolabeled substrate within complex microbial communities. More specifically, a sample-specific CIArray was used to identify anoxic phenol-degrading microorganisms in activated sludge treating synthetic coke-oven wastewater in a single-sludge predenitrification-nitrification process. Hybridization of the CIArray with DNA from the (14) C-phenol-amended sample indicated that bacteria assimilating (14) C-atoms, presumably directly from phenol, under nitrate-reducing conditions were abundant in the reactor, and taxonomic assignment of the fosmid clone end sequences suggested that they belonged to the Gammaproteobacteria. The specificity of the CIArray was validated by quantification of fosmid-clone-specific DNA in density-resolved DNA fractions from samples incubated with (13) C-phenol, which verified that all CIArray-positive probes stemmed from microorganisms that assimilated isotopically labeled carbon. This also demonstrated that the CIArray was more sensitive than DNA-SIP, as the former enabled positive detection at a phenol concentration that failed to yield a 'heavy' DNA fraction. Finally, two operational taxonomic units distantly related to marine Gammaproteobacteria were identified to account for more than half of 16S rRNA gene clones in the 'heavy' DNA library, corroborating the CIArray-based identification. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Deep Illumina-Based Shotgun Sequencing Reveals Dietary Effects on the Structure and Function of the Fecal Microbiome of Growing Kittens

PubMed Central

Deusch, Oliver; O’Flynn, Ciaran; Colyer, Alison; Morris, Penelope; Allaway, David; Jones, Paul G.; Swanson, Kelly S.

2014-01-01

Background Previously, we demonstrated that dietary protein:carbohydrate ratio dramatically affects the fecal microbial taxonomic structure of kittens using targeted 16S gene sequencing. The present study, using the same fecal samples, applied deep Illumina shotgun sequencing to identify the diet-associated functional potential and analyze taxonomic changes of the feline fecal microbiome. Methodology & Principal Findings Fecal samples from kittens fed one of two diets differing in protein and carbohydrate content (high–protein, low–carbohydrate, HPLC; and moderate-protein, moderate-carbohydrate, MPMC) were collected at 8, 12 and 16 weeks of age (n = 6 per group). A total of 345.3 gigabases of sequence were generated from 36 samples, with 99.75% of annotated sequences identified as bacterial. At the genus level, 26% and 39% of reads were annotated for HPLC- and MPMC-fed kittens, with HPLC-fed cats showing greater species richness and microbial diversity. Two phyla, ten families and fifteen genera were responsible for more than 80% of the sequences at each taxonomic level for both diet groups, consistent with the previous taxonomic study. Significantly different abundances between diet groups were observed for 324 genera (56% of all genera identified) demonstrating widespread diet-induced changes in microbial taxonomic structure. Diversity was not affected over time. Functional analysis identified 2,013 putative enzyme function groups were different (p<0.000007) between the two dietary groups and were associated to 194 pathways, which formed five discrete clusters based on average relative abundance. Of those, ten contained more (p<0.022) enzyme functions with significant diet effects than expected by chance. Six pathways were related to amino acid biosynthesis and metabolism linking changes in dietary protein with functional differences of the gut microbiome. Conclusions These data indicate that feline feces-derived microbiomes have large structural and functional differences relating to the dietary protein:carbohydrate ratio and highlight the impact of diet early in life. PMID:25010839

Diversity of kelp holdfast-associated fauna in an Arctic fjord - inconsistent responses to glacial mineral sedimentation across different taxa

NASA Astrophysics Data System (ADS)

Ronowicz, Marta; Kukliński, Piotr; Włodarska-Kowalczuk, Maria

2018-05-01

Kelp forests are complex underwater habitats that support diverse assemblages of animals ranging from sessile filter feeding invertebrates to fishes and marine mammals. In this study, the diversity of invertebrate fauna associated with kelp holdfasts was surveyed in a high Arctic glacial fjord (76 N, Hornsund, Svalbard). The effects of algal host identity (three kelp species: Laminaria digitata, Saccharina latissima and Alaria esculenta), depth (5 and 10 m) and glacier-derived disturbance (three sites with varying levels of mineral sedimentation) on faunal species richness and composition were studied based on 239 collected algal holdfasts. The species pool was mostly made up by three taxa: colonial Bryozoa and Hydrozoa, and Polychaeta. While the all-taxa species richness did not differ between depths, algal hosts and sites, the patterns varied when the two colonial sessile filter-feeding taxa were analysed alone (Hydrozoa and Bryozoa). The Hydrozoa sample species richness and average taxonomic distinctness were the highest at undisturbed sites, whereas Bryozoa species richness was higher in sediment-impacted localities, indicating relative insensitivity of this phylum to the increased level of mineral suspension in the water column. The average taxonomic distinctness of Bryozoa did not vary between sites. The species composition of kelp-associated fauna varied between sites and depths for the whole community and the most dominant taxa (Bryozoa, Hydrozoa). The high load of inorganic suspension and sedimentation did not cause pauperization of kelp holdfast-associated fauna but instead triggered the changes in species composition and shifts between dominant taxonomic groups.

Is Homo sapiens polytypic? Human taxonomic diversity and its implications.

PubMed

Woodley, Michael A

2010-01-01

The term race is a traditional synonym for subspecies, however it is frequently asserted that Homo sapiens is monotypic and that what are termed races are nothing more than biological illusions. In this manuscript a case is made for the hypothesis that H. sapiens is polytypic, and in this way is no different from other species exhibiting similar levels of genetic and morphological diversity. First it is demonstrated that the four major definitions of race/subspecies can be shown to be synonymous within the context of the framework of race as a correlation structure of traits. Next the issue of taxonomic classification is considered where it is demonstrated that H. sapiens possesses high levels morphological diversity, genetic heterozygosity and differentiation (F(ST)) compared to many species that are acknowledged to be polytypic with respect to subspecies. Racial variation is then evaluated in light of the phylogenetic species concept, where it is suggested that the least inclusive monophyletic units exist below the level of species within H. sapiens indicating the existence of a number of potential human phylogenetic species; and the biological species concept, where it is determined that racial variation is too small to represent differentiation at the level of biological species. Finally the implications of this are discussed in the context of anthropology where an accurate picture of the sequence and timing of events during the evolution of human taxa are required for a complete picture of human evolution, and medicine, where a greater appreciation of the role played by human taxonomic differences in disease susceptibility and treatment responsiveness will save lives in the future.

Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria

PubMed Central

Farrant, Gregory K.; Doré, Hugo; Cornejo-Castillo, Francisco M.; Partensky, Frédéric; Ratin, Morgane; Ostrowski, Martin; Pitt, Frances D.; Wincker, Patrick; Scanlan, David J.; Iudicone, Daniele; Acinas, Silvia G.; Garczarek, Laurence

2016-01-01

Prochlorococcus and Synechococcus are the two most abundant and widespread phytoplankton in the global ocean. To better understand the factors controlling their biogeography, a reference database of the high-resolution taxonomic marker petB, encoding cytochrome b6, was used to recruit reads out of 109 metagenomes from the Tara Oceans expedition. An unsuspected novel genetic diversity was unveiled within both genera, even for the most abundant and well-characterized clades, and 136 divergent petB sequences were successfully assembled from metagenomic reads, significantly enriching the reference database. We then defined Ecologically Significant Taxonomic Units (ESTUs)—that is, organisms belonging to the same clade and occupying a common oceanic niche. Three major ESTU assemblages were identified along the cruise transect for Prochlorococcus and eight for Synechococcus. Although Prochlorococcus HLIIIA and HLIVA ESTUs codominated in iron-depleted areas of the Pacific Ocean, CRD1 and the yet-to-be cultured EnvB were the prevalent Synechococcus clades in this area, with three different CRD1 and EnvB ESTUs occupying distinct ecological niches with regard to iron availability and temperature. Sharp community shifts were also observed over short geographic distances—for example, around the Marquesas Islands or between southern Indian and Atlantic Oceans—pointing to a tight correlation between ESTU assemblages and specific physico-chemical parameters. Together, this study demonstrates that there is a previously overlooked, ecologically meaningful, fine-scale diversity within some currently defined picocyanobacterial ecotypes, bringing novel insights into the ecology, diversity, and biology of the two most abundant phototrophs on Earth. PMID:27302952

DNA barcoding a nightmare taxon: assessing barcode index numbers and barcode gaps for sweat bees.

PubMed

Gibbs, Jason

2018-01-01

There is an ongoing campaign to DNA barcode the world's >20 000 bee species. Recent revisions of Lasioglossum (Dialictus) (Hymenoptera: Halictidae) for Canada and the eastern United States were completed using integrative taxonomy. DNA barcode data from 110 species of L. (Dialictus) are examined for their value in identification and discovering additional taxonomic diversity. Specimen identification success was estimated using the best close match method. Error rates were 20% relative to current taxonomic understanding. Barcode Index Numbers (BINs) assigned using Refined Single Linkage Analysis (RESL) and barcode gaps using the Automatic Barcode Gap Discovery (ABGD) method were also assessed. RESL was incongruent for 44.5% of species, although some cryptic diversity may exist. Forty-three of 110 species were part of merged BINs with multiple species. The barcode gap is non-existent for the data set as a whole and ABGD showed levels of discordance similar to the RESL. The viridatum species-group is particularly problematic, so that DNA barcodes alone would be misleading for species delimitation and specimen identification. Character-based methods using fixed nucleotide substitutions could improve specimen identification success in some cases. The use of DNA barcoding for species discovery for standard taxonomic practice in the absence of a well-defined barcode gap is discussed.

Taxonomic Notes on Nasutitermes and Bulbitermes (Termitidae, Nasutitermitinae) from the Sunda region of Southeast Asia based on morphological and molecular characters

PubMed Central

Syaukani; Thompson, Graham J.

2011-01-01

Abstract The Sunda region of Southeastern Asia is rich in termite fauna, but termites from this region have been poorly described. In this study, we described eight species from two diverse genera from this region, and from the family Termitidae. We describe Bulbitermes 4 spp. and Nasutitermes 4 spp. from new field collections. Where possible we examine original holotype specimens, and describe the essential morphological characters for soldier and worker castes. We devise two new bifurcating keys to guide the field identification of each species. In addition, we develop a nucleotide sequence profile for the COI gene. From this molecular character matrix, we use Neighbour-Joining analysis to test the monophyly of each morphospecies and genus. We find that the morphological and molecular characters are highly concordant, whereby all taxa appear to represent distinct molecular clades. For termites, there is therefore agreement between the morphological taxonomic characters used to sort species from a bifurcating key and the molecular taxonomic characters used to sort species on a bifurcating tree. This joint analysis suggests that DNA barcoding holds considerable promise for termite taxonomy, especially for diverse clades like Bulbitermes and Nasutitermes for which a global morphological key would be intractable. PMID:22287894

Fungal diversity in deep-sea sediments of a hydrothermal vent system in the Southwest Indian Ridge

NASA Astrophysics Data System (ADS)

Xu, Wei; Gong, Lin-feng; Pang, Ka-Lai; Luo, Zhu-Hua

2018-01-01

Deep-sea hydrothermal sediment is known to support remarkably diverse microbial consortia. In deep sea environments, fungal communities remain less studied despite their known taxonomic and functional diversity. High-throughput sequencing methods have augmented our capacity to assess eukaryotic diversity and their functions in microbial ecology. Here we provide the first description of the fungal community diversity found in deep sea sediments collected at the Southwest Indian Ridge (SWIR) using culture-dependent and high-throughput sequencing approaches. A total of 138 fungal isolates were cultured from seven different sediment samples using various nutrient media, and these isolates were identified to 14 fungal taxa, including 11 Ascomycota taxa (7 genera) and 3 Basidiomycota taxa (2 genera) based on internal transcribed spacers (ITS1, ITS2 and 5.8S) of rDNA. Using illumina HiSeq sequencing, a total of 757,467 fungal ITS2 tags were recovered from the samples and clustered into 723 operational taxonomic units (OTUs) belonging to 79 taxa (Ascomycota and Basidiomycota contributed to 99% of all samples) based on 97% sequence similarity. Results from both approaches suggest that there is a high fungal diversity in the deep-sea sediments collected in the SWIR and fungal communities were shown to be slightly different by location, although all were collected from adjacent sites at the SWIR. This study provides baseline data of the fungal diversity and biogeography, and a glimpse to the microbial ecology associated with the deep-sea sediments of the hydrothermal vent system of the Southwest Indian Ridge.

A waveform diversity method for optimizing 3-d power depositions generated by ultrasound phased arrays.

PubMed

Zeng, Xiaozheng Jenny; Li, Jian; McGough, Robert J

2010-01-01

A waveform-diversity-based approach for 3-D tumor heating is compared to spot scanning for hyperthermia applications. The waveform diversity method determines the excitation signals applied to the phased array elements and produces a beam pattern that closely matches the desired power distribution. The optimization algorithm solves the covariance matrix of the excitation signals through semidefinite programming subject to a series of quadratic cost functions and constraints on the control points. A numerical example simulates a 1444-element spherical-section phased array that delivers heat to a 3-cm-diameter spherical tumor located 12 cm from the array aperture, and the results show that waveform diversity combined with mode scanning increases the heated volume within the tumor while simultaneously decreasing normal tissue heating. Whereas standard single focus and multiple focus methods are often associated with unwanted intervening tissue heating, the waveform diversity method combined with mode scanning shifts energy away from intervening tissues where hotspots otherwise accumulate to improve temperature localization in deep-seated tumors.

Comparative genomics of biotechnologically important yeasts

USDA-ARS?s Scientific Manuscript database

Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the...

Fine-scale analysis of 16S rRNA sequences reveals a high level of taxonomic diversity among vaginal Atopobium spp.

PubMed Central

Mendes-Soares, Helena; Krishnan, Vandhana; Settles, Matthew L.; Ravel, Jacques; Brown, Celeste J.; Forney, Larry J.

2015-01-01

Although vaginal microbial communities of some healthy women have high proportions of Atopobium vaginae, the genus Atopobium is more commonly associated with bacterial vaginosis, a syndrome associated with an increased risk of adverse pregnancy outcomes and the transmission of sexually transmitted diseases. Genetic differences within Atopobium species may explain why single species can be associated with both health and disease. We used 16S rRNA gene sequences from previously published studies to explore the taxonomic diversity of the genus Atopobium in vaginal microbial communities of healthy women. Although A. vaginae was the species most commonly found, we also observed three other Atopobium species in the vaginal microbiota, one of which, A. parvulum, was not previously known to reside in the human vagina. Furthermore, we found several potential novel species of the genus Atopobium and multiple phylogenetic clades of A. vaginae. The diversity of Atopobium found in our study, which focused only on samples from healthy women, is greater than previously recognized, suggesting that analysis of samples from women with BV would yield even more diversity. Classification of microbes only to the genus level may thus obfuscate differences that might be important to better understand health or disease. PMID:25778779

Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches.

PubMed

Yahr, Rebecca; Schoch, Conrad L; Dentinger, Bryn T M

2016-09-05

The fungal kingdom is a hyperdiverse group of multicellular eukaryotes with profound impacts on human society and ecosystem function. The challenge of documenting and describing fungal diversity is exacerbated by their typically cryptic nature, their ability to produce seemingly unrelated morphologies from a single individual and their similarity in appearance to distantly related taxa. This multiplicity of hurdles resulted in the early adoption of DNA-based comparisons to study fungal diversity, including linking curated DNA sequence data to expertly identified voucher specimens. DNA-barcoding approaches in fungi were first applied in specimen-based studies for identification and discovery of taxonomic diversity, but are now widely deployed for community characterization based on sequencing of environmental samples. Collectively, fungal barcoding approaches have yielded important advances across biological scales and research applications, from taxonomic, ecological, industrial and health perspectives. A major outstanding issue is the growing problem of 'sequences without names' that are somewhat uncoupled from the traditional framework of fungal classification based on morphology and preserved specimens. This review summarizes some of the most significant impacts of fungal barcoding, its limitations, and progress towards the challenge of effective utilization of the exponentially growing volume of data gathered from high-throughput sequencing technologies.This article is part of the themed issue 'From DNA barcodes to biomes'. © 2016 The Authors.

DIVERSITY AND HOST SPECIFICITY OF AZOLLA CYANOBIONTS(1).

PubMed

Papaefthimiou, Dimitra; Van Hove, Charles; Lejeune, André; Rasmussen, Ulla; Wilmotte, Annick

2008-02-01

A unique, hereditary symbiosis exists between the water fern Azolla and cyanobacteria that reside within a cavity in the dorsal leaf-lobe of the plant. This association has been studied extensively, and questions have frequently been raised regarding the number and diversity of cyanobionts (cyanobacterial symbionts) among the different Azolla strains and species. In this work, denaturating gradient gel electrophoresis (DGGE) and a clone library based on the 16S rRNA gene were used to study the genetic diversity and host specificity of the cyanobionts in 35 Azolla strains covering a wide taxonomic and geographic range. DNA was extracted directly from the cyanobacterial packets, isolated after enzymatic digestion of the Azolla leaves. Our results indicated the existence of different cyanobiont strains among Azolla species, and diversity within a single Azolla species, independent of the geographic origin of the host. Furthermore, the cyanobiont exhibited host-species specificity and showed most divergence between the two sections of genus Azolla, Azolla and Rhizosperma. These findings are in agreement with the recent redefinition of the taxon Azolla cristata within the section Azolla. With regard to the taxonomic status of the cyanobiont, the genus Anabaena of the Nostocaceae family was identified as the closest relative by this work. © 2008 Phycological Society of America.

Analyses of the Microbial Diversity across the Human Microbiome

PubMed Central

Li, Kelvin; Bihan, Monika; Yooseph, Shibu; Methé, Barbara A.

2012-01-01

Analysis of human body microbial diversity is fundamental to understanding community structure, biology and ecology. The National Institutes of Health Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine microbial diversity within and across body habitats and individuals through pyrosequencing-based profiling of 16 S rRNA gene sequences (16 S) from habits of the oral, skin, distal gut, and vaginal body regions from over 200 healthy individuals enabling the application of statistical techniques. In this study, two approaches were applied to elucidate the nature and extent of human microbiome diversity. First, bootstrap and parametric curve fitting techniques were evaluated to estimate the maximum number of unique taxa, Smax, and taxa discovery rate for habitats across individuals. Next, our results demonstrated that the variation of diversity within low abundant taxa across habitats and individuals was not sufficiently quantified with standard ecological diversity indices. This impact from low abundant taxa motivated us to introduce a novel rank-based diversity measure, the Tail statistic, (“τ”), based on the standard deviation of the rank abundance curve if made symmetric by reflection around the most abundant taxon. Due to τ’s greater sensitivity to low abundant taxa, its application to diversity estimation of taxonomic units using taxonomic dependent and independent methods revealed a greater range of values recovered between individuals versus body habitats, and different patterns of diversity within habitats. The greatest range of τ values within and across individuals was found in stool, which also exhibited the most undiscovered taxa. Oral and skin habitats revealed variable diversity patterns, while vaginal habitats were consistently the least diverse. Collectively, these results demonstrate the importance, and motivate the introduction, of several visualization and analysis methods tuned specifically for next-generation sequence data, further revealing that low abundant taxa serve as an important reservoir of genetic diversity in the human microbiome. PMID:22719823

Coral Reef Health Indices versus the Biological, Ecological and Functional Diversity of Fish and Coral Assemblages in the Caribbean Sea

PubMed Central

Díaz-Pérez, Leopoldo; Ortiz, Marco; Cupul-Magaña, Amílcar Leví; Carriquiry, Jose D.; Ríos-Jara, Eduardo; Rodríguez-Troncoso, Alma Paola; García-Rivas, María del Carmen

2016-01-01

This study evaluated the relationship between the indices known as the Reef Health Index (RHI) and two-dimensional Coral Health Index (2D-CHI) and different representative metrics of biological, ecological and functional diversity of fish and corals in 101 reef sites located across seven zones in the western Caribbean Sea. Species richness and average taxonomic distinctness were used to asses biological estimation; while ecological diversity was evaluated with the indices of Shannon diversity and Pielou´s evenness, as well as by taxonomic diversity and distinctness. Functional diversity considered the number of functional groups, the Shannon diversity and the functional Pielou´s evenness. According to the RHI, 57.15% of the zones were classified as presenting a "poor" health grade, while 42.85% were in "critical" grade. Based on the 2D-CHI, 28.5% of the zones were in "degraded" condition and 71.5% were "very degraded". Differences in fish and coral diversity among sites and zones were demonstrated using permutational ANOVAs. Differences between the two health indices (RHI and 2D-CHI) and some indices of biological, ecological and functional diversity of fish and corals were observed; however, only the RHI showed a correlation between the health grades and the species and functional group richness of fish at the scale of sites, and with the species and functional group richness and Shannon diversity of the fish assemblages at the scale of zones. None of the health indices were related to the metrics analyzed for the coral diversity. In general, our study suggests that the estimation of health indices should be complemented with classic community indices, or should at least include diversity indices of fish and corals, in order to improve the accuracy of the estimated health status of coral reefs in the western Caribbean Sea. PMID:27579575

Coral Reef Health Indices versus the Biological, Ecological and Functional Diversity of Fish and Coral Assemblages in the Caribbean Sea.

PubMed

Díaz-Pérez, Leopoldo; Rodríguez-Zaragoza, Fabián Alejandro; Ortiz, Marco; Cupul-Magaña, Amílcar Leví; Carriquiry, Jose D; Ríos-Jara, Eduardo; Rodríguez-Troncoso, Alma Paola; García-Rivas, María Del Carmen

2016-01-01

This study evaluated the relationship between the indices known as the Reef Health Index (RHI) and two-dimensional Coral Health Index (2D-CHI) and different representative metrics of biological, ecological and functional diversity of fish and corals in 101 reef sites located across seven zones in the western Caribbean Sea. Species richness and average taxonomic distinctness were used to asses biological estimation; while ecological diversity was evaluated with the indices of Shannon diversity and Pielou´s evenness, as well as by taxonomic diversity and distinctness. Functional diversity considered the number of functional groups, the Shannon diversity and the functional Pielou´s evenness. According to the RHI, 57.15% of the zones were classified as presenting a "poor" health grade, while 42.85% were in "critical" grade. Based on the 2D-CHI, 28.5% of the zones were in "degraded" condition and 71.5% were "very degraded". Differences in fish and coral diversity among sites and zones were demonstrated using permutational ANOVAs. Differences between the two health indices (RHI and 2D-CHI) and some indices of biological, ecological and functional diversity of fish and corals were observed; however, only the RHI showed a correlation between the health grades and the species and functional group richness of fish at the scale of sites, and with the species and functional group richness and Shannon diversity of the fish assemblages at the scale of zones. None of the health indices were related to the metrics analyzed for the coral diversity. In general, our study suggests that the estimation of health indices should be complemented with classic community indices, or should at least include diversity indices of fish and corals, in order to improve the accuracy of the estimated health status of coral reefs in the western Caribbean Sea.

A taxonomic revision of Herminium L. (Orchidoideae, Orchidaceae)

PubMed Central

Raskoti, Bhakta Bahadur; Schuiteman, André; Jin, Wei-Tao; Jin, Xiao-Hua

2017-01-01

Abstract Herminium (Orchidaceae, Orchidoideae) is a medium-sized genus widespread in the northern hemisphere, with a clear centre of diversity in the Himalayas. We present a comprehensive taxonomic revision of Herminium based on field observations and morphological studies, for which we examined about 2500 specimens. We recognize 49 species grouped into six formal sections, including one new species, Herminium tibeticum, from Tibet. We provide an identification key to the species, descriptions of the species, notes on ecology and distribution, and complete nomenclature for each species, including typifications. We here designate lectotypes for five species and reduce four taxa to synonymy. PMID:28794677

Surfacing the deep data of taxonomy

PubMed Central

Page, Roderic D. M.

2016-01-01

Abstract Taxonomic databases are perpetuating approaches to citing literature that may have been appropriate before the Internet, often being little more than digitised 5 × 3 index cards. Typically the original taxonomic literature is either not cited, or is represented in the form of a (typically abbreviated) text string. Hence much of the “deep data” of taxonomy, such as the original descriptions, revisions, and nomenclatural actions are largely hidden from all but the most resourceful users. At the same time there are burgeoning efforts to digitise the scientific literature, and much of this newly available content has been assigned globally unique identifiers such as Digital Object Identifiers (DOIs), which are also the identifier of choice for most modern publications. This represents an opportunity for taxonomic databases to engage with digitisation efforts. Mapping the taxonomic literature on to globally unique identifiers can be time consuming, but need be done only once. Furthermore, if we reuse existing identifiers, rather than mint our own, we can start to build the links between the diverse data that are needed to support the kinds of inference which biodiversity informatics aspires to support. Until this practice becomes widespread, the taxonomic literature will remain balkanized, and much of the knowledge that it contains will linger in obscurity. PMID:26877663

Estimating the efficiency of fish cross-species cDNA microarray hybridization.

PubMed

Cohen, Raphael; Chalifa-Caspi, Vered; Williams, Timothy D; Auslander, Meirav; George, Stephen G; Chipman, James K; Tom, Moshe

2007-01-01

Using an available cross-species cDNA microarray is advantageous for examining multigene expression patterns in non-model organisms, saving the need for construction of species-specific arrays. The aim of the present study was to estimate relative efficiency of cross-species hybridizations across bony fishes, using bioinformatics tools. The methodology may serve also as a model for similar evaluations in other taxa. The theoretical evaluation was done by substituting comparative whole-transcriptome sequence similarity information into the thermodynamic hybridization equation. Complementary DNA sequence assemblages of nine fish species belonging to common families or suborders and distributed across the bony fish taxonomic branch were selected for transcriptome-wise comparisons. Actual cross-species hybridizations among fish of different taxonomic distances were used to validate and eventually to calibrate the theoretically computed relative efficiencies.

The family Rhabdoviridae: Mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins

USGS Publications Warehouse

Dietzgen, Ralf G.; Kondo, Hideki; Goodin, Michael M.; Kurath, Gael; Vasilakis, Nikos

2017-01-01

The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- and bipartite genomes.

Partitioning the impact of environment and spatial structure on alpha and beta components of taxonomic, functional, and phylogenetic diversity in European ants.

PubMed

Arnan, Xavier; Cerdá, Xim; Retana, Javier

2015-01-01

We analyze the relative contribution of environmental and spatial variables to the alpha and beta components of taxonomic (TD), phylogenetic (PD), and functional (FD) diversity in ant communities found along different climate and anthropogenic disturbance gradients across western and central Europe, in order to assess the mechanisms structuring ant biodiversity. To this aim we calculated alpha and beta TD, PD, and FD for 349 ant communities, which included a total of 155 ant species; we examined 10 functional traits and phylogenetic relatedness. Variation partitioning was used to examine how much variation in ant diversity was explained by environmental and spatial variables. Autocorrelation in diversity measures and each trait's phylogenetic signal were also analyzed. We found strong autocorrelation in diversity measures. Both environmental and spatial variables significantly contributed to variation in TD, PD, and FD at both alpha and beta scales; spatial structure had the larger influence. The different facets of diversity showed similar patterns along environmental gradients. Environment explained a much larger percentage of variation in FD than in TD or PD. All traits demonstrated strong phylogenetic signals. Our results indicate that environmental filtering and dispersal limitations structure all types of diversity in ant communities. Strong dispersal limitations appear to have led to clustering of TD, PD, and FD in western and central Europe, probably because different historical and evolutionary processes generated different pools of species. Remarkably, these three facets of diversity showed parallel patterns along environmental gradients. Trait-mediated species sorting and niche conservatism appear to structure ant diversity, as evidenced by the fact that more variation was explained for FD and that all traits had strong phylogenetic signals. Since environmental variables explained much more variation in FD than in PD, functional diversity should be a better indicator of community assembly processes than phylogenetic diversity.

[Some problems of the study and representation of Siberian flora biodiversity in connection with its conservation].

PubMed

Olonova, M V

2007-01-01

The present knowledge of flora of Siberia is quite insufficient, which is a considerable obstacle to the detection of its biodiversity for conserving the gene pool. Planning conservation measures should be focused not only on species, but also on intraspecific taxa and their phylogenetic uniqueness. In the absence of genetic data, available morphological and geographical methods should be used, so that, when it is impossible to establish the actual origin and relationship of taxa, the existing morphological diverstity is at least represented, as far as it is known to be based on genetic diversity. Phenetic maps can be of much use in the study of intraspecific morphological diversity. The estimation of geographic variability and morphological diversity, as well as the evaluation of territories, can be based on such maps. To represent adequately the biodiversity existing within poorly studied, presumably hybrid plant groups, until actual origin and relationship are known, they should probably be forcedly and provisionally considered as a special type of hybrid complexes, representing the unclear present day taxonomic situation. Such complexes could include populations and individuals with morphological characters of two or more different species, until the systematic position of such populations and individuals is further explored. Until the actual taxonomic status and relationship of the components are established, they could be regarded as subspecies permitted by the Code, or as certain recorded morphological deviations from the type, without assigning any taxonomic status to them--depending on the available data on variability and distribution. In the future, the resulting provisional information on morphological diversity would help to concentrate the efforts of biologists, in possession of the newest methods, on the most important objects, and serve as the scientific base for effective measures aimed at the conservation and management of the vast gene pool of the Siberian flora.

[Molecular phylogeny and systematics of flowering plants of the family Crassulaceae DC].

PubMed

Goncharova, S B; Goncharov, A A

2009-01-01

Crassulaceae is the most species rich (ca. 1400) family in the order Saxifragales. Most members of the family are succulent plants. Phenotypic diversity and a large number of species complicate systematics of the family and reconstruction of relationship within it. Phylogenetic analyses based on morphological and molecular markers placed Crassulaceae as one of the crown clades of Saxifragales. In this contribution a review of phylogenetic studies of the family Crassulaceae, based on DNA nucleotide sequence comparisons is presented; major clades established in the family are characterised; their structure and polyphylesis of some genera related to it are discussed. It was shown that the traditional taxonomic structure of Crassulaceae contradicts pattern of phylogenetic relationships between its members. We critically analysed recent taxonomic systems of the family and stress that homoplasy of morphological characters does not allow to use them to reconstruct relationships between crassulacean taxa even at the low taxonomic levels.

Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform.

PubMed

Kim, Junhyung; An, Jae-Uk; Kim, Woohyun; Lee, Soomin; Cho, Seongbeom

2017-01-01

Recent advances in next-generation sequencing technologies have enabled comprehensive analysis of the gut microbiota, which is closely linked to the health of the host. Consequently, several studies have explored the factors affecting gut microbiota composition. In recent years, increasing number of dog owners are feeding their pets a natural diet i.e., one consisting of bones, raw meat (such as chicken and beef), and vegetables, instead of commercial feed. However, the effect of these diets on the microbiota of dogs ( Canis lupus familiaris ) is unclear. Six dogs fed a natural diet and five dogs fed a commercial feed were selected; dog fecal metagenomic DNA samples were analyzed using the Illumina MiSeq platform. Pronounced differences in alpha and beta diversities, and taxonomic composition of the core gut microbiota were observed between the two groups. According to alpha diversity, the number of operational taxonomic units, the richness estimates, and diversity indices of microbiota were significantly higher ( p  < 0.05) in the natural diet group than in the commercial feed group. Based on beta diversity, most samples clustered together according to the diet type ( p  = 0.004). Additionally, the core microbiota between the two groups was different at the phylum, family, and species levels. Marked differences in the taxonomic composition of the core microbiota of the two groups were observed at the species level; Clostridium perfringens ( p  = 0.017) and Fusobacterium varium ( p  = 0.030) were more abundant in the natural diet group. The gut microbiota of dogs is significantly influenced by diet type (i.e., natural diet and commercial feed). Specifically, dogs fed a natural diet have more diverse and abundant microbial composition in the gut microbiota than dogs fed a commercial feed. In addition, this study suggests that in dogs fed a natural diet, the potential risk of opportunistic infection could be higher, than in dogs fed a commercial feed. The type of diet might therefore play a key role in animal health by affecting the gut microbiota. This study could be the basis for future gut microbiota research in dogs.

Why do different oceanic archipelagos harbour contrasting levels of species diversity? The macaronesian endemic genus Pericallis (Asteraceae) provides insight into explaining the 'Azores diversity Enigma'.

PubMed

Jones, K E; Pérez-Espona, S; Reyes-Betancort, J A; Pattinson, D; Caujapé-Castells, J; Hiscock, S J; Carine, M A

2016-10-08

Oceanic archipelagos typically harbour extensive radiations of flowering plants and a high proportion of endemics, many of which are restricted to a single island (Single Island Endemics; SIEs). The Azores represents an anomaly as overall levels of endemism are low; there are few SIEs and few documented cases of intra-archipelago radiations. The distinctiveness of the flora was first recognized by Darwin and has been referred to as the 'Azores Diversity Enigma' (ADE). Diversity patterns in the Macaronesian endemic genus Pericallis (Asteraceae) exemplify the ADE. In this study we used morphometric, Amplified Length Polymorphisms, and bioclimatic data for herbaceous Pericallis lineages endemic to the Azores and the Canaries, to test two key hypotheses proposed to explain the ADE: i) that it is a taxonomic artefact or Linnean shortfall, ie. the under description of taxa in the Azores or the over-splitting of taxa in the Canaries and (ii) that it reflects the greater ecological homogeneity of the Azores, which results in limited opportunity for ecological diversification compared to the Canaries. In both the Azores and the Canaries, morphological patterns were generally consistent with current taxonomic classifications. However, the AFLP data showed no genetic differentiation between the two currently recognized Azorean subspecies that are ecologically differentiated. Instead, genetic diversity in the Azores was structured geographically across the archipelago. In contrast, in the Canaries genetic differentiation was mostly consistent with morphology and current taxonomic treatments. Both Azorean and Canarian lineages exhibited ecological differentiation between currently recognized taxa. Neither a Linnean shortfall nor the perceived ecological homogeneity of the Azores fully explained the ADE-like pattern observed in Pericallis. Whilst variation in genetic data and morphological data in the Canaries were largely congruent, this was not the case in the Azores, where genetic patterns reflected inter-island geographical isolation, and morphology reflected intra-island bioclimatic variation. The combined effects of differences in (i) the extent of geographical isolation, (ii) population sizes and (iii) geographical occupancy of bioclimatic niche space, coupled with the morphological plasticity of Pericallis, may all have contributed to generating the contrasting patterns observed in the archipelagos.

Diversity and distribution patterns of the Oligocene and Miocene decapod crustaceans (Crustacea: Malacostraca) of the Western and Central Paratethys.

PubMed

Hyžný, Matúš

2016-10-01

Decapod associations have been significant components of marine habitats throughout the Cenozoic when the major diversification of the group occurred. In this respect, the circum-Mediterranean area is of particular interest due to its complex palaeogeographic history. During the Oligo-Miocene, it was divided in two major areas, Mediterranean and Paratethys. Decapod crustaceans from the Paratethys Sea have been reported in the literature since the 19 th century, but only recent research advances allow evaluation of the diversity and distribution patterns of the group. Altogether 176 species-level taxa have been identified from the Oligocene and Miocene of the Western and Central Paratethys. Using the three-dimensional NMDS analysis, the composition of decapod crustacean faunas of the Paratethys shows significant differences through time. The Ottnangian and Karpatian decapod associations were similar to each other both taxonomically and in the mode of preservation, and they differed taxonomically from the Badenian ones. The Early Badenian assemblages also differed taxonomically from the Late Badenian ones. The time factor, including speciation, immigration from other provinces and/or (local or global) extinction, can explain temporal differences among assemblages within the same environment. High decapod diversity during the Badenian was correlated with the presence of reefal settings. The Badenian was the time with the highest decapod diversity, which can, however, be a consequence of undersampling of other time slices. Whereas the Ottnangian and Karpatian decapod assemblages are preserved virtually exclusively in the siliciclastic "Schlier"-type facies that originated in non-reefal offshore environments, carbonate sedimentation and the presence of reefal environments during the Badenian in the Central Paratethys promoted thriving of more diverse reef-associated assemblages. In general, Paratethyan decapods exhibited homogeneous distribution during the Oligo-Miocene among the basins in the Paratethys. Based on the co-occurrence of certain decapod species, migration between the Paratethys and the North Sea during the Early Miocene probably occurred via the Rhine Graben. At larger spatial scales, our results suggest that the circum-Mediterranean marine decapod taxa migrated in an easterly direction during the Oligocene and/or Miocene, establishing present-day decapod communities in the Indo-West Pacific.

Diversity and distribution patterns of the Oligocene and Miocene decapod crustaceans (Crustacea: Malacostraca) of the Western and Central Paratethys

PubMed Central

Hyžný, Matúš

2017-01-01

Decapod associations have been significant components of marine habitats throughout the Cenozoic when the major diversification of the group occurred. In this respect, the circum-Mediterranean area is of particular interest due to its complex palaeogeographic history. During the Oligo-Miocene, it was divided in two major areas, Mediterranean and Paratethys. Decapod crustaceans from the Paratethys Sea have been reported in the literature since the 19th century, but only recent research advances allow evaluation of the diversity and distribution patterns of the group. Altogether 176 species-level taxa have been identified from the Oligocene and Miocene of the Western and Central Paratethys. Using the three-dimensional NMDS analysis, the composition of decapod crustacean faunas of the Paratethys shows significant differences through time. The Ottnangian and Karpatian decapod associations were similar to each other both taxonomically and in the mode of preservation, and they differed taxonomically from the Badenian ones. The Early Badenian assemblages also differed taxonomically from the Late Badenian ones. The time factor, including speciation, immigration from other provinces and/or (local or global) extinction, can explain temporal differences among assemblages within the same environment. High decapod diversity during the Badenian was correlated with the presence of reefal settings. The Badenian was the time with the highest decapod diversity, which can, however, be a consequence of undersampling of other time slices. Whereas the Ottnangian and Karpatian decapod assemblages are preserved virtually exclusively in the siliciclastic “Schlier”-type facies that originated in non-reefal offshore environments, carbonate sedimentation and the presence of reefal environments during the Badenian in the Central Paratethys promoted thriving of more diverse reef-associated assemblages. In general, Paratethyan decapods exhibited homogeneous distribution during the Oligo-Miocene among the basins in the Paratethys. Based on the co-occurrence of certain decapod species, migration between the Paratethys and the North Sea during the Early Miocene probably occurred via the Rhine Graben. At larger spatial scales, our results suggest that the circum-Mediterranean marine decapod taxa migrated in an easterly direction during the Oligocene and/or Miocene, establishing present-day decapod communities in the Indo-West Pacific. PMID:28239259

Gut microbiome diversity influenced more by the Westernized dietary regime than the body mass index as assessed using effect size statistic.

PubMed

Davis, Shannon C; Yadav, Jagjit S; Barrow, Stephanie D; Robertson, Boakai K

2017-08-01

Human gut microbiome dysbiosis has been associated with the onset of metabolic diseases and disorders. However, the critical factors leading to dysbiosis are poorly understood. In this study, we provide increasing evidence of the association of diet type and body mass index (BMI) and how they relatively influence the taxonomic structure of the gut microbiota with respect to the causation of gut microbiome dysbiosis. The study included randomly selected Alabama residents (n = 81), including females (n = 45) and males (n = 36). The demographics data included age (33 ± 13.3 years), height (1.7 ± 0.11 meters), and weight (82.3 ± 20.6 kg). The mean BMI was 28.3 ± 7.01, equating to an overweight BMI category. A cross-sectional case-control design encompassing the newly recognized effect size approach to bioinformatics analysis was used to analyze data from donated stool samples and accompanying nutrition surveys. We investigated the microbiome variations in the Bacteroidetes-Firmicutes ratio relative to BMI, food categories, and dietary groups at stratified abundance percentages of <20%, 20%, 30%, 40%, 50%, 60%, and ≥70%. We further investigated variation in the Firmicutes and Bacteroidetes phyla composition (at the genus and species level) in relation to BMI, food categories, and dietary groups (Westernized or healthy). The Pearson Correlation coefficient as an indication of effect size across Alpha diversity indices was used to test the hypothesis (H 0 ): increased BMI has greater effect on taxonomic diversity than Westernized diet type, (H a ): increased BMI does not have a greater effect on taxonomic diversity than Westernized diet type. In conclusion, we rejected the (H 0 ) as our results demonstrated that Westernized diet type had an effect size of 0.22 posing a greater impact upon the gut microbiota diversity than an increased BMI with an effect size of 0.16. This implied Westernized diet as a critical factor in causing dysbiosis as compared to an overweight or obese body mass index. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Algal taxonomy: a road to nowhere?

PubMed

De Clerck, Olivier; Guiry, Michael D; Leliaert, Frederik; Samyn, Yves; Verbruggen, Heroen

2013-04-01

The widespread view of taxonomy as an essentially retrogressive and outmoded science unable to cope with the current biodiversity crisis stimulated us to analyze the current status of cataloguing global algal diversity. Contrary to this largely pessimistic belief, species description rates of algae through time and trends in the number of active taxonomists, as revealed by the web resource AlgaeBase, show a much more positive picture. More species than ever before are being described by a large community of algal taxonomists. The lack of any decline in the rate at which new species and genera are described, however, is indicative of the large proportion of undiscovered diversity and bears heavily on any prediction of global algal species diversity and the time needed to catalogue it. The saturation of accumulation curves of higher taxa (family, order, and classes) on the other hand suggest that at these taxonomic levels most diversity has been discovered. This reasonably positive picture does not imply that algal taxonomy does not face serious challenges in the near future. The observed levels of cryptic diversity in algae, combined with the shift in methods used to characterize them, have resulted in a rampant uncertainty about the status of many older species. As a consequence, there is a tendency in phycology to move gradually away from traditional names to a more informal system whereby clade-, specimen- or strain-based identifiers are used to communicate biological information. Whether these informal names for species-level clades represent a temporary situation stimulated by the lag between species discovery and formal description, or an incipient alternative or parallel taxonomy, will be largely determined by how well we manage to integrate historical collections into modern taxonomic research. Additionally, there is a pressing need for a consensus about the organizational framework to manage the information about algal species names. An eventual strategy should preferably come out of an international working group that includes the various databases as well as the various phycological societies. In this strategy, phycologists should link up to major international initiatives that are currently being developed, such as the compulsory registration of taxonomic and nomenclatural acts and the introduction of Life Science Identifiers. © 2012 Phycological Society of America.

Diversity and distribution patterns of the Oligocene and Miocene decapod crustaceans (Crustacea: Malacostraca) of the Western and Central Paratethys

NASA Astrophysics Data System (ADS)

Hyžný, Matúš

2016-10-01

Decapod associations have been significant components of marine habitats throughout the Cenozoic when the major diversification of the group occurred. In this respect, the circum-Mediterranean area is of particular interest due to its complex palaeogeographic history. During the Oligo-Miocene, it was divided in two major areas, Mediterranean and Paratethys. Decapod crustaceans from the Paratethys Sea have been reported in the literature since the 19th century, but only recent research advances allow evaluation of the diversity and distribution patterns of the group. Altogether 176 species-level taxa have been identified from the Oligocene and Miocene of the Western and Central Paratethys. Using the three-dimensional NMDS analysis, the composition of decapod crustacean faunas of the Paratethys shows significant differences through time. The Ottnangian and Karpatian decapod associations were similar to each other both taxonomically and in the mode of preservation, and they differed taxonomically from the Badenian ones. The Early Badenian assemblages also differed taxonomically from the Late Badenian ones. The time factor, including speciation, immigration from other provinces and/or (local or global) extinction, can explain temporal differences among assemblages within the same environment. High decapod diversity during the Badenian was correlated with the presence of reefal settings. The Badenian was the time with the highest decapod diversity, which can, however, be a consequence of undersampling of other time slices. Whereas the Ottnangian and Karpatian decapod assemblages are preserved virtually exclusively in the siliciclastic "Schlier"-type facies that originated in non-reefal offshore environments, carbonate sedimentation and the presence of reefal environments during the Badenian in the Central Paratethys promoted thriving of more diverse reef-associated assemblages. In general, Paratethyan decapods exhibited homogeneous distribution during the Oligo-Miocene among the basins in the Paratethys. Based on the co-occurrence of certain decapod species, migration between the Paratethys and the North Sea during the Early Miocene probably occurred via the Rhine Graben. At larger spatial scales, our results suggest that the circum-Mediterranean marine decapod taxa migrated in an easterly direction during the Oligocene and/or Miocene, establishing present-day decapod communities in the Indo-West Pacific.

Integrating multiple evidences in taxonomy: species diversity and phylogeny of mustached bats (Mormoopidae: Pteronotus).

PubMed

Pavan, Ana Carolina; Marroig, Gabriel

2016-10-01

A phylogenetic systematic perspective is instrumental in recovering new species and their evolutionary relationships. The advent of new technologies for molecular and morphological data acquisition and analysis, allied to the integration of knowledge from different areas, such as ecology and population genetics, allows for the emergence of more rigorous, accurate and complete scientific hypothesis on species diversity. Mustached bats (genus Pteronotus) are a good model for the application of this integrative approach. They are a widely distributed and a morphologically homogeneous group, but comprising species with remarkable differences in their echolocation strategy and feeding behavior. The latest systematic review suggested six species with 17 subspecies in Pteronotus. Subsequent studies using discrete morphological characters supported the same arrangement. However, recent papers reported high levels of genetic divergence among conspecific taxa followed by bioacoustic and geographic agreement, suggesting an underestimated diversity in the genus. To date, no study merging genetic evidences and morphometric variation along the entire geographic range of this group has been attempted. Based on a comprehensive sampling including representatives of all current taxonomic units, we attempt to delimit species in Pteronotus through the application of multiple methodologies and hierarchically distinct datasets. The molecular approach includes six molecular markers from three genetic transmission systems; morphological investigations used 41 euclidean distances estimated through three-dimensional landmarks collected from 1628 skulls. The phylogenetic analysis reveals a greater diversity than previously reported, with a high correspondence among the genetic lineages and the currently recognized subspecies in the genus. Discriminant analysis of variables describing size and shape of cranial bones support the rising of the genetic groups to the specific status. Based on multiples evidences, we present an updated taxonomic arrangement composed by 16 extant species and a new and more robust phylogenetic hypothesis for the species included in the genus Pteronotus. Studies developed under such integrative taxonomic approach are timely for a deeper and wider comprehension of Neotropical diversity, representing the first step for answering broader questions on evolutionary and ecological aspects of Neotropical life history. Copyright © 2016 Elsevier Inc. All rights reserved.

Polar Lipids Analysis of Cultured Phytoplankton Reveals Significant Inter-taxa Changes, Low Influence of Growth Stage, and Usefulness in Chemotaxonomy.

PubMed

Cañavate, José Pedro; Armada, Isabel; Hachero-Cruzado, Ismael

2017-05-01

The high lipid diversity of microalgae has been used to taxonomically differentiate phytoplankton taxa at the class level. However, important lipids such as phospholipids (PL) and betaine lipids (BL) with potential chemotaxonomy application in phytoplankton ecology have been scarcely studied. The chemotaxonomy value of PL and BL depends on their intraspecific extent of variation as microalgae respond to external changing factors. To determine such effects, lipid class changes occurring at different growth stages in 15 microalgae from ten different classes were analyzed. BL occurred in 14 species and were the less affected lipids by growth stage with diacylglyceryl-hydroxymethyl-N,N,N-trimethyl-b-alanine (DGTA) showing the highest stability. PL were more influenced by growth stage with phosphatidylcholine (PC), phosphatidylglycerol (PG), and phosphatidyletanolamine (PE) declining towards older culture stages in some species. Glycolipids were the more common lipids, and no evident age-related variability pattern could be associated to taxonomic diversity. Selecting BL and PL as descriptor variables optimally distinguished microalgae taxonomic variability at all growth stages. Principal coordinate analysis arranged species through a main tendency from diacylglyceryl-hydroxymethyl-N,N,N-trimethyl-b-alanine (DGCC) containing species (mainly dinoflagellates and haptophytes) to DGTA or PC containing species (mainly cryptophytes). Two diatom classes with similar fatty acid profiles could be distinguished from their respective content in DGTA (Bacillariophyceae) or DGCC (Mediophyceae). In green lineage classes (Trebouxiophyceae, Porphyridophyceae, and Chlorodendrophyceae), PC was a better descriptor than BL. BL and PL explained a higher proportion of microalgae taxonomic variation than did fatty acids and played a complementary role as lipid markers.

Beta Diversity in a Highly Heterogeneous Area: Disentangling Species and Taxonomic Dissimilarity for Terrestrial Vertebrates

PubMed Central

Calderón-Patrón, Jaime M.; Goyenechea, Irene; Ortiz-Pulido, Raúl; Castillo-Cerón, Jesús; Manriquez, Norma; Ramírez-Bautista, Aurelio; Rojas-Martínez, Alberto E.; Sánchez-Rojas, Gerardo; Zuria, Iriana

2016-01-01

Quantifying differences in species composition among communities provides important information related to the distribution, conservation and management of biodiversity, especially when two components are recognized: dissimilarity due to turnover, and dissimilarity due to richness differences. The ecoregions in central Mexico, within the Mexican Transition Zone, have outstanding environmental heterogeneity and harbor huge biological richness, besides differences in the origin of the biota. Therefore, biodiversity studies in this area require the use of complementary measures to achieve appropriate information that may help in the design of conservation strategies. In this work we analyze the dissimilarity of terrestrial vertebrates, and the components of turnover and richness differences, among six ecoregions in the state of Hidalgo, central Mexico. We follow two approaches: one based on species level dissimilarity, and the second on taxonomic dissimilarity. We used databases from the project “Biodiversity in the state of Hidalgo”. Our results indicate that species dissimilarity is higher than taxonomic dissimilarity, and that turnover contributes more than richness differences, both for species and taxonomic total dissimilarity. Moreover, total dissimilarity, turnover dissimilarity and the dissimilarity due to richness differences were positively related in the four vertebrate groups. Reptiles had the highest values of dissimilarity, followed by mammals, amphibians and birds. For reptiles, birds, and mammals, species turnover was the most important component, while richness differences had a higher contribution for amphibians. The highest values of dissimilarity occurred between environmentally contrasting ecoregions (i.e., tropical and temperate forests), which suggests that environmental heterogeneity and differences in the origin of biotas are key factors driving beta diversity of terrestrial vertebrates among ecoregions in this complex area. PMID:27500934

Minimal Similarity between Biogeographic Patterns of Morphological Disparity and Taxonomic Richness in Extant Coccolithophores

NASA Astrophysics Data System (ADS)

Villarosa Garcia, M.

2016-02-01

Morphologic disparity, carries both an ecological and evolutionary signal and, where practical, might bridge ecological processes observed in modern seas with macroevolutionary processes observed in the fossil record, complementing taxonomic diversity studies. I compare the biogeography of morphologic disparity and taxonomic richness in extant coccolithophores to understand the role of environmental conditions in their spatial partitioning. I analyze 112 traits in 125 species and measure geographic extent as the occupation of pelagic biogeographic provinces (sensu Spalding et al. 2012). In the modern ocean, coccolithophorid species richness increases towards the equator, peaking in the subtropics, and certain biomes harbor more species. In contrast, their morphologic disparity does not vary across latitudes and biomes, yielding similar values of variance and mean pair-wise distances. Disparity is weakly correlated to richness across clades and biomes (no clear latitudinal pattern). I also study the morphological breadth of clades in a multivariate morphospace plotted as principal coordinate axes (PCO). Clades have distinct centroids but show some overlap in volume. However, they are completely separate when using canonical variates analysis (CVA) on these PCO axes. The centroids of latitudinal groups are closely spaced, and overlap in morphospace, but again separate with CVA. However biome groups can't be distinguished using PCO or CVA. Although clades with the most species tend to have high disparity, most clades are found in every region yielding similar group disparities. Despite the fact that taxonomic diversity is spatially partitioned on the globe, morphologic disparity has no such organization. Past studies using marine gastropods (Roy et al. 2001; McClain 2005), cuttlefish (Neige 2003), and birds (Jønsson et al. 2015) also find minimal support for a biogeographic structure of disparity, highlighting the profound nature of this differential response.

Body Size Is a Significant Predictor of Congruency in Species Richness Patterns: A Meta-Analysis of Aquatic Studies

PubMed Central

Velghe, Katherine; Gregory-Eaves, Irene

2013-01-01

Biodiversity losses over the next century are predicted to result in alterations of ecosystem functions that are on par with other major drivers of global change. Given the seriousness of this issue, there is a need to effectively monitor global biodiversity. Because performing biodiversity censuses of all taxonomic groups is prohibitively costly, indicator groups have been studied to estimate the biodiversity of different taxonomic groups. Quantifying cross-taxon congruence is a method of evaluating the assumption that the diversity of one taxonomic group can be used to predict the diversity of another. To improve the predictive ability of cross-taxon congruence in aquatic ecosystems, we evaluated whether body size, measured as the ratio of average body length between organismal groups, is a significant predictor of their cross-taxon biodiversity congruence. To test this hypothesis, we searched the published literature and screened for studies that used species richness correlations as their metric of cross-taxon congruence. We extracted 96 correlation coefficients from 16 studies, which encompassed 784 inland water bodies. With these correlation coefficients, we conducted a categorical meta-analysis, grouping data based on the body size ratio of organisms. Our results showed that cross-taxon congruence is variable among sites and between different groups (r values ranging between −0.53 to 0.88). In addition, our quantitative meta-analysis demonstrated that organisms most similar in body size showed stronger species richness correlations than organisms which differed increasingly in size (radj 2 = 0.94, p = 0.02). We propose that future studies applying biodiversity indicators in aquatic ecosystems consider functional traits such as body size, so as to increase their success at predicting the biodiversity of taxonomic groups where cost-effective conservation tools are needed. PMID:23468903

Beta Diversity in a Highly Heterogeneous Area: Disentangling Species and Taxonomic Dissimilarity for Terrestrial Vertebrates.

PubMed

Calderón-Patrón, Jaime M; Goyenechea, Irene; Ortiz-Pulido, Raúl; Castillo-Cerón, Jesús; Manriquez, Norma; Ramírez-Bautista, Aurelio; Rojas-Martínez, Alberto E; Sánchez-Rojas, Gerardo; Zuria, Iriana; Moreno, Claudia E

2016-01-01

Quantifying differences in species composition among communities provides important information related to the distribution, conservation and management of biodiversity, especially when two components are recognized: dissimilarity due to turnover, and dissimilarity due to richness differences. The ecoregions in central Mexico, within the Mexican Transition Zone, have outstanding environmental heterogeneity and harbor huge biological richness, besides differences in the origin of the biota. Therefore, biodiversity studies in this area require the use of complementary measures to achieve appropriate information that may help in the design of conservation strategies. In this work we analyze the dissimilarity of terrestrial vertebrates, and the components of turnover and richness differences, among six ecoregions in the state of Hidalgo, central Mexico. We follow two approaches: one based on species level dissimilarity, and the second on taxonomic dissimilarity. We used databases from the project "Biodiversity in the state of Hidalgo". Our results indicate that species dissimilarity is higher than taxonomic dissimilarity, and that turnover contributes more than richness differences, both for species and taxonomic total dissimilarity. Moreover, total dissimilarity, turnover dissimilarity and the dissimilarity due to richness differences were positively related in the four vertebrate groups. Reptiles had the highest values of dissimilarity, followed by mammals, amphibians and birds. For reptiles, birds, and mammals, species turnover was the most important component, while richness differences had a higher contribution for amphibians. The highest values of dissimilarity occurred between environmentally contrasting ecoregions (i.e., tropical and temperate forests), which suggests that environmental heterogeneity and differences in the origin of biotas are key factors driving beta diversity of terrestrial vertebrates among ecoregions in this complex area.

Community analysis of pigment patterns from 37 microalgae strains reveals new carotenoids and porphyrins characteristic of distinct strains and taxonomic groups

PubMed Central

Bérard, Jean-Baptiste; Kaas, Raymond; Pasquet, Virginie; Picot, Laurent; Cadoret, Jean-Paul

2017-01-01

Phytoplankton, with an estimated 30 000 to 1 000 000 species clustered in 12 phyla, presents a high taxonomic and ecophysiological diversity, reflected by the complex distribution of pigments among the different algal classes. High performance liquid chromatography is the gold standard method for qualitative and quantitative analysis of phytoplankton pigments in seawater and culture samples, but only a few pigments can be used as robust chemotaxonomic markers. A major challenge is thus to identify new ones, characteristic of a strain, species, class or taxon that cannot be currently identified on the basis of its pigment signature. Using an optimized extraction process coupled to a HPLC de-replication strategy, we examined the pigment composition of 37 microalgae strains, representative of the broad taxonomic diversity of marine and freshwater species (excluding cyanobacteria). For each species, the major pigments already described were unambiguously identified. We also observed the presence of several minor unidentified pigments in each chromatogram. The global analysis of pigment compositions revealed a total of 124 pigments, including 98 pigments or derivatives unidentified using the standards. Absorption spectra indicated that 35 corresponded to chlorophyll/porphyrin derivatives, 57 to carotenoids and six to derivatives having both spectral signatures. Sixty-one of these unidentified or new carotenoids and porphyrin derivatives were characteristic of particular strains or species, indicating their possible use as highly specific chemotaxonomic markers capable of identifying one strain out of the 37 selected. We developed a graphical analysis using Gephi software to give a clear representation of pigment communities among the various phytoplankton strains, and to reveal strain-characteristic and shared pigments. This made it possible to reconstruct the taxonomic evolution of microalgae classes, on the basis of the conservation, loss, and/or appearance of pigments. PMID:28231253

Botany, ethnomedicines, phytochemistry and pharmacology of Himalayan paeony (Paeonia emodi Royle.).

PubMed

Ahmad, Mushtaq; Malik, Khafsa; Tariq, Akash; Zhang, Guolin; Yaseen, Ghulam; Rashid, Neelam; Sultana, Shazia; Zafar, Muhammad; Ullah, Kifayat; Khan, Muhammad Pukhtoon Zada

2018-06-28

Himalayan paeony (Paeonia emodi Royle.) is an important species used to treat various diseases. This study aimed to compile the detailed traditional medicinal uses, phytochemistry, pharmacology and toxicological investigations on P. emodi. This study also highlights taxonomic validity, quality of experimental designs and shortcomings in previously reported information on Himalayan paeony. The data was extracted from unpublished theses (Pakistan, China, India and Nepal), and different published research articles confined to pharmacology, phytochemistry and antimicrobial activities using different databases through specific keywords. The relevant information regarding medicinal uses, taxonomic/common names, part used, collection and identification source, authentication, voucher specimen number, plant extracts and their characterization, isolation and identification of phytochemicals, methods of study in silico, in vivo or in vitro, model organism used, dose and duration, minimal active concentration, zone of inhibition (antimicrobial study), bioactive compound(s), mechanism of action on single or multiple targets, and toxicological information. P. emodi is reported for diverse medicinal uses with pharmacological properties like antioxidant, nephroprotective, lipoxygenase inhibitory, cognition and oxidative stress release, cytotoxic, anti-inflammatory, antiepileptic, anticonvulsant, haemaglutination, alpha-chymotrypsin inhibitory, hepatoprotective, hepatic chromes and pharmacokinetics of carbamazepine expression, β-glucuronidase inhibitory, spasmolytic and spasmogenic, and airway relaxant. Data confined to its taxonomic validity, shows 10% studies with correct taxonomic name while 90% studies with incorrect taxonomic, pharmacopeial and common names. The literature reviewed, shows lack of collection source (11 reports), without proper source of identification (15 reports), 33 studies without voucher specimen number, 26 reports lack information on authentic herbarium submission and most of the studies (90%) without validation of taxonomic names using recognized databases. In reported methods, 67% studies without characterization of extracts, 25% lack proper dose, 40% without duration and 31% reports lack information on proper controls. Similarly, only 18% studies reports active compound(s) responsible for pharmacological activities, 14% studies show minimal active concentration, only 2.5% studies report mechanism of action on target while none of the reports mentioned in silico approach. P. emodi is endemic to Himalayan region (Pakistan, China, India and Nepal) with diverse traditional therapeutic uses. Majority of reviewed studies showed confusion in its taxonomic validity, incomplete methodologies and ambiguous findings. Keeping in view the immense uses of P. emodi in various traditional medicinal systems, holistic pharmacological approaches in combination with reverse pharmacology, system biology, and "omics" technologies are recommended to improve the quality of research which leads to natural drug discovery development at global perspectives. Copyright © 2018 Elsevier B.V. All rights reserved.

Tandem-repeat protein domains across the tree of life.

PubMed

Jernigan, Kristin K; Bordenstein, Seth R

2015-01-01

Tandem-repeat protein domains, composed of repeated units of conserved stretches of 20-40 amino acids, are required for a wide array of biological functions. Despite their diverse and fundamental functions, there has been no comprehensive assessment of their taxonomic distribution, incidence, and associations with organismal lifestyle and phylogeny. In this study, we assess for the first time the abundance of armadillo (ARM) and tetratricopeptide (TPR) repeat domains across all three domains in the tree of life and compare the results to our previous analysis on ankyrin (ANK) repeat domains in this journal. All eukaryotes and a majority of the bacterial and archaeal genomes analyzed have a minimum of one TPR and ARM repeat. In eukaryotes, the fraction of ARM-containing proteins is approximately double that of TPR and ANK-containing proteins, whereas bacteria and archaea are enriched in TPR-containing proteins relative to ARM- and ANK-containing proteins. We show in bacteria that phylogenetic history, rather than lifestyle or pathogenicity, is a predictor of TPR repeat domain abundance, while neither phylogenetic history nor lifestyle predicts ARM repeat domain abundance. Surprisingly, pathogenic bacteria were not enriched in TPR-containing proteins, which have been associated within virulence factors in certain species. Taken together, this comparative analysis provides a newly appreciated view of the prevalence and diversity of multiple types of tandem-repeat protein domains across the tree of life. A central finding of this analysis is that tandem repeat domain-containing proteins are prevalent not just in eukaryotes, but also in bacterial and archaeal species.

Global loss of avian evolutionary uniqueness in urban areas.

PubMed

Ibáñez-Álamo, Juan Diego; Rubio, Enrique; Benedetti, Yanina; Morelli, Federico

2017-08-01

Urbanization, one of the most important anthropogenic impacts on Earth, is rapidly expanding worldwide. This expansion of urban land-covered areas is known to significantly reduce different components of biodiversity. However, the global evidence for this effect is mainly focused on a single diversity measure (species richness) with a few local or regional studies also supporting reductions in functional diversity. We have used birds, an important ecological group that has been used as surrogate for other animals, to investigate the hypothesis that urbanization reduces the global taxonomical and/or evolutionary diversity. We have also explored whether there is evidence supporting that urban bird communities are evolutionarily homogenized worldwide in comparison with nonurban ones by means of using evolutionary distinctiveness (how unique are the species) of bird communities. To our knowledge, this is the first attempt to quantify the effect of urbanization in more than one single diversity measure as well as the first time to look for associations between urbanization and phylogenetic diversity at a large spatial scale. Our findings show a strong and globally consistent reduction in taxonomic diversity in urban areas, which is also synchronized with the evolutionary homogenization of urban bird communities. Despite our general patterns, we found some regional differences in the intensity of the effect of cities on bird species richness or evolutionary distinctiveness, suggesting that conservation efforts should be adapted locally. Our findings might be useful for conservationists and policymakers to minimize the impact of urban development on Earth's biodiversity and help design more realistic conservation strategies. © 2016 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Assessing macroinvertebrate biodiversity in freshwater ecosystems: advances and challenges in DNA-based approaches

EPA Science Inventory

Assessing the biodiversity of macroinvertebrate faunas in freshwater ecosystems is an essential component of both basic ecological inquiry and applied ecological assessments. Aspects of taxonomic diversity and composition in freshwater communities are widely used to quantify wate...

Functional characterization of two concrete biofilms using pyrosequencing data

EPA Science Inventory

Phylogenetic studies of concrete biofilms using 16SrRNA-based approaches have demonstrated that concrete surfaces harbor a diverse microbial community. These approaches can provide information on the general taxonomical groups present in a sample but cannot shed light on the func...

Annotated checklist of fish cestodes from South America

PubMed Central

Alves, Philippe V.; de Chambrier, Alain; Scholz, Tomáš; Luque, José L.

2017-01-01

Abstract An exhaustive literature search supplemented by a critical examination of records made it possible to present an annotated checklist of tapeworms (Cestoda) that, as adults or larvae (metacestodes), parasitize freshwater, brackish water and marine fishes, i.e. cartilaginous and bony fishes, in South America. The current knowledge of their species diversity, host associations and geographical distribution is reviewed. Taxonomic problems are discussed based on a critical evaluation of the literature and information on DNA sequences of individual taxa is provided to facilitate future taxonomic and phylogenetic studies. As expected, the current knowledge is quite uneven regarding the number of taxa and host-associations reported from the principal river basins and marine ecoregions. These differences may not only reflect the actual cestode richness but may also be due to the research effort that has been devoted to unravelling the diversity of these endoparasitic helminths in individual countries. A total of 297 valid species, 61 taxa identified to the generic level, in addition to unidentified cestodes, were recorded from 401 species of fish hosts. Among the recognized cestode orders, 13 have been recorded in South America, with the Onchoproteocephalidea displaying the highest species richness, representing c. 50% of all species diversity. The majority of records include teleost fish hosts (79%) that harbour larval and adult stages of cestodes, whereas stingrays (Myliobatiformes) exhibit the highest proportion of records (39%) among the elasmobranch hosts. Fish cestodes are ubiquitous in South America, being mostly recorded from the Warm Temperate Southeastern Pacific (WTSP; 31%) for marine hosts and the Amazon River basin (45%) for freshwater ones. The following problems were detected during the compilation of literary data: (i) unreliability of many records; (ii) poor taxonomic resolution, i.e. identification made only to the genus or even family level; (iii) doubtful host identification; and (iv) the absence of voucher specimens that would enable us to verify identification. It is thus strongly recommended to always deposit representative specimens in any type of studies, including faunal surveys and ecological studies. An analysis of the proportion of three basic types of studies, i.e. surveys, taxonomic and ecological papers, has shown a considerable increase of ecological studies over the last decade. PMID:28331385

Annotated checklist of fish cestodes from South America.

PubMed

Alves, Philippe V; de Chambrier, Alain; Scholz, Tomáš; Luque, José L

2017-01-01

An exhaustive literature search supplemented by a critical examination of records made it possible to present an annotated checklist of tapeworms (Cestoda) that, as adults or larvae (metacestodes), parasitize freshwater, brackish water and marine fishes, i.e. cartilaginous and bony fishes, in South America. The current knowledge of their species diversity, host associations and geographical distribution is reviewed. Taxonomic problems are discussed based on a critical evaluation of the literature and information on DNA sequences of individual taxa is provided to facilitate future taxonomic and phylogenetic studies. As expected, the current knowledge is quite uneven regarding the number of taxa and host-associations reported from the principal river basins and marine ecoregions. These differences may not only reflect the actual cestode richness but may also be due to the research effort that has been devoted to unravelling the diversity of these endoparasitic helminths in individual countries. A total of 297 valid species, 61 taxa identified to the generic level, in addition to unidentified cestodes, were recorded from 401 species of fish hosts. Among the recognized cestode orders, 13 have been recorded in South America, with the Onchoproteocephalidea displaying the highest species richness, representing c. 50% of all species diversity. The majority of records include teleost fish hosts (79%) that harbour larval and adult stages of cestodes, whereas stingrays (Myliobatiformes) exhibit the highest proportion of records (39%) among the elasmobranch hosts. Fish cestodes are ubiquitous in South America, being mostly recorded from the Warm Temperate Southeastern Pacific (WTSP; 31%) for marine hosts and the Amazon River basin (45%) for freshwater ones. The following problems were detected during the compilation of literary data: (i) unreliability of many records; (ii) poor taxonomic resolution, i.e. identification made only to the genus or even family level; (iii) doubtful host identification; and (iv) the absence of voucher specimens that would enable us to verify identification. It is thus strongly recommended to always deposit representative specimens in any type of studies, including faunal surveys and ecological studies. An analysis of the proportion of three basic types of studies, i.e. surveys, taxonomic and ecological papers, has shown a considerable increase of ecological studies over the last decade.

Validation of the Hirst-Type Spore Trap for Simultaneous Monitoring of Prokaryotic and Eukaryotic Biodiversities in Urban Air Samples by Next-Generation Sequencing.

PubMed

Núñez, Andrés; Amo de Paz, Guillermo; Ferencova, Zuzana; Rastrojo, Alberto; Guantes, Raúl; García, Ana M; Alcamí, Antonio; Gutiérrez-Bustillo, A Montserrat; Moreno, Diego A

2017-07-01

Pollen, fungi, and bacteria are the main microscopic biological entities present in outdoor air, causing allergy symptoms and disease transmission and having a significant role in atmosphere dynamics. Despite their relevance, a method for monitoring simultaneously these biological particles in metropolitan environments has not yet been developed. Here, we assessed the use of the Hirst-type spore trap to characterize the global airborne biota by high-throughput DNA sequencing, selecting regions of the 16S rRNA gene and internal transcribed spacer for the taxonomic assignment. We showed that aerobiological communities are well represented by this approach. The operational taxonomic units (OTUs) of two traps working synchronically compiled >87% of the total relative abundance for bacterial diversity collected in each sampler, >89% for fungi, and >97% for pollen. We found a good correspondence between traditional characterization by microscopy and genetic identification, obtaining more-accurate taxonomic assignments and detecting a greater diversity using the latter. We also demonstrated that DNA sequencing accurately detects differences in biodiversity between samples. We concluded that high-throughput DNA sequencing applied to aerobiological samples obtained with Hirst spore traps provides reliable results and can be easily implemented for monitoring prokaryotic and eukaryotic entities present in the air of urban areas. IMPORTANCE Detection, monitoring, and characterization of the wide diversity of biological entities present in the air are difficult tasks that require time and expertise in different disciplines. We have evaluated the use of the Hirst spore trap (an instrument broadly employed in aerobiological studies) to detect and identify these organisms by DNA-based analyses. Our results showed a consistent collection of DNA and a good concordance with traditional methods for identification, suggesting that these devices can be used as a tool for continuous monitoring of the airborne biodiversity, improving taxonomic resolution and characterization together. They are also suitable for acquiring novel DNA amplicon-based information in order to gain a better understanding of the biological particles present in a scarcely known environment such as the air. Copyright © 2017 American Society for Microbiology.

Validation of the Hirst-Type Spore Trap for Simultaneous Monitoring of Prokaryotic and Eukaryotic Biodiversities in Urban Air Samples by Next-Generation Sequencing

PubMed Central

Núñez, Andrés; Amo de Paz, Guillermo; Ferencova, Zuzana; Rastrojo, Alberto; Guantes, Raúl; García, Ana M.; Alcamí, Antonio; Gutiérrez-Bustillo, A. Montserrat

2017-01-01

ABSTRACT Pollen, fungi, and bacteria are the main microscopic biological entities present in outdoor air, causing allergy symptoms and disease transmission and having a significant role in atmosphere dynamics. Despite their relevance, a method for monitoring simultaneously these biological particles in metropolitan environments has not yet been developed. Here, we assessed the use of the Hirst-type spore trap to characterize the global airborne biota by high-throughput DNA sequencing, selecting regions of the 16S rRNA gene and internal transcribed spacer for the taxonomic assignment. We showed that aerobiological communities are well represented by this approach. The operational taxonomic units (OTUs) of two traps working synchronically compiled >87% of the total relative abundance for bacterial diversity collected in each sampler, >89% for fungi, and >97% for pollen. We found a good correspondence between traditional characterization by microscopy and genetic identification, obtaining more-accurate taxonomic assignments and detecting a greater diversity using the latter. We also demonstrated that DNA sequencing accurately detects differences in biodiversity between samples. We concluded that high-throughput DNA sequencing applied to aerobiological samples obtained with Hirst spore traps provides reliable results and can be easily implemented for monitoring prokaryotic and eukaryotic entities present in the air of urban areas. IMPORTANCE Detection, monitoring, and characterization of the wide diversity of biological entities present in the air are difficult tasks that require time and expertise in different disciplines. We have evaluated the use of the Hirst spore trap (an instrument broadly employed in aerobiological studies) to detect and identify these organisms by DNA-based analyses. Our results showed a consistent collection of DNA and a good concordance with traditional methods for identification, suggesting that these devices can be used as a tool for continuous monitoring of the airborne biodiversity, improving taxonomic resolution and characterization together. They are also suitable for acquiring novel DNA amplicon-based information in order to gain a better understanding of the biological particles present in a scarcely known environment such as the air. PMID:28455334

Microbial analysis in primary and persistent endodontic infections by using pyrosequencing.

PubMed

Hong, Bo-Young; Lee, Tae-Kwon; Lim, Sang-Min; Chang, Seok Woo; Park, Joonhong; Han, Seung Hyun; Zhu, Qiang; Safavi, Kamran E; Fouad, Ashraf F; Kum, Kee Yeon

2013-09-01

The aim of this study was to investigate the bacterial community profile of intracanal microbiota in primary and persistent endodontic infections associated with asymptomatic chronic apical periodontitis by using GS-FLX Titanium pyrosequencing. The null hypothesis was that there is no difference in diversity of overall bacterial community profiles between primary and persistent infections. Pyrosequencing analysis from 10 untreated and 8 root-filled samples was conducted. Analysis from 18 samples yielded total of 124,767 16S rRNA gene sequences (with a mean of 6932 reads per sample) that were taxonomically assigned into 803 operational taxonomic units (3% distinction), 148 genera, and 10 phyla including unclassified. Bacteroidetes was the most abundant phylum in both primary and persistent infections. There were no significant differences in bacterial diversity between the 2 infection groups (P > .05). The bacterial community profile that was based on dendrogram showed that bacterial population in both infections was not significantly different in their structure and composition (P > .05). The present pyrosequencing study demonstrates that persistent infections have as diverse bacterial community as primary infections. Copyright © 2013 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures.

PubMed

Wilkins, Laetitia G E; Rogivue, Aude; Schütz, Frédéric; Fumagalli, Luca; Wedekind, Claus

2015-11-27

The taxonomic composition of egg-associated microbial communities can play a crucial role in the development of fish embryos. In response, hosts increasingly influence the composition of their associated microbial communities during embryogenesis, as concluded from recent field studies and laboratory experiments. However, little is known about the taxonomic composition and the diversity of egg-associated microbial communities within ecosystems; e.g., river networks. We sampled late embryonic stages of naturally spawned brown trout at nine locations within two different river networks and applied 16S rRNA pyrosequencing to describe their bacterial communities. We found no evidence for a significant isolation-by-distance effect on the composition of bacterial communities, and no association between neutral genetic divergence of fish host (based on 11 microsatellites) and phylogenetic distances of the composition of their associated bacterial communities. We characterized core bacterial communities on brown trout eggs and compared them to corresponding water samples with regard to bacterial composition and its presumptive function. Bacterial diversity was positively correlated with water temperature at the spawning locations. We discuss this finding in the context of the increased water temperatures that have been recorded during the last 25 years in the study area.

Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures

PubMed Central

Wilkins, Laetitia G. E.; Rogivue, Aude; Schütz, Frédéric; Fumagalli, Luca; Wedekind, Claus

2015-01-01

The taxonomic composition of egg-associated microbial communities can play a crucial role in the development of fish embryos. In response, hosts increasingly influence the composition of their associated microbial communities during embryogenesis, as concluded from recent field studies and laboratory experiments. However, little is known about the taxonomic composition and the diversity of egg-associated microbial communities within ecosystems; e.g., river networks. We sampled late embryonic stages of naturally spawned brown trout at nine locations within two different river networks and applied 16S rRNA pyrosequencing to describe their bacterial communities. We found no evidence for a significant isolation-by-distance effect on the composition of bacterial communities, and no association between neutral genetic divergence of fish host (based on 11 microsatellites) and phylogenetic distances of the composition of their associated bacterial communities. We characterized core bacterial communities on brown trout eggs and compared them to corresponding water samples with regard to bacterial composition and its presumptive function. Bacterial diversity was positively correlated with water temperature at the spawning locations. We discuss this finding in the context of the increased water temperatures that have been recorded during the last 25 years in the study area. PMID:26611640

Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing

PubMed Central

Logares, Ramiro; Audic, Stephane; Santini, Sebastien; Pernice, Massimo C; de Vargas, Colomban; Massana, Ramon

2012-01-01

Flagellated heterotrophic microeukaryotes have key roles for the functioning of marine ecosystems as they channel large amounts of organic carbon to the upper trophic levels and control the population sizes of bacteria and archaea. Still, we know very little on the diversity patterns of most groups constituting this evolutionary heterogeneous assemblage. Here, we investigate 11 groups of uncultured flagellates known as MArine STramenopiles (MASTs). MASTs are ecologically very important and branch at the base of stramenopiles. We explored the diversity patterns of MASTs using pyrosequencing (18S rDNA) in coastal European waters. We found that MAST groups range from highly to lowly diversified. Pyrosequencing (hereafter ‘454') allowed us to approach to the limits of taxonomic diversity for all MAST groups, which varied in one order of magnitude (tens to hundreds) in terms of operational taxonomic units (98% similarity). We did not evidence large differences in activity, as indicated by ratios of DNA:RNA-reads. Most groups were strictly planktonic, although we found some groups that were active in sediments and even in anoxic waters. The proportion of reads per size fraction indicated that most groups were composed of very small cells (∼2–5 μm). In addition, phylogenetically different assemblages appeared to be present in different size fractions, depths and geographic zones. Thus, MAST diversity seems to be highly partitioned in spatial scales. Altogether, our results shed light on these ecologically very important but poorly known groups of uncultured marine flagellates. PMID:22534609

Molecular diversity and distribution of marine fungi across 130 European environmental samples.

PubMed

Richards, Thomas A; Leonard, Guy; Mahé, Frédéric; Del Campo, Javier; Romac, Sarah; Jones, Meredith D M; Maguire, Finlay; Dunthorn, Micah; De Vargas, Colomban; Massana, Ramon; Chambouvet, Aurélie

2015-11-22

Environmental DNA and culture-based analyses have suggested that fungi are present in low diversity and in low abundance in many marine environments, especially in the upper water column. Here, we use a dual approach involving high-throughput diversity tag sequencing from both DNA and RNA templates and fluorescent cell counts to evaluate the diversity and relative abundance of fungi across marine samples taken from six European near-shore sites. We removed very rare fungal operational taxonomic units (OTUs) selecting only OTUs recovered from multiple samples for a detailed analysis. This approach identified a set of 71 fungal 'OTU clusters' that account for 66% of all the sequences assigned to the Fungi. Phylogenetic analyses demonstrated that this diversity includes a significant number of chytrid-like lineages that had not been previously described, indicating that the marine environment encompasses a number of zoosporic fungi that are new to taxonomic inventories. Using the sequence datasets, we identified cases where fungal OTUs were sampled across multiple geographical sites and between different sampling depths. This was especially clear in one relatively abundant and diverse phylogroup tentatively named Novel Chytrid-Like-Clade 1 (NCLC1). For comparison, a subset of the water column samples was also investigated using fluorescent microscopy to examine the abundance of eukaryotes with chitin cell walls. Comparisons of relative abundance of RNA-derived fungal tag sequences and chitin cell-wall counts demonstrate that fungi constitute a low fraction of the eukaryotic community in these water column samples. Taken together, these results demonstrate the phylogenetic position and environmental distribution of 71 lineages, improving our understanding of the diversity and abundance of fungi in marine environments. © 2015 The Authors.

Molecular diversity and distribution of marine fungi across 130 European environmental samples

PubMed Central

Richards, Thomas A.; Leonard, Guy; Mahé, Frédéric; del Campo, Javier; Romac, Sarah; Jones, Meredith D. M.; Maguire, Finlay; Dunthorn, Micah; De Vargas, Colomban; Massana, Ramon; Chambouvet, Aurélie

2015-01-01

Environmental DNA and culture-based analyses have suggested that fungi are present in low diversity and in low abundance in many marine environments, especially in the upper water column. Here, we use a dual approach involving high-throughput diversity tag sequencing from both DNA and RNA templates and fluorescent cell counts to evaluate the diversity and relative abundance of fungi across marine samples taken from six European near-shore sites. We removed very rare fungal operational taxonomic units (OTUs) selecting only OTUs recovered from multiple samples for a detailed analysis. This approach identified a set of 71 fungal ‘OTU clusters' that account for 66% of all the sequences assigned to the Fungi. Phylogenetic analyses demonstrated that this diversity includes a significant number of chytrid-like lineages that had not been previously described, indicating that the marine environment encompasses a number of zoosporic fungi that are new to taxonomic inventories. Using the sequence datasets, we identified cases where fungal OTUs were sampled across multiple geographical sites and between different sampling depths. This was especially clear in one relatively abundant and diverse phylogroup tentatively named Novel Chytrid-Like-Clade 1 (NCLC1). For comparison, a subset of the water column samples was also investigated using fluorescent microscopy to examine the abundance of eukaryotes with chitin cell walls. Comparisons of relative abundance of RNA-derived fungal tag sequences and chitin cell-wall counts demonstrate that fungi constitute a low fraction of the eukaryotic community in these water column samples. Taken together, these results demonstrate the phylogenetic position and environmental distribution of 71 lineages, improving our understanding of the diversity and abundance of fungi in marine environments. PMID:26582030

Fast Census of Moth Diversity in the Neotropics: A Comparison of Field-Assigned Morphospecies and DNA Barcoding in Tiger Moths

PubMed Central

Zenker, Mauricio M.; Rougerie, Rodolphe; Teston, José A.; Laguerre, Michel; Pie, Marcio R.; Freitas, André V. L.

2016-01-01

The morphological species delimitations (i.e. morphospecies) have long been the best way to avoid the taxonomic impediment and compare insect taxa biodiversity in highly diverse tropical and subtropical regions. The development of DNA barcoding, however, has shown great potential to replace (or at least complement) the morphospecies approach, with the advantage of relying on automated methods implemented in computer programs or even online rather than in often subjective morphological features. We sampled moths extensively for two years using light traps in a patch of the highly endangered Atlantic Forest of Brazil to produce a nearly complete census of arctiines (Noctuoidea: Erebidae), whose species richness was compared using different morphological and molecular approaches (DNA barcoding). A total of 1,075 barcode sequences of 286 morphospecies were analyzed. Based on the clustering method Barcode Index Number (BIN) we found a taxonomic bias of approximately 30% in our initial morphological assessment. However, a morphological reassessment revealed that the correspondence between morphospecies and molecular operational taxonomic units (MOTUs) can be up to 94% if differences in genitalia morphology are evaluated in individuals of different MOTUs originated from the same morphospecies (putative cases of cryptic species), and by recording if individuals of different genders in different morphospecies merge together in the same MOTU (putative cases of sexual dimorphism). The results of two other clustering methods (i.e. Automatic Barcode Gap Discovery and 2% threshold) were very similar to those of the BIN approach. Using empirical data we have shown that DNA barcoding performed substantially better than the morphospecies approach, based on superficial morphology, to delimit species of a highly diverse moth taxon, and thus should be used in species inventories. PMID:26859488

Pyrosequencing of mcrA and Archaeal 16S rRNA Genes Reveals Diversity and Substrate Preferences of Methanogen Communities in Anaerobic Digesters

PubMed Central

Wilkins, David; Lu, Xiao-Ying; Shen, Zhiyong; Chen, Jiapeng

2014-01-01

Methanogenic archaea play a key role in biogas-producing anaerobic digestion and yet remain poorly taxonomically characterized. This is in part due to the limitations of low-throughput Sanger sequencing of a single (16S rRNA) gene, which in the past may have undersampled methanogen diversity. In this study, archaeal communities from three sludge digesters in Hong Kong and one wastewater digester in China were examined using high-throughput pyrosequencing of the methyl coenzyme M reductase (mcrA) and 16S rRNA genes. Methanobacteriales, Methanomicrobiales, and Methanosarcinales were detected in each digester, indicating that both hydrogenotrophic and acetoclastic methanogenesis was occurring. Two sludge digesters had similar community structures, likely due to their similar design and feedstock. Taxonomic classification of the mcrA genes suggested that these digesters were dominated by acetoclastic methanogens, particularly Methanosarcinales, while the other digesters were dominated by hydrogenotrophic Methanomicrobiales. The proposed euryarchaeotal order Methanomassiliicoccales and the uncultured WSA2 group were detected with the 16S rRNA gene, and potential mcrA genes for these groups were identified. 16S rRNA gene sequencing also recovered several crenarchaeotal groups potentially involved in the initial anaerobic digestion processes. Overall, the two genes produced different taxonomic profiles for the digesters, while greater methanogen richness was detected using the mcrA gene, supporting the use of this functional gene as a complement to the 16S rRNA gene to better assess methanogen diversity. A significant positive correlation was detected between methane production and the abundance of mcrA transcripts in digesters treating sludge and wastewater samples, supporting the mcrA gene as a biomarker for methane yield. PMID:25381241

Morphology of Floral Papillae in Maxillaria Ruiz & Pav. (Orchidaceae)

PubMed Central

DAVIES, K. L.; TURNER, M. P.

2004-01-01

• Background and Aims The labellar papillae and trichomes of Maxillaria Ruiz & Pav. show great diversity. Although papillae also occur upon other parts of the flower (e.g. column and anther cap), these have not yet been studied. Labellar trichomes of Maxillaria are useful in taxonomy, but hitherto the taxonomic value of floral papillae has not been assessed. The aim of this paper is to describe the range of floral papillae found in Maxillaria and to determine whether papillae are useful as taxonomic characters. • Methods Light microscopy, histochemistry, low‐vacuum scanning and transmission electron microscopy. • Key Results A total of 75 taxa were studied. Conical papillae with rounded or pointed tips were the most common. The column and anther cap usually bear conical, obpyriform or villiform papillae, whereas those around the stigmatic surface and at the base of the anther are often larger and swollen. Labellar papillae show greater diversity, and may be conical, obpyriform, villiform, fusiform or clavate. Papillae may also occur on multiseriate trichomes that perhaps function as pseudostamens. Labellar papillae contain protein but most lack lipid. The occurrence of starch, however, is more variable. Many papillae contain pigment or act as osmophores, thereby attracting insects. Rewards such as nectar or a protein‐rich, wax‐like, lipoidal substance may be secreted by papillae onto the labellar surface. Some papillae may have a protective role in preventing desiccation. Species of diverse vegetative morphology may have identical floral papillae, whereas others of similar vegetative morphology may not. • Conclusions Generally, floral papillae in Maxillaria have little taxonomic value. Nevertheless, the absence of papillae from members of the M. cucullata alliance, the occurrence of clavate papillae with distended apices in the M. rufescens alliance and the presence of papillose trichomes in some species may yet prove to be useful. PMID:14630691

Morphology of floral papillae in Maxillaria Ruiz & Pav. (Orchidaceae).

PubMed

Davies, K L; Turner, M P

2004-01-01

The labellar papillae and trichomes of Maxillaria Ruiz & Pav. show great diversity. Although papillae also occur upon other parts of the flower (e.g. column and anther cap), these have not yet been studied. Labellar trichomes of Maxillaria are useful in taxonomy, but hitherto the taxonomic value of floral papillae has not been assessed. The aim of this paper is to describe the range of floral papillae found in Maxillaria and to determine whether papillae are useful as taxonomic characters. Light microscopy, histochemistry, low-vacuum scanning and transmission electron microscopy. A total of 75 taxa were studied. Conical papillae with rounded or pointed tips were the most common. The column and anther cap usually bear conical, obpyriform or villiform papillae, whereas those around the stigmatic surface and at the base of the anther are often larger and swollen. Labellar papillae show greater diversity, and may be conical, obpyriform, villiform, fusiform or clavate. Papillae may also occur on multiseriate trichomes that perhaps function as pseudostamens. Labellar papillae contain protein but most lack lipid. The occurrence of starch, however, is more variable. Many papillae contain pigment or act as osmophores, thereby attracting insects. Rewards such as nectar or a protein-rich, wax-like, lipoidal substance may be secreted by papillae onto the labellar surface. Some papillae may have a protective role in preventing desiccation. Species of diverse vegetative morphology may have identical floral papillae, whereas others of similar vegetative morphology may not. Generally, floral papillae in Maxillaria have little taxonomic value. Nevertheless, the absence of papillae from members of the M. cucullata alliance, the occurrence of clavate papillae with distended apices in the M. rufescens alliance and the presence of papillose trichomes in some species may yet prove to be useful.

Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major).

PubMed

Kropáčková, Lucie; Pechmanová, Hana; Vinkler, Michal; Svobodová, Jana; Velová, Hana; Těšičký, Martin; Martin, Jean-François; Kreisinger, Jakub

2017-01-01

The gastrointestinal tract of vertebrates is inhabited by diverse bacterial communities that induce marked effects on the host physiology and health status. The composition of the gastrointestinal microbiota is characterized by pronounced taxonomic and functional variability among different regions of the vertebrate gastrointestinal tract. Despite the relatively solid knowledge on the among-region variations of the gastrointestinal microbiota in model mammalian species, there are only a few studies concerning among-region variations of the gastrointestinal microbiota in free-living non-mammalian vertebrate taxa. We used Illumina MiSeq sequencing of bacterial 16S rRNA amplicons to compare the diversity as well as taxonomic composition of bacterial communities in proximal vs. distal parts of the gastrointestinal tract (represented by oral swabs and faecal samples, respectively) in a wild passerine bird, the great tit (Parus major). The diversity of the oral microbiota was significantly higher compared to the faecal microbiota, whereas interindividual variation was higher in faecal than in oral samples. We also observed a pronounced difference in taxonomic content between the oral and faecal microbiota. Bacteria belonging to the phyla Proteobacteria, Firmicutes and Actinobacteria typically dominated in both oral and faecal samples. A high abundance of bacteria belonging to Tenericutes was observed only in faecal samples. Surprisingly, we found only a slight correlation between the faecal and oral microbiota at the within-individual level, suggesting that the microbial composition in these body sites is shaped by independent regulatory processes. Given the independence of these two communities at the individual level, we propose that simultaneous sampling of the faecal and oral microbiota will extend our understanding of host vs. microbiota interactions in wild populations.

Fast Census of Moth Diversity in the Neotropics: A Comparison of Field-Assigned Morphospecies and DNA Barcoding in Tiger Moths.

PubMed

Zenker, Mauricio M; Rougerie, Rodolphe; Teston, José A; Laguerre, Michel; Pie, Marcio R; Freitas, André V L

2016-01-01

The morphological species delimitations (i.e. morphospecies) have long been the best way to avoid the taxonomic impediment and compare insect taxa biodiversity in highly diverse tropical and subtropical regions. The development of DNA barcoding, however, has shown great potential to replace (or at least complement) the morphospecies approach, with the advantage of relying on automated methods implemented in computer programs or even online rather than in often subjective morphological features. We sampled moths extensively for two years using light traps in a patch of the highly endangered Atlantic Forest of Brazil to produce a nearly complete census of arctiines (Noctuoidea: Erebidae), whose species richness was compared using different morphological and molecular approaches (DNA barcoding). A total of 1,075 barcode sequences of 286 morphospecies were analyzed. Based on the clustering method Barcode Index Number (BIN) we found a taxonomic bias of approximately 30% in our initial morphological assessment. However, a morphological reassessment revealed that the correspondence between morphospecies and molecular operational taxonomic units (MOTUs) can be up to 94% if differences in genitalia morphology are evaluated in individuals of different MOTUs originated from the same morphospecies (putative cases of cryptic species), and by recording if individuals of different genders in different morphospecies merge together in the same MOTU (putative cases of sexual dimorphism). The results of two other clustering methods (i.e. Automatic Barcode Gap Discovery and 2% threshold) were very similar to those of the BIN approach. Using empirical data we have shown that DNA barcoding performed substantially better than the morphospecies approach, based on superficial morphology, to delimit species of a highly diverse moth taxon, and thus should be used in species inventories.

Hiding deep in the trees: discovery of divergent mitochondrial lineages in Malagasy chameleons of the Calumma nasutum group

PubMed Central

Gehring, Philip-Sebastian; Tolley, Krystal A; Eckhardt, Falk Sebastian; Townsend, Ted M; Ziegler, Thomas; Ratsoavina, Fanomezana; Glaw, Frank; Vences, Miguel

2012-01-01

We conducted a comprehensive molecular phylogenetic study for a group of chameleons from Madagascar (Chamaeleonidae: Calumma nasutum group, comprising seven nominal species) to examine the genetic and species diversity in this widespread genus. Based on DNA sequences of the mitochondrial gene (ND2) from 215 specimens, we reconstructed the phylogeny using a Bayesian approach. Our results show deep divergences among several unnamed mitochondrial lineages that are difficult to identify morphologically. We evaluated lineage diversification using a number of statistical phylogenetic methods (general mixed Yule-coalescent model; SpeciesIdentifier; net p-distances) to objectively delimit lineages that we here consider as operational taxonomic units (OTUs), and for which the taxonomic status remains largely unknown. In addition, we compared molecular and morphological differentiation in detail for one particularly diverse clade (the C. boettgeri complex) from northern Madagascar. To assess the species boundaries within this group we used an integrative taxonomic approach, combining evidence from two independent molecular markers (ND2 and CMOS), together with genital and other external morphological characters, and conclude that some of the newly discovered OTUs are separate species (confirmed candidate species, CCS), while others should best be considered as deep conspecific lineages (DCLs). Our analysis supports a total of 33 OTUs, of which seven correspond to described species, suggesting that the taxonomy of the C. nasutum group is in need of revision. PMID:22957155

Land scale biogeography of arsenic biotransformation genes in estuarine wetland.

PubMed

Zhang, Si-Yu; Su, Jian-Qiang; Sun, Guo-Xin; Yang, Yunfeng; Zhao, Yi; Ding, Junjun; Chen, Yong-Shan; Shen, Yu; Zhu, Guibing; Rensing, Christopher; Zhu, Yong-Guan

2017-06-01

As an analogue of phosphorus, arsenic (As) has a biogeochemical cycle coupled closely with other key elements on the Earth, such as iron, sulfate and phosphate. It has been documented that microbial genes associated with As biotransformation are widely present in As-rich environments. Nonetheless, their presence in natural environment with low As levels remains unclear. To address this issue, we investigated the abundance levels and diversities of aioA, arrA, arsC and arsM genes in estuarine sediments at low As levels across Southeastern China to uncover biogeographic patterns at a large spatial scale. Unexpectedly, genes involved in As biotransformation were characterized by high abundance and diversity. The functional microbial communities showed a significant decrease in similarity along the geographic distance, with higher turnover rates than taxonomic microbial communities based on the similarities of 16S rRNA genes. Further investigation with niche-based models showed that deterministic processes played primary roles in shaping both functional and taxonomic microbial communities. Temperature, pH, total nitrogen concentration, carbon/nitrogen ratio and ferric iron concentration rather than As content in these sediments were significantly linked to functional microbial communities, while sediment temperature and pH were linked to taxonomic microbial communities. We proposed several possible mechanisms to explain these results. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Characterization of fatty acid-producing wastewater microbial communities using next generation sequencing technologies

EPA Science Inventory

While wastewater represents a viable source of bacterial biodiesel production, very little is known on the composition of these microbial communities. We studied the taxonomic diversity and succession of microbial communities in bioreactors accumulating fatty acids using 454-pyro...

Activity and bacterial diversity of snow around Russian Antarctic stations.

PubMed

Lopatina, Anna; Krylenkov, Vjacheslav; Severinov, Konstantin

2013-11-01

The diversity and temporal dynamics of bacterial communities in pristine snow around two Russian Antarctic stations was investigated. Taxonomic analysis of rDNA libraries revealed that snow communities were dominated by bacteria from a small number of operational taxonomic units (OTUs) that underwent dramatic swings in abundance between the 54th (2008-2009) and 55th (2009-2010) Russian Antarctic expeditions. Moreover, analysis of the 55th expedition samples indicated that there was very little, if any, correspondence in abundance of clones belonging to the same OTU present in rDNA and rRNA libraries. The latter result suggests that most rDNA clones originate from bacteria that are not alive and/or active and may have been deposited on the snow surface from the atmosphere. In contrast, clones most abundant in rRNA libraries (mostly belonging to Variovorax, Janthinobacterium, Pseudomonas, and Sphingomonas genera) may be considered as endogenous Antarctic snow inhabitants. Copyright © 2013 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Eukaryotic organisms in Proterozoic oceans

PubMed Central

Knoll, A.H; Javaux, E.J; Hewitt, D; Cohen, P

2006-01-01

The geological record of protists begins well before the Ediacaran and Cambrian diversification of animals, but the antiquity of that history, its reliability as a chronicle of evolution and the causal inferences that can be drawn from it remain subjects of debate. Well-preserved protists are known from a relatively small number of Proterozoic formations, but taphonomic considerations suggest that they capture at least broad aspects of early eukaryotic evolution. A modest diversity of problematic, possibly stem group protists occurs in ca 1800–1300 Myr old rocks. 1300–720 Myr fossils document the divergence of major eukaryotic clades, but only with the Ediacaran–Cambrian radiation of animals did diversity increase within most clades with fossilizable members. While taxonomic placement of many Proterozoic eukaryotes may be arguable, the presence of characters used for that placement is not. Focus on character evolution permits inferences about the innovations in cell biology and development that underpin the taxonomic and morphological diversification of eukaryotic organisms. PMID:16754612

Efficacy of DNA barcoding for the species identification of spiders from Western Ghats of India.

PubMed

Gaikwad, Swapnil; Warudkar, Ashwin; Shouche, Yogesh

2017-09-01

DNA barcoding has emerged as an additional tool for taxonomy and as an aid to taxonomic impediments. Due to their extensive morphological variation, spiders are taxonomically challenging. Therefore, all over the world, attempts are being made to DNA barcode species of spiders. Till now no attempts were made to DNA barcode Indian spiders despite their rich diversity. We have generated DNA barcodes for 60 species (n = 112) of spiders for the first time from India. Although only 17 species were correctly identified at the species level, DNA barcoding correctly discriminated 99% of the species studied here. We have also found high intraspecies nucleotide divergence in Plexippus paykulli suggesting cryptic diversity that needs to be studied in detail. Our study also showed non-specific amplification of the Cytochrome Oxidase I (COI) gene of endosymbiont bacteria Wolbachia. However, these cases are very rare and could be resolved by the use of modified or group specific primers.

Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome

PubMed Central

Li, Kelvin; Bihan, Monika; Methé, Barbara A.

2013-01-01

Analyses of the taxonomic diversity associated with the human microbiome continue to be an area of great importance. The study of the nature and extent of the commonly shared taxa (“core”), versus those less prevalent, establishes a baseline for comparing healthy and diseased groups by quantifying the variation among people, across body habitats and over time. The National Institutes of Health (NIH) sponsored Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine and better define what constitutes the taxonomic core within and across body habitats and individuals through pyrosequencing-based profiling of 16S rRNA gene sequences from oral, skin, distal gut (stool), and vaginal body habitats from over 200 healthy individuals. A two-parameter model is introduced to quantitatively identify the core taxonomic members of each body habitat’s microbiota across the healthy cohort. Using only cutoffs for taxonomic ubiquity and abundance, core taxonomic members were identified for each of the 18 body habitats and also for the 4 higher-level body regions. Although many microbes were shared at low abundance, they exhibited a relatively continuous spread in both their abundance and ubiquity, as opposed to a more discretized separation. The numbers of core taxa members in the body regions are comparatively small and stable, reflecting the relatively high, but conserved, interpersonal variability within the cohort. Core sizes increased across the body regions in the order of: vagina, skin, stool, and oral cavity. A number of “minor” oral taxonomic core were also identified by their majority presence across the cohort, but with relatively low and stable abundances. A method for quantifying the difference between two cohorts was introduced and applied to samples collected on a second visit, revealing that over time, the oral, skin, and stool body regions tended to be more transient in their taxonomic structure than the vaginal body region. PMID:23671663

Species Diversity of Hypogeous Ascomycetes in Israel

PubMed Central

Wasser, Solomon P.

2010-01-01

We conducted a species diversity study of the hypogeous Ascomycetes of Israel. The hypogeous Ascomycetes in Israel include members of the families Pyronemataceae, Pezizaceae, and Tuberaceae, which are represented by seven species: Hydnocystis piligera, Terfezia arenaria, T. claveryi, T. oligosperma, Tirmania africana, Tuber asa, and T. nitidum; only T. asa is new to Israeli mycobiota. Synonymy, locations, collection data, general distribution, distribution in Israel, descriptions, a key to identification, illustrations, and taxonomic remarks are provided. PMID:23956647

Phylogeny, Traits, and Biodiversity of a Neotropical Bat Assemblage: Close Relatives Show Similar Responses to Local Deforestation.

PubMed

Frank, Hannah K; Frishkoff, Luke O; Mendenhall, Chase D; Daily, Gretchen C; Hadly, Elizabeth A

2017-08-01

If species' evolutionary pasts predetermine their responses to evolutionarily novel stressors, then phylogeny could predict species survival in an increasingly human-dominated world. To understand the role of phylogenetic relatedness in structuring responses to rapid environmental change, we focused on assemblages of Neotropical bats, an ecologically diverse and functionally important group. We examined how taxonomic and phylogenetic diversity shift between tropical forest and farmland. We then explored the importance of evolutionary history by ascertaining whether close relatives share similar responses to environmental change and which species traits might mediate these trends. We analyzed a 5-year data set (5,011 captures) from 18 sites in a countryside landscape in southern Costa Rica using statistical models that account and correct for imperfect detection of species across sites, spatial autocorrelation, and consideration of spatial scale. Taxonomic and phylogenetic diversity decreased with deforestation, and assemblages became more phylogenetically clustered. Species' responses to deforestation were strongly phylogenetically correlated. Body mass and absolute wing loading explained a substantial portion of species variation in species' habitat preferences, likely related to these traits' influence on maneuverability in cluttered forest environments. Our findings highlight the role that evolutionary history plays in determining which species will survive human impacts and the need to consider diversity metrics, evolutionary history, and traits together when making predictions about species persistence for conservation or ecosystem functioning.

Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes.

PubMed

Takeuchi, Yayoi; Chaffron, Samuel; Salcher, Michaela M; Shimizu-Inatsugi, Rie; Kobayashi, Masaki J; Diway, Bibian; von Mering, Christian; Pernthaler, Jakob; Shimizu, Kentaro K

2015-07-01

Pitchers are modified leaves used by carnivorous plants for trapping prey. Their fluids contain digestive enzymes from the plant and they harbor abundant microbes. In this study, the diversity of bacterial communities was assessed in Nepenthes pitcher fluids and the composition of the bacterial community was compared to that in other environments, including the phyllosphere of Arabidopsis, animal guts and another pitcher plant, Sarracenia. Diversity was measured by 454 pyrosequencing of 16S rRNA gene amplicons. A total of 232,823 sequences were obtained after chimera and singleton removal that clustered into 3260 distinct operational taxonomic units (OTUs) (3% dissimilarity), which were taxonomically distributed over 17 phyla, 25 classes, 45 orders, 100 families, and 195 genera. Pyrosequencing and fluorescence in situ hybridization yielded similar estimates of community composition. Most pitchers contained high proportions of unique OTUs, and only 22 OTUs (<0.6%) were shared by ≥14/16 samples, suggesting a unique bacterial assemblage in each pitcher at the OTU level. Diversity analysis at the class level revealed that the bacterial communities of both opened and unopened pitchers were most similar to that of Sarracenia and to that in the phyllosphere. Therefore, the bacterial community in pitchers may be formed by environmental filtering and/or by phyllosphere bacteria. Copyright © 2015 The Authors. Published by Elsevier GmbH.. All rights reserved.

Censusing marine eukaryotic diversity in the twenty-first century

PubMed Central

Knowlton, Nancy

2016-01-01

The ocean constitutes one of the vastest and richest biomes on our planet. Most recent estimations, all based on indirect approaches, suggest that there are millions of marine eukaryotic species. Moreover, a large majority of these are small (less than 1 mm), cryptic and still unknown to science. However, this knowledge gap, caused by the lack of diagnostic morphological features in small organisms and the limited sampling of the global ocean, is currently being filled, thanks to new DNA-based approaches. The molecular technique of PCR amplification of homologous gene regions combined with high-throughput sequencing, routinely used to census unculturable prokaryotes, is now also being used to characterize whole communities of marine eukaryotes. Here, we review how this methodological advancement has helped to better quantify the magnitude and patterns of marine eukaryotic diversity, with an emphasis on taxonomic groups previously largely overlooked. We then discuss obstacles remaining to achieve a global understanding of marine eukaryotic diversity. In particular, we argue that 18S variable regions do not provide sufficient taxonomic resolution to census marine life, and suggest combining broad eukaryotic surveys targeting the 18S rRNA region with more taxon-focused analyses of hypervariable regions to improve our understanding of the diversity of species, the functional units of marine ecosystems. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481783

Metacommunity versus Biogeography: A Case Study of Two Groups of Neotropical Vegetation-Dwelling Arthropods

PubMed Central

Gonçalves-Souza, Thiago; Romero, Gustavo Q.; Cottenie, Karl

2014-01-01

Biogeography and metacommunity ecology provide two different perspectives on species diversity. Both are spatial in nature but their spatial scales do not necessarily match. With recent boom of metacommunity studies, we see an increasing need for clear discrimination of spatial scales relevant for both perspectives. This discrimination is a necessary prerequisite for improved understanding of ecological phenomena across scales. Here we provide a case study to illustrate some spatial scale-dependent concepts in recent metacommunity studies and identify potential pitfalls. We presented here the diversity patterns of Neotropical lepidopterans and spiders viewed both from metacommunity and biogeographical perspectives. Specifically, we investigated how the relative importance of niche- and dispersal-based processes for community assembly change at two spatial scales: metacommunity scale, i.e. within a locality, and biogeographical scale, i.e. among localities widely scattered along a macroclimatic gradient. As expected, niche-based processes dominated the community assembly at metacommunity scale, while dispersal-based processes played a major role at biogeographical scale for both taxonomical groups. However, we also observed small but significant spatial effects at metacommunity scale and environmental effects at biogeographical scale. We also observed differences in diversity patterns between the two taxonomical groups corresponding to differences in their dispersal modes. Our results thus support the idea of continuity of processes interactively shaping diversity patterns across scales and emphasize the necessity of integration of metacommunity and biogeographical perspectives. PMID:25549332

Molecular identification of Amazonian stingless bees using polymerase chain reaction single-strand conformation polymorphism.

PubMed

Souza, M T; Carvalho-Zilse, G A

2014-07-25

In countries containing a mega diversity of wildlife, such as Brazil, identifying and characterizing biological diversity is a continuous process for the scientific community, even in face of technological and scientific advances. This activity demands initiatives for the taxonomic identification of highly diverse groups, such as stingless bees, including molecular analysis strategies. This type of bee is distributed in all of the Brazilian states, with the highest species diversity being found in the State of Amazônia. However, the estimated number of species diverges among taxonomists. These bees are considered the main pollinators in the Amazon rainforest, in which they obtain food and shelter; however, their persistence is constantly threatened by deforestation pressure. Hence, it is important to classify the number and abundance of bee specie, to measure their decline and implement meaningful, priority conservation strategies. This study aims to maximize the implementation of more direct, economic and successful techniques for the taxonomic identification of stingless bees. Specifically, the genes 16S rRNA and COI from mitochondrial DNA were used as molecular markers to differentiate 9 species of Amazonian stingless bees based on DNA polymorphism, using the polymerase chain reaction-single-strand conformation polymorphism technique. We registered different, exclusive SSCP haplotypes for both genes in all species analyzed. These results demonstrate that SSCP is a simple and cost-effective technique that is applicable to the molecular identification of stingless bee species.

Microbial community structure and diversity within hypersaline Keke Salt Lake environments.

PubMed

Han, Rui; Zhang, Xin; Liu, Jing; Long, Qifu; Chen, Laisheng; Liu, Deli; Zhu, Derui

2017-11-01

Keke Salt Lake is located in the Qaidamu Basin of China. It is a unique magnesium sulfate-subtype hypersaline lake that exhibits a halite domain ecosystem, yet its microbial diversity has remained unstudied. Here, the microbial community structure and diversity was investigated via high-throughput sequencing of the V3-V5 regions of 16S rRNA genes. A high diversity of operational taxonomic units was detected for Bacteria and Archaea (734 and 747, respectively), comprising 21 phyla, 43 classes, and 201 genera of Bacteria and 4 phyla, 4 classes, and 39 genera of Archaea. Salt-saturated samples were dominated by the bacterial genera Bacillus (51.52%-58.35% relative abundance), Lactococcus (9.52%-10.51%), and Oceanobacillus (8.82%-9.88%) within the Firmicutes phylum (74.81%-80.99%), contrasting with other hypersaline lakes. The dominant Archaea belonged to the Halobacteriaceae family, and in particular, the genera (with an abundance of >10% of communities) Halonotius, Halorubellus, Halapricum, Halorubrum, and Natronomonas. Additionally, we report the presence of Nanohaloarchaeota and Woesearchaeota in Qinghai-Tibet Plateau lakes, which has not been previously documented. Total salinity (especially Mg 2+ , Cl - , Na + , and K + ) mostly correlated with taxonomic distribution across samples. These results expand our understanding of microbial resource utilization within hypersaline lakes and the potential adaptations of dominant microorganisms that allow them to inhabit such environments.

Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing.

PubMed

Massana, Ramon; Gobet, Angélique; Audic, Stéphane; Bass, David; Bittner, Lucie; Boutte, Christophe; Chambouvet, Aurélie; Christen, Richard; Claverie, Jean-Michel; Decelle, Johan; Dolan, John R; Dunthorn, Micah; Edvardsen, Bente; Forn, Irene; Forster, Dominik; Guillou, Laure; Jaillon, Olivier; Kooistra, Wiebe H C F; Logares, Ramiro; Mahé, Frédéric; Not, Fabrice; Ogata, Hiroyuki; Pawlowski, Jan; Pernice, Massimo C; Probert, Ian; Romac, Sarah; Richards, Thomas; Santini, Sébastien; Shalchian-Tabrizi, Kamran; Siano, Raffaele; Simon, Nathalie; Stoeck, Thorsten; Vaulot, Daniel; Zingone, Adriana; de Vargas, Colomban

2015-10-01

Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together, while communities from the same site but different seasons were unrelated. Both DNA and RNA-based surveys provided similar relative abundances for most class-level taxonomic groups. Yet, particular groups were overrepresented in one of the two templates, such as marine alveolates (MALV)-I and MALV-II that were much more abundant in DNA surveys. Overall, the groups displaying the highest relative contribution were Dinophyceae, Diatomea, Ciliophora and Acantharia. Also, well represented were Mamiellophyceae, Cryptomonadales, marine alveolates and marine stramenopiles in the picoplankton, and Monadofilosa and basal Fungi in sediments. Our extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

The family Rhabdoviridae: mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins.

PubMed

Dietzgen, Ralf G; Kondo, Hideki; Goodin, Michael M; Kurath, Gael; Vasilakis, Nikos

2017-01-02

The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- and bipartite genomes. Copyright © 2016 Elsevier B.V. All rights reserved.

Diversity and evolution of marine phytoplankton.

PubMed

Simon, Nathalie; Cras, Anne-Lise; Foulon, Elodie; Lemée, Rodolphe

2009-01-01

Marine phytoplankton organisms account for more than 45% of the photosynthetic net primary production on Earth. They are distributed across many of the major clades of the tree of life and include prokaryotes, and eukaryotes that acquired photosynthesis through the process of endosymbiosis. If the number of extant described species is relatively low compared to the diversity of the terrestrial plants, recent insights into the genetic diversity of natural assemblages have revealed a large unsuspected diversity at different taxonomic levels. Wide infra-specific diversity is also being discovered in many widespread and well known morphological species. This review summarizes data obtained in the fields of ecology, evolutionary biology, physiology and genomics that have improved our understanding of the biodiversity and evolution of marine phytoplankton.

Small Scale Biodiversity of an Alkaline Hot Spring in Yellowstone National Park

NASA Astrophysics Data System (ADS)

Walther, K.; Oiler, J.; Meyer-Dombard, D. R.

2012-12-01

To date, many phylogenetic diversity studies have been conducted in Yellowstone National Park (YNP) [1-7] focusing on the amplification of the 16S rRNA gene and "metagenomic" datasets. However, few reports focus on diversity at small scales. Here, we report on a small scale biodiversity study of sediment and biofilm communities within a confined area of a YNP hot spring, compare and contrast these communities to other sediment and biofilm communities from previous studies [1-7], and with other sediment and biofilm communities in the same system. Sediment and biofilm samples were collected, using a 30 x 50 cm sampling grid divided in 5 x 5 cm squares, which was placed in the outflow channel of "Bat Pool", an alkaline (pH 7.9) hot spring in YNP. Accompanying geochemical data included a full range of spectrophotometry measurements along with major ions, trace elements, and DIC/DOC. In addition, in situ temperature and conductivity arrays were placed within the grid location. The temperature array closest to the source varied between 83-88°C, while the temperature array 40 cm downstream varied between ~83.5-86.5°C. The two conductivity arrays yielded measurements of 5632 μS and 5710 μS showing little variation within the sampling area. Within the grid space, DO ranged from 0.5-1.33 mg/L, with relatively similar, but slightly lower values down the outflow channel. Sulfide values within the grid ranged from 1020-1671 μg/L, while sulfide values outside of the grid region fluctuated, but generally followed the trend of decreasing from source down the outflow. Despite the relative heterogeneity of chemical and physical parameters in the grid space, there was biological diversity in sediments and biofilms at the 5 cm scale. Small scale biodiversity was analyzed by selecting a representative number of samples from within the grid. DNA was extracted and variable regions V3 and V6 (Archaea and Bacteria, respectively) were sequenced with 454 pyrosequencing. The datasets from each of the samples were randomly subsampled and the same number of sequences was taken from each dataset so that the samples could be directly compared. Using the Ribosomal Database Project Pyrosequencing Pipeline (http://rdp.cme.msu.edu/), the sequences were aligned, complete linkage clustering was performed, Shannon and Chao1 indices were calculated, and rarefaction curves were made. The RDP Classifier tool afforded classification in a taxonomical hierarchy and the samples were compared on the order level to determine the variation of the microbial communities within the sampling grid. Additional alpha and beta diversity indices were also established. Through comparing the samples on the order level, it was determined that there is variation within a small sampling area despite similar geochemical and temperature conditions at the time of sampling. This variation is seen in both the sediment and biofilm communities, primarily seen among Bacteria. [1] Barns, S.M. et al. (1994) PNAS. 91: 1609-1613. [2] Barns, S.M. et al. (1996) PNAS. 93: 9188-9193. [3] Hall, J.R. et al. (2008) AEM. 74(15): 4910-4922. [4] Hugenholtz, P. et al. (1998) JofBac. 180(2): 366-376. [5] Meyer-Dombard, D. R. et al. (2005) Geobio. 3: 211-227. [6] Meyer-Dombard, D.R. et al. (2011) EM. 13(8): 2216-2231. [7] Reysenbach, A.L. et al. (1994) AEM. 60 (6): 2113-2119.

Social calls provide novel insights into the evolution of vocal learning

PubMed Central

Sewall, Kendra B.; Young, Anna M.; Wright, Timothy F.

2016-01-01

Learned song is among the best-studied models of animal communication. In oscine songbirds, where learned song is most prevalent, it is used primarily for intrasexual selection and mate attraction. Learning of a different class of vocal signals, known as contact calls, is found in a diverse array of species, where they are used to mediate social interactions among individuals. We argue that call learning provides a taxonomically rich system for studying testable hypotheses for the evolutionary origins of vocal learning. We describe and critically evaluate four nonmutually exclusive hypotheses for the origin and current function of vocal learning of calls, which propose that call learning (1) improves auditory detection and recognition, (2) signals local knowledge, (3) signals group membership, or (4) allows for the encoding of more complex social information. We propose approaches to testing these four hypotheses but emphasize that all of them share the idea that social living, not sexual selection, is a central driver of vocal learning. Finally, we identify future areas for research on call learning that could provide new perspectives on the origins and mechanisms of vocal learning in both animals and humans. PMID:28163325

Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array

USDA-ARS?s Scientific Manuscript database

High-density single nucleotide polymorphism (SNP) genotyping chips are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships among individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array includ...

Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias.

PubMed

Clarke, Laurence J; Soubrier, Julien; Weyrich, Laura S; Cooper, Alan

2014-11-01

Studies of insect assemblages are suited to the simultaneous DNA-based identification of multiple taxa known as metabarcoding. To obtain accurate estimates of diversity, metabarcoding markers ideally possess appropriate taxonomic coverage to avoid PCR-amplification bias, as well as sufficient sequence divergence to resolve species. We used in silico PCR to compare the taxonomic coverage and resolution of newly designed insect metabarcodes (targeting 16S) with that of existing markers [16S and cytochrome oxidase c subunit I (COI)] and then compared their efficiency in vitro. Existing metabarcoding primers amplified in silico <75% of insect species with complete mitochondrial genomes available, whereas new primers targeting 16S provided >90% coverage. Furthermore, metabarcodes targeting COI appeared to introduce taxonomic PCR-amplification bias, typically amplifying a greater percentage of Lepidoptera and Diptera species, while failing to amplify certain orders in silico. To test whether bias predicted in silico was observed in vitro, we created an artificial DNA blend containing equal amounts of DNA from 14 species, representing 11 insect orders and one arachnid. We PCR-amplified the blend using five primer sets, targeting either COI or 16S, with high-throughput amplicon sequencing yielding more than 6 million reads. In vitro results typically corresponded to in silico PCR predictions, with newly designed 16S primers detecting 11 insect taxa present, thus providing equivalent or better taxonomic coverage than COI metabarcodes. Our results demonstrate that in silico PCR is a useful tool for predicting taxonomic bias in mixed template PCR and that researchers should be wary of potential bias when selecting metabarcoding markers. © 2014 John Wiley & Sons Ltd.

Minimal standards for describing new species belonging to the families Campylobacteraceae and Helicobacteraceae: Campylobacter, Arcobacter, Helicobacter and Wolinella spp.

PubMed Central

On, Stephen L. W.; Miller, William G.; Houf, Kurt; Fox, James G.; Vandamme, Peter

2017-01-01

Ongoing changes in taxonomic methods, and in the rapid development of the taxonomic structure of species assigned to the Epsilonproteobacteria have lead the International Committee of Systematic Bacteriology Subcommittee on the Taxonomy of Campylobacter and Related Bacteria to discuss significant updates to previous minimal standards for describing new species of Campylobacteraceae and Helicobacteraceae. This paper is the result of these discussions and proposes minimum requirements for the description of new species belonging to the families Campylobacteraceae and Helicobacteraceae, thus including species in Campylobacter, Arcobacter, Helicobacter, and Wolinella. The core underlying principle remains the use of appropriate phenotypic and genotypic methods to characterise strains sufficiently so as to effectively and unambiguously determine their taxonomic position in these families, and provide adequate means by which the new taxon can be distinguished from extant species and subspecies. This polyphasic taxonomic approach demands the use of appropriate reference data for comparison to ensure the novelty of proposed new taxa, and the recommended study of at least five strains to enable species diversity to be assessed. Methodological approaches for phenotypic and genotypic (including whole-genome sequence comparisons) characterisation are recommended. PMID:29034857

Towards a Global Names Architecture: The future of indexing scientific names

PubMed Central

Pyle, Richard L.

2016-01-01

Abstract For more than 250 years, the taxonomic enterprise has remained almost unchanged. Certainly, the tools of the trade have improved: months-long journeys aboard sailing ships have been reduced to hours aboard jet airplanes; advanced technology allows humans to access environments that were once utterly inaccessible; GPS has replaced crude maps; digital hi-resolution imagery provides far more accurate renderings of organisms that even the best commissioned artists of a century ago; and primitive candle-lit microscopes have been replaced by an array of technologies ranging from scanning electron microscopy to DNA sequencing. But the basic paradigm remains the same. Perhaps the most revolutionary change of all – which we are still in the midst of, and which has not yet been fully realized – is the means by which taxonomists manage and communicate the information of their trade. The rapid evolution in recent decades of computer database management software, and of information dissemination via the Internet, have both dramatically improved the potential for streamlining the entire taxonomic process. Unfortunately, the potential still largely exceeds the reality. The vast majority of taxonomic information is either not yet digitized, or digitized in a form that does not allow direct and easy access. Moreover, the information that is easily accessed in digital form is not yet seamlessly interconnected. In an effort to bring reality closer to potential, a loose affiliation of major taxonomic resources, including GBIF, the Encyclopedia of Life, NBII, Catalog of Life, ITIS, IPNI, ICZN, Index Fungorum, and many others have been crafting a “Global Names Architecture” (GNA). The intention of the GNA is not to replace any of the existing taxonomic data initiatives, but rather to serve as a dynamic index to interconnect them in a way that streamlines the entire taxonomic enterprise: from gathering specimens in the field, to publication of new taxa and related data. PMID:26877664

Towards a Global Names Architecture: The future of indexing scientific names.

PubMed

Pyle, Richard L

2016-01-01

For more than 250 years, the taxonomic enterprise has remained almost unchanged. Certainly, the tools of the trade have improved: months-long journeys aboard sailing ships have been reduced to hours aboard jet airplanes; advanced technology allows humans to access environments that were once utterly inaccessible; GPS has replaced crude maps; digital hi-resolution imagery provides far more accurate renderings of organisms that even the best commissioned artists of a century ago; and primitive candle-lit microscopes have been replaced by an array of technologies ranging from scanning electron microscopy to DNA sequencing. But the basic paradigm remains the same. Perhaps the most revolutionary change of all - which we are still in the midst of, and which has not yet been fully realized - is the means by which taxonomists manage and communicate the information of their trade. The rapid evolution in recent decades of computer database management software, and of information dissemination via the Internet, have both dramatically improved the potential for streamlining the entire taxonomic process. Unfortunately, the potential still largely exceeds the reality. The vast majority of taxonomic information is either not yet digitized, or digitized in a form that does not allow direct and easy access. Moreover, the information that is easily accessed in digital form is not yet seamlessly interconnected. In an effort to bring reality closer to potential, a loose affiliation of major taxonomic resources, including GBIF, the Encyclopedia of Life, NBII, Catalog of Life, ITIS, IPNI, ICZN, Index Fungorum, and many others have been crafting a "Global Names Architecture" (GNA). The intention of the GNA is not to replace any of the existing taxonomic data initiatives, but rather to serve as a dynamic index to interconnect them in a way that streamlines the entire taxonomic enterprise: from gathering specimens in the field, to publication of new taxa and related data.

The iPhyClassifier, an interactive online tool for phytoplasma classification and taxonomic assignment

USDA-ARS?s Scientific Manuscript database

The iPhyClassifier is an Internet-based research tool for quick identification and classification of diverse phytoplasmas. The iPhyClassifier simulates laboratory restriction enzyme digestions and subsequent gel electrophoresis and generates virtual restriction fragment length polymorphism (RFLP) p...

Genetic diversity of Talaromyces species isolated from maize in North America

USDA-ARS?s Scientific Manuscript database

Talaromyces species isolated from maize in the U.S., primarily between 1970 and 2014 were grown up from lyophilized storage to identify potential seed endophytes. These isolates had been predominantly identified as Penicillium funiculosum following the taxonomic system of Raper & Thom (1949), althou...

Genetic identity and diversity of perennial pepperweed (Lepidium latifolium) in its native and invaded ranges

USDA-ARS?s Scientific Manuscript database

Perennial pepperweed is an invasive plant species in North America, native to temperate Eurasia and northern Africa. Effective biological control depends upon correct taxonomic identification. Therefore, we investigated morphological and genetic data (DNA sequences and Amplified Fragment Length Poly...

Taxonomic concepts and practice with complex microbial communities

USDA-ARS?s Scientific Manuscript database

This brief review discusses the main points of the Keynote Lecture to be given at the 3rd International Conference on Microbial Diversity, October 27-29, 2015, Perugia, Italy. Key points include the necessity of molecular identification of microorganisms in order to understand their ecology. DNA-bas...

Diversity in nuclear DNA content and ploidy level of Hedychium species and hybrids

USDA-ARS?s Scientific Manuscript database

Hedychiums are multipurpose plants cultivated as ornamentals because of their multicolor, showy, and scented flowers, and as medicinal plants because of their essential oils that have been found to possess antimicrobial and insecticidal properties. There is often taxonomic and botanical confusion ab...

Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment.

PubMed

Wurzbacher, Christian; Fuchs, Andrea; Attermeyer, Katrin; Frindte, Katharina; Grossart, Hans-Peter; Hupfer, Michael; Casper, Peter; Monaghan, Michael T

2017-04-08

Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments. We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to 137 Cs dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota. Community β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5-14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO 2 and CH 4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions. By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper "replacement horizon" is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower "depauperate horizon" is characterized by low taxonomic richness, more stable "low-energy" conditions, and a dominance of enigmatic Archaea.

Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression.

PubMed

Kadam, Anagha; Janto, Benjamin; Eutsey, Rory; Earl, Joshua P; Powell, Evan; Dahlgren, Margaret E; Hu, Fen Z; Ehrlich, Garth D; Hiller, N Luisa

2015-02-02

There is extensive genomic diversity among Streptococcus pneumoniae isolates. Approximately half of the comprehensive set of genes in the species (the supragenome or pangenome) is present in all the isolates (core set), and the remaining is unevenly distributed among strains (distributed set). The Streptococcus pneumoniae Supragenome Hybridization (SpSGH) array provides coverage for an extensive set of genes and polymorphisms encountered within this species, capturing this genomic diversity. Further, the capture is quantitative. In this manner, the SpSGH array allows for both genomic and transcriptomic analyses of diverse S. pneumoniae isolates on a single platform. In this unit, we present the SpSGH array, and describe in detail its design and implementation for both genomic and transcriptomic analyses. The methodology can be applied to construction and modification of SpSGH array platforms, as well to other bacterial species as long as multiple whole-genome sequences are available that collectively capture the vast majority of the species supragenome. Copyright © 2015 John Wiley & Sons, Inc.

High-throughput genotyping of hop (Humulus lupulus L.) utilising diversity arrays technology (DArT)

USDA-ARS?s Scientific Manuscript database

Implementation of molecular methods in hop breeding is dependent on the availability of sizeable numbers of polymorphic markers and a comprehensive understanding of genetic variation. Diversity Arrays Technology (DArT) is a high-throughput cost-effective method for the discovery of large numbers of...

Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array

PubMed Central

Wang, Shichen; Wong, Debbie; Forrest, Kerrie; Allen, Alexandra; Chao, Shiaoman; Huang, Bevan E; Maccaferri, Marco; Salvi, Silvio; Milner, Sara G; Cattivelli, Luigi; Mastrangelo, Anna M; Whan, Alex; Stephen, Stuart; Barker, Gary; Wieseke, Ralf; Plieske, Joerg; International Wheat Genome Sequencing Consortium; Lillemo, Morten; Mather, Diane; Appels, Rudi; Dolferus, Rudy; Brown-Guedira, Gina; Korol, Abraham; Akhunova, Alina R; Feuillet, Catherine; Salse, Jerome; Morgante, Michele; Pozniak, Curtis; Luo, Ming-Cheng; Dvorak, Jan; Morell, Matthew; Dubcovsky, Jorge; Ganal, Martin; Tuberosa, Roberto; Lawley, Cindy; Mikoulitch, Ivan; Cavanagh, Colin; Edwards, Keith J; Hayden, Matthew; Akhunov, Eduard

2014-01-01

High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker–trait associations in mapping experiments. We developed a genotyping array including about 90 000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence–absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat. PMID:24646323

A study of lagoonal and estuarine processes in the area of Merritt Island encompassing the space center

NASA Technical Reports Server (NTRS)

1974-01-01

A study was conducted to determine the marine biology and dynamic oceanographic properties of the Indian River in Florida. One of the major areas of concentration involved the compilation of a taxonomic list of marine animals in the river. An important conclusion of the study is that diversity of the benthic community is substantially higher than expected. The effect of major climatic factors on the diversity and structure of the benthic community is analyzed.

Bacterial diversity in Fe-rich hydrothermal sediments at two South Tonga Arc submarine volcanoes.

PubMed

Forget, N L; Murdock, S A; Juniper, S K

2010-12-01

Seafloor iron oxide deposits are a common feature of submarine hydrothermal systems. Morphological study of these deposits has led investigators to suggest a microbiological role in their formation, through the oxidation of reduced Fe in hydrothermal fluids. Fe-oxidizing bacteria, including the recently described Zetaproteobacteria, have been isolated from a few of these deposits but generally little is known about the microbial diversity associated with this habitat. In this study, we characterized bacterial diversity in two Fe oxide samples collected on the seafloor of Volcanoes 1 and 19 on the South Tonga Arc. We were particularly interested in confirming the presence of Zetaproteobacteria at these two sites and in documenting the diversity of groups other than Fe oxidizers. Our results (small subunit rRNA gene sequence data) showed a surprisingly high bacterial diversity, with 150 operational taxonomic units belonging to 19 distinct taxonomic groups. Both samples were dominated by Zetaproteobacteria Fe oxidizers. This group was most abundant at Volcano 1, where sediments were richer in Fe and contained more crystalline forms of Fe oxides. Other groups of bacteria found at these two sites include known S- and a few N-metabolizing bacteria, all ubiquitous in marine environments. The low similarity of our clones with the GenBank database suggests that new species and perhaps new families were recovered. The results of this study suggest that Fe-rich hydrothermal sediments, while dominated by Fe oxidizers, can be exploited by a variety of autotrophic and heterotrophic micro-organisms. © 2010 Blackwell Publishing Ltd.

Differential organization of taxonomic and functional diversity in an urban woody plant metacommunity

Treesearch

Christopher M. Swan; Anna Johnson; David J. Nowak; Alicia Acosta

2016-01-01

Questions: Urban ecosystems present an opportunity to study ecological communities in the context of unprecedented environmental change. In the face of urban land conversion, ecologists observe new patterns of species composition, dominance, behaviour and dispersal.We propose a hypothetical socioeconomic template that describes a gradient...

The Generalizability of the Youth Self-Report Syndrome Structure in 23 Societies

ERIC Educational Resources Information Center

Ivanova, Masha Y.; Achenbach, Thomas M.; Rescorla, Leslie A.; Dumenci, Levent; Almqvist, Fredrik; Bilenberg, Niels; Bird, Hector; Broberg, Anders G.; Dobrean, Anca; Dopfner, Manfred; Erol, Nese; Forns, Maria; Hannesdottir, Helga; Kanbayashi, Yasuko; Lambert, Michael C.; Leung, Patrick; Minaei, Asghar; Mulatu, Mesfin S.; Novik, Torunn; Oh, Kyung Ja; Roussos, Alexandra; Sawyer, Michael; Simsek, Zeynep; Steinhausen, Hans- Christoph; Weintraub, Sheila; Winkler Metzke, Christa; Wolanczyk, Tomasz; Zilber, Nelly; Zukauskiene, Rita; Verhulst, Frank C.

2007-01-01

As a basis for theories of psychopathology, clinical psychology and related disciplines need sound taxonomies that are generalizable across diverse populations. To test the generalizability of a statistically derived 8-syndrome taxonomic model for youth psychopathology, confirmatory factor analyses (CFAs) were performed on the Youth Self-Report…

Genetic diversity-seeing the forest through the trees

Treesearch

M. Thompson Conkle

1992-01-01

Forest trees, populations, races, species, and taxonomic groups above the species level display rich variation in biochemical markers. The variation stems from inherited modifications that trace back in time, through converging ancestries, towards common progenitors. Past movements of continents, mountain building events, and climate changes isolated forest populations...

Pangenome and taxonomic analysis of Salmonella enterica subspecies enterica

USDA-ARS?s Scientific Manuscript database

Salmonella enterica subspecies enterica (S. enterica ssp. I) contains almost all the major pathogens in this genus. We sequenced 354 new S. enterica ssp. I genomes using paired end 100 base reads to ~80-fold coverage. These genomes were chosen to maximize genetic diversity, representing at least 100...

Biodiversity research sets sail: showcasing the diversity of marine life.

PubMed

Webb, Thomas J

2009-04-23

The World Congress on Marine Biodiversity was held in the City of Arts and Sciences, Valencia, from 10 to 15 November 2008, showcasing research on all aspects of marine biodiversity from basic taxonomic exploration to innovative conservation strategies and methods to integrate research into environmental policy.

SSRs are useful to assess genetic diversity among Lagerstroemia species

USDA-ARS?s Scientific Manuscript database

The most recent and widely accepted taxonomic revision of Lagerstroemia occurred in 1969 and is based on morphological characters. As described, the genus is split into three sections and includes more than 50 species, several of which are grown for lumber in Asia and the Philippines. Three species,...

Restoration of Delta Streams: A Case History and Conceptual Model

DTIC Science & Technology

2008-02-01

Hydrobiologia 303:211-9. Raup, D. M. 1975. Taxonomic diversity estimation using rarefaction. Paleobiology 1: 333-342. Schlosser, I. J. 1995. Critical...Rarefaction and rarefiction — The use and abuse of a method in paleoecology. Paleobiology 5: 423-434. U.S. Environmental Protection Agency (USEPA). 1986

LARVAL FISH DIVERSITY IN SUISAN MARSH, CALIFORNIA: ARE INTERMEDIATE FLOWS THE BEST?

EPA Science Inventory

We sampled larval fish in Suisun Marsh, in the San Francisco Bay estuary from February to June 1995-1999. We used principal components analysis (PCA) and canonical correspondence analysis (CCA) on 13 taxonomic groups making up 99.7% of the catch and several environmental variable...

GENETIC DIVERSITY OF STREAM FISH IN THE MID-ATLANTIC INTEGRATED ASSESSMENT AREA

EPA Science Inventory

In this report, we describe the results of research to assess the genetics of three stream fish species in the Mid-Atlantic region. This research had three specific goals. First, we sought to examine the utility of genetic analysis for purposes of taxonomic identification. Bioa...

A conservation framework for the Critically Endangered endemic species of the Caribbean palm Coccothrinax.

USDA-ARS?s Scientific Manuscript database

With 30 threatened species [14 Critically Endangered (CR) and 16 Endangered, sensu IUCN)] Coccothrinax (c. 54 species) is the flagship palm genus for conservation in the Caribbean Island Biodiversity Hotspot. Coccothrinax has its center of taxonomic diversity in these islands, with c. 51 endemic spe...

Species-level assessment of secondary metabolite diversity among Hamigera species and a taxonomic note on the genus

USDA-ARS?s Scientific Manuscript database

Secondary metabolite phenotypes in nine species of the Hamigera clade were analysed to assess their correlations to a multi-gene species-level phylogeny. High-pressure-liquid-chromatography-based chemical analysis revealed three distinctive patterns of secondary metabolite production: (1) the nine s...

The amphibians and reptiles of Luzon Island, Philippines, VIII: the herpetofauna of Cagayan and Isabela Provinces, northern Sierra Madre Mountain Range

PubMed Central

Brown, Rafe M.; Siler, Cameron D.; Oliveros, Carl. H; Welton, Luke J.; Rock, Ashley; Swab, John; Weerd, Merlijn Van; van Beijnen, Jonah; Jose, Edgar; Rodriguez, Dominic; Jose, Edmund; Diesmos, Arvin C.

2013-01-01

Abstract We provide the first report on the herpetological biodiversity (amphibians and reptiles) of the northern Sierra Madre Mountain Range (Cagayan and Isabela provinces), northeast Luzon Island, Philippines. New data from extensive previously unpublished surveys in the Municipalities of Gonzaga, Gattaran, Lasam, Santa Ana, and Baggao (Cagayan Province), as well as fieldwork in the Municipalities of Cabagan, San Mariano, and Palanan (Isabela Province), combined with all available historical museum records, suggest this region is quite diverse. Our new data indicate that at least 101 species are present (29 amphibians, 30 lizards, 35 snakes, two freshwater turtles, three marine turtles, and two crocodilians) and now represented with well-documented records and/or voucher specimens, confirmed in institutional biodiversity repositories. A high percentage of Philippine endemic species constitute the local fauna (approximately 70%). The results of this and other recent studies signify that the herpetological diversity of the northern Philippines is far more diverse than previously imagined. Thirty-eight percent of our recorded species are associated with unresolved taxonomic issues (suspected new species or species complexes in need of taxonomic partitioning). This suggests that despite past and present efforts to comprehensively characterize the fauna, the herpetological biodiversity of the northern Philippines is still substantially underestimated and warranting of further study. PMID:23653519

Phylogenomics and species delimitation of a complex radiation of Neotropical suboscine birds (Pachyramphus).

PubMed

Musher, Lukas J; Cracraft, Joel

2018-01-01

Phylogeographic studies within the Neotropics continue to uncover hidden diversity, the extent of which remains poorly known. In birds, molecular studies are producing evidence that species-level diversity is substantially underestimated. Many avian taxa comprise large complexes of subspecies that often represent species-level taxa by various criteria. One such group of Neotropical suboscine birds, the becards (Pachyramphus), ranges from Argentina through northern Mexico. Their taxonomic limits have been complex and controversial as the genus has bounced around a number of suboscine families. Additionally, the phylogenetic relationships within Pachyramphus are unresolved due to insufficient sampling of taxa and populations across species' ranges. We used target capture of ultraconserved elements for 62 individuals representing 42 taxa, and sequenced two mitochondrial genes and two nuclear introns covering 265 individuals of 51 taxa, including all recognized species, resulting in the most densely and completely sampled phylogenetic hypothesis for Pachyramphus to date. We delimited species using a traditional taxonomic approach and then tested them under a Bayesian multi-species coalescent framework. In doing so, we provide evidence for multiple young, previously undetected evolutionary lineages within Pachyramphus. Deep, well-supported branches and a high number of intraspecific lineages across the tree suggest that at least 50% of species diversity may be unrecognized. Copyright © 2017 Elsevier Inc. All rights reserved.

The amphibians and reptiles of Luzon Island, Philippines, VIII: the herpetofauna of Cagayan and Isabela Provinces, northern Sierra Madre Mountain Range.

PubMed

Brown, Rafe M; Siler, Cameron D; Oliveros, Carl H; Welton, Luke J; Rock, Ashley; Swab, John; Weerd, Merlijn Van; van Beijnen, Jonah; Jose, Edgar; Rodriguez, Dominic; Jose, Edmund; Diesmos, Arvin C

2013-01-01

We provide the first report on the herpetological biodiversity (amphibians and reptiles) of the northern Sierra Madre Mountain Range (Cagayan and Isabela provinces), northeast Luzon Island, Philippines. New data from extensive previously unpublished surveys in the Municipalities of Gonzaga, Gattaran, Lasam, Santa Ana, and Baggao (Cagayan Province), as well as fieldwork in the Municipalities of Cabagan, San Mariano, and Palanan (Isabela Province), combined with all available historical museum records, suggest this region is quite diverse. Our new data indicate that at least 101 species are present (29 amphibians, 30 lizards, 35 snakes, two freshwater turtles, three marine turtles, and two crocodilians) and now represented with well-documented records and/or voucher specimens, confirmed in institutional biodiversity repositories. A high percentage of Philippine endemic species constitute the local fauna (approximately 70%). The results of this and other recent studies signify that the herpetological diversity of the northern Philippines is far more diverse than previously imagined. Thirty-eight percent of our recorded species are associated with unresolved taxonomic issues (suspected new species or species complexes in need of taxonomic partitioning). This suggests that despite past and present efforts to comprehensively characterize the fauna, the herpetological biodiversity of the northern Philippines is still substantially underestimated and warranting of further study.

Diversity and distribution patterns of root-associated fungi on herbaceous plants in alpine meadows of southwestern China.

PubMed

Gao, Qian; Yang, Zhu L

2016-01-01

The diversity of root-associated fungi associated with four ectomycorrhizal herbaceous species, Kobresia capillifolia, Carex parva, Polygonum macrophyllum and Potentilla fallens, collected in three sites of alpine meadows in southwestern China, was estimated based on internal transcribed spacer (ITS) rDNA sequence analysis of root tips. Three hundred seventy-seven fungal sequences sorted to 154 operational taxonomical units (sequence similarity of ≥ 97% across the ITS) were obtained from the four plant species across all three sites. Similar taxa (in GenBank with ≥ 97% similarity) were not found in GenBank and/or UNITE for most of the OTUs. Ectomycorrhiz a made up 64% of the fungi operational taxonomic units (OTUs), endophytes constituted 4% and the other 33% were unidentified root-associated fungi. Fungal OTUs were represented by 57% basidiomycetes and 43% ascomycetes. Inocybe, Tomentella/Thelophora, Sebacina, Hebeloma, Pezizomycotina, Cenococcum geophilum complex, Cortinarius, Lactarius and Helotiales were OTU-rich fungal lineages. Across the sites and host species the root-associated fungal communities generally exhibited low host and site specificity but high host and sampling site preference. Collectively our study revealed noteworthy diversity and endemism of root-associated fungi of alpine plants in this global biodiversity hotspot. © 2016 by The Mycological Society of America.

Dynamic evolutionary change in post-Paleozoic echinoids and the importance of scale when interpreting changes in rates of evolution.

PubMed

Hopkins, Melanie J; Smith, Andrew B

2015-03-24

How ecological and morphological diversity accrues over geological time has been much debated by paleobiologists. Evidence from the fossil record suggests that many clades reach maximal diversity early in their evolutionary history, followed by a decline in evolutionary rates as ecological space fills or due to internal constraints. Here, we apply recently developed methods for estimating rates of morphological evolution during the post-Paleozoic history of a major invertebrate clade, the Echinoidea. Contrary to expectation, rates of evolution were lowest during the initial phase of diversification following the Permo-Triassic mass extinction and increased over time. Furthermore, although several subclades show high initial rates and net decreases in rates of evolution, consistent with "early bursts" of morphological diversification, at more inclusive taxonomic levels, these bursts appear as episodic peaks. Peak rates coincided with major shifts in ecological morphology, primarily associated with innovations in feeding strategies. Despite having similar numbers of species in today's oceans, regular echinoids have accrued far less morphological diversity than irregular echinoids due to lower intrinsic rates of morphological evolution and less morphological innovation, the latter indicative of constrained or bounded evolution. These results indicate that rates of evolution are extremely heterogenous through time and their interpretation depends on the temporal and taxonomic scale of analysis.

Phytoplankton Diversity and Geologically Relevant Carbon: Using metagenomics to determine phytoplankton biomarker production

NASA Astrophysics Data System (ADS)

Kodner, R. B.; Armbrust, E.

2008-12-01

Phytoplankton play an important role in the global carbon cycle, on short and long time scales. On long time scales, organic carbon, especially recalcitrant forms of biomass such as lipids, can be preserved and thus sequestered in sediments and rocks on geologic time scales. If the preserved lipids have some taxonomic specificity, they can be used as fossil biomarkers to characterize the community of organisms that contributed to ancient carbon sinks. Currently, it is not well understood how well the complex mixture of organic compounds preserved in geological carbon sinks represents the original community that produced those molecules or how the diversity of organism in a community is reflected in the lipid biomarkers they collectively synthesize. We have begun to investigate these questions by characterizing lipid biomarker production in modern phytoplankton communities with metagenomic data sets. Here we evaluate the information on community biomarker biosynthesis gathered from this type of data set using sterols as a case study. We have identified genes involved in sterol biosynthesis in a number of metagenomes and placed these genes in a phylogenetic context using a method designed to deal with short metagenomic sequences. The degree of taxonomic diversity of biomarker production measured with gene sequences can be more specific than lipid analysis alone.

Metaphor, symbolic play, and logical thought in early childhood.

PubMed

Seitz, J A

1997-11-01

Development of the ability to understand diverse types of metaphor was examined in terms of play context (symbolic vs. constructive-object play), Piagetian operational level (preoperational vs. concrete-operational), and medium of presentation (pictures vs. words). Forty 4-year-olds and 80 6-year-olds (40 preoperational, 40 concrete-operational) were presented with six different types of metaphorical relationships (color, shape, physiognomic, cross-modal, psychological-physical, and taxonomic matches) in both pictures and words in a match-to-sample design. Results indicated that (a) constructive-object play, rather than symbolic play, facilitated the understanding of perceptual and taxonomic metaphor, suggesting differences in early styles of metaphoric usage; (b) despite previous findings, the study failed to replicate a relationship between operativity and metaphoric understanding; and (c) younger children did significantly better in the pictorial medium, suggesting a picture-superiority effect for more perceptible metaphorical relations (perceptual and physiognomic), whereas older children showed a word-superiority effect for more conceptual metaphors (psychological-physical and taxonomic).

Is the plant-associated microbiota of Thymus spp. adapted to plant essential oil?

PubMed

Checcucci, Alice; Maida, Isabel; Bacci, Giovanni; Ninno, Cristina; Bilia, Anna Rita; Biffi, Sauro; Firenzuoli, Fabio; Flamini, Guido; Fani, Renato; Mengoni, Alessio

2017-04-01

We examined whether the microbiota of two related aromatic thyme species, Thymus vulgaris and Thymus citriodorus, differs in relation to the composition of the respective essential oil (EO). A total of 576 bacterial isolates were obtained from three districts (leaves, roots and rhizospheric soil). They were taxonomically characterized and inspected for tolerance to the EO from the two thyme species. A district-related taxonomic pattern was found. In particular, high taxonomic diversity among the isolates from leaves was detected. Moreover, data obtained revealed a differential pattern of resistance of the isolates to EOs extracted from T. vulgaris and T. citriodorus, which was interpreted in terms of differing chemical composition of the EO of their respective host plants. In conclusion, we suggest that bacterial colonization of leaves in Thymus spp. is influenced by the EO present in leaf glandular tissue as one of the selective forces shaping endophytic community composition. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Tephritid Integrative Taxonomy: Where We Are Now, with a Focus on the Resolution of Three Tropical Fruit Fly Species Complexes.

PubMed

Schutze, Mark K; Virgilio, Massimiliano; Norrbom, Allen; Clarke, Anthony R

2017-01-31

Accurate species delimitation underpins good taxonomy. Formalization of integrative taxonomy in the past decade has provided a framework for using multidisciplinary data to make species delimitation hypotheses more rigorous. We address the current state of integrative taxonomy by using as a case study an international project targeted at resolving three important tephritid species complexes: Bactrocera dorsalis complex, Anastrepha fraterculus complex, and Ceratitis FAR (C. fasciventris, C. anonae, C. rosa) complex. The integrative taxonomic approach has helped deliver significant advances in resolving these complexes: It has been used to identify some taxa as belonging to the same biological species as well as to confirm hidden cryptic diversity under a single taxonomic name. Nevertheless, the general application of integrative taxonomy has not been without issue, revealing challenges that must be considered when undertaking an integrative taxonomy project. Scrutiny of this international case study provides a unique opportunity to document lessons learned for the benefit of not only tephritid taxonomists, but also the wider taxonomic community.

Phenex: ontological annotation of phenotypic diversity.

PubMed

Balhoff, James P; Dahdul, Wasila M; Kothari, Cartik R; Lapp, Hilmar; Lundberg, John G; Mabee, Paula; Midford, Peter E; Westerfield, Monte; Vision, Todd J

2010-05-05

Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge. Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices. Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

Diversity Arrays Technology (DArT) platform for genotyping and mapping in carrot (Daucus carota L.)

USDA-ARS?s Scientific Manuscript database

Carrot is one of the most important root vegetable crops grown worldwide on more than one million hectares. Its progenitor, wild Daucus carota, is a weed commonly occurring across continents in the temperate climatic zone. Diversity Array Technology (DArT) is a microarray-based molecular marker syst...

Characterization of a Wheat Breeders' Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum).

PubMed

Allen, Alexandra M; Winfield, Mark O; Burridge, Amanda J; Downie, Rowena C; Benbow, Harriet R; Barker, Gary L A; Wilkinson, Paul A; Coghill, Jane; Waterfall, Christy; Davassi, Alessandro; Scopes, Geoff; Pirani, Ali; Webster, Teresa; Brew, Fiona; Bloor, Claire; Griffiths, Simon; Bentley, Alison R; Alda, Mark; Jack, Peter; Phillips, Andrew L; Edwards, Keith J

2017-03-01

Targeted selection and inbreeding have resulted in a lack of genetic diversity in elite hexaploid bread wheat accessions. Reduced diversity can be a limiting factor in the breeding of high yielding varieties and crucially can mean reduced resilience in the face of changing climate and resource pressures. Recent technological advances have enabled the development of molecular markers for use in the assessment and utilization of genetic diversity in hexaploid wheat. Starting with a large collection of 819 571 previously characterized wheat markers, here we describe the identification of 35 143 single nucleotide polymorphism-based markers, which are highly suited to the genotyping of elite hexaploid wheat accessions. To assess their suitability, the markers have been validated using a commercial high-density Affymetrix Axiom ® genotyping array (the Wheat Breeders' Array), in a high-throughput 384 microplate configuration, to characterize a diverse global collection of wheat accessions including landraces and elite lines derived from commercial breeding communities. We demonstrate that the Wheat Breeders' Array is also suitable for generating high-density genetic maps of previously uncharacterized populations and for characterizing novel genetic diversity produced by mutagenesis. To facilitate the use of the array by the wheat community, the markers, the associated sequence and the genotype information have been made available through the interactive web site 'CerealsDB'. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Conservation Genetics of the Philippine Tarsier: Cryptic Genetic Variation Restructures Conservation Priorities for an Island Archipelago Primate

PubMed Central

Brown, Rafe M.; Weghorst, Jennifer A.; Olson, Karen V.; Duya, Mariano R. M.; Barley, Anthony J.; Duya, Melizar V.; Shekelle, Myron; Neri-Arboleda, Irene; Esselstyn, Jacob A.; Dominy, Nathaniel J.; Ong, Perry S.; Moritz, Gillian L.; Luczon, Adrian; Diesmos, Mae Lowe L.; Diesmos, Arvin C.; Siler, Cameron D.

2014-01-01

Establishment of conservation priorities for primates is a particular concern in the island archipelagos of Southeast Asia, where rates of habitat destruction are among the highest in the world. Conservation programs require knowledge of taxonomic diversity to ensure success. The Philippine tarsier is a flagship species that promotes environmental awareness and a thriving ecotourism economy in the Philippines. However, assessment of its conservation status has been impeded by taxonomic uncertainty, a paucity of field studies, and a lack of vouchered specimens and genetic samples available for study in biodiversity repositories. Consequently, conservation priorities are unclear. In this study we use mitochondrial and nuclear DNA to empirically infer geographic partitioning of genetic variation and to identify evolutionarily distinct lineages for conservation action. The distribution of Philippine tarsier genetic diversity is neither congruent with expectations based on biogeographical patterns documented in other Philippine vertebrates, nor does it agree with the most recent Philippine tarsier taxonomic arrangement. We identify three principal evolutionary lineages that do not correspond to the currently recognized subspecies, highlight the discovery of a novel cryptic and range-restricted subcenter of genetic variation in an unanticipated part of the archipelago, and identify additional geographically structured genetic variation that should be the focus of future studies and conservation action. Conservation of this flagship species necessitates establishment of protected areas and targeted conservation programs within the range of each genetically distinct variant of the Philippine tarsier. PMID:25136854

The global distribution of diet breadth in insect herbivores

PubMed Central

Forister, Matthew L.; Novotny, Vojtech; Panorska, Anna K.; Baje, Leontine; Basset, Yves; Butterill, Philip T.; Cizek, Lukas; Coley, Phyllis D.; Dem, Francesca; Diniz, Ivone R.; Drozd, Pavel; Fox, Mark; Glassmire, Andrea E.; Hazen, Rebecca; Hrcek, Jan; Jahner, Joshua P.; Kaman, Ondrej; Kozubowski, Tomasz J.; Kursar, Thomas A.; Lewis, Owen T.; Lill, John; Marquis, Robert J.; Miller, Scott E.; Morais, Helena C.; Murakami, Masashi; Nickel, Herbert; Pardikes, Nicholas A.; Ricklefs, Robert E.; Singer, Michael S.; Smilanich, Angela M.; Stireman, John O.; Villamarín-Cortez, Santiago; Vodka, Stepan; Volf, Martin; Wagner, David L.; Walla, Thomas; Weiblen, George D.; Dyer, Lee A.

2015-01-01

Understanding variation in resource specialization is important for progress on issues that include coevolution, community assembly, ecosystem processes, and the latitudinal gradient of species richness. Herbivorous insects are useful models for studying resource specialization, and the interaction between plants and herbivorous insects is one of the most common and consequential ecological associations on the planet. However, uncertainty persists regarding fundamental features of herbivore diet breadth, including its relationship to latitude and plant species richness. Here, we use a global dataset to investigate host range for over 7,500 insect herbivore species covering a wide taxonomic breadth and interacting with more than 2,000 species of plants in 165 families. We ask whether relatively specialized and generalized herbivores represent a dichotomy rather than a continuum from few to many host families and species attacked and whether diet breadth changes with increasing plant species richness toward the tropics. Across geographic regions and taxonomic subsets of the data, we find that the distribution of diet breadth is fit well by a discrete, truncated Pareto power law characterized by the predominance of specialized herbivores and a long, thin tail of more generalized species. Both the taxonomic and phylogenetic distributions of diet breadth shift globally with latitude, consistent with a higher frequency of specialized insects in tropical regions. We also find that more diverse lineages of plants support assemblages of relatively more specialized herbivores and that the global distribution of plant diversity contributes to but does not fully explain the latitudinal gradient in insect herbivore specialization. PMID:25548168

Snake species of the world: A taxonomic and geographic reference. v. 1

USGS Publications Warehouse

McDiarmid, R.W.; Campbell, J.A.; Toure, T.

1999-01-01

Given the absence of a current source on snake diversity and nomenclature and the expressed global need to understand better the diversity of our biota, we think that a catalogue of the world snake fauna complete with synonymies at the familial, generic, and specific levels is essential. We provide that here beginning with publication of the first volume. This compendium will facilitate comparative studies on the ecology, genetics, and behavior of snakes and, we hope, contribute to their conservation. At the very least, this work, when completed, will provide a readily available reference to the current taxonomic statuses and geographic distributions of snakes on a global scale. No comprehensive, up-to-date catalogue of snake species exists, and it is obvious that a detailed and inclusive treatment is long overdue. Snake Species of the World provides a comprehensive treatment of 31 families, 450 genera, and more than 2500 species of living snakes. The magnitude of the compilation requires publication in several volumes. This volume, the first of three, covers 682 species. A primary goal of this synthesis is to provide interested readers with a means for tracking scientific names that have been applied to a snake and determining the currently accepted name of that species. A secondary goal is to alert those interested in snakes as research subjects that in general many species are poorly known, that some have limited distributions, and that several are characterized by taxonomic problems.

[Population structure of soil arthropod in different age Pinus massoniana plantations].

PubMed

Tan, Bo; Wu, Fu-zhong; Yang, Wan-qin; Zhang, Jian; Xu, Zhen-feng; Liu, Yang; Gou, Xiao-lin

2013-04-01

An investigation was conducted on the population structure of soil arthropod community in the 3-, 8-, 14-, 31-, and 40-years old Pinus massoniana plantations in the upper reaches of the Yangtze River in spring (May) and autumn (October), 2011, aimed to search for the scientific management of the plantation. A total of 4045 soil arthropods were collected, belonging to 57 families. Both the individual density and the taxonomic group number of the soil arthropod community decreased obviously with increasing soil depth, and this trend increased with increasing stand age. The dominant groups and ordinary groups of the soil arthropod community varied greatly with the stand age of P. massoniana plantation, and a significant difference (P<0.05) was observed in the individual density and taxonomic group number among different age P. massoniana plantations. In comparison with other stand age P. massoniana plantations, 3years old P. massoniana plantation had a significant difference in the structure and diversity of soil arthropod community, and the similarity index of the soil arthropod community was lower. The individual density, taxonomic group number, and diversity of soil arthropod community were the highest in 8-years old P. massoniana plantation, and then, decreased obviously with increasing stand age. It was suggested that the land fertility of the P. massoniana plantations could be degraded with increasing stand age, and it would be appropriate to make artificial regulation and restoration in 8-years old P. massoniana plantation.

Predicting taxonomic and functional structure of microbial communities in acid mine drainage

PubMed Central

Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

2016-01-01

Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray–Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural acidophilic microbial communities. PMID:26943622

Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

PubMed

Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

2016-06-01

Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural acidophilic microbial communities.

Coastal habitats as surrogates for taxonomic, functional and trophic structures of benthic faunal communities.

PubMed

Törnroos, Anna; Nordström, Marie C; Bonsdorff, Erik

2013-01-01

Due to human impact, there is extensive degradation and loss of marine habitats, which calls for measures that incorporate taxonomic as well as functional and trophic aspects of biodiversity. Since such data is less easily quantifiable in nature, the use of habitats as surrogates or proxies for biodiversity is on the rise in marine conservation and management. However, there is a critical gap in knowledge of whether pre-defined habitat units adequately represent the functional and trophic structure of communities. We also lack comparisons of different measures of community structure in terms of both between- (β) and within-habitat (α) variability when accounting for species densities. Thus, we evaluated a priori defined coastal habitats as surrogates for traditional taxonomic, functional and trophic zoobenthic community structure. We focused on four habitats (bare sand, canopy-forming algae, seagrass above- and belowground), all easily delineated in nature and defined through classification systems. We analyzed uni- and multivariate data on species and trait diversity as well as stable isotope ratios of benthic macrofauna. A good fit between habitat types and taxonomic and functional structure was found, although habitats were more similar functionally. This was attributed to within-habitat heterogeneity so when habitat divisions matched the taxonomic structure, only bare sand was functionally distinct. The pre-defined habitats did not meet the variability of trophic structure, which also proved to differentiate on a smaller spatial scale. The quantification of trophic structure using species density only identified an epi- and an infaunal unit. To summarize the results we present a conceptual model illustrating the match between pre-defined habitat types and the taxonomic, functional and trophic community structure. Our results show the importance of including functional and trophic aspects more comprehensively in marine management and spatial planning.

Genetic Structure of Natural Populations of Escherichia coli in Wild Hosts on Different Continents

PubMed Central

Souza, Valeria; Rocha, Martha; Valera, Aldo; Eguiarte, Luis E.

1999-01-01

Current knowledge of genotypic and phenotypic diversity in the species Escherichia coli is based almost entirely on strains recovered from humans or zoo animals. In this study, we analyzed a collection of 202 strains obtained from 81 mammalian species representing 39 families and 14 orders in Australia and the Americas, as well as several reference strains; we also included a strain from a reptile and 10 from different families of birds collected in Mexico. The strains were characterized genotypically by multilocus enzyme electrophoresis (MLEE) and phenotypically by patterns of sugar utilization, antibiotic resistance, and plasmid profile. MLEE analysis yielded an estimated genetic diversity (H) of 0.682 for 11 loci. The observed genetic diversity in this sample is the greatest yet reported for E. coli. However, this genetic diversity is not randomly distributed; geographic effects and host taxonomic group accounted for most of the genetic differentiation. The genetic relationship among the strains showed that they are more associated by origin and host order than is expected by chance. In a dendrogram, the ancestral cluster includes primarily strains from Australia and ECOR strains from groups B and C. The most differentiated E. coli in our analysis are strains from Mexican carnivores and strains from humans, including those in the ECOR group A. The kinds and numbers of sugars utilized by the strains varied by host taxonomic group and country of origin. Strains isolated from bats were found to exploit the greatest range of sugars, while those from primates utilized the fewest. Toxins are more frequent in strains from rodents from both continents than in any other taxonomic group. Strains from Mexican wild mammals were, on average, as resistant to antibiotics as strains from humans in cities. On average, the Australian strains presented a lower antibiotic resistance than the Mexican strains. However, strains recovered from hosts in cities carried significantly more plasmids than did strains isolated from wild mammals. Previous studies have shown that natural populations of E. coli harbor an extensive genetic diversity that is organized in a limited number of clones. However, knowledge of this worldwide bacterium has been limited. Here, we suggest that the strains from a wide range of wild hosts from different regions of the world are organized in an ecotypic structure where adaptation to the host plays an important role in the population structure. PMID:10427022

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

PubMed

He, Yan; Caporaso, J Gregory; Jiang, Xiao-Tao; Sheng, Hua-Fang; Huse, Susan M; Rideout, Jai Ram; Edgar, Robert C; Kopylova, Evguenia; Walters, William A; Knight, Rob; Zhou, Hong-Wei

2015-01-01

The operational taxonomic unit (OTU) is widely used in microbial ecology. Reproducibility in microbial ecology research depends on the reliability of OTU-based 16S ribosomal subunit RNA (rRNA) analyses. Here, we report that many hierarchical and greedy clustering methods produce unstable OTUs, with membership that depends on the number of sequences clustered. If OTUs are regenerated with additional sequences or samples, sequences originally assigned to a given OTU can be split into different OTUs. Alternatively, sequences assigned to different OTUs can be merged into a single OTU. This OTU instability affects alpha-diversity analyses such as rarefaction curves, beta-diversity analyses such as distance-based ordination (for example, Principal Coordinate Analysis (PCoA)), and the identification of differentially represented OTUs. Our results show that the proportion of unstable OTUs varies for different clustering methods. We found that the closed-reference method is the only one that produces completely stable OTUs, with the caveat that sequences that do not match a pre-existing reference sequence collection are discarded. As a compromise to the factors listed above, we propose using an open-reference method to enhance OTU stability. This type of method clusters sequences against a database and includes unmatched sequences by clustering them via a relatively stable de novo clustering method. OTU stability is an important consideration when analyzing microbial diversity and is a feature that should be taken into account during the development of novel OTU clustering methods.

DNA metabarcoding uncovers fungal diversity of mixed airborne samples in Italy

PubMed Central

Banchi, Elisa; Ametrano, Claudio Gennaro; Stanković, David; Verardo, Pierluigi; Moretti, Olga; Gabrielli, Francesca; Lazzarin, Stefania; Borney, Maria Francesca; Tassan, Francesca; Tretiach, Mauro; Pallavicini, Alberto

2018-01-01

Fungal spores and mycelium fragments are particles which become and remain airborne and have been subjects of aerobiological studies. The presence and the abundance of taxa in aerobiological samples can be very variable and impaired by changeable climatic conditions. Because many fungi produce mycotoxins and both their mycelium fragments and spores are potential allergens, monitoring the presence of these taxa is of key importance. So far data on exposure and sensitization to fungal allergens are mainly based on the assessment of few, easily identifiable taxa and focused only on certain environments. The microscopic method used to analyze aerobiological samples and the inconspicuous fungal characters do not allow a in depth taxonomical identification. Here, we present a first assessment of fungal diversity from airborne samples using a DNA metabarcoding analysis. The nuclear ITS2 region was selected as barcode to catch fungal diversity in mixed airborne samples gathered during two weeks in four sites of North-Eastern and Central Italy. We assessed the taxonomic composition and diversity within and among the sampled sites and compared the molecular data with those obtained by traditional microscopy. The molecular analyses provide a tenfold more comprehensive determination of the taxa than the traditional morphological inspections. Our results prove that the metabarcoding analysis is a promising approach to increases quality and sensitivity of the aerobiological monitoring. The laboratory and bioinformatic workflow implemented here is now suitable for routine, high-throughput, regional analyses of airborne fungi. PMID:29558527

Covariance in species diversity and facilitation among non-interactive parasite taxa: all against the host.

PubMed

Krasnov, B R; Mouillot, D; Khokhlova, I S; Shenbrot, G I; Poulin, R

2005-10-01

Different parasite taxa exploit different host resources and are often unlikely to interact directly. It is unclear, however, whether the diversity of any given parasite taxon is indirectly influenced by that of other parasite taxa on the same host. Some components of host immune defences may operate simultaneously against all kinds of parasites, whereas investment by the host in specific defences against one type of parasite may come at the expense of defence against other parasites. We investigated the relationships between the species diversity of 4 higher taxa of ectoparasites (fleas, sucking lice, mesostigmatid mites, and ixodid ticks), and between the species richness of ectoparasites and endoparasitic helminths, across different species of rodent hosts. Our analyses used 2 measures of species diversity, species richness and taxonomic distinctness, and controlled for the potentially confounding effects of sampling effort and phylogenetic relationships among host species. We found positive pairwise correlations between the species richness of fleas, mites and ticks; however, there was no association between species richness of any of these 3 groups and that of lice. We also found a strong positive relationship between the taxonomic distinctness of ecto- and endoparasite assemblages across host species. These results suggest the existence of a process of apparent facilitation among unrelated taxa in the organization of parasite communities. We propose explanations based on host immune responses, involving acquired cross-resistance to infection and interspecific variation in immunocompetence among hosts, to account for these patterns.

Metagenomic Insights of Microbial Feedbacks to Elevated CO2 (Invited)

NASA Astrophysics Data System (ADS)

Zhou, J.; Tu, Q.; Wu, L.; He, Z.; Deng, Y.; Van Nostrand, J. D.

2013-12-01

Understanding the responses of biological communities to elevated CO2 (eCO2) is a central issue in ecology and global change biology, but its impacts on the diversity, composition, structure, function, interactions and dynamics of soil microbial communities remain elusive. In this study, we first examined microbial responses to eCO2 among six FACE sites/ecosystems using a comprehensive functional gene microarray (GeoChip), and then focused on details of metagenome sequencing analysis in one particular site. GeoChip is a comprehensive functional gene array for examining the relationships between microbial community structure and ecosystem functioning and is a very powerful technology for biogeochemical, ecological and environmental studies. The current version of GeoChip (GeoChip 5.0) contains approximately 162,000 probes from 378,000 genes involved in C, N, S and P cycling, organic contaminant degradation, metal resistance, antibiotic resistance, stress responses, metal homeostasis, virulence, pigment production, bacterial phage-mediated lysis, soil beneficial microorganisms, and specific probes for viruses, protists, and fungi. Our experimental results revealed that both ecosystem and CO2 significantly (p < 0.05) affected the functional composition, structure and metabolic potential of soil microbial communities with the ecosystem having much greater influence (~47%) than CO2 (~1.3%) or CO2 and ecosystem (~4.1%). On one hand, microbial responses to eCO2 shared some common patterns among different ecosystems, such as increased abundances for key functional genes involved in nitrogen fixation, carbon fixation and degradation, and denitrification. On the other hand, more ecosystem-specific microbial responses were identified in each individual ecosystem. Such changes in the soil microbial community structure were closely correlated with geographic distance, soil NO3-N, NH4-N and C/N ratio. Further metagenome sequencing analysis of soil microbial communities in one particular site showed eCO2 altered the overall structure of soil microbial communities with ambient CO2 samples retaining a higher functional gene diversity than eCO2 samples. Also the taxonomic diversity of functional genes decreased at eCO2. Random matrix theory (RMT)-based network analysis showed that the identified networks under ambient and elevated CO2 were substantially different in terms of overall network topology, network composition, node overlap, module preservation, module-based higher order organization (meta-modules), topological roles of individual nodes, and network hubs, indicating that elevated CO2 dramatically altered the network interactions among different phylogenetic and functional groups/populations. In addition, the changes in network structure were significantly correlated with soil carbon and nitrogen content, indicating the potential importance of network interactions in ecosystem functioning. Taken together, this study indicates that eCO2 may decrease the overall functional and taxonomic diversity of soil microbial communities, but such effects appeared to be ecosystem-specific, which makes it more challenging for predicting global or regional terrestrial ecosystems responses to eCO2.

Tandem-repeat protein domains across the tree of life

PubMed Central

Jernigan, Kristin K.

2015-01-01

Tandem-repeat protein domains, composed of repeated units of conserved stretches of 20–40 amino acids, are required for a wide array of biological functions. Despite their diverse and fundamental functions, there has been no comprehensive assessment of their taxonomic distribution, incidence, and associations with organismal lifestyle and phylogeny. In this study, we assess for the first time the abundance of armadillo (ARM) and tetratricopeptide (TPR) repeat domains across all three domains in the tree of life and compare the results to our previous analysis on ankyrin (ANK) repeat domains in this journal. All eukaryotes and a majority of the bacterial and archaeal genomes analyzed have a minimum of one TPR and ARM repeat. In eukaryotes, the fraction of ARM-containing proteins is approximately double that of TPR and ANK-containing proteins, whereas bacteria and archaea are enriched in TPR-containing proteins relative to ARM- and ANK-containing proteins. We show in bacteria that phylogenetic history, rather than lifestyle or pathogenicity, is a predictor of TPR repeat domain abundance, while neither phylogenetic history nor lifestyle predicts ARM repeat domain abundance. Surprisingly, pathogenic bacteria were not enriched in TPR-containing proteins, which have been associated within virulence factors in certain species. Taken together, this comparative analysis provides a newly appreciated view of the prevalence and diversity of multiple types of tandem-repeat protein domains across the tree of life. A central finding of this analysis is that tandem repeat domain-containing proteins are prevalent not just in eukaryotes, but also in bacterial and archaeal species. PMID:25653910

The Genomic Diversification of the Whole Acinetobacter Genus: Origins, Mechanisms, and Consequences

PubMed Central

Touchon, Marie; Cury, Jean; Yoon, Eun-Jeong; Krizova, Lenka; Cerqueira, Gustavo C.; Murphy, Cheryl; Feldgarden, Michael; Wortman, Jennifer; Clermont, Dominique; Lambert, Thierry; Grillot-Courvalin, Catherine; Nemec, Alexandr; Courvalin, Patrice; Rocha, Eduardo P.C.

2014-01-01

Bacterial genomics has greatly expanded our understanding of microdiversification patterns within a species, but analyses at higher taxonomical levels are necessary to understand and predict the independent rise of pathogens in a genus. We have sampled, sequenced, and assessed the diversity of genomes of validly named and tentative species of the Acinetobacter genus, a clade including major nosocomial pathogens and biotechnologically important species. We inferred a robust global phylogeny and delimited several new putative species. The genus is very ancient and extremely diverse: Genomes of highly divergent species share more orthologs than certain strains within a species. We systematically characterized elements and mechanisms driving genome diversification, such as conjugative elements, insertion sequences, and natural transformation. We found many error-prone polymerases that may play a role in resistance to toxins, antibiotics, and in the generation of genetic variation. Surprisingly, temperate phages, poorly studied in Acinetobacter, were found to account for a significant fraction of most genomes. Accordingly, many genomes encode clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems with some of the largest CRISPR-arrays found so far in bacteria. Integrons are strongly overrepresented in Acinetobacter baumannii, which correlates with its frequent resistance to antibiotics. Our data suggest that A. baumannii arose from an ancient population bottleneck followed by population expansion under strong purifying selection. The outstanding diversification of the species occurred largely by horizontal transfer, including some allelic recombination, at specific hotspots preferentially located close to the replication terminus. Our work sets a quantitative basis to understand the diversification of Acinetobacter into emerging resistant and versatile pathogens. PMID:25313016

Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish

PubMed Central

Barton, Carrie L.; Proffitt, Sarah; Tanguay, Robert L.; Sharpton, Thomas J.

2016-01-01

Growing evidence indicates that disrupting the microbial community that comprises the intestinal tract, known as the gut microbiome, can contribute to the development or severity of disease. As a result, it is important to discern the agents responsible for microbiome disruption. While animals are frequently exposed to a diverse array of environmental chemicals, little is known about their effects on gut microbiome stability and structure. Here, we demonstrate how zebrafish can be used to glean insight into the effects of environmental chemical exposure on the structure and ecological dynamics of the gut microbiome. Specifically, we exposed forty-five adult zebrafish to triclosan-laden food for four or seven days or a control diet, and analyzed their microbial communities using 16S rRNA amplicon sequencing. Triclosan exposure was associated with rapid shifts in microbiome structure and diversity. We find evidence that several operational taxonomic units (OTUs) associated with the family Enterobacteriaceae appear to be susceptible to triclosan exposure, while OTUs associated with the genus Pseudomonas appeared to be more resilient and resistant to exposure. We also found that triclosan exposure is associated with topological alterations to microbial interaction networks and results in an overall increase in the number of negative interactions per microbe in these networks. Together these data indicate that triclosan exposure results in altered composition and ecological dynamics of microbial communities in the gut. Our work demonstrates that because zebrafish afford rapid and inexpensive interrogation of a large number of individuals, it is a useful experimental system for the discovery of the gut microbiome’s interaction with environmental chemicals. PMID:27191725

A model of onshore-offshore change in faunal diversity

NASA Technical Reports Server (NTRS)

Sepkoski, J. J. Jr; Sepkoski JJ, J. r. (Principal Investigator)

1991-01-01

Onshore-offshore patterns of faunal change occurred at many taxonomic scales during the Paleozoic Era, ranging from replacement of the Cambrian evolutionary fauna by the Paleozoic fauna to the environmental expansion of many orders and classes. A simple mathematical model is constructed to investigate such change. The environmental gradient across the marine shelf-slope is treated as a linear array of discrete habitats, each of which holds a set number of species, as observed in the fossil record. During any interval of time, some portion of the species in each habitat becomes extinct by background processes, with rates of extinction varying among both clades and habitats, as also observed in the record. After extinction, species are replaced from within the habitat and from immediately adjacent habitats, with proportions dependent on surviving species. This model leads to the prediction that extinction-resistant clades will always diversify at the expense of extinction-prone clades. But if extinction intensity is highest in nearshore habitats, extinction-resistant clades will expand preferentially in the onshore direction, build up diversity there, and then diversify outward toward the offshore. Thus, onshore-offshore patterns of diversification may be the expectation for faunal change quite independently of whether or not clades originate onshore. When the model is parameterized for Paleozoic trilobites and brachiopods, numerical solutions exhibit both a pattern of faunal change and a time span for diversification similar to that seen in the fossil record. They also generate structure similar to that seen in global diversification, including logistic patterns of growth, declining origination but constant extinction within clades through time, and declining overall extinction across clades through time.

Pyrosequencing-based assessment of the bacteria diversity in surface and subsurface peat layers of a northern wetland, with focus on poorly studied phyla and candidate divisions.

PubMed

Serkebaeva, Yulia M; Kim, Yongkyu; Liesack, Werner; Dedysh, Svetlana N

2013-01-01

Northern peatlands play a key role in the global carbon and water budget, but the bacterial diversity in these ecosystems remains poorly described. Here, we compared the bacterial community composition in the surface (0-5 cm depth) and subsurface (45-50 cm) peat layers of an acidic (pH 4.0) Sphagnum-dominated wetland, using pyrosequencing of 16S rRNA genes. The denoised sequences (37,229 reads, average length ∼430 bp) were affiliated with 27 bacterial phyla and corresponded to 1,269 operational taxonomic units (OTUs) determined at 97% sequence identity. Abundant OTUs were affiliated with the Acidobacteria (35.5±2.4% and 39.2±1.2% of all classified sequences in surface and subsurface peat, respectively), Alphaproteobacteria (15.9±1.7% and 25.8±1.4%), Actinobacteria (9.5±2.0% and 10.7±0.5%), Verrucomicrobia (8.5±1.4% and 0.6±0.2%), Planctomycetes (5.8±0.4% and 9.7±0.6%), Deltaproteobacteria (7.1±0.4% and 4.4%±0.3%), and Gammaproteobacteria (6.6±0.4% and 2.1±0.1%). The taxonomic patterns of the abundant OTUs were uniform across all the subsamples taken from each peat layer. In contrast, the taxonomic patterns of rare OTUs were different from those of the abundant OTUs and varied greatly among subsamples, in both surface and subsurface peat. In addition to the bacterial taxa listed above, rare OTUs represented the following groups: Armatimonadetes, Bacteroidetes, Chlamydia, Chloroflexi, Cyanobacteria, Elusimicrobia, Fibrobacteres, Firmicutes, Gemmatimonadetes, Spirochaetes, AD3, WS1, WS4, WS5, WYO, OD1, OP3, BRC1, TM6, TM7, WPS-2, and FCPU426. OTU richness was notably higher in the surface layer (882 OTUs) than in the anoxic subsurface peat (483 OTUs), with only 96 OTUs common to both data sets. Most members of poorly studied phyla, such as the Acidobacteria, Verrucomicrobia, Planctomycetes and the candidate division TM6, showed a clear preference for growth in either oxic or anoxic conditions. Apparently, the bacterial communities in surface and subsurface layers of northern peatlands are highly diverse and taxonomically distinct, reflecting the different abiotic conditions in microhabitats within the peat profile.

Changes in the microbial community structure of bacteria, archaea and fungi in response to elevated CO(2) and warming in an Australian native grassland soil.

PubMed

Hayden, Helen L; Mele, Pauline M; Bougoure, Damian S; Allan, Claire Y; Norng, Sorn; Piceno, Yvette M; Brodie, Eoin L; Desantis, Todd Z; Andersen, Gary L; Williams, Amity L; Hovenden, Mark J

2012-12-01

The microbial community structure of bacteria, archaea and fungi is described in an Australian native grassland soil after more than 5 years exposure to different atmospheric CO2 concentrations ([CO2]) (ambient, +550 ppm) and temperatures (ambient, + 2°C) under different plant functional types (C3 and C4 grasses) and at two soil depths (0-5 cm and 5-10 cm). Archaeal community diversity was influenced by elevated [CO2], while under warming archaeal 16S rRNA gene copy numbers increased for C4 plant Themeda triandra and decreased for the C3 plant community (P < 0.05). Fungal community diversity resulted in three groups based upon elevated [CO2], elevated [CO2] plus warming and ambient [CO2]. Overall bacterial community diversity was influenced primarily by depth. Specific bacterial taxa changed in richness and relative abundance in response to climate change factors when assessed by a high-resolution 16S rRNA microarray (PhyloChip). Operational taxonomic unit signal intensities increased under elevated [CO2] for both Firmicutes and Bacteroidetes, and increased under warming for Actinobacteria and Alphaproteobacteria. For the interaction of elevated [CO2] and warming there were 103 significant operational taxonomic units (P < 0.01) representing 15 phyla and 30 classes. The majority of these operational taxonomic units increased in abundance for elevated [CO2] plus warming plots, while abundance declined in warmed or elevated [CO2] plots. Bacterial abundance (16S rRNA gene copy number) was significantly different for the interaction of elevated [CO2] and depth (P < 0.05) with decreased abundance under elevated [CO2] at 5-10 cm, and for Firmicutes under elevated [CO2] (P < 0.05). Bacteria, archaea and fungi in soil responded differently to elevated [CO2], warming and their interaction. Taxa identified as significantly climate-responsive could show differing trends in the direction of response ('+' or '-') under elevated CO2 or warming, which could then not be used to predict their interactive effects supporting the need to investigate interactive effects for climate change. The approach of focusing on specific taxonomic groups provides greater potential for understanding complex microbial community changes in ecosystems under climate change. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Increasing zooplankton size diversity enhances the strength of top-down control on phytoplankton through diet niche partitioning.

PubMed

Ye, Lin; Chang, Chun-Yi; García-Comas, Carmen; Gong, Gwo-Ching; Hsieh, Chih-Hao

2013-09-01

1. The biodiversity-ecosystem functioning debate is a central topic in ecology. Recently, there has been a growing interest in size diversity because body size is sensitive to environmental changes and is one of the fundamental characteristics of organisms linking many ecosystem properties. However, how size diversity affects ecosystem functioning is an important yet unclear issue. 2. To fill the gap, with large-scale field data from the East China Sea, we tested the novel hypothesis that increasing zooplankton size diversity enhances top-down control on phytoplankton (H1) and compared it with five conventional hypotheses explaining the top-down control: flatter zooplankton size spectrum enhances the strength of top-down control (H2); nutrient enrichment lessens the strength of top-down control (H3); increasing zooplankton taxonomic diversity enhances the strength of top-down control (H4); increasing fish predation decreases the strength of top-down control of zooplankton on phytoplankton through trophic cascade (H5); increasing temperature intensifies the strength of top-down control (H6). 3. The results of univariate analyses support the hypotheses based on zooplankton size diversity (H1), zooplankton size spectrum (H2), nutrient (H3) and zooplankton taxonomic diversity (H4), but not the hypotheses based on fish predation (H5) and temperature (H6). More in-depth analyses indicate that zooplankton size diversity is the most important factor in determining the strength of top-down control on phytoplankton in the East China Sea. 4. Our results suggest a new potential mechanism that increasing predator size diversity enhances the strength of top-down control on prey through diet niche partitioning. This mechanism can be explained by the optimal predator-prey body-mass ratio concept. Suppose each size group of zooplankton predators has its own optimal phytoplankton prey size, increasing size diversity of zooplankton would promote diet niche partitioning of predators and thus elevates the strength of top-down control. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

The Gills of Reef Fish Support a Distinct Microbiome Influenced by Host-Specific Factors.

PubMed

Pratte, Zoe A; Besson, Marc; Hollman, Rebecca D; Stewart, Frank J

2018-05-01

Teleost fish represent the most diverse of the vertebrate groups and play important roles in food webs, as ecosystem engineers, and as vectors for microorganisms. However, the microbial ecology of fishes remains underexplored for most host taxa and for certain niches on the fish body. This is particularly true for the gills, the key sites of respiration and waste exchange in fishes. Here we provide a comprehensive analysis of the gill microbiome. We focus on ecologically diverse taxa from coral reefs around Moorea, sampling the gills and intestines of adults and juveniles representing 15 families. The gill microbiome composition differed significantly from that of the gut for both adults and juveniles, with fish-associated niches having lower alpha diversity values and higher beta diversity values than those for seawater, sediment, and alga-associated microbiomes. Of ∼45,000 operational taxonomic units (OTUs) detected across all samples, 11% and 13% were detected only in the gill and the intestine, respectively. OTUs most enriched in the gill included members of the gammaproteobacterial genus Shewanella and the family Endozoicimonaceae In adult fish, both gill and intestinal microbiomes varied significantly among host species grouped by diet category. Gill and intestinal microbiomes from the same individual were more similar to one another than to gill and intestinal microbiomes from different individuals. These results demonstrate that distinct body sites are jointly influenced by host-specific organizing factors operating at the level of the host individual. The results also identify taxonomic signatures unique to the gill and the intestine, confirming fish-associated niches as distinct reservoirs of marine microbial diversity. IMPORTANCE Fish breathe and excrete waste through their gills. The gills are also potential sites of pathogen invasion and colonization by other microbes. However, we know little about the microbial communities that live on the gill and the factors shaping their diversity. Focusing on ecologically distinct types of coral reef fish, we provide a comprehensive analysis of the fish gill microbiome. By comparison to microbiomes of the gut and the surrounding environment, we identify microbes unique to the gill niche. These microbes may be targets for further studies to determine the contribution of the microbiome to waste exchange or host immunity. We also show that despite exhibiting a unique taxonomic signature, the gill microbiome is influenced by factors that also influence the gut microbiome. These factors include the specific identity of the host individual. These results suggest basic principles describing how association with fishes structures the composition of microbial communities. Copyright © 2018 American Society for Microbiology.

Can biotic indicators distinguish between natural and anthropogenic environmental stress in estuaries?

NASA Astrophysics Data System (ADS)

Tweedley, J. R.; Warwick, R. M.; Potter, I. C.

2015-08-01

Because estuaries are naturally stressed, due to variations in salinity, organic loadings, sediment stability and oxygen concentrations over both spatial and temporal scales, it is difficult both to set baseline reference conditions and to distinguish between natural and anthropogenic environmental stresses. This contrasts with the situation in marine coastal and offshore locations. A very large benthic macroinvertebrate dataset and matching concentrations for seven toxic heavy metals (i.e. Cr, Ni, Cu, Zn, Cd, Hg and Pb), compiled over three years as part of the UK's National Marine Monitoring Programme (NMMP) for 27 subtidal sites in 16 estuaries and 34 coastal marine sites in the United Kingdom, have been analysed. The results demonstrate that species composition and most benthic biotic indicators (number of taxa, overall density, Shannon-Wiener diversity, Simpson's index and AZTI's Marine Biotic Index [AMBI]) for sites in estuarine and coastal areas were significantly different, reflecting natural differences between these two environments. Shannon-Wiener diversity and AMBI were not significantly correlated either with overall heavy metal contaminant loadings or with individual heavy metal concentrations ('normalized' as heavy metal/aluminium ratios) in estuaries. In contrast, average taxonomic distinctness (Δ+) and variation in taxonomic distinctness (Λ+) did not differ significantly between estuarine and coastal environments, i.e. they were unaffected by natural differences between these two environments, but both were significantly correlated with overall heavy metal concentrations. Furthermore, Δ+ was correlated significantly with the Cu, Zn, Cd, Hg and Pb concentrations and Λ+ was correlated significantly with the Cr, Ni, Cu, Cd and Hg concentrations. Thus, one or both of these two taxonomic distinctness indices are significantly correlated with the concentrations for each of these seven heavy metals. These taxonomic distinctness indices are therefore considered appropriate indicators of anthropogenic disturbance in estuaries, as they allow a regional reference condition to be set from which significant departures can then be determined.

The blind men meet the elephant at the dam: Alternative spatial and taxonomic components reveal different insights about how low-head dams impact fish biodiversity

USGS Publications Warehouse

Fencl, Jane S.; Mather, Martha E.; Smith, Joseph M.; Hitchman, Sean M.

2017-01-01

Dams are ubiquitous environmental impacts that threaten aquatic ecosystems. The ability to compare across research studies is essential to conserve the native biodiversity that is impacted by the millions of low‐head dams that currently fragment streams and rivers. Here, we identify a previously unaddressed obstacle that impedes this generalization. Specifically, divergent spatial and taxonomic approaches that result from different conceptualizations of the dam‐biodiversity problem can produce conflicting science‐based conclusions about the same dam impact. In this research, using the same dammed and undammed sites, we evaluated the scientific generality of different conceptualizations of the dam‐biodiversity problem. We compared two different but commonly used spatial approaches—(1) above dam–below dam vs. (2) undammed–dammed comparisons—and 11 different, commonly used taxonomic approaches (three assemblage summaries, eight guilds). Sites above the dam structure had less diverse fish assemblages than sites below dams, whereas sites below the dam structure were similar to undammed sites. Thus, spatial approach 1 detected a large dam effect and spatial approach 2 detected a small dam effect. Similarly, some taxonomic responses (species richness, diversity, abundance, and number of guilds) detected large dam effects; other responses detected small (riffle specialist guild) or no dam effects (pool generalists). In summary, our results showed that how the problem was framed altered scientific conclusions and created different dam realities. The metaphor of how individual blind men disagree about the structure of an elephant, based on examinations of different body parts, reinforces the need for a coordinated, holistic perspective on dam research. Although no single approach is adequate for all problems, identifying the form, consequences of, and relationships among different research conceptualizations will set the stage for future syntheses of dam‐biodiversity research to advance science‐based conservation.

Quantification of bioluminescence from the surface to the deep sea demonstrates its predominance as an ecological trait

PubMed Central

Martini, Séverine; Haddock, Steven H. D.

2017-01-01

The capability of animals to emit light, called bioluminescence, is considered to be a major factor in ecological interactions. Because it occurs across diverse taxa, measurements of bioluminescence can be powerful to detect and quantify organisms in the ocean. In this study, 17 years of video observations were recorded by remotely operated vehicles during surveys off the California Coast, from the surface down to 3,900 m depth. More than 350,000 observations are classified for their bioluminescence capability based on literature descriptions. The organisms represented 553 phylogenetic concepts (species, genera or families, at the most precise taxonomic level defined from the images), distributed within 13 broader taxonomic categories. The importance of bioluminescent marine taxa is highlighted in the water column, as we showed that 76% of the observed individuals have bioluminescence capability. More than 97% of Cnidarians were bioluminescent, and 9 of the 13 taxonomic categories were found to be bioluminescent dominant. The percentage of bioluminescent animals is remarkably uniform over depth. Moreover, the proportion of bioluminescent and non-bioluminescent animals within taxonomic groups changes with depth for Ctenophora, Scyphozoa, Chaetognatha, and Crustacea. Given these results, bioluminescence has to be considered an important ecological trait from the surface to the deep-sea. PMID:28374789

The application of DNA sequence data for the identification of benthic nematodes from the North Sea

NASA Astrophysics Data System (ADS)

Vogt, Philipp; Miljutina, Maria; Raupach, Michael J.

2014-12-01

Nematodes or roundworms represent one of the most diverse and dominant taxon in marine benthic habitats. Whereas a morphological identification of many species is challenging, the application of molecular markers represents a promising approach for species discrimination and identification. In this study, we used an integrative taxonomic approach, combining both molecular and morphological methods, to characterize nematodes of distinct sex and ontogenetic stages from three sampling sites of the North Sea. Morphospecies were discriminated after first visual determination, followed by a molecular analysis of the nuclear 28S rDNA: D2-D3 marker. By linking each sequence to a morphological voucher, discordant morphological identification was subjected to a so-called reverse taxonomic approach. Molecular operational taxonomic units (MOTUs) and morphospecies were compared for all of the three sampling sites to assess concordance of methodology. In total, 32 MOTUs and 26 morphospecies were assigned, of which 12 taxa were identified as described species. Both approaches showed high concordance in taxon assignment (84.4 %) except for a cluster comprising various Sabatieria species. Our study revealed the high potential of the analyzed fragment as a useful molecular marker for the identification of the North Sea nematodes and highlighted the applicability of this combined taxonomic approach in general.

Notes on the taxonomic position of several species of the genus Diphascon (Tardigrada, Hypsibiidae).

PubMed

Tumanov, Denis V

2018-03-20

For this paper I analysed the descriptions of all species, attributed to the genus Diphascon Plate, 1889, to ascertain if they fit the diagnosis of this genus, provided by Bertolani et al. 2014. Thirty four species (the majority of the species diversity classified within the genus) fully match its emended diagnosis, while three: Diphascon opisthoglyptum Maucci, 1987, Diphascon procerum Pilato, Sabella Lisi, 2014 and Diphascon ziliense Lisi, Sabella Pilato, 2014, demonstrate a combination of characters, typical to the genus Pilatobius Bertolani et al., 2014. I propose the transfer these three species to the genus Pilatobius, thus their new taxonomic positions are as follows: Pilatobius opisthoglyptus (Maucci, 1987) comb. nov., Pilatobius procerus (Pilato, Sabella Lisi, 2014) comb. nov. and Pilatobius ziliense (Lisi, Sabella Pilato, 2014) comb. nov. Descriptions of three other Diphascon species (Diphascon mariae (Mihelčič, 1951), Diphascon rivulare (Mihelčič, 1967) and Diphascon punctatum (Iharos, 1962)) contain too little detail to conclude on their taxonomic position. The species Pilatobius halapiense (Iharos, 1964) was erroneously transferred from the genus Diphascon, and here I suggest it is transferred back to Diphascon. The new taxonomic position of this species is: Diphascon halapiense (Iharos, 1964) comb. nov. Emended list of species, attributed to the genus Diphascon is given.

Taxonomical and functional microbial community selection in soybean rhizosphere

PubMed Central

Mendes, Lucas W; Kuramae, Eiko E; Navarrete, Acácio A; van Veen, Johannes A; Tsai, Siu M

2014-01-01

This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors. PMID:24553468

Quantification of bioluminescence from the surface to the deep sea demonstrates its predominance as an ecological trait

NASA Astrophysics Data System (ADS)

Martini, Séverine; Haddock, Steven H. D.

2017-04-01

The capability of animals to emit light, called bioluminescence, is considered to be a major factor in ecological interactions. Because it occurs across diverse taxa, measurements of bioluminescence can be powerful to detect and quantify organisms in the ocean. In this study, 17 years of video observations were recorded by remotely operated vehicles during surveys off the California Coast, from the surface down to 3,900 m depth. More than 350,000 observations are classified for their bioluminescence capability based on literature descriptions. The organisms represented 553 phylogenetic concepts (species, genera or families, at the most precise taxonomic level defined from the images), distributed within 13 broader taxonomic categories. The importance of bioluminescent marine taxa is highlighted in the water column, as we showed that 76% of the observed individuals have bioluminescence capability. More than 97% of Cnidarians were bioluminescent, and 9 of the 13 taxonomic categories were found to be bioluminescent dominant. The percentage of bioluminescent animals is remarkably uniform over depth. Moreover, the proportion of bioluminescent and non-bioluminescent animals within taxonomic groups changes with depth for Ctenophora, Scyphozoa, Chaetognatha, and Crustacea. Given these results, bioluminescence has to be considered an important ecological trait from the surface to the deep-sea.

Multivariate analysis of maize disease resistances suggests a pleiotropic genetic basis and implicates a glutathione S-transferase gene

USDA-ARS?s Scientific Manuscript database

Plants are attacked by pathogens representing diverse taxonomic groups, such that genes providing multiple disease resistance (MDR) would likely be under positive selection pressure. We examined the novel proposition that naturally occurring allelic variants may confer MDR. To do so, we applied a ...

Maintaining saproxylic insects in Canada's extensively managed boreal forests: a review

Treesearch

David W. Langor; John R. Spence; H.E. James Hammond; Joshua Jacobs; Tyler P. Cobb

2006-01-01

Recent work on saproxylic insect assemblages in western Canadian boreal forests has demonstrated high faunal diversity and variability, and that adequate assessment of these insects involves significant sampling and taxonomic challenges. Some major determinants of assemblage structure include tree species, degree of decay, stand age and cause of tree death. Experiments...

Species rarity: definition, causes, and classification

Treesearch

Curtis H. Flather; Carolyn Hull Sieg

2007-01-01

In virtually all ecological communities around the world, most species are represented by few individuals, and most individuals come from only a few of the most common species. Why this distribution of species abundances is so regularly observed among different taxonomic sets in geographically diverse systems is a question that has received considerable theoretical and...

Not as ubiquitous as we thought: taxonomic crypsis, hidden diversity and cryptic speciation in the cosmopolitan fungus Thelonectria discophora (Nectriaceae, Hypocreales, Ascomycota)

USDA-ARS?s Scientific Manuscript database

The distribution of microbial species, including fungi, has long been considered cosmopolitan. Recently, this perception has been challenged by molecular studies in historical biogeography, phylogeny and population genetics. Here we explore this issue using the fungal morphological species Thelonect...

Testing Times for Plant Family Recognition

ERIC Educational Resources Information Center

Burrows, Geoffrey E.

2010-01-01

Plant families are the level of the taxonomic hierarchy that many biologists use to organise their understanding of plant diversity. Consequently, from many perspectives, it is very useful to be able to recognise the major plant families "on sight". To this end numerous books and web sites have described and illustrated plant families,…

Delineation of taxonomic species within complex of species: Aeromonas media and related species as a test case

USDA-ARS?s Scientific Manuscript database

Aeromonas media is an opportunistic pathogen for human and animals mainly found in aquatic habitats and which has been noted for significant genomic and phenotypic heterogeneities. We aimed to better understand the population structure and diversity of strains currently affiliated to A. media and th...

Recto-anal junction (RAJ) microbiota composition in Escherichia coli O157:H7 shedding cattle

USDA-ARS?s Scientific Manuscript database

Introduction: Cattle are the asymptomatic reservoirs of Escherichia coli O157:H7 (O157) that tend to preferentially colonize the bovine recto-anal junction (RAJ). Therefore, understanding the taxonomic profile, microbial diversity, and microbiota-O157 interactions at the RAJ could give insights into...

Insect Gut Bacterial Diversity Determined by Environmental Habitat, Diet, Developmental Stage, and Phylogeny of Host

PubMed Central

Yun, Ji-Hyun; Roh, Seong Woon; Whon, Tae Woong; Jung, Mi-Ja; Kim, Min-Soo; Park, Doo-Sang; Yoon, Changmann; Nam, Young-Do; Kim, Yun-Ji; Choi, Jung-Hye; Kim, Joon-Yong; Shin, Na-Ri; Kim, Sung-Hee; Lee, Won-Jae

2014-01-01

Insects are the most abundant animals on Earth, and the microbiota within their guts play important roles by engaging in beneficial and pathological interactions with these hosts. In this study, we comprehensively characterized insect-associated gut bacteria of 305 individuals belonging to 218 species in 21 taxonomic orders, using 454 pyrosequencing of 16S rRNA genes. In total, 174,374 sequence reads were obtained, identifying 9,301 bacterial operational taxonomic units (OTUs) at the 3% distance level from all samples, with an average of 84.3 (±97.7) OTUs per sample. The insect gut microbiota were dominated by Proteobacteria (62.1% of the total reads, including 14.1% Wolbachia sequences) and Firmicutes (20.7%). Significant differences were found in the relative abundances of anaerobes in insects and were classified according to the criteria of host environmental habitat, diet, developmental stage, and phylogeny. Gut bacterial diversity was significantly higher in omnivorous insects than in stenophagous (carnivorous and herbivorous) insects. This insect-order-spanning investigation of the gut microbiota provides insights into the relationships between insects and their gut bacterial communities. PMID:24928884

Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics

PubMed Central

Eiler, Alexander; Zaremba-Niedzwiedzka, Katarzyna; Martínez-García, Manuel; McMahon, Katherine D; Stepanauskas, Ramunas; Andersson, Siv G E; Bertilsson, Stefan

2014-01-01

Little is known about the diversity and structuring of freshwater microbial communities beyond the patterns revealed by tracing their distribution in the landscape with common taxonomic markers such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial lineages was also reflected in phylogenies of functional genes, and there were also significant differences in functional beta-diversity. The pathways and functions that accounted for these differences are involved in osmoregulation, active transport, carbohydrate and amino acid metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes. This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic- compared with freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities. PMID:24118837

Taxonomic revision and phylogenetic analysis of the flightless Mancallinae (Aves, Pan-Alcidae)

PubMed Central

Smith, Neil Adam

2011-01-01

Abstract Although flightless alcids from the Miocene and Pliocene of the eastern Pacific Ocean have been known for over 100 years, there is no detailed evaluation of diversity and systematic placement of these taxa. This is the first combined analysis of morphological and molecular data to include all extant alcids, the recently extinct Great Auk Pinguinus impennis, the mancalline auks, and a large outgroup sampling of 29 additional non-alcid charadriiforms. Based on the systematic placement of Mancallinae outside of crown clade Alcidae, the clade name Pan-Alcidae is proposed to include all known alcids. An extensive review of the Mancallinae fossil record resulted in taxonomic revision of the clade, and identification of three new species. In addition to positing the first hypothesis of inter-relationships between Mancallinae species, phylogenetic results support placement of Mancallinae as the sister taxon to all other Alcidae, indicating that flightlessness evolved at least twice in the alcid lineage. Convergent osteological characteristics of Mancallinae, the flightless Great Auk, and Spheniscidae are summarized, and implications of Mancallinae diversity, radiation, and extinction in the context of paleoclimatic changes are discussed. PMID:21594108

Soil protists: a fertile frontier in soil biology research.

PubMed

Geisen, Stefan; Mitchell, Edward A D; Adl, Sina; Bonkowski, Michael; Dunthorn, Micah; Ekelund, Flemming; Fernández, Leonardo D; Jousset, Alexandre; Krashevska, Valentyna; Singer, David; Spiegel, Frederick W; Walochnik, Julia; Lara, Enrique

2018-05-01

Protists include all eukaryotes except plants, fungi and animals. They are an essential, yet often forgotten, component of the soil microbiome. Method developments have now furthered our understanding of the real taxonomic and functional diversity of soil protists. They occupy key roles in microbial foodwebs as consumers of bacteria, fungi and other small eukaryotes. As parasites of plants, animals and even of larger protists, they regulate populations and shape communities. Pathogenic forms play a major role in public health issues as human parasites, or act as agricultural pests. Predatory soil protists release nutrients enhancing plant growth. Soil protists are of key importance for our understanding of eukaryotic evolution and microbial biogeography. Soil protists are also useful in applied research as bioindicators of soil quality, as models in ecotoxicology and as potential biofertilizers and biocontrol agents. In this review, we provide an overview of the enormous morphological, taxonomical and functional diversity of soil protists, and discuss current challenges and opportunities in soil protistology. Research in soil biology would clearly benefit from incorporating more protistology alongside the study of bacteria, fungi and animals.

High Diversity in Cretaceous Ichthyosaurs from Europe Prior to Their Extinction

PubMed Central

Fischer, Valentin; Bardet, Nathalie; Guiomar, Myette; Godefroit, Pascal

2014-01-01

Background Ichthyosaurs are reptiles that inhabited the marine realm during most of the Mesozoic. Their Cretaceous representatives have traditionally been considered as the last survivors of a group declining since the Jurassic. Recently, however, an unexpected diversity has been described in Upper Jurassic–Lower Cretaceous deposits, but is widely spread across time and space, giving small clues on the adaptive potential and ecosystem control of the last ichthyosaurs. The famous but little studied English Gault Formation and ‘greensands’ deposits (the Upper Greensand Formation and the Cambridge Greensand Member of the Lower Chalk Formation) offer an unprecedented opportunity to investigate this topic, containing thousands of ichthyosaur remains spanning the Early–Late Cretaceous boundary. Methodology/Principal Findings To assess the diversity of the ichthyosaur assemblage from these sedimentary bodies, we recognized morphotypes within each type of bones. We grouped these morphotypes together, when possible, by using articulated specimens from the same formations and from new localities in the Vocontian Basin (France); a revised taxonomic scheme is proposed. We recognize the following taxa in the ‘greensands’: the platypterygiines ‘Platypterygius’ sp. and Sisteronia seeleyi gen. et sp. nov., indeterminate ophthalmosaurines and the rare incertae sedis Cetarthrosaurus walkeri. The taxonomic diversity of late Albian ichthyosaurs now matches that of older, well-known intervals such as the Toarcian or the Tithonian. Contrasting tooth shapes and wear patterns suggest that these ichthyosaurs colonized three distinct feeding guilds, despite the presence of numerous plesiosaur taxa. Conclusion/Significance Western Europe was a diversity hot-spot for ichthyosaurs a few million years prior to their final extinction. By contrast, the low diversity in Australia and U.S.A. suggests strong geographical disparities in the diversity pattern of Albian–early Cenomanian ichthyosaurs. This provides a whole new context to investigate the extinction of these successful marine reptiles, at the end of the Cenomanian. PMID:24465427

Community level patterns in diverse systems: A case study of litter fauna in a Mexican pine-oak forest using higher taxa surrogates and re-sampling methods

NASA Astrophysics Data System (ADS)

Moreno, Claudia E.; Guevara, Roger; Sánchez-Rojas, Gerardo; Téllez, Dianeis; Verdú, José R.

2008-01-01

Environmental assessment at the community level in highly diverse ecosystems is limited by taxonomic constraints and statistical methods requiring true replicates. Our objective was to show how diverse systems can be studied at the community level using higher taxa as biodiversity surrogates, and re-sampling methods to allow comparisons. To illustrate this we compared the abundance, richness, evenness and diversity of the litter fauna in a pine-oak forest in central Mexico among seasons, sites and collecting methods. We also assessed changes in the abundance of trophic guilds and evaluated the relationships between community parameters and litter attributes. With the direct search method we observed differences in the rate of taxa accumulation between sites. Bootstrap analysis showed that abundance varied significantly between seasons and sampling methods, but not between sites. In contrast, diversity and evenness were significantly higher at the managed than at the non-managed site. Tree regression models show that abundance varied mainly between seasons, whereas taxa richness was affected by litter attributes (composition and moisture content). The abundance of trophic guilds varied among methods and seasons, but overall we found that parasitoids, predators and detrivores decreased under management. Therefore, although our results suggest that management has positive effects on the richness and diversity of litter fauna, the analysis of trophic guilds revealed a contrasting story. Our results indicate that functional groups and re-sampling methods may be used as tools for describing community patterns in highly diverse systems. Also, the higher taxa surrogacy could be seen as a preliminary approach when it is not possible to identify the specimens at a low taxonomic level in a reasonable period of time and in a context of limited financial resources, but further studies are needed to test whether the results are specific to a system or whether they are general with regards to land management.

Global Patterns of Guild Composition and Functional Diversity of Spiders

PubMed Central

Cardoso, Pedro; Pekár, Stano; Jocqué, Rudy; Coddington, Jonathan A.

2011-01-01

The objectives of this work are: (1) to define spider guilds for all extant families worldwide; (2) test if guilds defined at family level are good surrogates of species guilds; (3) compare the taxonomic and guild composition of spider assemblages from different parts of the world; (4) compare the taxonomic and functional diversity of spider assemblages and; (5) relate functional diversity with habitat structure. Data on foraging strategy, prey range, vertical stratification and circadian activity was collected for 108 families. Spider guilds were defined by hierarchical clustering. We searched for inconsistencies between family guild placement and the known guild of each species. Richness and abundance per guild before and after correcting guild placement were compared, as were the proportions of each guild and family between all possible pairs of sites. Functional diversity per site was calculated based on hierarchical clustering. Eight guilds were discriminated: (1) sensing, (2) sheet, (3) space, and (4) orb web weavers; (5) specialists; (6) ambush, (7) ground, and (8) other hunters. Sixteen percent of the species richness corresponding to 11% of all captured individuals was incorrectly attributed to a guild by family surrogacy; however, the correlation of uncorrected vs. corrected guilds was invariably high. The correlation of guild richness or abundances was generally higher than the correlation of family richness or abundances. Functional diversity was not always higher in the tropics than in temperate regions. Families may potentially serve as ecological surrogates for species. Different families may present similar roles in the ecosystems, with replacement of some taxa by other within the same guild. Spiders in tropical regions seem to have higher redundancy of functional roles and/or finer resource partitioning than in temperate regions. Although species and family diversity were higher in the tropics, functional diversity seems to be also influenced by altitude and habitat structure. PMID:21738772

Are different facets of plant diversity well protected against climate and land cover changes? A test study in the French Alps

PubMed Central

Thuiller, Wilfried; Guéguen, Maya; Georges, Damien; Bonet, Richard; Chalmandrier, Loïc; Garraud, Luc; Renaud, Julien; Roquet, Cristina; Van Es, Jérémie; Zimmermann, Niklaus E.; Lavergne, Sébastien

2014-01-01

Climate and land cover changes are important drivers of the plant species distributions and diversity patterns in mountainous regions. Although the need for a multifaceted view of diversity based on taxonomic, functional and phylogenetic dimensions is now commonly recognized, there are no complete risk assessments concerning their expected changes. In this paper, we used a range of species distribution models in an ensemble-forecasting framework together with regional climate and land cover projections by 2080 to analyze the potential threat for more than 2,500 plant species at high resolution (2.5 km × 2.5 km) in the French Alps. We also decomposed taxonomic, functional and phylogenetic diversity facets into α and β components and analyzed their expected changes by 2080. Overall, plant species threats from climate and land cover changes in the French Alps were expected to vary depending on the species’ preferred altitudinal vegetation zone, rarity, and conservation status. Indeed, rare species and species of conservation concern were the ones projected to experience less severe change, and also the ones being the most efficiently preserved by the current network of protected areas. Conversely, the three facets of plant diversity were also projected to experience drastic spatial re-shuffling by 2080. In general, the mean α-diversity of the three facets was projected to increase to the detriment of regional β-diversity, although the latter was projected to remain high at the montane-alpine transition zones. Our results show that, due to a high-altitude distribution, the current protection network is efficient for rare species, and species predicted to migrate upward. Although our modeling framework may not capture all possible mechanisms of species range shifts, our work illustrates that a comprehensive risk assessment on an entire floristic region combined with functional and phylogenetic information can help delimitate future scenarios of biodiversity and better design its protection. PMID:25722539

Diversity, Productivity, and Stability of an Industrial Microbial Ecosystem

PubMed Central

Tang, Pei-Zhong; Becker, Scott; Hoang, Tony; Bilgin, Damla; Lim, Yan Wei; Peterson, Todd C.; Mayfield, Stephen; Haerizadeh, Farzad; Shurin, Jonathan B.; Bafna, Vineet; McBride, Robert

2016-01-01

Managing ecosystems to maintain biodiversity may be one approach to ensuring their dynamic stability, productivity, and delivery of vital services. The applicability of this approach to industrial ecosystems that harness the metabolic activities of microbes has been proposed but has never been tested at relevant scales. We used a tag-sequencing approach with bacterial small subunit rRNA (16S) genes and eukaryotic internal transcribed spacer 2 (ITS2) to measuring the taxonomic composition and diversity of bacteria and eukaryotes in an open pond managed for bioenergy production by microalgae over a year. Periods of high eukaryotic diversity were associated with high and more-stable biomass productivity. In addition, bacterial diversity and eukaryotic diversity were inversely correlated over time, possibly due to their opposite responses to temperature. The results indicate that maintaining diverse communities may be essential to engineering stable and productive bioenergy ecosystems using microorganisms. PMID:26896141

Microbial diversity arising from thermodynamic constraints

PubMed Central

Großkopf, Tobias; Soyer, Orkun S

2016-01-01

The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments. PMID:27035705

Diversity, Productivity, and Stability of an Industrial Microbial Ecosystem.

PubMed

Beyter, Doruk; Tang, Pei-Zhong; Becker, Scott; Hoang, Tony; Bilgin, Damla; Lim, Yan Wei; Peterson, Todd C; Mayfield, Stephen; Haerizadeh, Farzad; Shurin, Jonathan B; Bafna, Vineet; McBride, Robert

2016-04-01

Managing ecosystems to maintain biodiversity may be one approach to ensuring their dynamic stability, productivity, and delivery of vital services. The applicability of this approach to industrial ecosystems that harness the metabolic activities of microbes has been proposed but has never been tested at relevant scales. We used a tag-sequencing approach with bacterial small subunit rRNA (16S) genes and eukaryotic internal transcribed spacer 2 (ITS2) to measuring the taxonomic composition and diversity of bacteria and eukaryotes in an open pond managed for bioenergy production by microalgae over a year. Periods of high eukaryotic diversity were associated with high and more-stable biomass productivity. In addition, bacterial diversity and eukaryotic diversity were inversely correlated over time, possibly due to their opposite responses to temperature. The results indicate that maintaining diverse communities may be essential to engineering stable and productive bioenergy ecosystems using microorganisms. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

System-Level Performance of Antenna Arrays in CDMA-Based Cellular Mobile Radio Systems

NASA Astrophysics Data System (ADS)

Czylwik, Andreas; Dekorsy, Armin

2004-12-01

Smart antennas exploit the inherent spatial diversity of the mobile radio channel, provide an antenna gain, and also enable spatial interference suppression leading to reduced intracell as well as intercell interference. Especially, for the downlink of future CDMA-based mobile communications systems, transmit beamforming is seen as a well-promising smart antenna technique. The main objective of this paper is to study the performance of diverse antenna array topologies when applied for transmit beamforming in the downlink of CDMA-based networks. In this paper, we focus on uniform linear array (ULA) and uniform circular array (UCA) topologies. For the ULA, we consider three-sector base stations with one linear array per sector. While recent research on downlink beamforming is often restricted to one single cell, this study takes into account the important impact of intercell interference on the performance by evaluating complete networks. Especially, from the operator perspective, system capacity and system coverage are very essential parameters of a cellular system so that there is a clear necessity of intensive system level investigations. Apart from delivering assessments on the performance of the diverse antenna array topologies, in the paper also different antenna array parameters, such as element spacing and beamwidth of the sector antennas, are optimized. Although we focus on the network level, fast channel fluctuations are taken into account by including them analytically into the signal-to-interference calculation.

Parametric scaling from species to growth-form diversity: an interesting analogy with multifractal functions.

PubMed

Ricotta, Carlo; Pacini, Alessandra; Avena, Giancarlo

2002-01-01

We propose a measure of divergence from species to life-form diversity aimed at summarizing the ecological similarity among different plant communities without losing information on traditional taxonomic diversity. First, species and life-form relative abundances within a given plant community are determined. Next, using Rényi's generalized entropy, the diversity profiles of the analyzed community are computed both from species and life-form relative abundances. Finally, the speed of decrease from species to life-form diversity is obtained by combining the outcome of both profiles. Interestingly, the proposed measure shows some formal analogies with multifractal functions developed in statistical physics for the analysis of spatial patterns. As an application for demonstration, a small data set from a plant community sampled in the archaeological site of Paestum (southern Italy) is used.

Decoupled temporal patterns of evolution and ecology in two post-Paleozoic clades

NASA Technical Reports Server (NTRS)

McKinney, F. K.; Lidgard, S.; Sepkoski, J. J. Jr; Taylor, P. D.

1998-01-01

Counts of taxonomic diversity are the prevailing standards for documenting large-scale patterns of evolution in the fossil record. However, the secular pattern of relative ecological importance between the bryozoan clades Cyclostomata and Cheilostomata is not reflected fully in compilations of generic diversity or within-fauna species richness, and the delayed ecological recovery of the Cheilostomata after the mass extinction at the Cretaceous-Tertiary boundary is missed entirely. These observations demonstrate that evolutionary success and ecological dominance can be decoupled and profoundly different, even over tens of millions of years.

Characterization of the vaginal microbiota among sexual risk behavior groups of women with bacterial vaginosis.

PubMed

Muzny, Christina A; Sunesara, Imran R; Kumar, Ranjit; Mena, Leandro A; Griswold, Michael E; Martin, David H; Lefkowitz, Elliot J; Schwebke, Jane R; Swiatlo, Edwin

2013-01-01

The pathogenesis of bacterial vaginosis (BV) remains elusive. BV may be more common among women who have sex with women (WSW). The objective of this study was to use 454 pyrosequencing to investigate the vaginal microbiome of WSW, women who have sex with women and men (WSWM), and women who have sex with men (WSM) with BV to determine if there are differences in organism composition between groups that may inform new hypotheses regarding the pathogenesis of BV. Vaginal swab specimens from eligible women with BV at the Mississippi State Department of Health STD Clinic were used. After DNA extraction, 454 pyrosequencing of PCR-amplified 16S rRNA gene sequences was performed. Sequence data was classified using the Ribosomal Database Program classifer. Complete linkage clustering analysis was performed to compare bacterial community composition among samples. Differences in operational taxonomic units with an abundance of ≥ 2% between risk behavior groups were determined. Alpha and beta diversity were measured using Shannon's Index implemented in QIIME and Unifrac analysis, respectively. 33 WSW, 35 WSWM, and 44 WSM were included. The vaginal bacterial communities of all women clustered into four taxonomic groups with the dominant taxonomic group in each being Lactobacillus, Lachnospiraceae, Prevotella, and Sneathia. Regarding differences in organism composition between risk behavior groups, the abundance of Atopobium (relative ratio (RR)=0.24; 95%CI 0.11-0.54) and Parvimonas (RR=0.33; 95%CI 0.11-0.93) were significantly lower in WSW than WSM, the abundance of Prevotella was significantly higher in WSW than WSWM (RR=1.77; 95%CI 1.10-2.86), and the abundance of Atopobium (RR=0.41; 95%CI 0.18-0.88) was significantly lower in WSWM than WSM. Overall, WSM had the highest diversity of bacterial taxa. The microbiology of BV among women in different risk behavior groups is heterogeneous. WSM in this study had the highest diversity of bacterial taxa. Additional studies are needed to better understand these differences.

Functional diversity measures revealed impacts of non-native species and habitat degradation on species-poor freshwater fish assemblages.

PubMed

Colin, Nicole; Villéger, Sébastien; Wilkes, Martin; de Sostoa, Adolfo; Maceda-Veiga, Alberto

2018-06-01

Trait-based ecology has been developed for decades to infer ecosystem responses to stressors based on the functional structure of communities, yet its value in species-poor systems is largely unknown. Here, we used an extensive dataset in a Spanish region highly prone to non-native fish invasions (15 catchments, N=389 sites) to assess for the first time how species-poor communities respond to large-scale environmental gradients using a taxonomic and functional trait-based approach in riverine fish. We examined total species richness and three functional trait-based indices available when many sites have ≤3 species (specialization, FSpe; originality, FOri and entropy, FEnt). We assessed the responses of these taxonomic and functional indices along gradients of altitude, water pollution, physical habitat degradation and non-native fish biomass. Whilst species richness was relatively sensitive to spatial effects, functional diversity indices were responsive across natural and anthropogenic gradients. All four diversity measures declined with altitude but this decline was modulated by physical habitat degradation (richness, FSpe and FEnt) and the non-native:total fish biomass ratio (FSpe and FOri) in ways that varied between indices. Furthermore, FSpe and FOri were significantly correlated with Total Nitrogen. Non-native fish were a major component of the taxonomic and functional structure of fish communities, raising concerns about potential misdiagnosis between invaded and environmentally-degraded river reaches. Such misdiagnosis was evident in a regional fish index widely used in official monitoring programs. We recommend the application of FSpe and FOri to extensive datasets from monitoring programs in order to generate valuable cross-system information about the impacts of non-native species and habitat degradation, even in species-poor systems. Scoring non-native species apart from habitat degradation in the indices used to determine ecosystem health is essential to develop better management strategies. Copyright © 2018 Elsevier B.V. All rights reserved.

Microbial community profiling of fresh basil and pitfalls in taxonomic assignment of enterobacterial pathogenic species based upon 16S rRNA amplicon sequencing.

PubMed

Ceuppens, Siele; De Coninck, Dieter; Bottledoorn, Nadine; Van Nieuwerburgh, Filip; Uyttendaele, Mieke

2017-09-18

Application of 16S rRNA (gene) amplicon sequencing on food samples is increasingly applied for assessing microbial diversity but may as unintended advantage also enable simultaneous detection of any human pathogens without a priori definition. In the present study high-throughput next-generation sequencing (NGS) of the V1-V2-V3 regions of the 16S rRNA gene was applied to identify the bacteria present on fresh basil leaves. However, results were strongly impacted by variations in the bioinformatics analysis pipelines (MEGAN, SILVAngs, QIIME and MG-RAST), including the database choice (Greengenes, RDP and M5RNA) and the annotation algorithm (best hit, representative hit and lowest common ancestor). The use of pipelines with default parameters will lead to discrepancies. The estimate of microbial diversity of fresh basil using 16S rRNA (gene) amplicon sequencing is thus indicative but subject to biases. Salmonella enterica was detected at low frequencies, between 0.1% and 0.4% of bacterial sequences, corresponding with 37 to 166 reads. However, this result was dependent upon the pipeline used: Salmonella was detected by MEGAN, SILVAngs and MG-RAST, but not by QIIME. Confirmation of Salmonella sequences by real-time PCR was unsuccessful. It was shown that taxonomic resolution obtained from the short (500bp) sequence reads of the 16S rRNA gene containing the hypervariable regions V1-V3 cannot allow distinction of Salmonella with closely related enterobacterial species. In conclusion 16S amplicon sequencing, getting the status of standard method in microbial ecology studies of foods, needs expertise on both bioinformatics and microbiology for analysis of results. It is a powerful tool to estimate bacterial diversity but amenable to biases. Limitations concerning taxonomic resolution for some bacterial species or its inability to detect sub-dominant (pathogenic) species should be acknowledged in order to avoid overinterpretation of results. Copyright © 2017 Elsevier B.V. All rights reserved.

Mammalian niche conservation through deep time.

PubMed

DeSantis, Larisa R G; Beavins Tracy, Rachel A; Koontz, Cassandra S; Roseberry, John C; Velasco, Matthew C

2012-01-01

Climate change alters species distributions, causing plants and animals to move north or to higher elevations with current warming. Bioclimatic models predict species distributions based on extant realized niches and assume niche conservation. Here, we evaluate if proxies for niches (i.e., range areas) are conserved at the family level through deep time, from the Eocene to the Pleistocene. We analyze the occurrence of all mammalian families in the continental USA, calculating range area, percent range area occupied, range area rank, and range polygon centroids during each epoch. Percent range area occupied significantly increases from the Oligocene to the Miocene and again from the Pliocene to the Pleistocene; however, mammalian families maintain statistical concordance between rank orders across time. Families with greater taxonomic diversity occupy a greater percent of available range area during each epoch and net changes in taxonomic diversity are significantly positively related to changes in percent range area occupied from the Eocene to the Pleistocene. Furthermore, gains and losses in generic and species diversity are remarkably consistent with ~2.3 species gained per generic increase. Centroids demonstrate southeastern shifts from the Eocene through the Pleistocene that may correspond to major environmental events and/or climate changes during the Cenozoic. These results demonstrate range conservation at the family level and support the idea that niche conservation at higher taxonomic levels operates over deep time and may be controlled by life history traits. Furthermore, families containing megafauna and/or terminal Pleistocene extinction victims do not incur significantly greater declines in range area rank than families containing only smaller taxa and/or only survivors, from the Pliocene to Pleistocene. Collectively, these data evince the resilience of families to climate and/or environmental change in deep time, the absence of terminal Pleistocene "extinction prone" families, and provide valuable insights to understanding mammalian responses to current climate change.

Mammalian Niche Conservation through Deep Time

PubMed Central

DeSantis, Larisa R. G.; Beavins Tracy, Rachel A.; Koontz, Cassandra S.; Roseberry, John C.; Velasco, Matthew C.

2012-01-01

Climate change alters species distributions, causing plants and animals to move north or to higher elevations with current warming. Bioclimatic models predict species distributions based on extant realized niches and assume niche conservation. Here, we evaluate if proxies for niches (i.e., range areas) are conserved at the family level through deep time, from the Eocene to the Pleistocene. We analyze the occurrence of all mammalian families in the continental USA, calculating range area, percent range area occupied, range area rank, and range polygon centroids during each epoch. Percent range area occupied significantly increases from the Oligocene to the Miocene and again from the Pliocene to the Pleistocene; however, mammalian families maintain statistical concordance between rank orders across time. Families with greater taxonomic diversity occupy a greater percent of available range area during each epoch and net changes in taxonomic diversity are significantly positively related to changes in percent range area occupied from the Eocene to the Pleistocene. Furthermore, gains and losses in generic and species diversity are remarkably consistent with ∼2.3 species gained per generic increase. Centroids demonstrate southeastern shifts from the Eocene through the Pleistocene that may correspond to major environmental events and/or climate changes during the Cenozoic. These results demonstrate range conservation at the family level and support the idea that niche conservation at higher taxonomic levels operates over deep time and may be controlled by life history traits. Furthermore, families containing megafauna and/or terminal Pleistocene extinction victims do not incur significantly greater declines in range area rank than families containing only smaller taxa and/or only survivors, from the Pliocene to Pleistocene. Collectively, these data evince the resilience of families to climate and/or environmental change in deep time, the absence of terminal Pleistocene “extinction prone” families, and provide valuable insights to understanding mammalian responses to current climate change. PMID:22539985

Antifungal bacteria on woodland salamander skin exhibit high taxonomic diversity and geographic variability

USGS Publications Warehouse

Muletz-Wolz, Carly R.; DiRenzo, Graziella V.; Yarwood, Stephanie A.; Grant, Evan H. Campbell; Fleischer, Robert C.; Lips, Karen R.

2017-01-01

Diverse bacteria inhabit amphibian skin; some of those bacteria inhibit growth of the fungal pathogen Batrachochytrium dendrobatidis. Yet there has been no systematic survey of anti-B. dendrobatidis bacteria across localities, species, and elevations. This is important given geographic and taxonomic variations in amphibian susceptibility to B. dendrobatidis. Our collection sites were at locations within the Appalachian Mountains where previous sampling had indicated low B. dendrobatidis prevalence. We determined the numbers and identities of anti-B. dendrobatidis bacteria on 61 Plethodon salamanders (37 P. cinereus, 15 P. glutinosus, 9 P. cylindraceus) via culturing methods and 16S rRNA gene sequencing. We sampled co-occurring species at three localities and sampled P. cinereus along an elevational gradient (700 to 1,000 meters above sea level [masl]) at one locality. We identified 50 anti-B. dendrobatidis bacterial operational taxonomic units (OTUs) and found that the degree of B. dendrobatidis inhibition was not correlated with relatedness. Five anti-B. dendrobatidis bacterial strains occurred on multiple amphibian species at multiple localities, but none were shared among all species and localities. The prevalence of anti-B. dendrobatidis bacteria was higher at Shenandoah National Park (NP), VA, with 96% (25/26) of salamanders hosting at least one anti-B. dendrobatidis bacterial species compared to 50% (7/14) at Catoctin Mountain Park (MP), MD, and 38% (8/21) at Mt. Rogers National Recreation Area (NRA), VA. At the individual level, salamanders at Shenandoah NP had more anti-B. dendrobatidis bacteria per individual (μ = 3.3) than those at Catoctin MP (μ = 0.8) and at Mt. Rogers NRA (μ = 0.4). All salamanders tested negative for B. dendrobatidis. Anti-B. dendrobatidis bacterial species are diverse in central Appalachian Plethodon salamanders, and their distribution varied geographically. The antifungal bacterial species that we identified may play a protective role for these salamanders.

Marine benthic ecological functioning over decreasing taxonomic richness

NASA Astrophysics Data System (ADS)

Törnroos, Anna; Bonsdorff, Erik; Bremner, Julie; Blomqvist, Mats; Josefson, Alf B.; Garcia, Clement; Warzocha, Jan

2015-04-01

Alterations to ecosystem function due to reductions in species richness are predicted to increase as humans continue to affect the marine environment, especially in coastal areas, which serve as the interface between land and sea. The potential functional consequences due to reductions in species diversity have attracted considerable attention recently but little is known about the consequence of such loss in natural communities. We examined how the potential for function is affected by natural reductions in taxon richness using empirical (non-simulated) coastal marine benthic macrofaunal data from the Skagerrak-Baltic Sea region (N. Europe), where taxon richness decreases 25-fold, from 151 to 6 taxa. To estimate functional changes we defined multiple traits (10 traits and 51 categories) on which trait category richness, functional diversity (FD) and number of taxa per trait category were calculated. Our results show that decrease in taxon richness leads to an overall reduction in function but functional richness remains comparatively high even at the lowest level of taxon richness. Although the taxonomic reduction was sharp, up to 96% of total taxon richness, we identified both potential thresholds in functioning and subtler changes where function was maintained along the gradient. The functional changes were not only caused by reductions in taxa per trait category, some categories were maintained or even increased. Primarily, the reduction in species richness altered trait categories related to feeding, living and movement and thus potentially could have an effect on various ecosystem processes. This highlights the importance of recognising ecosystem multifunctionality, especially at low taxonomic richness. We also found that in this system rare species (singletons) did not stand for the functional complexities and changes. Our findings were consistent with theoretical and experimental predictions and suggest that a large proportion of the information about alterations of function is found in measures such as functional diversity and number of taxa per trait category.

Vertical Structure of Phyllosphere Fungal Communities in a Tropical Forest in Thailand Uncovered by High-Throughput Sequencing.

PubMed

Izuno, Ayako; Kanzaki, Mamoru; Artchawakom, Taksin; Wachrinrat, Chongrak; Isagi, Yuji

2016-01-01

Phyllosphere fungi harbor a tremendous species diversity and play important ecological roles. However, little is known about their distribution patterns within forest ecosystems. We examined how species diversity and community composition of phyllosphere fungi change along a vertical structure in a tropical forest in Thailand. Fungal communities in 144 leaf samples from 19 vertical layers (1.28-34.4 m above ground) of 73 plant individuals (27 species) were investigated by metabarcoding analysis using Ion Torrent sequencing. In total, 1,524 fungal operational taxonomic units (OTUs) were detected among 890,710 reads obtained from the 144 leaf samples. Taxonomically diverse fungi belonging to as many as 24 orders of Ascomycota and 21 orders of Basidiomycota were detected, most of which inhabited limited parts of the lowest layers closest to the forest floor. Species diversity of phyllosphere fungi was the highest in the lowest layers closest to the forest floor, decreased with increasing height, and lowest in the canopy; 742 and 55 fungal OTUs were detected at the lowest and highest layer, respectively. On the layers close to the forest floor, phyllosphere fungal communities were mainly composed of low frequency OTUs and largely differentiated among plant individuals. Conversely, in the canopy, fungal communities consisted of similar OTUs across plant individuals, and as many as 86.1%-92.7% of the OTUs found in the canopy (≥22 m above ground) were also distributed in the lower layers. Overall, our study showed the variability of phyllosphere fungal communities along the vertical gradient of plant vegetation and environmental conditions, suggesting the significance of biotic and abiotic variation for the species diversity of phyllosphere fungi.

How anthropogenic changes may affect soil-borne parasite diversity? Plant-parasitic nematode communities associated with olive trees in Morocco as a case study.

PubMed

Ali, Nadine; Tavoillot, Johannes; Besnard, Guillaume; Khadari, Bouchaib; Dmowska, Ewa; Winiszewska, Grażyna; Fossati-Gaschignard, Odile; Ater, Mohammed; Aït Hamza, Mohamed; El Mousadik, Abdelhamid; El Oualkadi, Aïcha; Moukhli, Abdelmajid; Essalouh, Laila; El Bakkali, Ahmed; Chapuis, Elodie; Mateille, Thierry

2017-02-06

Plant-parasitic nematodes (PPN) are major crop pests. On olive (Olea europaea), they significantly contribute to economic losses in the top-ten olive producing countries in the world especially in nurseries and under cropping intensification. The diversity and the structure of PPN communities respond to environmental and anthropogenic forces. The olive tree is a good host plant model to understand the impact of such forces on PPN diversity since it grows according to different modalities (wild, feral and cultivated olives). A wide soil survey was conducted in several olive-growing regions in Morocco. The taxonomical and the functional diversity as well as the structures of PPN communities were described and then compared between non-cultivated (wild and feral forms) and cultivated (traditional and high-density olive cultivation) olives. A high diversity of PPN with the detection of 117 species and 47 genera was revealed. Some taxa were recorded for the first time on olive trees worldwide and new species were also identified. Anthropogenic factors (wild vs cultivated conditions) strongly impacted the PPN diversity and the functional composition of communities because the species richness, the local diversity and the evenness of communities significantly decreased and the abundance of nematodes significantly increased in high-density conditions. Furthermore, these conditions exhibited many more obligate and colonizer PPN and less persister PPN compared to non-cultivated conditions. Taxonomical structures of communities were also impacted: genera such as Xiphinema spp. and Heterodera spp. were dominant in wild olive, whereas harmful taxa such as Meloidogyne spp. were especially enhanced in high-density orchards. Olive anthropogenic practices reduce the PPN diversity in communities and lead to changes of the community structures with the development of some damaging nematodes. The study underlined the PPN diversity as a relevant indicator to assess community pathogenicity. That could be taken into account in order to design control strategies based on community rearrangements and interactions between species instead of reducing the most pathogenic species.

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering

PubMed Central

Ekanayake, Saliya; Ruan, Yang; Schütte, Ursel M. E.; Kaonongbua, Wittaya; Fox, Geoffrey; Ye, Yuzhen; Bever, James D.

2016-01-01

ABSTRACT Arbuscular mycorrhizal (AM) fungi form mutualisms with plant roots that increase plant growth and shape plant communities. Each AM fungal cell contains a large amount of genetic diversity, but it is unclear if this diversity varies across evolutionary lineages. We found that sequence variation in the nuclear large-subunit (LSU) rRNA gene from 29 isolates representing 21 AM fungal species generally assorted into genus- and species-level clades, with the exception of species of the genera Claroideoglomus and Entrophospora. However, there were significant differences in the levels of sequence variation across the phylogeny and between genera, indicating that it is an evolutionarily constrained trait in AM fungi. These consistent patterns of sequence variation across both phylogenetic and taxonomic groups pose challenges to interpreting operational taxonomic units (OTUs) as approximations of species-level groups of AM fungi. We demonstrate that the OTUs produced by five sequence clustering methods using 97% or equivalent sequence similarity thresholds failed to match the expected species of AM fungi, although OTUs from AbundantOTU, CD-HIT-OTU, and CROP corresponded better to species than did OTUs from mothur or UPARSE. This lack of OTU-to-species correspondence resulted both from sequences of one species being split into multiple OTUs and from sequences of multiple species being lumped into the same OTU. The OTU richness therefore will not reliably correspond to the AM fungal species richness in environmental samples. Conservatively, this error can overestimate species richness by 4-fold or underestimate richness by one-half, and the direction of this error will depend on the genera represented in the sample. IMPORTANCE Arbuscular mycorrhizal (AM) fungi form important mutualisms with the roots of most plant species. Individual AM fungi are genetically diverse, but it is unclear whether the level of this diversity differs among evolutionary lineages. We found that the amount of sequence variation in an rRNA gene that is commonly used to identify AM fungal species varied significantly between evolutionary groups that correspond to different genera, with the exception of two genera that are genetically indistinguishable from each other. When we clustered groups of similar sequences into operational taxonomic units (OTUs) using five different clustering methods, these patterns of sequence variation caused the number of OTUs to either over- or underestimate the actual number of AM fungal species, depending on the genus. Our results indicate that OTU-based inferences about AM fungal species composition from environmental sequences can be improved if they take these taxonomically structured patterns of sequence variation into account. PMID:27260357

Molecular analysis reveals hidden diversity in Zungaro (Siluriformes: Pimelodidade): a genus of giant South American catfish.

PubMed

Pires, Antonio A; Ramirez, Jorge L; Galetti, Pedro M; Troy, Waldo P; Freitas, Patricia D

2017-06-01

The genus Zungaro contains some of the largest catfish in South America. Two valid species are currently recognized: Zungaro jahu, inhabiting the Paraná and Paraguay basins, and Zungaro zungaro, occurring in the Amazonas and Orinoco basins. Analysing Zungaro specimens from the Amazonas, Orinoco, Paraguay and Paraná basins, based on the sequencing of COI and D-loop, we found at least three MOTUs, indicating the existence of hidden diversity within this fish group. Considering the ecological and economic values of this fish, our results are surely welcomed for its conservation, disclosing new findings on its diversity and pointing out the necessity for a detailed taxonomic revision.

Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment

PubMed Central

Kinsela, Andrew S.; Bligh, Mark W.; Harrison, Jennifer J.; Payne, Timothy E.

2017-01-01

ABSTRACT During the 1960s, small quantities of radioactive materials were codisposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in 3-meter-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess the impact of changing water levels upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically diverse microbial community played in this transition. In particular, aerobes dominated in the first day, followed by an increase of facultative anaerobes/denitrifiers at day 4. Toward the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs. IMPORTANCE The role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and contaminant mobility. Results demonstrate that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the important role that the taxonomically diverse microbial community played in this transition. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs. PMID:28667104

Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment.

PubMed

Vázquez-Campos, Xabier; Kinsela, Andrew S; Bligh, Mark W; Harrison, Jennifer J; Payne, Timothy E; Waite, T David

2017-09-01

During the 1960s, small quantities of radioactive materials were codisposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in 3-meter-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess the impact of changing water levels upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically diverse microbial community played in this transition. In particular, aerobes dominated in the first day, followed by an increase of facultative anaerobes/denitrifiers at day 4. Toward the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs. IMPORTANCE The role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and contaminant mobility. Results demonstrate that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the important role that the taxonomically diverse microbial community played in this transition. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs. Copyright © 2017 Vázquez-Campos et al.

Fluctuating environments, sexual selection and the evolution of flexible mate choice in birds.

PubMed

Botero, Carlos A; Rubenstein, Dustin R

2012-01-01

Environmentally-induced fluctuation in the form and strength of natural selection can drive the evolution of morphology, physiology, and behavior. Here we test the idea that fluctuating climatic conditions may also influence the process of sexual selection by inducing unexpected reversals in the relative quality or sexual attractiveness of potential breeding partners. Although this phenomenon, known as 'ecological cross-over', has been documented in a variety of species, it remains unclear the extent to which it has driven the evolution of major interspecific differences in reproductive behavior. We show that after controlling for potentially influential life history and demographic variables, there are significant positive associations between the variability and predictability of annual climatic cycles and the prevalence of infidelity and divorce within populations of a taxonomically diverse array of socially monogamous birds. Our results are consistent with the hypothesis that environmental factors have shaped the evolution of reproductive flexibility and suggest that in the absence of severe time constraints, secondary mate choice behaviors can help prevent, correct, or minimize the negative consequences of ecological cross-overs. Our findings also illustrate how a basic evolutionary process like sexual selection is susceptible to the increasing variability and unpredictability of climatic conditions that is resulting from climate change.

The Pathogen-Host Interactions database (PHI-base): additions and future developments

PubMed Central

Urban, Martin; Pant, Rashmi; Raghunath, Arathi; Irvine, Alistair G.; Pedro, Helder; Hammond-Kosack, Kim E.

2015-01-01

Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-base) catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and protist pathogens. Mutant phenotypes are associated with gene information. The included pathogens infect a wide range of hosts including humans, animals, plants, insects, fish and other fungi. The current version, PHI-base 3.6, available at http://www.phi-base.org, stores information on 2875 genes, 4102 interactions, 110 host species, 160 pathogenic species (103 plant, 3 fungal and 54 animal infecting species) and 181 diseases drawn from 1243 references. Phenotypic and gene function information has been obtained by manual curation of the peer-reviewed literature. A controlled vocabulary consisting of nine high-level phenotype terms permits comparisons and data analysis across the taxonomic space. PHI-base phenotypes were mapped via their associated gene information to reference genomes available in Ensembl Genomes. Virulence genes and hotspots can be visualized directly in genome browsers. Future plans for PHI-base include development of tools facilitating community-led curation and inclusion of the corresponding host target(s). PMID:25414340

Improved protocols to accelerate the assembly of DNA barcode reference libraries for freshwater zooplankton.

PubMed

Elías-Gutiérrez, Manuel; Valdez-Moreno, Martha; Topan, Janet; Young, Monica R; Cohuo-Colli, José Angel

2018-03-01

Currently, freshwater zooplankton sampling and identification methodologies have remained virtually unchanged since they were first established in the beginning of the XX century. One major contributing factor to this slow progress is the limited success of modern genetic methodologies, such as DNA barcoding, in several of the main groups. This study demonstrates improved protocols which enable the rapid assessment of most animal taxa inhabiting any freshwater system by combining the use of light traps, careful fixation at low temperatures using ethanol, and zooplankton-specific primers. We DNA-barcoded 2,136 specimens from a diverse array of taxonomic assemblages (rotifers, mollusks, mites, crustaceans, insects, and fishes) from several Canadian and Mexican lakes with an average sequence success rate of 85.3%. In total, 325 Barcode Index Numbers (BINs) were detected with only three BINs (two cladocerans and one copepod) shared between Canada and Mexico, suggesting a much narrower distribution range of freshwater zooplankton than previously thought. This study is the first to broadly explore the metazoan biodiversity of freshwater systems with DNA barcodes to construct a reference library that represents the first step for future programs which aim to monitor ecosystem health, track invasive species, or improve knowledge of the ecology and distribution of freshwater zooplankton.

Innovativeness as an emergent property: a new alignment of comparative and experimental research on animal innovation

PubMed Central

Griffin, Andrea S.

2016-01-01

Innovation and creativity are key defining features of human societies. As we face the global challenges of the twenty-first century, they are also facets upon which we must become increasingly reliant. But what makes Homo sapiens so innovative and where does our high innovation propensity come from? Comparative research on innovativeness in non-human animals allows us to peer back through evolutionary time and investigate the ecological factors that drove the evolution of innovativeness, whereas experimental research identifies and manipulates underpinning creative processes. In commenting on the present theme issue, I highlight the controversies that have typified this research field and show how a paradigmatic shift in our thinking about innovativeness will contribute to resolving these tensions. In the past decade, innovativeness has been considered by many as a trait, a direct product of cognition, and a direct target of selection. The evidence I review here suggests that innovativeness will be hereon viewed as one component, or even an emergent property of a larger array of traits, which have evolved to deal with environmental variation. I illustrate how research should capitalize on taxonomic diversity to unravel the full range of psychological processes that underpin innovativeness in non-human animals. PMID:26926287

Understanding fungal functional biodiversity during the mitigation of environmentally dispersed pentachlorophenol in cork oak forest soils.

PubMed

Varela, Adélia; Martins, Celso; Núñez, Oscar; Martins, Isabel; Houbraken, Jos A M P; Martins, Tiago M; Leitão, M Cristina; McLellan, Iain; Vetter, Walter; Galceran, M Teresa; Samson, Robert A; Hursthouse, Andrew; Silva Pereira, Cristina

2015-08-01

Pentachlorophenol (PCP) is globally dispersed and contamination of soil with this biocide adversely affects its functional biodiversity, particularly of fungi - key colonizers. Their functional role as a community is poorly understood, although a few pathways have been already elucidated in pure cultures. This constitutes here our main challenge - elucidate how fungi influence the pollutant mitigation processes in forest soils. Circumstantial evidence exists that cork oak forests in N. W. Tunisia - economically critical managed forests are likely to be contaminated with PCP, but the scientific evidence has previously been lacking. Our data illustrate significant forest contamination through the detection of undefined active sources of PCP. By solving the taxonomic diversity and the PCP-derived metabolomes of both the cultivable fungi and the fungal community, we demonstrate here that most strains (predominantly penicillia) participate in the pollutant biotic degradation. They form an array of degradation intermediates and by-products, including several hydroquinone, resorcinol and catechol derivatives, either chlorinated or not. The degradation pathway of the fungal community includes uncharacterized derivatives, e.g. tetrachloroguaiacol isomers. Our study highlights fungi key role in the mineralization and short lifetime of PCP in forest soils and provide novel tools to monitor its degradation in other fungi dominated food webs. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Integrative analyses unveil speciation linked to host plant shift in Spialia butterflies.

PubMed

Hernández-Roldán, Juan L; Dapporto, Leonardo; Dincă, Vlad; Vicente, Juan C; Hornett, Emily A; Šíchová, Jindra; Lukhtanov, Vladimir A; Talavera, Gerard; Vila, Roger

2016-09-01

Discovering cryptic species in well-studied areas and taxonomic groups can have profound implications in understanding eco-evolutionary processes and in nature conservation because such groups often involve research models and act as flagship taxa for nature management. In this study, we use an array of techniques to study the butterflies in the Spialia sertorius species group (Lepidoptera, Hesperiidae). The integration of genetic, chemical, cytogenetic, morphological, ecological and microbiological data indicates that the sertorius species complex includes at least five species that differentiated during the last three million years. As a result, we propose the restitution of the species status for two taxa often treated as subspecies, Spialia ali (Oberthür, 1881) stat. rest. and Spialia therapne (Rambur, 1832) stat. rest., and describe a new cryptic species Spialia rosae Hernández-Roldán, Dapporto, Dincă, Vicente & Vila sp. nov. Spialia sertorius (Hoffmannsegg, 1804) and S. rosae are sympatric and synmorphic, but show constant differences in mitochondrial DNA, chemical profiles and ecology, suggesting that S. rosae represents a case of ecological speciation involving larval host plant and altitudinal shift, and apparently associated with Wolbachia infection. This study exemplifies how a multidisciplinary approach can reveal elusive cases of hidden diversity. © 2016 John Wiley & Sons Ltd.

DNA barcoding using skin exuviates can improve identification and biodiversity studies of snakes.

PubMed

Khedkar, Trupti; Sharma, Rashmi; Tiknaik, Anita; Khedkar, Gulab; Naikwade, Bhagwat S; Ron, Tetsuzan Benny; Haymer, David

2016-01-01

Snakes represent a taxonomically underdeveloped group of animals in India with a lack of experts and incomplete taxonomic descriptions being the main deterrents to advances in this area. Molecular taxonomic approaches using DNA barcoding could aid in snake identification as well as studies of biodiversity. Here a non-invasive sampling method using DNA barcoding is tested using skin exuviates. Taxonomically authenticated samples were collected and tested for validation and comparisons to unknown snake exuviate samples. This approach was also used to construct the first comprehensive study targeting the snake species from Maharashtra state in India. A total of 92 skin exuviate samples were collected and tested for this study. Of these, 81 samples were successfully DNA barcoded and compared with unknown samples for assignment of taxonomic identity. Good quality DNA was obtained irrespective of age and quality of the exuviate material, and all unknown samples were successfully identified. A total of 23 species of snakes were identified, six of which were in the list of Endangered species (Red Data Book). Intra- and inter-specific distance values were also calculated, and these were sufficient to allow discrimination among species and between species without ambiguity in most cases. Two samples were suspected to represent cryptic species based on deep K2P divergence values (>3%), and one sample could be identified to the genus level only. Eleven samples failed to amplify COI sequences, suggesting the need for alternative PCR primer pairs. This study clearly documents how snake skin exuviates can be used for DNA barcoding, estimates of diversity and population genetic structuring in a noninvasive manner.

Taxonomic and functional assignment of cloned sequences from high Andean forest soil metagenome.

PubMed

Montaña, José Salvador; Jiménez, Diego Javier; Hernández, Mónica; Angel, Tatiana; Baena, Sandra

2012-02-01

Total metagenomic DNA was isolated from high Andean forest soil and subjected to taxonomical and functional composition analyses by means of clone library generation and sequencing. The obtained yield of 1.7 μg of DNA/g of soil was used to construct a metagenomic library of approximately 20,000 clones (in the plasmid p-Bluescript II SK+) with an average insert size of 4 Kb, covering 80 Mb of the total metagenomic DNA. Metagenomic sequences near the plasmid cloning site were sequenced and them trimmed and assembled, obtaining 299 reads and 31 contigs (0.3 Mb). Taxonomic assignment of total sequences was performed by BLASTX, resulting in 68.8, 44.8 and 24.5% classification into taxonomic groups using the metagenomic RAST server v2.0, WebCARMA v1.0 online system and MetaGenome Analyzer v3.8 software, respectively. Most clone sequences were classified as Bacteria belonging to phlya Actinobacteria, Proteobacteria and Acidobacteria. Among the most represented orders were Actinomycetales (34% average), Rhizobiales, Burkholderiales and Myxococcales and with a greater number of sequences in the genus Mycobacterium (7% average), Frankia, Streptomyces and Bradyrhizobium. The vast majority of sequences were associated with the metabolism of carbohydrates, proteins, lipids and catalytic functions, such as phosphatases, glycosyltransferases, dehydrogenases, methyltransferases, dehydratases and epoxide hydrolases. In this study we compared different methods of taxonomic and functional assignment of metagenomic clone sequences to evaluate microbial diversity in an unexplored soil ecosystem, searching for putative enzymes of biotechnological interest and generating important information for further functional screening of clone libraries.

Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities

PubMed Central

Emerson, Brent C.; Cicconardi, Francesco; Fanciulli, Pietro P.; Shaw, Peter J. A.

2011-01-01

There has been much recent interest and progress in the characterization of community structure and community assembly processes through the application of phylogenetic methods. To date most focus has been on groups of taxa for which some relevant detail of their ecology is known, for which community composition is reasonably easily quantified and where the temporal scale is such that speciation is not likely to feature. Here, we explore how we might apply a molecular genetic approach to investigate community structure and assembly at broad taxonomic and geographical scales, where we have little knowledge of species ecology, where community composition is not easily quantified, and where speciation is likely to be of some importance. We explore these ideas using the class Collembola as a focal group. Gathering molecular evidence for cryptic diversity suggests that the ubiquity of many species of Collembola across the landscape may belie greater community complexity than would otherwise be assumed. However, this morphologically cryptic species-level diversity poses a challenge for attempts to characterize diversity both within and among local species assemblages. Recent developments in high throughput parallel sequencing technology, combined with mtDNA barcoding, provide an advance that can bring together the fields of phylogenetic and phylogeographic analysis to bear on this problem. Such an approach could be standardized for analyses at any geographical scale for a range of taxonomic groups to quantify the formation and composition of species assemblages. PMID:21768154

The diversity of ice algal communities on the Greenland Ice Sheet as revealed by oligotyping

PubMed Central

Lutz, Stefanie; McCutcheon, Jenine; McQuaid, James B.; Benning, Liane G.

2018-01-01

The Arctic is being disproportionally affected by climate change compared with other geographic locations, and is currently experiencing unprecedented melt rates. The Greenland Ice Sheet (GrIS) can be regarded as the largest supraglacial ecosystem on Earth, and ice algae are the dominant primary producers on bare ice surfaces throughout the course of a melt season. Ice-algal-derived pigments cause a darkening of the ice surface, which in turn decreases albedo and increases melt rates. The important role of ice algae in changing melt rates has only recently been recognized, and we currently know little about their community compositions and functions. Here, we present the first analysis of ice algal communities across a 100 km transect on the GrIS by high-throughput sequencing and subsequent oligotyping of the most abundant taxa. Our data reveal an extremely low algal diversity with Ancylonema nordenskiöldii and a Mesotaenium species being by far the dominant taxa at all sites. We employed an oligotyping approach and revealed a hidden diversity not detectable by conventional clustering of operational taxonomic units and taxonomic classification. Oligotypes of the dominant taxa exhibit a site-specific distribution, which may be linked to differences in temperatures and subsequently the extent of the melting. Our results help to better understand the distribution patterns of ice algal communities that play a crucial role in the GrIS ecosystem. PMID:29547098

Dynamic evolutionary change in post-Paleozoic echinoids and the importance of scale when interpreting changes in rates of evolution

PubMed Central

Hopkins, Melanie J.; Smith, Andrew B.

2015-01-01

How ecological and morphological diversity accrues over geological time has been much debated by paleobiologists. Evidence from the fossil record suggests that many clades reach maximal diversity early in their evolutionary history, followed by a decline in evolutionary rates as ecological space fills or due to internal constraints. Here, we apply recently developed methods for estimating rates of morphological evolution during the post-Paleozoic history of a major invertebrate clade, the Echinoidea. Contrary to expectation, rates of evolution were lowest during the initial phase of diversification following the Permo-Triassic mass extinction and increased over time. Furthermore, although several subclades show high initial rates and net decreases in rates of evolution, consistent with “early bursts” of morphological diversification, at more inclusive taxonomic levels, these bursts appear as episodic peaks. Peak rates coincided with major shifts in ecological morphology, primarily associated with innovations in feeding strategies. Despite having similar numbers of species in today’s oceans, regular echinoids have accrued far less morphological diversity than irregular echinoids due to lower intrinsic rates of morphological evolution and less morphological innovation, the latter indicative of constrained or bounded evolution. These results indicate that rates of evolution are extremely heterogenous through time and their interpretation depends on the temporal and taxonomic scale of analysis. PMID:25713369

Dynamics of origination and extinction in the marine fossil record

PubMed Central

Alroy, John

2008-01-01

The discipline-wide effort to database the fossil record at the occurrence level has made it possible to estimate marine invertebrate extinction and origination rates with much greater accuracy. The new data show that two biotic mechanisms have hastened recoveries from mass extinctions and confined diversity to a relatively narrow range over the past 500 million years (Myr). First, a drop in diversity of any size correlates with low extinction rates immediately afterward, so much so that extinction would almost come to a halt if diversity dropped by 90%. Second, very high extinction rates are followed by equally high origination rates. The two relationships predict that the rebound from the current mass extinction will take at least 10 Myr, and perhaps 40 Myr if it rivals the Permo-Triassic catastrophe. Regardless, any large event will result in a dramatic ecological and taxonomic restructuring of the biosphere. The data also confirm that extinction and origination rates both declined through the Phanerozoic and that several extinctions in addition to the Permo-Triassic event were particularly severe. However, the trend may be driven by taxonomic biases and the rates vary in accord with a simple log normal distribution, so there is no sharp distinction between background and mass extinctions. Furthermore, the lack of any significant autocorrelation in the data is inconsistent with macroevolutionary theories of periodicity or self-organized criticality. PMID:18695240

A comprehensive insight into bacterial virulence in drinking water using 454 pyrosequencing and Illumina high-throughput sequencing.

PubMed

Huang, Kailong; Zhang, Xu-Xiang; Shi, Peng; Wu, Bing; Ren, Hongqiang

2014-11-01

In order to comprehensively investigate bacterial virulence in drinking water, 454 pyrosequencing and Illumina high-throughput sequencing were used to detect potential pathogenic bacteria and virulence factors (VFs) in a full-scale drinking water treatment and distribution system. 16S rRNA gene pyrosequencing revealed high bacterial diversity in the drinking water (441-586 operational taxonomic units). Bacterial diversity decreased after chlorine disinfection, but increased after pipeline distribution. α-Proteobacteria was the most dominant taxonomic class. Alignment against the established pathogen database showed that several types of putative pathogens were present in the drinking water and Pseudomonas aeruginosa had the highest abundance (over 11‰ of total sequencing reads). Many pathogens disappeared after chlorine disinfection, but P. aeruginosa and Leptospira interrogans were still detected in the tap water. High-throughput sequencing revealed prevalence of various pathogenicity islands and virulence proteins in the drinking water, and translocases, transposons, Clp proteases and flagellar motor switch proteins were the predominant VFs. Both diversity and abundance of the detectable VFs increased after the chlorination, and decreased after the pipeline distribution. This study indicates that joint use of 454 pyrosequencing and Illumina sequencing can comprehensively characterize environmental pathogenesis, and several types of putative pathogens and various VFs are prevalent in drinking water. Copyright © 2014 Elsevier Inc. All rights reserved.

Non-Ischemic Heart Failure With Reduced Ejection Fraction Is Associated With Altered Intestinal Microbiota.

PubMed

Katsimichas, Themistoklis; Ohtani, Tomohito; Motooka, Daisuke; Tsukamoto, Yasumasa; Kioka, Hidetaka; Nakamoto, Kei; Konishi, Shozo; Chimura, Misato; Sengoku, Kaoruko; Miyawaki, Hiroshi; Sakaguchi, Taiki; Okumura, Ryu; Theofilis, Konstantinos; Iida, Tetsuya; Takeda, Kiyoshi; Nakamura, Shota; Sakata, Yasushi

2018-05-25

Research suggests that heart failure with reduced ejection fraction (HFrEF) is a state of systemic inflammation that may be triggered by microbial products passing into the bloodstream through a compromised intestinal barrier. However, whether the intestinal microbiota exhibits dysbiosis in HFrEF patients is largely unknown.Methods and Results:Twenty eight non-ischemic HFrEF patients and 19 healthy controls were assessed by 16S rRNA analysis of bacterial DNA extracted from stool samples. After processing of sequencing data, bacteria were taxonomically classified, diversity indices were used to examine microbial ecology, and relative abundances of common core genera were compared between groups. Furthermore, we predicted gene carriage for bacterial metabolic pathways and inferred microbial interaction networks on multiple taxonomic levels.Bacterial communities of both groups were dominated by the Firmicutes and Bacteroidetes phyla. The most abundant genus in both groups wasBacteroides. Although α diversity did not differ between groups, ordination by β diversity metrics revealed a separation of the groups across components of variation.StreptococcusandVeillonellawere enriched in the common core microbiota of patients, whileSMB53was depleted. Gene families in amino acid, carbohydrate, vitamin, and xenobiotic metabolism showed significant differences between groups. Interaction networks revealed a higher degree of correlations between bacteria in patients. Non-ischemic HFrEF patients exhibited multidimensional differences in intestinal microbial communities compared with healthy subjects.

Taxonomic composition of phytoplankton in the Vakh River (Western Siberia)

NASA Astrophysics Data System (ADS)

Skorobogatova, O. N.

2018-03-01

This paper provides data on the hydrological and hydrochemical parameters of the Vakh River in the Middle Ob region. In 2005-2008 we have identified 404 taxonomic units represented by 463 species, types and forms of algae, belonging to 140 genera, 52 families, 13 classes and 7 divisions. 386 species were identified for the first time, 141 taxa were identified as rare and 22 taxa as new for Western Siberia. Leading divisions, Bacillariophyta and Chlorophyta, make up for 78.9% of total phytoplankton diversity. Cyanobacteria, Chrysophyta and Euglenophyta form a community of 88 taxonomic units having a rank lower than genus level, and represent 19.0% of the total number. The floral role of Xanthophyta and Dinophyta is insignificant (2.1%). The main structure-forming species are 14: vegetating throughout the year (Aulacoseira italica, Asterionella formosa), summer taxa (Microcystis aeruginosa, Melosira varians, Aulacoseira granulata, Pandorina morum, Pediastrum boryanum, P. duplex, Lacunastrum gracillimum, Scenedesmus quadricauda) and summer-autumn (Microcystis pulverea, Tabellaria fenestrata, T. flocculosa, Mucidosphaerium pulchellum). The Vakh River demonstrates specific characteristics of boreal flowing waterways. The northern composition is represented in a big rate of families (44.2%) and genera (109 77.9) with one to three species. The richest genera Closterium (31 taxa), Eunotia (27 taxa), Pinnularia (22 taxa), Desmidium (11 taxa) and the family Desmidiaceae (45 taxa) ensure diversity of phytoplankton. Ecological and geographical analysis demonstrates predominance of cosmopolitan algae (56.6%). Plankton represents 44.7% of all algae, oligogalobs - 78.8% and indifferent algae – 36.7%. Water meets the requirements for β-mezosaprobian pollution zone, class of satisfactory purity (III class).

Mass coral bleaching causes biotic homogenization of reef fish assemblages.

PubMed

Richardson, Laura E; Graham, Nicholas A J; Pratchett, Morgan S; Eurich, Jacob G; Hoey, Andrew S

2018-04-06

Global climate change is altering community composition across many ecosystems due to nonrandom species turnover, typically characterized by the loss of specialist species and increasing similarity of biological communities across spatial scales. As anthropogenic disturbances continue to alter species composition globally, there is a growing need to identify how species responses influence the establishment of distinct assemblages, such that management actions may be appropriately assigned. Here, we use trait-based analyses to compare temporal changes in five complementary indices of reef fish assemblage structure among six taxonomically distinct coral reef habitats exposed to a system-wide thermal stress event. Our results revealed increased taxonomic and functional similarity of previously distinct reef fish assemblages following mass coral bleaching, with changes characterized by subtle, but significant, shifts toward predominance of small-bodied, algal-farming habitat generalists. Furthermore, while the taxonomic or functional richness of fish assemblages did not change across all habitats, an increase in functional originality indicated an overall loss of functional redundancy. We also found that prebleaching coral composition better predicted changes in fish assemblage structure than the magnitude of coral loss. These results emphasize how measures of alpha diversity can mask important changes in the structure and functioning of ecosystems as assemblages reorganize. Our findings also highlight the role of coral species composition in structuring communities and influencing the diversity of responses of reef fishes to disturbance. As new coral species configurations emerge, their desirability will hinge upon the composition of associated species and their capacity to maintain key ecological processes in spite of ongoing disturbances. © 2018 John Wiley & Sons Ltd.

Diversity and abundance of invertebrate epifaunal assemblages associated with gorgonians are driven by colony attributes

NASA Astrophysics Data System (ADS)

Cúrdia, João; Carvalho, Susana; Pereira, Fábio; Guerra-García, José Manuel; Santos, Miguel N.; Cunha, Marina R.

2015-06-01

The present study aimed to explicitly quantify the link between the attributes of shallow-water gorgonian colonies (Octocorallia: Alcyonacea) and the ecological patterns of associated non-colonial epifaunal invertebrates. Based on multiple regression analysis, we tested the contribution of several attributes (colony height, width, and area, fractal dimension as a measure of colony complexity, lacunarity as a measure of the heterogeneity, and "colonial" epibiont cover) to abundance and taxonomic richness of associated assemblages. The results highlight the variation in the response of epifaunal assemblages to the gorgonian colony characteristics. The nature and intensity of the relationships were gorgonian species-dependent and varied from one taxonomic group to another. For both gorgonian species analyzed, the strongest predictor of species richness and abundance of the epifaunal assemblages was "colonial" epibiont cover, possibly due to a trophic effect (direct or indirect enhancement of food availability) combined with the surface available for colonization (species-area effect). Although structural complexity is usually indicated as the main driver for rich and abundant coral-associated assemblages, no significant relationship was observed between fractal dimension and the community descriptors; lacunarity, which reflects the sizes of the inter-branch spaces, was only linked to taxonomic richness in the assemblages associated with Leptogorgia lusitanica. The validity of the paradigm that structural complexity enhances biodiversity may be scale-dependent. In the case of gorgonians, the effect of complexity at the "garden" level may be more relevant than at the individual colony level. This reinforces the need for the conservation of gorgonian aggregation areas as a whole in order to preserve host diversity and size structure.

Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil.

PubMed

Mendes, Lucas William; Tsai, Siu Mui

2018-01-01

Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters. Our data showed that the microbiome is shaped by soil properties, with pH, base saturation, boron and iron content significantly correlated to overall community structure. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as boron, copper, sulfur, potassium and aluminum presented significant correlation with the most number of bacterial groups. Mangrove soil was the most distinct site and presented the highest taxonomic and functional diversity in comparison with forest and restinga soils. From the total 34 microbial phyla identified, 14 were overrepresented in mangrove soils, including several archaeal groups. Mangrove soils hosted a high abundance of sequences related to replication, survival and adaptation; forest soils included high numbers of sequences related to the metabolism of nutrients and other composts; while restinga soils included abundant genes related to the metabolism of carbohydrates. Overall, our finds show that the microbial community structure and functional potential were clearly different across the environmental gradient, followed by functional adaptation and both were related to the soil properties.

Variability of airborne bacteria in an urban Mediterranean area (Thessaloniki, Greece)

NASA Astrophysics Data System (ADS)

Genitsaris, Savvas; Stefanidou, Natassa; Katsiapi, Matina; Kormas, Konstantinos A.; Sommer, Ulrich; Moustaka-Gouni, Maria

2017-05-01

The abundance, biomass and the taxonomic composition of the total airborne bacterial communities in a coastal urban area of Northeastern Mediterranean Sea were examined. In total, 27 air samples were collected across three seasons from a sampling point of approximately 30 m altitude in the center of the city. The abundance and biomass were determined with the use of epifluorescent microscopy, while the taxonomic composition was characterized by next-generation sequencing methods. Overall, the highest values of bacterial abundance were recorded during summer, with values exceeding abundances recorded in other urban sites across Europe, reaching 41 × 104 cells m-3. Out of 6 core meteorological parameters, only air temperature was found to significantly affect the abundance and biomass of airborne bacteria. Concerning the taxonomic composition of the airborne bacterial community, the group of Proteobacteria was the most diverse, with 47% of the total number of OTUs belonging to them, followed by Firmicutes, Actinobacteria and Bacteroidetes. The most dominant OTU belonged to γ-Proteobacteria, and was closely affiliated to Pseudomonas sp., a taxon commonly found to actively participate in the formation of ice-nuclei in the atmosphere. Finally, 19 OTUs were shared between all seasons and were found to be among the most dominant overall. The majority of these OTUs were affiliated to genera from soil and wastewater origin, while several were affiliated to genera that include known or opportunistic pathogens. Yet, only rare OTUs were affiliated to taxa with possible marine origin (e.g. Synechococcus sp.). The results showed that the atmosphere of the study area harbors a diverse and abundant bacterial community.

GSD Update: Ushering in a new age of genetics to restore lands and conserve species

Treesearch

Deborah M. Finch

2013-01-01

Plant genetic information provides critical knowledge necessary to mitigate the impacts of climate change through ecological restoration. The first step in restoration is recognizing and delineating genetic boundaries at different taxonomic and spatial hierarchies (e.g., species, subspecies and populations). The second step is an assessment of the genetic diversity...

Under Pressure: A Study of Issues in Oceanography

ERIC Educational Resources Information Center

Payne, Diana

2006-01-01

The world's greatest cities and centers of civilization arose near or along major waterways providing access to the sea. Many people, no matter where they live, find the ocean and the life associated with it a fascinating topic. Although the ocean is characterized by high taxonomic diversity (over 90% of the animal phyla are represented in the…

DIVERSITY SURFACES AND SPECIES WAVE FRONTS IN A SOIL MICROARTHROPOD ASSEMBLAGE: ADDING THE DIMENSION OF TIME

EPA Science Inventory

As a general rule, animal species of intermediate size within a given taxonomic group are most abundant in nature. It is not known if these patterns occur in small-bodied taxa, such as soil microarthropods, or how these patterns change through time. Here I show that Oribatida (Ac...

Utilization of data estimation via existing models, within a tiered data quality system, for populating species sensitivity distributions

EPA Science Inventory

The acquisition toxicity test data of sufficient quality from open literature to fulfill taxonomic diversity requirements can be a limiting factor in the creation of new 304(a) Aquatic Life Criteria. The use of existing models (WebICE and ACE) that estimate acute and chronic eff...

Polyphasic characterization of Trichocoleus desertorum sp. nov. (Pseudanabaenales, Cyanobacteria) from desert soils and phylogenetic placement of the genus Trichocoleus

Treesearch

Radka Muhlsteinova; Jeffrey R. Johansen; Nicole Pietrasiak; Michael P. Martin; Karina Osorio-Santos; Steven D. Warren

2014-01-01

Little is known about the taxonomic diversity of cyanobacteria in deserts, despite their important ecological roles in these ecosystems. In this study, cyanobacterial strains from the Atacama, Colorado, and Mojave Deserts were isolated and characterized using molecular, morphological, and ecological information. Phylogenetic placement of these strains was revealed...

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

Treesearch

C.L. Schoch; B. Robbertse; V. Robert; R.G. Haight; K. Kovacs; B. Leung; W. Meyer; R.H. Nilsson; K. Hughes; A.N. Miller; P.M. Kirk; K. Abarenkov; M.C. Aime; H.A. Ariyawansa; M. Bidartondo; T. Boekhout; B. Buyck; Q. Cai; J. Chen; A. Crespo; P.W. Crous; U. Damm; Z.W. De Beer; B.T.M. Dentinger; P.K. Divakar; M. Duenas; N. Feau; K. Fliegerova; M.A. Garcia; Z.-W. Ge; G.W. Griffith; J.Z. Groenewald; M. Groenewald; M. Grube; M. Gryzenhout; C. Gueidan; L. Guo; S. Hambleton; R. Hamelin; K. Hansen; V. Hofstetter; S.-B. Hong; J. Houbraken; K.D. Hyde; P. Inderbitzin; P.R. Johnston; S.C. Karunarathna; U. Koljalg; G.M. Kovacs; E. Kraichak; K. Krizsan; C.P. Kurtzman; K.-H. Larsson; S. Leavitt; P.M. Letcher; K. Liimatainen; J.-K. Liu; D.J. Lodge; J. Jennifer Luangsa-ard; H.T. Lumbsch; S.S.N. Maharachchikumbura; D. Manamgoda; M.P. Martin; A.M. Minnis; J.-M. Moncalvo; G. Mule; K.K. Nakasone; T. Niskanen; I. Olariaga; T. Papp; T. Petkovits; R. Pino-Bodas; M.J. Powell; H.A. Raja; D. Redecker; J.M. Sarmiento-Ramirez; K.A. Seifert; B. Shrestha; S. Stenroos; B. Stielow; S.-O. Suh; K. Tanaka; L. Tedersoo; M.T. Telleria; D. Udayanga; W.A. Untereiner; J. Dieguez Uribeondo; K.V. Subbarao; C. Vagvolgyi; C. Visagie; K. Voigt; D.M. Walker; B.S. Weir; M. Weiss; N.N. Wijayawardene; M.J. Wingfield; J.P. Xu; Z.L. Yang; N. Zhang; W.-Y. Zhuang; S. Federhen

2014-01-01

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput...

Conservation of ectomycorrhizal fungi: exploring the linkages between functional and taxonomic responses to anthropogenic N deposition

Treesearch

E.A. Lilleskov; E.A. Hobbie; T.R. Horton

2011-01-01

Anthropogenic nitrogen (N) deposition alters ectomycorrhizal fungal communities, but the effect on functional diversity is not clear. In this review we explore whether fungi that respond differently to N deposition also differ in functional traits, including organic N use, hydrophobicity and exploration type (extent and pattern of extraradical hyphae). ...

Conservation Implications of Changes in Endemic Hawaiian Drosophilidae Diversity across Land Use Gradients

PubMed Central

Leblanc, Luc; Rubinoff, Daniel; Wright, Mark G.

2013-01-01

Endemic Hawaiian Drosophilidae, a radiation of nearly 1000 species including 13 federally listed as endangered, occur mostly in intact native forest, 500–1500 m above sea level. But their persistence in disturbed forest and agricultural areas has not been documented. Thus, control efforts for agricultural pests may impact endemic species if previously undocumented refugia in agricultural areas may play a role in their conservation. To quantify whether invasive plants and agriculture habitats may harbor endemic Drosophilidae, we established standardized trapping arrays, with traps typically designed to control invasive fruit flies (Tephritidae), with 81 sites across native, disturbed and agricultural land use gradients on the islands of Hawai’i and Maui. We collected and identified, to species level, over 22,000 specimens. We found 121 of the possible 292 species expected to occur in the sampled areas, and the majority (91%) of the captured specimens belonged to 24 common species. Species diversity and numbers were greatest in the native forest, but 55% of the species occurred in the invasive strawberry guava belt and plantation forest, adjacent to and almost 500 m from native forest, and 22 species were collected in orchards and nonnative forest as far as 10 km from native habitats. Their persistence outside of native forest suggests that more careful management of disturbed forest and a reassessment of its conservation value are in order. Conservation efforts and assessments of native forest integrity should include the subset of species restricted to intact native forest, since these species are highly localized and particularly sensitive. Additionally, future efforts to control invasive pest fruit flies should consider the nontarget impacts of maintaining traps in and near native forest. This survey project demonstrates the utility of thorough biotic surveys and taxonomic expertise in developing both sensitive species lists and baseline diversity indices for future conservation and monitoring efforts. PMID:23650514

Outlook for coastal plain forests: a subregional report from the Southern Forest Futures Project

Treesearch

Kier Klepzig; Richard Shelfer; Zanethia Choice

2014-01-01

The U.S. Coastal Plain consists of seven sections: the Northern Atlantic, Eastern Atlantic, Peninsular Florida, Southern Gulf, Middle Gulf-East, Middle Gulf-West, and Western Gulf. It covers a large area, consists of a diverse array of habitats, and supports a diverse array of uses. This report presents forecasts from the Southern Forest Futures Project that are...

Microbial Diversity in Engineered Haloalkaline Environments Shaped by Shared Geochemical Drivers Observed in Natural Analogues

PubMed Central

Warren, Lesley A.; Kendra, Kathryn E.

2015-01-01

Microbial communities in engineered terrestrial haloalkaline environments have been poorly characterized relative to their natural counterparts and are geologically recent in formation, offering opportunities to explore microbial diversity and assembly in dynamic, geochemically comparable contexts. In this study, the microbial community structure and geochemical characteristics of three geographically dispersed bauxite residue environments along a remediation gradient were assessed and subsequently compared with other engineered and natural haloalkaline systems. In bauxite residues, bacterial communities were similar at the phylum level (dominated by Proteobacteria and Firmicutes) to those found in soda lakes, oil sands tailings, and nuclear wastes; however, they differed at lower taxonomic levels, with only 23% of operational taxonomic units (OTUs) shared with other haloalkaline environments. Although being less diverse than natural analogues, bauxite residue harbored substantial novel bacterial taxa, with 90% of OTUs nonmatchable to cultured representative sequences. Fungal communities were dominated by Ascomycota and Basidiomycota, consistent with previous studies of hypersaline environments, and also harbored substantial novel (73% of OTUs) taxa. In bauxite residues, community structure was clearly linked to geochemical and physical environmental parameters, with 84% of variation in bacterial and 73% of variation in fungal community structures explained by environmental parameters. The major driver of bacterial community structure (salinity) was consistent across natural and engineered environments; however, drivers differed for fungal community structure between natural (pH) and engineered (total alkalinity) environments. This study demonstrates that both engineered and natural terrestrial haloalkaline environments host substantial repositories of microbial diversity, which are strongly shaped by geochemical drivers. PMID:25979895

Accurate phylogenetic classification of DNA fragments based onsequence composition

DOE Office of Scientific and Technical Information (OSTI.GOV)

McHardy, Alice C.; Garcia Martin, Hector; Tsirigos, Aristotelis

2006-05-01

Metagenome studies have retrieved vast amounts of sequenceout of a variety of environments, leading to novel discoveries and greatinsights into the uncultured microbial world. Except for very simplecommunities, diversity makes sequence assembly and analysis a verychallenging problem. To understand the structure a 5 nd function ofmicrobial communities, a taxonomic characterization of the obtainedsequence fragments is highly desirable, yet currently limited mostly tothose sequences that contain phylogenetic marker genes. We show that forclades at the rank of domain down to genus, sequence composition allowsthe very accurate phylogenetic 10 characterization of genomic sequence.We developed a composition-based classifier, PhyloPythia, for de novophylogenetic sequencemore » characterization and have trained it on adata setof 340 genomes. By extensive evaluation experiments we show that themethodis accurate across all taxonomic ranks considered, even forsequences that originate fromnovel organisms and are as short as 1kb.Application to two metagenome datasets 15 obtained from samples ofphosphorus-removing sludge showed that the method allows the accurateclassification at genus level of most sequence fragments from thedominant populations, while at the same time correctly characterizingeven larger parts of the samples at higher taxonomic levels.« less

Dynamics of clade diversification on the morphological hypercube

PubMed Central

Gavrilets, S.

1999-01-01

Understanding the relationship between taxonomic and morphological changes is important in identifying the reasons for accelerated morphological diversification early in the history of animal phyla. Here, a simple general model describing the joint dynamics of taxonomic diversity and morphological disparity is presented and applied to the data on the diversification of blastozoans. I show that the observed patterns of deceleration in clade diversification can be explicable in terms of the geometric structure of the morphospace and the effects of extinction and speciation on morphological disparity without invoking major declines in the size of morphological transitions or taxonomic turnover rates. The model allows testing of hypotheses about patterns of diversification and estimation of rates of morphological evolution. In the case of blastozoans, I find no evidence that major changes in evolutionary rates and mechanisms are responsible for the deceleration of morphological diversification seen during the period of this clade's expansion. At the same time, there is evidence for a moderate decline in overall rates of morphological diversification concordant with a major change (from positive to negative values) in the clade's growth rate.

Biotechnological application and taxonomical distribution of plant growth promoting actinobacteria.

PubMed

Hamedi, Javad; Mohammadipanah, Fatemeh

2015-02-01

Plant growth promoting (PGP) bacteria are involved in various interactions known to affect plant fitness and soil quality, thereby increasing the productivity of agriculture and stability of soil. Although the potential of actinobacteria in antibiotic production is well-investigated, their capacity to enhance plant growth is not fully surveyed. Due to the following justifications, PGP actinobacteria (PGPA) can be considered as a more promising taxonomical group of PGP bacteria: (1) high numbers of actinobacteria per gram of soil and their filamentous nature, (2) genome dedicated to the secondary metabolite production (~5 to 10 %) is distinctively more than that of other bacteria and (3) number of plant growth promoter genera reported from actinobacteria is 1.3 times higher than that of other bacteria. Mechanisms by which PGPA contribute to the plant growth by association are: (a) enhancing nutrients availability, (b) regulation of plant metabolism, (c) decreasing environmental stress, (d) control of phytopathogens and (e) improvement of soil texture. Taxonomical and chemical diversity of PGPA and their biotechnological application along with their associated challenges are summarized in this paper.

Five New Wood Decay Fungi (Polyporales and Hymenochaetales) in Korea.

PubMed

Kim, Nam Kyu; Park, Jae Young; Park, Myung Soo; Lee, Hyun; Cho, Hae Jin; Eimes, John A; Kim, Changmu; Lim, Young Woon

2016-09-01

The wood decay fungi are a diverse taxonomic group that plays a pivotal role in forest carbon cycling. Wood decay fungi use various enzymatic pathways to digest dead or living wood in order to obtain carbon and other nutrients and these enzymatic systems have been exploited for both industrial and medical applications. Over 600 wood decay fungi species have been described in Korea; however, the recent application of molecular markers has dramatically altered the taxonomy of many of these wood decay fungi at both the genus and species levels. By combining molecular methods, specifically sequences of the internal transcribed spacer region, with traditional morphological characters, this study identified five new species records for Korea in five genera: Aurantiporus , Favolus , Neofavolus , Loweomyces , and Hymenochaetopsis . Three of these genera ( Aurantiporus , Favolus , and Loweomyces ) were previously unknown in Korea. The relatively simple morphology of the wood decay fungi often leads to ambiguous taxonomic assignment. Therefore, molecular markers are a necessary component of any taxonomic or evolutionary study of wood decay fungi. Our study highlights the need for a more robust and multifaceted approach in investigating new wood decay fungi in Korea.

Greatest soil microbial diversity found in micro-habitats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bach, Elizabeth M.; Williams, Ryan J.; Hargreaves, Sarah K.

Microbial interactions occur in habitats much smaller than typically considered in classic ecological studies. This study uses soil aggregates to examine soil microbial community composition and structure of both bacteria and fungi at a microbially relevant scale. Aggregates were isolated from three land management systems in central Iowa, USA to test if aggregate-level microbial responses were sensitive to large-scale shifts in plant community and management practices. Bacteria and fungi exhibited similar patterns of community structure and diversity among soil aggregates, regardless of land management. Microaggregates supported more diverse microbial communities, both taxonomically and functionally. Calculation of a weighted proportional wholemore » soil diversity, which accounted for microbes found in aggregate fractions, resulted in 65% greater bacterial richness and 100% greater fungal richness over independently sampled whole soil. Our results show microaggregates support a previously unrecognized diverse microbial community that likely effects microbial access and metabolism of soil substrates.« less

Temperature mediates continental-scale diversity of microbes in forest soils

PubMed Central

Zhou, Jizhong; Deng, Ye; Shen, Lina; Wen, Chongqing; Yan, Qingyun; Ning, Daliang; Qin, Yujia; Xue, Kai; Wu, Liyou; He, Zhili; Voordeckers, James W.; Nostrand, Joy D. Van; Buzzard, Vanessa; Michaletz, Sean T.; Enquist, Brian J.; Weiser, Michael D.; Kaspari, Michael; Waide, Robert; Yang, Yunfeng; Brown, James H.

2016-01-01

Climate warming is increasingly leading to marked changes in plant and animal biodiversity, but it remains unclear how temperatures affect microbial biodiversity, particularly in terrestrial soils. Here we show that, in accordance with metabolic theory of ecology, taxonomic and phylogenetic diversity of soil bacteria, fungi and nitrogen fixers are all better predicted by variation in environmental temperature than pH. However, the rates of diversity turnover across the global temperature gradients are substantially lower than those recorded for trees and animals, suggesting that the diversity of plant, animal and soil microbial communities show differential responses to climate change. To the best of our knowledge, this is the first study demonstrating that the diversity of different microbial groups has significantly lower rates of turnover across temperature gradients than other major taxa, which has important implications for assessing the effects of human-caused changes in climate, land use and other factors. PMID:27377774

Bee communities along a prairie restoration chronosequence: similar abundance and diversity, distinct composition.

PubMed

Tonietto, Rebecca K; Ascher, John S; Larkin, Daniel J

2017-04-01

Recognition of the importance of bee conservation has grown in response to declines of managed honey bees and some wild bee species. Habitat loss has been implicated as a leading cause of declines, suggesting that ecological restoration is likely to play an increasing role in bee conservation efforts. In the midwestern United States, restoration of tallgrass prairie has traditionally targeted plant community objectives without explicit consideration for bees. However, restoration of prairie vegetation is likely to provide ancillary benefits to bees through increased foraging and nesting resources. We investigated community assembly of bees across a chronosequence of restored eastern tallgrass prairies and compared patterns to those in control and reference habitats (old fields and prairie remnants, respectively). We collected bees for 3 yr and measured diversity and abundance of in-bloom flowering plants, vegetation structure, ground cover, and surrounding land use as predictors of bee abundance and bee taxonomic and functional diversity. We found that site-level variables, but not site type or restoration age, were significant predictors of bee abundance (bloom diversity, P = 0.004; bare ground cover, P = 0.02) and bee diversity (bloom diversity, P = 0.01). There were significant correlations between overall composition of bee and blooming plant communities (Mantel test, P = 0.002), and both plant and bee assemblages in restorations were intermediate between those of old fields and remnant prairies. Restorations exhibited high bee beta diversity, i.e., restored sites' bee assemblages were taxonomically and functionally differentiated from each other. This pattern was strong in younger restorations (<20 yr old), but absent from older restorations (>20 yr), suggesting restored prairie bee communities become more similar to one another and more similar to remnant prairie bee communities over time with the arrival of more species and functional groups of bees. Our results indicate that old fields, restorations, and remnants provide habitat for diverse and abundant bee communities, but continued restoration of old fields will help support and conserve bee communities more similar to reference bee communities characteristic of remnant prairies. © 2016 by the Ecological Society of America.

The marine diversity spectrum

PubMed Central

Reuman, Daniel C; Gislason, Henrik; Barnes, Carolyn; Mélin, Frédéric; Jennings, Simon

2014-01-01

Distributions of species body sizes within a taxonomic group, for example, mammals, are widely studied and important because they help illuminate the evolutionary processes that produced these distributions. Distributions of the sizes of species within an assemblage delineated by geography instead of taxonomy (all the species in a region regardless of clade) are much less studied but are equally important and will illuminate a different set of ecological and evolutionary processes. We develop and test a mechanistic model of how diversity varies with body mass in marine ecosystems. The model predicts the form of the ‘diversity spectrum’, which quantifies the distribution of species' asymptotic body masses, is a species analogue of the classic size spectrum of individuals, and which we have found to be a new and widely applicable description of diversity patterns. The marine diversity spectrum is predicted to be approximately linear across an asymptotic mass range spanning seven orders of magnitude. Slope −0·5 is predicted for the global marine diversity spectrum for all combined pelagic zones of continental shelf seas, and slopes for large regions are predicted to lie between −0·5 and −0·1. Slopes of −0·5 and −0·1 represent markedly different communities: a slope of −0·5 depicts a 10-fold reduction in diversity for every 100-fold increase in asymptotic mass; a slope of −0·1 depicts a 1·6-fold reduction. Steeper slopes are predicted for larger or colder regions, meaning fewer large species per small species for such regions. Predictions were largely validated by a global empirical analysis. Results explain for the first time a new and widespread phenomenon of biodiversity. Results have implications for estimating numbers of species of small asymptotic mass, where taxonomic inventories are far from complete. Results show that the relationship between diversity and body mass can be explained from the dependence of predation behaviour, dispersal, and life history on body mass, and a neutral assumption about speciation and extinction. PMID:24588547

Challenges of pedodiversity in soil science

NASA Astrophysics Data System (ADS)

Toomanian, N.; Esfandiarpoor, I.

2010-12-01

Soil diversity is not a completely new concept in soil science. It has been discussed from early times but it was not challenged this much broad. Ibañez with introducing the pedodiversity opened a new conceptual window to ease the induction of the soils complexity, spatial and temporal evolution and distribution. Pedodiversity now attracts more attention and goes to open new windows in soil science. Pedodiversity faces now with different challenges, which could be critical in its way on. Do the current soil diversity indices conceptually define all aspects of soil variability, or do we need to bind them with other characteristics like taxonomic distances? How is the soil individualism defined within the context of spatial variability and soil continuum? How are pedocomplexity, connectance, pedodiversity and soil spatial structure related? Can the changes of soil diversity be accounted as the rate of soil development? Can a range of pedodiversity index be a scale for soil series definition? Initial and some of current pedodiversity studies were/are focused on the concepts and measurement of pedodiversity and soil complexity indices of soilscape compared with the biological diversity and complexity. However, for the pedogenetic studies, the most important issues are the evolutionary concerns out of this approach compared with the other biotic systems. The new contexts, which should be more undertaken in future studies are: functional diversity, temporal diversity, study of soil and landform extinction and preservation. The last question could be: how pedodiversity could be changed under different understanding levels? A case study has been carried out in Charmahal and Bakhtiary province, Iran. Its objectives are the following: comparing the pedodiversity indices combined with and without taxonomic distances within tow replication of a geomorphic surface (Pi 111). What the pedodiversity says here? Did the unique calcification process which rules the soil formation here result in endemism or soil zonality? Do different pedodiversity indices correlate with the soil patterns?